Biology subjects

Smith, J.

Publications and source records attributed to Smith, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Valine overproduction with metabolically engineered Methanothermobacter marburgensis

In times of a climate crisis caused by extreme emissions of green-house gases on a global scale, mitigation solutions need to be found. One solution is the system of carbon capture and utilization (CCU), where C1 gases, such as carbon monoxide (CO), carbon dioxide (CO2), or methane, are either redirected from industrial off-gas streams or directly air-captured. A biotechnological process for CCU is the use of Methanothermobacter marburgensis for CO2 fixation and production of value-added compounds. In this study, we focused on valine production, an amino acid important for human or feed stock nutrition. We demonstrated overproduction of valine from CO2 in M. marburgensis with temperature-induced promoters. Here, we reached a 12.9-fold increase in valine production between the OFF- and ON states of the inducible promoter with a maximal specific production rate of 14.17 mg gCDW-1 h-1 of valine in closed batch experiments. In the second approach for valine production, we overexpressed acetolactate synthase genes with resistance to allosteric valine inhibition from Methanothermobacter thermautotrophicus recombinant in M. marburgensis. We identified a strong reduction in allosteric inhibition towards valine. This resulted in specific valine productivity of up to 40 mg gCDW-1 h-1 and states the highest specific productivity on an individual amino acid in methanogens. With those findings, we expanded the toolbox for genetic modification of M. marburgensis by a thermo-inducible promoter system and applied protein engineering for enhanced production of value-added compounds to M. marburgensis. This proof of concept shows the feasibility of archaeal cell factories generation via genetic engineering for industrial production of value-added compounds with thermophilic methanogens.

molecular biology↗

bioRxiv2025

Populus trichocarpa associated microbiomes vary across a natural temperature, elevation and rainfall gradient

Abiotic stresses associated with warming and drought are increasing in frequency and severity due to climate change. However, microbial associations can partially mitigate their adverse effects on plant physiology. We examined the bacterial/archaeal and fungal communities with 16S rRNA and ITS2 gene region amplicon sequencing of bulk soil, rhizosphere soil, and root endosphere samples of Populus trichocarpa trees from 11 sites along a 200 km transect with highly variable precipitation, temperature, and soil conditions over the Cascade Mountains in Washington, USA. Foliar stress response was examined with qRT-PCR and field physiological measurements. Soil conditions were examined with physiochemical sample analysis and site climate conditions were approximated using DAYMET. For each niche sampled, bacterial/archaeal and fungal communities clustered into three distinct micro-climate groups: a high-precipitation, low-stress community on the western side of the range, and two stressed climate communities: a high-elevation community nearer the crest of the pass, and a warmer and drier community along the eastern slope. The differences between these micro-climate communities, though still distinct, were notably diminished within the P. trichocarpa root endosphere, indicating that P. trichocarpa likely has a homogenizing effect on the microbiome under stress, but climate plays a major role in shaping these microbial communities.

ecology↗

bioRxiv2025

Synthesis of stable isotope labeled analogs of phytanic acid for separate and combined tracing of alpha-, beta- and omega-oxidation

Phytanic acid (3,7,11,15-tetramethylhexadecanoic acid) is a branched very long chain fatty acid (VLCFA) derived in humans from the diet and catabolized via peroxisomal metabolism. Catabolism of phytanic acid is important in humans as certain inborn errors of peroxisomal metabolism, including Refsum Disease, manifest when catabolism of diet derived phytanic acid is impaired. We developed a novel, linear, unified, unoptimized synthesis of all-racemic phytanic acid along with its 2,3,6,7,10,11,14,15-d8, 1,2-13C2, and 1,2-13C2-2,3,6,7,10,11,14,15-d8 stable isotope labeled analogs from commercially available materials including the common starting material ethyl 2-bromoacetate and ethyl 2-bromoacetate-13C2. This improves upon previous synthetic work to provide a simple synthetic route to produce amounts of stable isotope labeled analogs useful for biochemical studies. The neutron encoded position of the stable isotope enrichment allow distinct examination of oxidative pathways of catabolism, allowing comparison of alpha, beta, and omega oxidation through the combination of labels. This provides a useful set of stable isotope labeled analogs for studies of phytanic acid and branched VLCFA metabolism.

biochemistry↗

bioRxiv2025

Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus).

