Biology subjects

Fugmann, S. D.

Publications and source records attributed to Fugmann, S. D..

6 recordsLinked to original sources

bioRxiv2025

An ancient evolutionary origin for IL-1 cytokines as mediators of immunity

Inflammation is a hallmark of immune responses. Its mechanistic underpinnings in mammals are well-defined: pro-inflammatory cytokines of the interleukin 1 (IL-1) superfamily establish and support microenvironments that promote immune cell activities. Despite a growing number of reports on inflammatory processes and components of the IL-1 signaling axis in several invertebrate lineages, orthologs of these central cytokines have not been detected outside of the jawed vertebrates. Here, protein structure prediction algorithms were applied to identify genes encoding a family of IL-1 proteins with homologs throughout Eumetazoa (termed "IL-1anc" to reflect their ancestral evolutionary origin). Using Petromyzon marinus (sea lamprey) and Strongylocentrotus purpuratus (purple sea urchin) as model systems, we demonstrate that IL-1anc proteins share important features with mammalian IL-1/IL-1{beta} including expression patterns, protein localization, and processing. Together, our data indicate that the IL-1 superfamily and associated circuitry represent a foundational module of animal immunity that far predates the jawed vertebrates.

immunology↗

bioRxiv2025

Mesophilic compostability of polylactic acid and the associated microbiome as revealed by metagenomics

Polylactic acid (PLA), the most popular bioplastic, has high sustainability potential as it is bio-sourced and also harbors biodegradability. A form of its biodegradability is via composting, and it was previously established that thermophilic temperatures are needed for PLA breakdown in composts. Here we report the development of composts that have overcome the temperature requirement needed for PLA composting. Our mesophilic composts exhibited clear PLA biodegradability, and this is due to specific biological activity enriched in our material. To investigate the nature of this mesophilic activity, we conducted metagenomics analysis to reveal the microbial composition and enzyme-coding potential associated with PLA biodegradation. These efforts revealed multiple enzyme subtypes with strong enrichment on PLA surfaces in our trained composts, and the top candidate was a type of hydro-lyase, an enzyme that can cleave carbon-carbon and carbon-oxygen bonds, both present in the chemical structure of PLA, in the absence of water. Hydro-lyases represent a novel class of enzymes that could facilitate PLA degradation, and our results point to the model that the combinatorial action of multiple types of enzymes is what drives PLA biodegradation and how the temperature barrier for PLA composting is overcome.

microbiology↗

bioRxiv2025

The classical MHC class I and II genes of O. m. formosanus exhibit different polymorphism levels

Oncorhynchus masou formosanus (Formosa landlocked salmon) is a salmonid fish endemic to Taiwan with a critically endangered extant small population in high-altitude mountain streams. To begin to assess the remaining genetic diversity we characterized the single classical MHC class I (UBA) and MHC class II (DAA and DAB) genes of teleost fish in a small cohort of eight unrelated O. m. formosanus individuals. We focused on the exons encoding the peptide binding regions of these complexes as they are considered the most highly polymorphic regions in vertebrate genomes. Surprisingly, the DAA and DAB genes appeared homozygous and identical among all eight fish indicating that the encoded class II complex is monomorphic. In contrast, three distinct UBA alleles were discovered with one dominant allele present in every single individual. Notably, 75% were heterozygous indicating a selective advantage of heterozygosity at this locus. Lastly, our MHC alleles differ from those present in the genome of the closely related Japanese O. m. masou, suggesting that the loss of DAA/DAB diversity and the emergence of the dominant UBA allele occurred after their populations were isolated. Together we discovered residual genetic diversity at the classical MHC class I locus in O. m. formosanus and maintaining this allelic variation unlike the homozygous DAA and DAB genes is likely important for its survival in its geographically restricted unique habitat.

immunology↗

bioRxiv2023

The cytokine genes of Oncorhynchus masou formosanus include a defective interleukin-4A gene.

Oncorhynchus masou formosanus (Formosa land-locked salmon) is a critically endangered salmonid fish endemic to Taiwan. To begin to understand how its drastic change in lifestyle from anadromous to exclusively river-dwelling is reflected in its immune genes, we characterized the genes encoding six cytokines (IL-2A, IL-2B, IL-4A, IL-4B1, IL-4B2, and IL-17A/F2a) important for T cell responses as no genomic data is available for this fish. Interestingly, all genes appeared homozygous indicative of a genetic bottleneck. The IL2 and IL17A/F2a genes and their products are highly similar to their characterized homologs in Oncorhynchus mykiss (rainbow trout) and other salmonid fish. Two notable differences were observed in IL4 family important for type 2 immune responses. First, O. m. formosanus carries not only one but two genes encoding IL-4B1 proteins and expansions of these genes are present in other salmonid fish. Second, the OmfoIL4A gene carries a 228 bp deletion that results in a premature stop codon and hence a non-functional IL-4A cytokine. This suggests a reduced ability for T cell responses against parasitic infections in this species.

immunology↗

bioRxiv2022

Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways

One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that have exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment in PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization of different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.

microbiology↗

bioRxiv2020

Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Determination

Germ cells in D. melanogaster are specified maternally shortly after fertilization and are transcriptionally quiescent until their zygotic genome is activated to sustain further development. To understand the molecular basis of this process, we analyzed the progressing transcriptomes of early male and female germ cells at the single-cell level between germline specification and coalescence with somatic gonadal cells. Our data comprehensively covered zygotic activation in the germline genome, and analyses on genes that exhibit germline-restricted expression revealed that polymerase pausing and differential RNA stability are important mechanisms that establish gene expression differences between the germline and soma. In addition, we observed an immediate bifurcation between the male and female germ cells as zygotic transcription begins. The main difference between the two sexes is an elevation in X chromosome expression in females relative to males signifying incomplete dosage compensation with a few select genes exhibiting even higher expression increases. These indicate that the male program is the default mode in the germline that is driven to female development with a second X chromosome.

developmental biology↗