scholarly journals Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating

2021 ◽  
Vol 7 (8) ◽  
pp. 661
Author(s):  
Hannah M Edwards ◽  
Johanna Rhodes
Keyword(s):  
Drug Resistance ◽  
Bacterial Pathogen ◽  
Pathogenic Fungi ◽  
Epidemiological Data ◽  
Phylogeny Reconstruction ◽  
Rate Variation ◽  
Biological Processes ◽  
Antifungal Drug Resistance ◽  
The Past ◽  
Mutation Rate Variation

In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.

Role of Mediator in virulence and antifungal drug resistance in pathogenic fungi

2019 ◽  
Vol 65 (3) ◽  
pp. 621-630 ◽  
Author(s):  
Gary P. Moran ◽  
Matthew Z. Anderson ◽  
Lawrence C. Myers ◽  
Derek J. Sullivan
Keyword(s):  
Drug Resistance ◽  
Pathogenic Fungi ◽  
Antifungal Drug ◽  
Antifungal Drug Resistance

Antifungal drug resistance of pathogenic fungi

The Lancet ◽  
2002 ◽  
Vol 359 (9312) ◽  
pp. 1135-1144 ◽  
Author(s):  
Dimitrios P Kontoyiannis ◽  
Russell E Lewis
Keyword(s):  
Drug Resistance ◽  
Pathogenic Fungi ◽  
Antifungal Drug ◽  
Antifungal Drug Resistance

scholarly journals Large-Scale Biochemical Profiling of the Candida albicans Biofilm Matrix: New Compositional, Structural, and Functional Insights

mBio ◽  
2014 ◽  
Vol 5 (5) ◽  
Author(s):  
Jose L. Lopez-Ribot
Keyword(s):  
Drug Resistance ◽  
Candida Albicans ◽  
Large Scale ◽  
Pathogenic Fungi ◽  
Antifungal Drug ◽  
Content Type ◽  
Antifungal Drug Resistance ◽  
Functional Aspects ◽  
Main Components ◽  
Biofilm Matrix

ABSTRACTAmong pathogenic fungi,Candida albicansis most frequently associated with biofilm formation, a lifestyle that is entirely different from the planktonic state. One of the distinguishing features of these biofilms is the presence of extracellular material, commonly referred to as the “biofilm matrix.” The fungal biofilm matrix embeds sessile cells within these communities and plays important structural and physiological functions, including antifungal drug resistance with important clinical repercussions. This matrix is mostly self-produced by the fungal cells themselves and is composed of different types of biopolymers. InC. albicans, the main components of the biofilm matrix are carbohydrates, proteins, lipids, and DNA, but many of them remain unidentified and/or poorly characterized. In their recent article, Zarnowski et al. [mBio 5(4):e01333-14, 2014, doi:10.1128/mBio.01333-14] used a variety of biochemical and state-of-the-art “omic” approaches (glycomics, proteomics, and lipidomics) to identify and characterize unique biopolymers present in theC. albicansbiofilm matrix. Besides generating a true “encyclopedic” catalog of individual moieties from each of the different macromolecular categories, results also provide important insights into structural and functional aspects of the fungal biofilm matrix, particularly the interaction between different components and the contribution of multiple matrix constituents to biofilm antifungal drug resistance.

scholarly journals Advances in Molecular Tools and In Vivo Models for the Study of Human Fungal Pathogenesis

2020 ◽  
Vol 8 (6) ◽  
pp. 803 ◽  
Author(s):  
Dhara Malavia ◽  
Neil A. R. Gow ◽  
Jane Usher
Keyword(s):  
Drug Resistance ◽  
Fungal Pathogens ◽  
Galleria Mellonella ◽  
Pathogenic Fungi ◽  
Targeted Mutagenesis ◽  
Molecular Tools ◽  
In Vivo Models ◽  
Antifungal Drug Resistance ◽  
Made In

Pathogenic fungi represent an increasing infectious disease threat to humans, especially with an increasing challenge of antifungal drug resistance. Over the decades, numerous tools have been developed to expedite the study of pathogenicity, initiation of disease, drug resistance and host-pathogen interactions. In this review, we highlight advances that have been made in the use of molecular tools using CRISPR technologies, RNA interference and transposon targeted mutagenesis. We also discuss the use of animal models in modelling disease of human fungal pathogens, focusing on zebrafish, the silkworm, Galleria mellonella and the murine model.

Fluorescent potentiometric dyes for membrane-potential imaging

1994 ◽  
Vol 52 ◽  
pp. 166-167
Author(s):  
Leslie M. Loew
Keyword(s):  
Membrane Potential ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Optical Recording ◽  
Biological Processes ◽  
Major Focus ◽  
The Past ◽  
Excitable Systems ◽  
Major Application ◽  
The Impact

A major application of potentiometric dyes has been the multisite optical recording of electrical activity in excitable systems. After being championed by L.B. Cohen and his colleagues for the past 20 years, the impact of this technology is rapidly being felt and is spreading to an increasing number of neuroscience laboratories. A second class of experiments involves using dyes to image membrane potential distributions in single cells by digital imaging microscopy - a major focus of this lab. These studies usually do not require the temporal resolution of multisite optical recording, being primarily focussed on slow cell biological processes, and therefore can achieve much higher spatial resolution. We have developed 2 methods for quantitative imaging of membrane potential. One method uses dual wavelength imaging of membrane-staining dyes and the other uses quantitative 3D imaging of a fluorescent lipophilic cation; the dyes used in each case were synthesized for this purpose in this laboratory.