Sturgeon and paddlefish represent some of the most early diverging branches of ray-finned fishes and have undergone at least one global and several lineage-specific whole genome duplication events. White sturgeon (Acipenser transmontanus), the largest freshwater fish in North America, have experienced at least two rounds of whole genome duplication, and may exhibit both di- and multi-valent meiotic segregation. Moreover, they exhibit contemporary ploidy variants due to spontaneous autopolyploidy, particularly in aquaculture. Nonetheless, as a species with several population segments that exhibit chronic recruitment failure, conservation aquaculture is an important part of their management. To facilitate the development of genetic tools to aid white sturgeon conservation, as well as a basis to understand how ploidy changes and variation historically and contemporarily shape the evolution of this species, we present a genome assembly for a white sturgeon from the Snake River, Idaho, USA. Analysis of sequence data used for assembly indicated a haploid genome size of approximately 1.5Gbp, implying tetraploidy (4N), while analysis of heterozygous k-mers from 21 to 41 bp suggest the genome reflects both 4N and 8N variants. The final genome assembly, scaffolded using linkage maps constructed from Fraser River and Snake River F1 families, contained 6.26Gbp in 832,145 scaffolds, consistent with published genome size estimates. Conserved ortholog completeness for this genome (90.5%; 22.8% single-copy and 67.7% duplicated) was similar to the putatively diploid sterlet sturgeon, and the largest linkage map-based scaffold was 55.2Gbp, though the N50 for this assembly was only 416Kbp, indicating the assembly remains fragmented. We demonstrate the utility of this assembly by identifying genomic regions significantly associated with sex. Genetic markers, designed for inclusion in an amplicon genotyping panel, predicted sex 96.6% and 81.5% correctly in females and males, respectively, providing a strong overall association ({square}2 p-value < 2.7x10-37) with some variation by geographic region. Article summaryFunctional polysomes (more than two chromosomes that pair in meiosis) are rare among vertebrates. White sturgeon, the largest freshwater fish in North America, are tetraploid and occasionally hexaploid. Several populations of this species are stagnant or declining, requiring aquaculture to bolster reproduction. We analyzed whole genomic data and assembled the genome of an individual from the unique Snake River, Idaho, population. Results indicate most genetic variants are consistent with tetraploidy, and the genome assembly, while fragmented, is largely complete. We demonstrate its utility by designing genetic markers for sex for use in conservation and commercial aquaculture.

genomics↗

bioRxiv2025

Axonemal dynein contributions to flagellar beat types and waveforms

Eukaryotic flagella, or motile cilia, are iconic molecular machines whose beating drives cell propulsion and fluid transport across diverse organisms. Beat type and waveform are tailored to function, differing between species and cell types, and individual flagella can switch between beat types. Aberrant beating causes ciliopathies and infertility in humans1 and prevents unicellular parasite transmission2. Eight distinct dynein motor protein complexes bind to axonemal doublet microtubules (DMTs) within flagella and drive beating, yet despite extensive structural analysis3-5, how this machinery achieves different beat types is unknown. Here, using the flagellate unicellular parasite Leishmania, we show a division of labour where specific dyneins drive specific beat types. Using cryo-EM, we determined the structure of the 96-nm repeat unit of the DMT and identified its dynein composition. We used CRISPR-Cas9 to systematically delete all 96-nm repeat proteins, comprehensively mapping necessity for swimming, and determined the contribution of each dynein to incidence and waveform of the preferred beat types. Outer dynein arms (ODAs) were required for symmetric tip-to-base beats, specific single-headed inner dynein arms (IDAs) were important for asymmetric base-to-tip beats (IDAd), and double-headed IDAf important for both. This systematic analysis indicates that the prevailing dogma that ODAs drive and IDAs shape the beat6-9 is either incomplete or not universal, and establishes new hypotheses for how different species, cell types and individual flagella achieve their necessary beat types.

biophysics↗

bioRxiv2025

Pilot-scale production of leucine from CO2

On a cellular level, proteinogenic amino acids (AAs) are the building blocks of proteins. On a global scale, AAs serve as important nutrients for humans and animals. Beyond their nutritional value, AAs are of relevance in medicine, and, due to their chemical properties, they are indispensable for applications in many different realms, such as pharmaceutics, cosmetics, animal feed, food, and the beverage industry. Here, we report the first archaeal cell factory for leucine production from CO2 that has been generated by rational design, random mutagenesis and pathway engineering. The cell factory has been bioprocess-technologically examined and successfully scaled-up with regard to productivity, product quality, and operational stability. In a 2-day fed-batch campaign, we produced 181 g of leucine from CO2 at 150 L pilot-plant scale at a mean volumetric leucine productivity of 65 mg L-1 h-1. A thorough techno-economic analysis indicates that the roll-out of leucine production from CO2 is nearly economically feasible on a global scale.

bioengineering↗

bioRxiv2025

An efficient eukaryotic cell-free expression and correlative cryo-electron tomography platform for structural biology of macromolecular complexes

