Biology subjects

Miller, S. L.

Publications and source records attributed to Miller, S. L..

6 recordsLinked to original sources

bioRxiv2025

Description of Gopheromyces tardescens, gen. nov., sp.nov., Gigasporangiomyces pilosus, gen. nov., sp.nov., Kelyphomyces adhaerens, gen. nov., sp. nov., proposal of Testudinimycetales ord. nov. and Testudinimycetaceae fam. nov., and emended description of the order Neocallimastigales.

Anaerobic gut fungi (AGF, Neocallimastigomycota) represent a phylum of zoospore-producing fungi inhabiting the gastrointestinal tracts of herbivores. Twenty mammalian-affiliated genera (M-AGF) and two tortoise-affiliated genera (T-AGF) have been described so far. Here, we report on three additional novel T-AGF isolates obtained from Texas and sulcata tortoises. Phylogenetic analysis using the D1-D2 regions of the large ribosomal RNA subunit (D1-D2 LSU), RNA polymerase II large subunit (RPB1), internal transcribed spacer-1 region (ITS1), and transcriptomics-enabled phylogenomic analysis clustered these strains into three distinct, deep-branching clades, closely related to previously described T-AGF genus Testudinimyces. All isolates displayed filamentous rhizoidal growth patterns and produced monoflagellated zoospores. Unique morphological characteristics included the production of elongated, thick, nucleated structures in GX isolates, the formation of thin hair-like projections on sporangial walls in SR isolates, and irregularly shaped sporangia in TM isolates. All strains grew optimally at 32-35 {degrees}C and showed distinct substrate utilization capacity (e.g., growth on pectin, chitin, galactose). LSU analyses revealed GX isolates as the first cultured representatives of tortoise-affiliated but previously uncultured lineage NY56, while SR and TM strains have not been encountered in prior culture-independent AGF surveys. We propose to accommodate these isolates in three new genera and species - Gopheromyces tardescens (GXA2), Gigasporangiomyces pilosus (SR0.6), and Kelyphomyces adhaerens (TM0.3). Further, based on the ecological, physiological, and phylogenetic distinctions between T-AGF and M-AGF, we propose to establish a new family (Testudinimycetaceae) to accommodate the genera Testudinimyces, Gopheromyces, Gigasporangiomyces, and Kelyphomyces, within a new order (Testudinimycetales), and amend the description of Neocallimastigales to circumscribe M-AGF genera only.

microbiology↗

bioRxiv2025

Perinatal Asphyxia Alters Physiological Responses and Ex Vivo Cardiovascular Function of Preterm Growth-Restricted Lambs

IntroductionFetal growth restriction (FGR) arises from chronic hypoxia and increases the risk of cardiovascular dysfunction following perinatal asphyxia, although the underlying mechanisms are unknown. We investigated whether FGR lambs have altered cardiovascular responses to perinatal asphyxia compared to control lambs, and whether impairments in 1 and {beta}1 adrenergic receptor function underlie these responses. MethodsSingle or twin-bearing ewes underwent sterile fetal surgery at 89 days gestation (dGA; term=148d) to induce FGR (single umbilical artery ligation) or sham surgery (Control). At 126dGA, lambs were delivered via caesarean section, instrumented and randomised to immediate ventilation (ControlVENT n=6; FGRVENT n=6), or asphyxia (ControlASPHYXIA n=12; FGRASPHYXIA n=11) induced by umbilical cord occlusion while withholding resuscitation until diastolic blood pressure (BP) decreased to 10mmHg. Lambs were ventilated for 8 hours before baseline ex vivo cardiac function was assessed via Langendorff perfusion to measure left ventricular developed pressure (LVDP), heart rate (HR) and coronary perfusion pressure (CPP). Ex vivo 1 and {beta}1 adrenergic responses were assessed via phenylephrine (10-5 to 10-2 mmol/L) and dobutamine (10-7 to 10-4) administration, respectively. ResultsFGRASPHYXIA lambs had lower BP during asphyxia (p<0.05 vs ControlASPHYXIA) and took longer to reach a diastolic BP of 10mmHg (14.5 {+/-} 0.8 min vs. 19.2 {+/-} 1.3 min; p=0.005). FGRASPHYXIA lambs had lower BP in the first 5 minutes after return of spontaneous circulation (p<0.05) due to impaired vascular contractility, with reduced Tau, dP/dtmax and dP/dtmin (p<0.03 vs ControlASPHYXIA). Baseline LVDP, HR and CPP were similar between groups, however FGRASPHYXIA lambs had increased LVDP responses to phenylephrine and dobutamine (p<0.05 vs ControlASPHYXIA), without significant changes to HR or CPP. ConclusionFGR lambs have altered physiological responses to perinatal asphyxia due to impaired vascular contractility and dysregulated cardiac 1 and {beta}1 adrenergic receptor function, which may increase susceptibility to cardiovascular dysfunction in the neonatal period.

