Article
Biotechnology & Applied Microbiology
Claire Oget-Ebrad, Naveen Kumar Kadri, Gabriel Costa Monteiro Moreira, Latifa Karim, Wouter Coppieters, Michel Georges, Tom Druet
Summary: This study evaluates several population-based haplotype phasing methods in a Holstein cattle pedigree using whole-genome sequence data. The results show that ShapeIT4.1 and Beagle5.2 are the most accurate methods, particularly for phasing long segments and in the first scenario.
Article
Biotechnology & Applied Microbiology
Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
Summary: nPhase is a tool that does not consider ploidy, using long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy. Through testing on simulated and real polyploids, nPhase achieves an average accuracy of over 95% and obtains an average of 1.25 contiguous haplotigs per haplotype to cover more than 90% of each chromosome.
Article
Chemistry, Analytical
Prakhar Dutta, Yi-Jung Lu, Han-Yu Hsieh, Tyng-Yuh Lee, Yi-Tzu Lee, Chao-Min Cheng, Yu-Jui Fan
Summary: This study developed a rapid screening procedure for detecting Candida albicans using electrochemical sensors, breaking down the cell wall with hemicellulase and detecting soluble sugars with a glucose meter. Spiked samples of C. albicans suspended in urine and serum demonstrated the feasibility of the method in a simulated real situation.
Article
Genetics & Heredity
Veronica Mixao, Ester Saus, Teun Boekhout, Toni Gabaldon
Summary: Candida albicans is the most commonly reported species causing candidiasis, with controversial taxonomic classification and potential hybrid origin with Candida africana. Recent genomic analyses suggest a shared hybrid origin of C. albicans and C. africana, with parallel massive loss of heterozygosity in C. stellatoidea as in C. africana.
Review
Biochemical Research Methods
Ziad Al Bkhetan, Gursharan Chana, Kotagiri Ramamohanarao, Karin Verspoor, Benjamin Goudey
Summary: This study comprehensively evaluated consensus strategies for haplotype phasing, exploring the performance of different consensus paradigms and the impact on the downstream task of genotype imputation across various datasets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Microbiology
Elise Iracane, Samuel Vega-Estevez, Alessia Buscaino
Summary: Candida albicans is a dimorphic opportunistic pathogen that can colonize most humans without harm, but can also cause life-threatening infections in immunocompromised individuals. The ability to grow as yeast and hyphae, as well as to form biofilms, is critical for its survival in the host. Transcriptional regulatory networks are well understood in controlling the switching between different forms, but the role of non-DNA based epigenetic modulation in morphological transitions is still not fully explored.
Article
Immunology
Weidong Qian, Xinchen Li, Qiming Liu, Jiaxing Lu, Ting Wang, Qian Zhang
Summary: Paeonol exhibits antifungal and antibiofilm activities against Candida albicans and Cryptococcus neoformans, disrupting cell membrane integrity, inhibiting biofilm formation, and affecting yeast-to-hyphal transition.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Microbiology
Nicole Robbins, Leah E. Cowen
Summary: Fungi have a significant impact on human health, causing numerous infections and deaths worldwide each year. The emergence of drug-resistant fungal pathogens and the lack of effective treatment options exacerbate the public health burden. However, scientific advances in chemistry, genetics, and biochemistry methodologies have enabled the discovery of novel antifungal compounds and exploration of potential therapeutic approaches.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Angelique N. Besold, Vinit Shanbhag, Michael J. Petris, Valeria C. Culotta
Summary: Copper is essential for all organisms, with ceruloplasmin being the most abundant extracellular copper-binding molecule in serum. Studies suggest that ceruloplasmin may be a preferred source of copper for fungal pathogens.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Robert Zarnowski, Andrea Noll, Marc G. Chevrette, Hiram Sanchez, Ryley Jones, Hanna Anhalt, Jen Fossen, Anna Jaromin, Cameron Currie, Jeniel E. Nett, Aaron Mitchell, David R. Andes
Summary: The fungal pathogen Candida albicans can form biofilms that protect it from drugs and the immune system by releasing extracellular vesicles (EVs) that promote extracellular matrix formation and resistance to antifungal drugs. The study identifies functions for numerous EV cargo proteins in biofilm matrix assembly, drug resistance, fungal cell adhesion, and dissemination. The findings suggest that EVs play a crucial role in coordinating biofilm development in C. albicans.