Cell-free expression using Leishmania tarentolae lysates allows rapid expression of eukaryotic proteins directly from DNA templates. We develop a pipeline that combines cell-free expression system with cryogenic fluorescence microscopy that we term CC-FLEXCET (Correlative Cell-Free Leishmania EXpression and Cryo-Electron Tomography), to target and visualize expressed protein complexes by cryo-electron tomography at high resolution. We demonstrate the utility of this method by structurally characterising the filaments of the full-length apoptosis-associated speck like protein containing CARD (ASC) protein. Cell-free expression of ASC results in a polymeric structure characteristic of its cellular speck assembly. Sub-tomogram averaging allows us to resolve both the pyrin domain (PYD) to medium resolution, and show, for the first time, the arrangement of the flexibly linked caspase recruitment domain (CARD). Finally, we observed an interaction between the ASC filament and the L. tarentolae ribosome. Using template matching and quantitative approaches, we characterise this interaction and determine that there is a random structural association between the filament and the ribosome, with 57% of ribosomes oriented with the LSU toward the ASC polymer. CC-FLEXCET facilitates structural analysis of macromolecules and protein-lipid assemblies without need of purification, providing a pipeline from DNA template to protein expression to cryo-tilt series acquisition, within a single day.

biochemistry↗

bioRxiv2025

Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment

Myogenic commitment is a decisive and irreversible step in skeletal muscle regeneration, necessitating proliferating myoblasts to integrate metabolic cues with nuclear transcriptional programs. Among amino acids, glutamine is uniquely positioned to influence this transition by coupling energy production to macromolecule biosynthesis and epigenetic regulation. We reasoned that myoblasts must sense glutamine availability to ensure orderly progression toward commitment, and we tested this by examining the molecular consequences of acute glutamine withdrawal. We find that continued glutamine oxidation is required to sustain glycolysis, maintain mitochondrial fission, and preserve a redox balance that supports progression towards myogenic commitment. In its absence, myoblasts undergo a reductive shift, characterized by mitochondrial elongation, membrane depolarization, and suppression of glycolysis, ultimately leading to growth arrest. Transcriptomic profiling reveals reduced MyoD and MKi67, accompanied by increased Sprouty1 levels, defining a reversible non-proliferative state that resembles but is distinct from quiescent and reserve cells. We term this state Poised Metabolic Arrest (PMA), a cellular response to glutamine limitation during myogenic progression. Mechanistically, PMA is driven by Nrf2-dependent increased glutathione (GSH) biosynthesis and upregulation of mitochondrial GSH carrier Slc25a39 when glutamine is limited. Depleting mitochondrial glutathione or silencing Slc25a39 forces exit from PMA. However, this premature exit compromises subsequent differentiation potential, indicating PMA serves to preserve differentiation competence when glutamine is limited. Consistent with this, both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt regeneration in vivo. Together, these data suggest that a reciprocal Slc25a39-Nrf2 redox axis functions as a nutrient-dependent checkpoint, coupling glutamine availability to mitochondrial remodeling and metabolic reprogramming, necessary to establish irreversible myogenic commitment.

biochemistry↗

bioRxiv2025

Is it chaotic? Chicken Linkage Disequilibrium and quantitative trait loci

Linkage disequilibrium (LD) underpins genome-wide association studies (GWAS) to map Quantitative Trait Loci Regions (QTLRs). A common yet misled assumption is that the closest sites to a significant marker are the prime candidates as the causative mutation. However, LD blocks are typically fragmented and intermingled. We studied chicken LD of mapped QTLRs for Mareks Disease in numerous chicken populations. We estimated background LD by random sampling of non-syntenic or syntenic marker pairs from different or same chromosomes. We defined LD blocks as a group of markers located on the same chromosome having significant moderate (0.15 [≥] r2 < 0.7) or high (r2 [≥] 0.7) LD, regardless of distance and the number of mixed markers with no LD. Next, we studied QTLR LD by all SNP markers within the QTLRs. We found very complex, nearly chaotic, LD patterns, with fragmented and interdigitated LD blocks. Exceptional LD was found between QTLRs 4-5. LD blocks and protein networks shared by the two QTLRs suggest possible functional relationships. Thus, potential causative candidates could be found beyond non-LD sites, occasionally at a very large distance from a significant marker, and even in another QTLR. Multiple effects might make LD intrinsically chaotic, thus limiting GWAS informativity and repeatability. Chaotic complexity challenges the practical use of LD across populations, and must be accounted for while interpreting genetic mapping studies.

genetics↗

bioRxiv2025

RHO1-2 meganuclease gene editing targets human P23H rhodopsin-induced retinitis pigmentosa to rejuvenate rods and maintain cones

