Publications by authors named "Michael Tassia"

Article Synopsis
  • The study presents detailed genomes of six ape species, achieving high accuracy and complete sequencing of all their chromosomes.
  • It addresses complex genomic regions, leading to enhanced understanding of evolutionary relationships among these species.
  • The findings will serve as a crucial resource for future research on human evolution and our closest ape relatives.
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Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity. Although invaluable, studies investigating these links in humans have been strongly biased towards participants of European ancestries, which constrains generalizability and hinders evolutionary research. Here to address these limitations, we developed MAGE, an open-access RNA sequencing dataset of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project, spread across 5 continental groups and 26 populations.

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Article Synopsis
  • Apes have two sex chromosomes: the essential Y chromosome for male reproduction and the X chromosome necessary for both reproduction and cognition, with differences in mating patterns affecting their function.
  • Studying these chromosomes is challenging due to their repetitive structures, but researchers created gapless assemblies for five great apes and one lesser ape to explore their evolutionary complexities.
  • The Y chromosomes are highly variable and undergo significant changes compared to the more stable X chromosomes, and this research can provide insights into human evolution and aid in the conservation of endangered ape species.
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Article Synopsis
  • Apes have two main sex chromosomes, X and Y, where Y is crucial for male reproduction and its deletions can lead to infertility, while X is important for both reproduction and brain function.
  • Recent advancements in genomic techniques helped researchers create complete structures of the X and Y chromosomes for multiple great ape species, allowing them to explore their evolutionary complexities.
  • Findings indicate that Y chromosomes are highly variable and undergo rapid changes due to unique genetic regions and transposable elements, while X chromosomes are more stable, highlighting differing evolutionary paths among great ape species.
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Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research. To address these limitations, we developed MAGE, an open-access RNA-seq data set of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project spread across 5 continental groups and 26 populations.

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Cnidarians are commonly recognized as sea jellies, corals, or complex colonies such as the Portuguese man-of-war. While some cnidarians possess rigid internal calcareous skeletons (e.g.

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Hummingbirds are very well adapted to sustain efficient and rapid metabolic shifts. They oxidize ingested nectar to directly fuel flight when foraging but have to switch to oxidizing stored lipids derived from ingested sugars during the night or long-distance migratory flights. Understanding how this organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation.

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Background: Telomere shortening is a well-characterized cellular aging mechanism, and short telomere syndromes cause age-related disease. However, whether long telomere length is advantageous is poorly understood.

Methods: We examined the clinical and molecular features of aging and cancer in persons carrying heterozygous loss-of-function mutations in the telomere-related gene and noncarrier relatives.

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Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Although their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes-the animal clade composed of chordates, hemichordates, and echinoderms.

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Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species.

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Background: Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth.

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The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates.

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Tunicata, a diverse clade of approximately 3000 described species of marine, filter-feeding chordates, is of great interest to researchers because tunicates are the closest living relatives of vertebrates and they facilitate comparative studies of our own biology. The group also includes numerous invasive species that cause considerable economic damage and some species of tunicates are edible. Despite their diversity and importance, relationships among major lineages of Tunicata are not completely resolved.

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Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Toll-like receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen.

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Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates.

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