physiology↗

bioRxiv2025

Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation

Intronic GGGGCC hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Despite its intronic location, this repeat avidly supports synthesis of pathogenic dipeptide repeat (DPR) proteins via repeat-associated non-AUG (RAN) translation. However, the template RNA species that undergoes RAN translation endogenously remains unclear. Using long-read based 5 RNA ligase-mediated rapid amplification of cDNA ends (5 Repeat-RLM-RACE), we identified novel C9orf72 transcripts initiating within intron 1 in a C9BAC mouse model, patient-derived iNeurons, and iNeuron-derived polysomes. These cryptic m7G-capped mRNAs are at least partially polyadenylated and are more abundant than transcripts derived from intron retention or circular intron lariats. In RAN translation reporter assays, novel intronic template transcripts - even those with short (32 nucleotide) leaders - exhibited robust expression compared to exon-intron and repeat-containing lariat reporters. To assess endogenous lariat repeat RNA contributions to RAN translation, we enhanced endogenous lariat stability by knocking down the lariat debranching enzyme Dbr1. However, this modulation did not impact DPR production in patient-derived iNeurons. These findings identify cryptic, linear, m7G-capped intronic-initiating C9orf72 mRNAs as an endogenous template for RAN translation and DPR production, with implications for disease pathogenesis and therapeutic development. SIGNIFICANCE STATEMENTAn intronic GGGGCC repeat expansion in C9orf72 supports an unusual translational initiation process known as repeat-associated non-AUG (RAN) translation to produce toxic dipeptide repeat (DPR) proteins that contribute to neurodegeneration in ALS and FTD. How an intronic repeat RNA engages with ribosomes to support such translation is unclear. Here we identify a series of novel mRNA transcripts that initiate within the repeat-containing intron to create linear m7G-capped templates for RAN translation from GGGGCC repeats. These cryptic mRNAs are present in patient iNeurons, engage with ribosomes, and robustly support RAN translation. This finding has important implications for both our understanding of the mechanism by which RAN translation occurs and on therapeutic development in this currently untreatable class of neurodegenerative disorders.

neuroscience↗

bioRxiv2023

Growth dynamics and genetic variation in attached and free-living populations of the filamentous brown seaweed, Pilayella littoralis

We used common garden growth experiments to study genetic variation among geographic isolates (Greenland, Massachusetts, and Connecticut, USA) of the filamentous brown seaweed Pilayella littoralis, including the free-living form unique to Nahant Bay, Massachusetts. Ecotypic variation for temperature growth maximum was demonstrated for a west Greenland isolate (10{degrees} C versus 15{degrees} C for other attached isolates) and between Nahant Bay attached (narrower phenotypic plasticity) and free-living forms (broader phenotypic plasticity) of the species. Morphological and reproductive characteristics of attached and free-living isolates remained distinctive under identical culture conditions after four years. The attached forms were characteristically cabled, twisted, and clumped; unilocular reproductive cells were common and plurilocular reproductive cells were present. The free-living form was characteristically loosely branched and ball-like; only vegetative reproduction occurred, with a few unilocular reproductive cells observed in one experiment. Free-living and attached isolates cultured using no water movement and turbulent conditions to mimic surf and surge conditions did not develop forms that resembled each other after eight months. We additionally used starch gel electrophoresis to study genetic variability in attached and free-living forms of P. littoralis from Nahant Bay. Free-living and attached populations were not different at the isozyme level because a limited number of isozymes were resolved (six out of 39 enzymes tested). One isozyme (PGI) was polymorphic, with two alleles present. The two alleles shared in the attached and free-living populations suggest that the free-living form is not one large identical clone. For attached and free-living P. littoralis, both transplant and growth studies in the laboratory provide convincing evidence of ecotypic differentiation.

ecology↗

bioRxiv2023

Grazing of the free-living filamentous brown seaweed, Pilayella littoralis, by the amphipod Gammarus tigrinis

Pilayella littoralis is a common brown alga with a cosmopolitan distribution. A distinct form of the alga is found free-living in Nahant Bay, Massachusetts. Characteristics that distinguish the free-living form include radial branching that results in a ball-like morphology, reproduction by fragmentation of filaments rather than by spores, and year-round persistence of the population. The amphipod Gammarus tigrinis is frequently found within the floating drifts of P. littoralis. We conducted gut content analyses to document that G. tigrinis consumes P. littoralis. Culture studies revealed that ingested P. littoralis could survive and grow from fecal pellets produced by G. tigrinis. In addition, inefficient grazing produces vegetative fragments (propagules) that can increase numbers within the free-living population. {delta}13C values for the amphipods and P. littoralis averaged -17.4 o/oo and -17.7 o/oo, respectively, suggesting that G. tigrinis acquires most of its carbon from P. littoralis.

ecology↗

bioRxiv2021

DENR/MCTS1 knockdown modulates repeat-associated non-AUG translation

Repeat associated non-AUG (RAN) translation of mRNAs containing repeat-expansion mutations produces toxic peptides in neurons of patients suffering from neurodegenerative diseases. Recent findings indicate that RAN translation in diverse model systems is not inhibited by cellular stressors that impair global translation through phosphorylation of the alpha subunit of eIF2, the essential eukaryotic translation initiation factor that brings the initiator tRNA to the 40S ribosome. Using in vitro, cell-based, and Drosophila models, we examined the role of alternative ternary complex factors that may function in place of eIF2, including eIF2A, eIF2D, and DENR/MCTS1. Among these factors, DENR knockdown had the greatest inhibitory effect on RAN translation of expanded GGGGCC and CGG repeat reporters, and its reduction improved survival of Drosophila expressing expanded GGGGCC repeats. Taken together, these data support a role for alternative initiation factors in RAN translation and suggest they may serve as novel therapeutic targets in neurodegenerative disease.

neuroscience↗