IU Indianapolis ScholarWorks :: Browsing by Subject "Yeast"

Browsing by Subject "Yeast"

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A 20-year retrospective clinical analysis of Candida infections in tertiary centre: Single-center experience
(Elsevier, 2022) Muzaheed; Alshehri, Bashayer A.; Rabaan, Ali A.; El-Masry, Omar S.; Acharya, Sadananda; Alzahrani, Faisal M.; Al Mutair, Abbas; Alhumaid, Saad; Al-Tawfiq, Jaffar A.; Muhammad, Javed; Khan, Amjad; Dhama, Kuldeep; Al-Omari, Awad; Medicine, School of Medicine
Introduction: Fungal infections have risen exponentially in the last decade. In fact, candidiasis has become the most frequent type of hospital acquired infection especially in patients receiving treatment for chronic and terminal illnesses in a hospital. A retrospective analysis for a period of twenty year was undertaken to analyze the incidence rate of candidiasis, especially of Candida species, patients treated in a tertiary care center. Materials and methods: Clinical data was collected from samples of patients who were receiving tertiary care were presenting with clinically suspected fungal infections. Direct microscopy with 10% potassium hydroxide was done to visualize the presence of fungal elements, and Gram staining was done for any suspected yeast infection. The samples were inoculated on Sabouraud's Dextrose Agar and kept at 22 °C. Results: A total of 1256 samples with presumed fungal etiology were included in the study. The maximum number of fungal infections were present in elderly (70-79 years age). Females (53.8%) were more affected (45.5%). 21% isolates were identified as yeast but belonged to non-Candida fungi. Among Candida species, Candida albicans was the most dominant species (58.3%) followed by Candida glabrata (6.4%). The year-round data of fungal cases showed that the highest incident of Candida albicans infection were in January with a mean value of 3.80, while the lowest infections were reported in June, with prevalence of 2.32 of C. albicans. The twenty-year data analysis showed that the years 2001 and 2000 showed the highest incidents of C. albicans, with a mean prevalence of 7.50 and 6.83, respectively. Specimen vs fungal prevalence data showed that 38% of the C. albicans were isolated from body aspirate specimens, followed by 26% from swab specimens. Conclusion: The high prevalence of Candida spp. in the present study suggests increased susceptibility of patients with critical or chronic illnesses to fungal infections.
Altered sterol metabolism in budding yeast affects mitochondrial iron–sulfur (Fe-S) cluster synthesis
(American Society for Biochemistry and Molecular Biology, 2018-07-06) Ward, Diane M.; Chen, Opal S.; Li, Liangtao; Kaplan, Jerry; Bhuiyan, Shah Alam; Natarajan, Selvamuthu K.; Bard, Martin; Cox, James E.; Microbiology & Immunology, IU School of Medicine
Ergosterol synthesis is essential for cellular growth and viability of the budding yeast Saccharomyces cerevisiae, and intracellular sterol distribution and homeostasis are therefore highly regulated in this species. Erg25 is an iron-containing C4-methyl sterol oxidase that contributes to the conversion of 4,4-dimethylzymosterol to zymosterol, a precursor of ergosterol. The ERG29 gene encodes an endoplasmic reticulum (ER)-associated protein, and here we identified a role for Erg29 in the methyl sterol oxidase step of ergosterol synthesis. ERG29 deletion resulted in lethality in respiring cells, but respiration-incompetent (Rho- or Rho0) cells survived, suggesting that Erg29 loss leads to accumulation of oxidized sterol metabolites that affect cell viability. Down-regulation of ERG29 expression in Δerg29 cells indeed led to accumulation of methyl sterol metabolites, resulting in increased mitochondrial oxidants and a decreased ability of mitochondria to synthesize iron-sulfur (Fe-S) clusters due to reduced levels of Yfh1, the mammalian frataxin homolog, which is involved in mitochondrial iron metabolism. Using a high-copy genomic library, we identified suppressor genes that permitted growth of Δerg29 cells on respiratory substrates, and these included genes encoding the mitochondrial proteins Yfh1, Mmt1, Mmt2, and Pet20, which reversed all phenotypes associated with loss of ERG29 Of note, loss of Erg25 also resulted in accumulation of methyl sterol metabolites and also increased mitochondrial oxidants and degradation of Yfh1. We propose that accumulation of toxic intermediates of the methyl sterol oxidase reaction increases mitochondrial oxidants, which affect Yfh1 protein stability. These results indicate an interaction between sterols generated by ER proteins and mitochondrial iron metabolism.
