Laura A. Katz
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View article: Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae
Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae Open
Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved met…
View article: A geothermal amoeba sets a new upper temperature limit for eukaryotes
A geothermal amoeba sets a new upper temperature limit for eukaryotes Open
The study of temperature limits has transformed our knowledge of the boundaries of life but has been largely focused on bacteria and archaea. We isolated a novel geothermal amoeba, Incendiamoeba cascadensis, that divides at 63°C (145.4°F),…
View article: Rethinking large-scale phylogenomics with EukPhylo v.1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages
Rethinking large-scale phylogenomics with EukPhylo v.1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages Open
Eukaryotic diversity is largely microbial, with macroscopic lineages (plants, animals, and fungi) nesting among a plethora of diverse protists. Our understanding of the evolutionary relationships among eukaryotes is rapidly advancing throu…
View article: Freshwater Foraminifera Biodiversity in New England (<scp>USA</scp>): Evaluation of Field Sites and a Botanical Garden
Freshwater Foraminifera Biodiversity in New England (<span>USA</span>): Evaluation of Field Sites and a Botanical Garden Open
Despite textbook definitions of foraminifera as marine organisms, foraminifera also occur in freshwater habitats, with first reports from ~150 years ago. Yet, to date, very few freshwater foraminifera have been described in part because th…
View article: Genome content reorganization in the non-model ciliate <i>Chilodonella uncinata</i> : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development
Genome content reorganization in the non-model ciliate <i>Chilodonella uncinata</i> : insights into nuclear architecture, DNA content, and chromosome fragmentation during macronuclear development Open
Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following …
View article: Visualizing Epigenetics: A Review of Microscopy Techniques for Investigating DNA Methylation Patterns, Chromatin Structure, and Gene Expression
Visualizing Epigenetics: A Review of Microscopy Techniques for Investigating DNA Methylation Patterns, Chromatin Structure, and Gene Expression Open
Microscopy approaches are frequently used to decipher the localization and quantify the abundance of biologically relevant molecular targets within single cells. Recent research has applied many optical imaging techniques to specifically v…
View article: Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera
Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera Open
Analyses of codon usage in eukaryotes suggest that amino acid usage responds to GC pressure so AT-biased substitutions drive higher usage of amino acids with AT-ending codons. Here, we combine single-cell transcriptomics and phylogenomics …
View article: Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes
Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes Open
View article: Protists as mediators of complex microbial and viral associations
Protists as mediators of complex microbial and viral associations Open
Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ culti…
View article: Correction: Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates
Correction: Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates Open
[This corrects the article DOI: 10.1371/journal.pone.0291688.].
View article: Genome content in the non-model ciliate<i>Chilodonella uncinata</i>: insights into nuclear architecture, gene-sized chromosomes among the total DNA in their somatic macronuclei during their development
Genome content in the non-model ciliate<i>Chilodonella uncinata</i>: insights into nuclear architecture, gene-sized chromosomes among the total DNA in their somatic macronuclei during their development Open
Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following …
View article: Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict
Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict Open
In contrast to the typified view of genome cycling only between haploidy and diploidy, there is evidence from across the tree of life of genome dynamics that alter both copy number (i.e. ploidy) and chromosome complements. Here, we highlig…
View article: Rethinking large scale phylogenomics with EukPhylo v1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages
Rethinking large scale phylogenomics with EukPhylo v1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages Open
Eukaryotic diversity is largely microbial, with macroscopic lineages (plant, animals and fungi) nesting among a plethora of diverse protists. Understanding the evolutionary relationships among eukaryotes is rapidly advancing through omics …
View article: Phylogeny and species delimitation of ciliates in the genus<i>Spirostomum</i>(Class, Heterotrichea) using single-cell transcriptomes
Phylogeny and species delimitation of ciliates in the genus<i>Spirostomum</i>(Class, Heterotrichea) using single-cell transcriptomes Open
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing signific…
View article: Correction to: Editorial 2024
Correction to: Editorial 2024 Open
View article: Foraminifera as a model of eukaryotic genome dynamism
Foraminifera as a model of eukaryotic genome dynamism Open
In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual’s life cycle. However, the few detailed studies of microeukaryo…
View article: Editorial 2024
Editorial 2024 Open
View article: Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates
Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates Open
The evolution of lineage-specific gene families remains poorly studied across the eukaryotic tree of life, with most analyses focusing on the recent evolution of de novo genes in model species. Here we explore the origins of lineage-specif…
View article: Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution
Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution Open
We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolut…
View article: Phylogenomics Reveals Potential Low-Oxygen Adaptations in Free-Living Testate Amoebae
Phylogenomics Reveals Potential Low-Oxygen Adaptations in Free-Living Testate Amoebae Open
View article: Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing
Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing Open
View article: Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes
Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes Open
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostl…
View article: Updated Virophage Taxonomy and Distinction from Polinton-like Viruses
Updated Virophage Taxonomy and Distinction from Polinton-like Viruses Open
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful…
View article: Illuminating protist diversity in pitcher plants and bromeliad tanks
Illuminating protist diversity in pitcher plants and bromeliad tanks Open
Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The …
View article: Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages
Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages Open
Advances in phylogenomics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypo…
View article: Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events
Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events Open
Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfe…
View article: Macronuclear development in ciliates, with a focus on nuclear architecture
Macronuclear development in ciliates, with a focus on nuclear architecture Open
Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei vary treme…
View article: Editorial
Editorial Open
View article: Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution
Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution Open
Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered “junk” DNA (i.e., deleterious or at best neutral), more r…
View article: Genome architecture used to supplement species delineation in two cryptic marine ciliates (study on congeneric tintinnid ciliates Schmidingerella arcuata and Schmidingerella meunieri (published as Smith et al. 2022 in Molecular Ecology Resources)
Genome architecture used to supplement species delineation in two cryptic marine ciliates (study on congeneric tintinnid ciliates Schmidingerella arcuata and Schmidingerella meunieri (published as Smith et al. 2022 in Molecular Ecology Resources) Open
These data are associated with the following publication: Genome architecture used to supplement species delineation in two cryptic marine ciliates Susan A. Smith, Luciana F. Santoferrara, Laura A. Katz, George …