NATURE COMMUNICATIONS
(2021)
Review
Food Science & Technology
Lohith Kunyeit, Reeta P. Rao, K. A. Anu-Appaiah
Summary: Yeasts derived from fermented foods have various characteristics, such as larger cells, a rigid cell wall composed primarily of glucans and mannans, natural resistance to antibiotics, and the secretion of beneficial secondary metabolites. This review also focuses on the therapeutic applications of probiotic yeasts from fermented foods in treating Candida-associated infections and preventing health complications caused by opportunistic fungal colonization, including drug-resistant superbugs.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Microbiology
Leandro Honorato, Joana Feital Demetrio de Araujo, Cameron C. Ellis, Alicia Corbellini Piffer, Yan Pereira, Susana Frases, Glauber Ribeiro de Sousa Araujo, Bruno Pontes, Maria Tays Mendes, Marcos Dias Pereira, Allan J. Guimaraes, Natalia Martins da Silva, Gabriele Vargas, Luna Joffe, Maurizio Del Poeta, Joshua D. Nosanchuk, Daniel Zamith-Miranda, Flavia Coelho Garcia dos Reis, Haroldo Cesar de Oliveira, Marcio L. Rodrigues, Sharon de Toledo Martins, Lysangela Ronalte Alves, Igor C. Almeida, Leonardo Nimrichter
Summary: This study investigates the impact of fungal extracellular vesicles (EVs) on biofilm formation and virulence in Candida albicans. The researchers found that C. albicans EVs inhibit biofilm formation and promote pseudohyphae formation. EVs from different strains of C. albicans, S. cerevisiae, and H. capsulatum also inhibit yeast-to-hyphae differentiation. The inhibitory effect of C. albicans EVs is attributed to a combination of lipid compounds.
Article
Biotechnology & Applied Microbiology
Hua Ling, Ruirui Liu, Qi Hui Sam, Haosheng Shen, Louis Yi Ann Chai, Matthew Wook Chang
Summary: In this study, a commercial boulardii strain was engineered to produce medium-chain fatty acids (MCFAs) with antagonistic effects against Candida albicans. The engineered boulardii strain constitutively produced and secreted a mixture of C6:0, C8:0, and C10:0, which reduced biofilm and hyphal formations in C. albicans. The secreted MCFAs also upregulated the expression of virulence-related genes and immune response genes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Infectious Diseases
Nashwa Mohamed Reda, Reem Mostafa Hassan, Sherifa Tarek Salem, Reham Hamed A. Yousef
Summary: Candidemia remains a significant problem in healthcare settings, with a changing distribution of Candida species. C. albicans is still the most prevalent species, but non-albicans species are increasing, particularly in pediatric patients. The emergence of uncommon Candida species is concerning and requires prompt management.
Article
Microbiology
Mingzhu Guo, Kuan Yang, Zhifei Zhou, Yujiang Chen, Ziye Zhou, Peng Chen, Ruizhe Huang, Xiaojing Wang
Summary: This study confirms that stevioside has anti-caries effects on Streptococcus mutans and Candida albicans in a dual-species biofilm. It inhibits biofilm formation and reduces the risk of developing dental caries more effectively than sucrose and xylitol in this model.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Eduardo F. C. Scopel, James Hose, Douda Bensasson, Audrey P. Gasch
Summary: Individuals with abnormal numbers of chromosomes can vary significantly in their expression of aneuploidy phenotypes. The genetic makeup of an individual has a greater impact on tolerance of karyotypic imbalance than ecology. Chromosome gain and loss prevalence and tolerance are influenced by genetic background and can potentially lead to phenotypic benefits in evolutionary trajectories.
Article
Multidisciplinary Sciences
Guilherme B. Dias, Musaad A. Altammami, Hamadttu A. F. El-Shafie, Fahad M. Alhoshani, Mohamed B. Al-Fageeh, Casey M. Bergman, Manee M. Manee
Summary: This study generated a haplotype-resolved diploid genome assembly for R. ferrugineus using 10x Genomics linked-read sequencing, which showed a high completeness in gene content without suffering from haplotype-induced duplication artifacts.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
S. Earl Kang, Brandi N. Celia, Douda Bensasson, Michelle Momany
Summary: Aspergillus fumigatus causes over 300,000 life-threatening infections annually and is genetically identical dormant spores wind-dispersed in various environments, where they can germinate and cause disease in susceptible hosts. High-throughput single-cell analysis revealed that genetically identical individuals exhibit different germination phenotypes, the environment of spore production affects spore size and germination heterogeneity, and impacts the virulence in a Galleria mellonella host.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Shunhua Han, Preston J. Basting, Guilherme B. Dias, Arthur Luhur, Andrew C. Zelhof, Casey M. Bergman
Summary: Cell culture systems can be improved by leveraging transposable element insertions to authenticate Drosophila cell lines and understand the forces impacting metazoan genomes during evolution in cell culture. A new bioinformatics approach, ngs_te_mapper2, has been developed to detect TE insertions and estimate allele frequencies in legacy whole-genome sequencing data.