A Broad-Based Mosquito Yeast Interfering RNA Pesticide Targeting Rbfox1 Represses Notch Signaling and Kills Both Larvae and Adult Mosquitoes
(MDPI, 2021-09-28) Mysore, Keshava; Sun, Longhua; Hapairai, Limb K.; Wang, Chien-Wei; Roethele, Joseph B.; Igiede, Jessica; Scheel, Max P.; Scheel, Nicholas D.; Li, Ping; Wei, Na; Severson, David W.; Duman-Scheel, Molly; Medical and Molecular Genetics, School of Medicine
Prevention of mosquito-borne infectious diseases will require new classes of environmentally safe insecticides and novel mosquito control technologies. Saccharomyces cerevisiae was engineered to express short hairpin RNA (shRNA) corresponding to mosquito Rbfox1 genes. The yeast induced target gene silencing, resulting in larval death that was observed in both laboratory and outdoor semi-field trials conducted on Aedes aegypti. High levels of mortality were also observed during simulated field trials in which adult females consumed yeast delivered through a sugar bait. Mortality correlated with defects in the mosquito brain, in which a role for Rbfox1 as a positive regulator of Notch signaling was identified. The larvicidal and adulticidal activities of the yeast were subsequently confirmed in trials conducted on Aedes albopictus, Anopheles gambiae, and Culex quinquefasciatus, yet the yeast had no impact on survival of select non-target arthropods. These studies indicate that yeast RNAi pesticides targeting Rbfox1 could be further developed as broad-based mosquito larvicides and adulticides for deployment in integrated biorational mosquito control programs. These findings also suggest that the species-specificity of attractive targeted sugar baits, a new paradigm for vector control, could potentially be enhanced through RNAi technology, and specifically through the use of yeast-based interfering RNA pesticides.
A conserved female-specific larval requirement for MtnB function facilitates sex separation in multiple species of disease vector mosquitoes
(BMC, 2021-06-26) Mysore, Keshava; Sun, Longhua; Roethele, Joseph B.; Li, Ping; Igiede, Jessica; Misenti, Joi K.; Duman‑Scheel, Molly; Medical and Molecular Genetics, School of Medicine
Background: Clusters of sex-specific loci are predicted to shape the boundaries of the M/m sex-determination locus of the dengue vector mosquito Aedes aegypti, but the identities of these genes are not known. Identification and characterization of these loci could promote a better understanding of mosquito sex chromosome evolution and lead to the elucidation of new strategies for male mosquito sex separation, a requirement for several emerging mosquito population control strategies that are dependent on the mass rearing and release of male mosquitoes. This investigation revealed that the methylthioribulose-1-phosphate dehydratase (MtnB) gene, which resides adjacent to the M/m locus and encodes an evolutionarily conserved component of the methionine salvage pathway, is required for survival of female larvae. Results: Larval consumption of Saccharomyces cerevisiae (yeast) strains engineered to express interfering RNA corresponding to MtnB resulted in target gene silencing and significant female death, yet had no impact on A. aegypti male survival or fitness. Integration of the yeast larvicides into mass culturing protocols permitted scaled production of fit adult male mosquitoes. Moreover, silencing MtnB orthologs in Aedes albopictus, Anopheles gambiae, and Culex quinquefasciatus revealed a conserved female-specific larval requirement for MtnB among different species of mosquitoes. Conclusions: The results of this investigation, which may have important implications for the study of mosquito sex chromosome evolution, indicate that silencing MtnB can facilitate sex separation in multiple species of disease vector insects.
Correction: Mysore et al. A Broad-Based Mosquito Yeast Interfering RNA Pesticide Targeting Rbfox1 Represses Notch Signaling and Kills Both Larvae and Adult Mosquitoes. Pathogens 2021, 10, 1251
(MDPI, 2022-08-23) Mysore, Keshava; Sun, Longhua; Hapairai, Limb K.; Wang, Chien-Wei; Roethele, Joseph B.; Igiede, Jessica; Scheel, Max P.; Scheel, Nicholas D.; Li, Ping; Wei, Na; Severson, David W.; Duman-Scheel, Molly; Medical and Molecular Genetics, School of Medicine
In the original publication [1], there was a mistake in Figure 1 as published. The wrong graph was inadvertently included in panel 1f (dose–response curve). Additionally, the original image for the gel shown in panel 1a is now included in the Supplementary Materials.