Comparison and Analysis of Computational Methods for Identifying N6 - methyladenosine Sites in Saccharomyces Cerevisiae

2020 ◽  
Vol 26 ◽  
Author(s):  
Pengmian Feng ◽  
Lijing Feng ◽  
Chaohui Tang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Computational Methods ◽  
Computational Analysis ◽  
Computational Prediction ◽  
Experimental Methods ◽  
Biological Processes ◽  
Biological Functions ◽  
Precise Location ◽  
Future Directions ◽  
The Past

Background and Purpose: N 6 -methyladenosine (m6A) plays critical roles in a broad set of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As good complements to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. Methods: In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to give a comprehensive review and comparison on existing methods. Results: Since researches on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progresses on computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites were presented. Conclusion: Taken together, we anticipate that this review will provide important guides for computational analysis of m 6A modifications.

scholarly journals Research supporting malaria control and elimination in China over four decades: a bibliometric analysis of academic articles published in chinese from 1980 to 2019

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yan-Qiu Du ◽  
Guo-Ding Zhu ◽  
Jun Cao ◽  
Jia-Yan Huang
Keyword(s):  
Drug Resistance ◽  
Bibliometric Analysis ◽  
Malaria Control ◽  
China National Knowledge Infrastructure ◽  
Malaria Research ◽  
The Past ◽  
Imported Case ◽  
Multidisciplinary Cooperation ◽  
Malaria Epidemic ◽  
Occurrence Matrix

Abstract Background China has accumulated considerable experience in malaria control and elimination over the past decades. Many research papers have been published in Chinese journals. This study intends to describe the development and experience of malaria control and elimination in China by quantitatively analysing relevant research using a bibliometric analysis. Methods A long-term, multistage bibliometric analysis was performed. Research articles published in Chinese journals from 1980 to 2019 were retrieved from the Wanfang and China National Knowledge Infrastructure (CNKI) databases. Year of publication, journal name and keywords were extracted by the Bibliographic Items Co-occurrence Matrix Builder (BICOMB). The K/A ratio (the frequency of a keyword among the total number of articles within a certain period) was considered an indicator of the popularity of a keyword in different decades. VOSviewer software was used to construct keyword co-occurrence network maps. Results A total of 16,290 articles were included. The overall number of articles continually increased. However, the number of articles published in the last three years decreased. There were two kinds of keyword frequency trends among the different decades. The K/A ratio of the keyword ‘Plasmodium falciparum’ decreased (17.05 in the 1980s, 13.04% in the 1990s, 9.86 in the 2000s, 5.28 in the 2010s), but those of ‘imported case’ and ‘surveillance’ increased. Drug resistance has been a continuous concern. The keyword co-occurrence network maps showed that the themes of malaria research diversified, and the degree of multidisciplinary cooperation gradually increased. Conclusions This bibliometric analysis revealed the trends in malaria research in China over the past 40 years. The results suggest emphasis on investigation, multidisciplinary participation and drug resistance by researchers and policymakers in malaria epidemic areas. The results also provide domestic experts with qualitative evidence of China’s experience in malaria control and elimination.

scholarly journals Mode of Selection and Experimental Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1287-1298
Author(s):  
James B Anderson ◽  
Caroline Sirjusingh ◽  
Ainslie B Parsons ◽  
Charles Boone ◽  
Claire Wickens ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Pleiotropic Effect ◽  
Antifungal Drug ◽  
Recessive Mutation ◽  
High Concentration ◽  
Gene Encoding ◽  
Antifungal Drug Resistance ◽  
Degree Of Dominance ◽  
A Genome ◽  
Abc Transporter Genes

Abstract We show that mode of selection, degree of dominance of mutations, and ploidy are determining factors in the evolution of resistance to the antifungal drug fluconazole in yeast. In experiment 1, yeast populations were subjected to a stepwise increase in fluconazole concentration over 400 generations. Under this regimen, two mutations in the same two chromosomal regions rose to high frequency in parallel in three replicate populations. These mutations were semidominant and additive in their effect on resistance. The first of these mutations mapped to PDR1 and resulted in the overexpression of the ABC transporter genes PDR5 and SNQ2. These mutations had an unexpected pleiotropic effect of reducing the residual ability of the wild type to reproduce at the highest concentrations of fluconazole. In experiment 2, yeast populations were subjected to a single high concentration of fluconazole. Under this regimen, a single recessive mutation appeared in each of three replicate populations. In a genome-wide screen of ∼4700 viable deletion strains, 13 were classified as resistant to fluconazole (ERG3, ERG6, YMR102C, YMR099C, YPL056C, ERG28, OSH1, SCS2, CKA2, SML1, YBR147W, YGR283C, and YLR407W). The mutations in experiment 2 all mapped to ERG3 and resulted in the overexpression of the gene encoding the drug target ERG11, but not PDR5 and SNQ2. Diploid hybrids from experiments 1 and 2 were less fit than the parents in the presence of fluconazole. In a variation of experiment 2, haploids showed a higher frequency of resistance than diploids, suggesting that degree of dominance and ploidy are important factors in the evolution of antifungal drug resistance.

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