Article
Genetics & Heredity
Mirela Pelizaro Valeri, Guilherme Borges Dias, Alice Alves do Espirito Santo, Camila Nascimento Moreira, Yatiyo Yonenaga-Yassuda, Iara Braga Sommer, Gustavo C. S. Kuhn, Marta Svartman
Summary: This study identified a novel satellite DNA in Trichechus manatus using the sequenced genome and TAREAN technology, describing its proportion and structure in the genome and detecting similar sequences in related species. By constructing a neighbor-joining tree, the evolutionary relationship between these sequences was revealed.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Daniel Mariyappa, Douglas B. Rusch, Shunhua Han, Arthur Luhur, Danielle Overton, David F. B. Miller, Casey M. Bergman, Andrew C. Zelhof
Summary: This study developed a PCR-based next-generation sequencing protocol to identify Drosophila cell lines using transposable element insertions as markers. The results showed that the protocol can reliably identify different cell lines, and there is minimal change in the genome-wide distribution of transposable element families after 50 cell passages.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Guilherme B. Dias, Ahmad M. Aldossary, Hamadttu A. F. El-Shafie, Fahad M. Alhoshani, Mohamed B. Al-Fageeh, Casey M. Bergman, Manee M. Manee
Summary: The mitochondrial genome of Jebusaea hammerschmidtii was assembled, annotated, and compared to other longhorn beetles, showing typical gene content. Phylogenetic analysis placed J. hammerschmidtii within the Cerambycinae subfamily and supported the monophyly of Cerambycinae, Lamiinae, and Prioninae subfamilies.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Microbiology
Jingxuan Chen, David J. Garfinkel, Casey M. Bergman
Summary: This study presents a long-read genome assembly of Saccharomyces uvarum strain CBS 7001 based on PacBio whole-genome shotgun sequence data, providing an improved reference genome for an important yeast in the Saccharomyces sensu stricto clade.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Genetics & Heredity
Shunhua Han, Guilherme B. Dias, Preston J. Basting, Michael G. Nelson, Sanjai Patel, Mar Marzo, Casey M. Bergman
Summary: This study sequenced the genomes of 25 sublines of Drosophila S2 cells and found that transposable element insertions can be used as markers for phylogenetic reconstruction in a model cell culture system. Comparison of DNA copy number evolution across sublines revealed different patterns of genome organization, which supported the overall evolutionary history reconstructed using transposable element insertions. Analysis showed that ongoing transposition in cell culture is dominated by episodic activity of a small number of retrotransposon families. This study demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, potentially impacting the reproducibility of experiments that do not control for subline identity.
Article
Biochemistry & Molecular Biology
Shunhua Han, Guilherme B. Dias, Preston J. Basting, Raghuvir Viswanatha, Norbert Perrimon, Casey M. Bergman
Summary: Animal cell lines often undergo extreme genome restructuring events that hinder de novo whole-genome assembly. This study used long-read and linked-read technologies to sequence the genome of a tetraploid Drosophila cell line and developed a novel method called TELR for TE analysis. The results shed light on the role and mechanism of transposable elements in animal cell culture genome evolution.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Entomology
Manee M. Manee, Fahad H. Alqahtani, Badr M. Al-Shomrani, Hamadttu A. F. El-Shafie, Guilherme B. Dias
Summary: The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is a devastating pest of palm trees worldwide. Understanding its biology and genetics is crucial for mitigating its economic and biodiversity impact. Advances in omics approaches have provided new avenues for pest control, such as genetic engineering. This review summarizes the use of omics technologies in RPW research, highlights important findings for pest management, and discusses future opportunities and challenges in this area of study.
Article
Genetics & Heredity
Jingxuan Chen, Preston J. Basting, Shunhua Han, David J. Garfinkel, Casey M. Bergman
Summary: Researchers have re-implemented the TE insertion detection tool McClintock, improving its installation, speed, stability, and extensibility using Python, Snakemake, and Conda. The new version includes 12 TE detectors, interactive HTML reports, and a simulation framework. Testing on simulated data showed that RelocaTE2 had the highest recall and precision for identifying non-reference TE insertions. The tool also successfully revealed fine-scale target preferences for retrotransposons in yeast using resequencing data.