Data on the identity of non-canonical complexes formed from proteasome subunits in vivo
(Elsevier, 2016-11-22) Hammack, Lindsay J.; Kusmierczyk, Andrew R.; Department of Biology, School of Science
The dataset presented here represents analysis supplied by the local proteomics core facility on samples submitted to it in support of the article "Assembly of proteasome subunits into non-canonical complexes in vivo" Hammack and Kusmierczyk (2016) [1]. This article provides the detailed protein contents of gel slices, cut from non-denaturing polyacrylamide gels, containing distinct protein complexes visualized following gel staining. The identification of the protein contents of these complexes was carried out by liquid chromatography tandem mass-spectrometry (LC-MS/MS).
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes
(PLOS, 2006-08-04) Haynes, Chad; Oldfield, Christopher J.; Ji, Fei; Klitgord, Niels; Cusick, Michael E.; Radivojac, Predrag; Uversky, Vladimir N.; Vidal, Marc; Iakoucheva, Lilia M.; Biochemistry and Molecular Biology, School of Medicine
Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted structural disorder, the disorder propensities of proteins with various numbers of interacting partners from four eukaryotic organisms (Caenorhabditis elegans, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens) were investigated. The results of PONDR VL-XT disorder analysis show that for all four studied organisms, hub proteins, defined here as those that interact with ≥10 partners, are significantly more disordered than end proteins, defined here as those that interact with just one partner. The proportion of predicted disordered residues, the average disorder score, and the number of predicted disordered regions of various lengths were higher overall in hubs than in ends. A binary classification of hubs and ends into ordered and disordered subclasses using the consensus prediction method showed a significant enrichment of wholly disordered proteins and a significant depletion of wholly ordered proteins in hubs relative to ends in worm, fly, and human. The functional annotation of yeast hubs and ends using GO categories and the correlation of these annotations with disorder predictions demonstrate that proteins with regulation, transcription, and development annotations are enriched in disorder, whereas proteins with catalytic activity, transport, and membrane localization annotations are depleted in disorder. The results of this study demonstrate that intrinsic structural disorder is a distinctive and common characteristic of eukaryotic hub proteins, and that disorder may serve as a determinant of protein interactivity.
Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins
(PLOS, 2008-02-13) Warden, Charles D.; Kim, Seong-Ho; Yi, Soojin V.; Biostatistics, School of Public Health
Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.
Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase
(Oxford University Press, 2017-05-19) Rogers, Cody M.; Wang, Joseph Che-Yen; Noguchi, Hiroki; Imasaki, Tsuyoshi; Takagi, Yuichiro; Bochman, Matthew L.; Biochemistry and Molecular Biology, School of Medicine
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops. Consistent with their roles at telomeres, telomeric repeat sequence DNA also stimulated binding and unwinding by these enzymes. Finally, electron microscopy revealed that Hrq1 and RecQ4 share similar structural features. These results solidify Hrq1 as a true RecQ4 homolog and position it as the premier model to determine how RecQ4 mutations lead to genomic instability and disease.
A Yeast RNA-Interference Pesticide Targeting the Irx Gene Functions as a Broad-Based Mosquito Larvicide and Adulticide
(MDPI, 2021-11-02) Mysore, Keshava; Sun, Longhua; Hapairai, Limb K.; Wang, Chien-Wei; Igiede, Jessica; Roethele, Joseph B.; Scheel, Nicholas D.; Scheel, Max P.; Li, Ping; Wei, Na; Severson, David W.; Duman-Scheel, Molly; Medical and Molecular Genetics, School of Medicine
Concerns for widespread insecticide resistance and the unintended impacts of insecticides on nontarget organisms have generated a pressing need for mosquito control innovations. A yeast RNAi-based insecticide that targets a conserved site in mosquito Irx family genes, but which has not yet been identified in the genomes of nontarget organisms, was developed and characterized. Saccharomyces cerevisiae constructed to express short hairpin RNA (shRNA) matching the target site induced significant Aedes aegypti larval death in both lab trials and outdoor semi-field evaluations. The yeast also induced high levels of mortality in adult females, which readily consumed yeast incorporated into an attractive targeted sugar bait (ATSB) during simulated field trials. A conserved requirement for Irx function as a regulator of proneural gene expression was observed in the mosquito brain, suggesting a possible mode of action. The larvicidal and adulticidal properties of the yeast were also verified in Aedes albopictus, Anopheles gambiae, and Culexquinquefasciatus mosquitoes, but the yeast larvicide was not toxic to other nontarget arthropods. These results indicate that further development and evaluation of this technology as an ecofriendly control intervention is warranted, and that ATSBs, an emerging mosquito control paradigm, could potentially be enriched through the use of yeast-based RNAi technology.

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