Autosomal dominant retinitis pigmentosa (adRP) is an inherited retinal dystrophy characterized by progressive vision loss and eventual blindness. The P23H mutation (proline to histidine substitution at codon 23) in the rhodopsin (RHO) gene represents the most common form of adRP in North Americans. Currently, there is no cure for P23H adRP. Genome editing targeting the mutant RHO allele, leaving a functional wildtype (WT) allele, is an attractive approach for P23H adRP, as only one copy of RHO is needed for normal retinal function. We re-engineered an I-Cre meganuclease, called RHO1-2, to target a 22bp recognition sequence encompassing the mutation responsible for the p.P23H RHO mutation. In vitro, RHO1-2, cuts human P23H RHO but not WT RHO. In vivo, we delivered scAAV5:GRK1:RHO1-2 via subretinal injection in early-stage degeneration using the only large animal model of human p.P23H RHO adRP (TgP23H pigs). We tested RHO1-2 efficacy and durability, on retinal function using full-field electroretinograms and on retinal structure using spectral domain optical coherence tomography and immunohistochemistry. We observe that RHO1-2 treatment: arrests rod photoreceptor degeneration, resurrects rod-driven retinal function that does not exist in untreated TgP23H pigs, restores mislocalized rhodopsin expression and rebuilds rod inner and outer segments (IS/OS). Rod rescue maintains cones. A year after RHO1-2 treatment, we show that TgP23H pigs use rod-driven vision to navigate a maze. Our results demonstrate that genome editing via RHO1-2 meganuclease is a viable treatment to cure human p.P23H RHO adRP. They also suggest that meganuclease-based editors can be effective for other IRDs. One Sentence SummaryEngineered meganuclease, RHO1-2 is a safe and promising therapeutic genome editing approach to cure human p.P23H RHO adRP.

neuroscience↗

bioRxiv2025

Murine limb ischaemia induces structural and functional remodelling of local and distant bone marrow

Peripheral arterial disease (PAD) can induce bone marrow (BM) ischaemia, although little is known about the implications of this for local and systemic haematopoiesis. We explored the impact of murine unilateral hind-limb ischaemia (HLI) surgery on the structure and function of the ischaemic and non-ischaemic BM, versus control mice without HLI surgery. Abnormal BM hypoxia was present in the ischaemic limb 7-days post-HLI, with normalisation by 28-days. Histological analysis revealed the ischaemic BM to undergo profound vascular remodelling at 7-days that normalised by 61-days, along with a progressive accumulation of BM lipid droplets between 7- and 61-days; no structural changes were observed in the non-ischaemic limb BM. Flow cytometry revealed increased abundance of monocytes and inflammatory monocytes in the non-ischaemic and ischaemic BM 7-days post-HLI, with this persisting at 61-days in the non-ischaemic limb. In both limbs, we observed a progressive decline in the abundance of lineage-Sca-1+c-Kit+ haematopoietic stem cells. RNA-sequencing of BM-derived macrophages (BMDMs) revealed substantial transcriptomic differences between unstimulated control, ischaemic limb and non-ischaemic limb BMDMs. Moreover, there were also substantial transcriptomic differences between lipopolysaccharide-stimulated control and ischaemic limb BMDMs. However, we observed minimal differences in chromatin accessibility of unstimulated BMDMs from the 3 groups. Collectively, our data show that BM ischaemia has transient and sustained structural implications, along with both local and systemic effects on haematopoiesis and myeloid cell function. These findings suggest that PAD may have important consequences for systemic immune responses.

immunology↗

bioRxiv2025

Rats Exposed to a Low Resource Environment in Early Life Display Sex Differences in Blood Pressure, Autonomic Activity, and Brain and Kidney Pro-inflammatory Markers During Adulthood

Introduction: Poverty, a low resource state, is a common adverse childhood experience (ACE) and early life stress (ELS). People who experienced childhood poverty are at greater risk for developing hypertension during adulthood, with sex differences. To determine the possible mechanisms of these sex differences, we investigated the alterations in blood pressure (BP), autonomic activity, and inflammation in the brain and kidneys of rats exposed to an impoverished environment during the early postnatal period, by using the limited bedding and nesting (LBN) model. Methods: The LBN model mimics childhood poverty by creating a low resource environment on postnatal days 2-9. After weaning, offspring were separated by sex and LBN exposure and were evaluated at 16-18 weeks of age (Adulthood). Results: LBN males displayed an increase in BP compared to the control (CON), whereas LBN females showed no changes. Sympathetic nerve activity (SNA) was increased in LBN males and females compared to the CON, while only parasympathetic nerve activity (PNA) was increased in LBN vs. CON females. Pro-inflammatory cytokines, IL-17 and TNF-, were decreased in the brains of LBN vs. CON males, with no alterations in females. Conclusion: Adult LBN males have elevated BP, due to increased SNA, while LBN females may be protected from increased BP due to a simultaneous increase in SNA and PNA. The reduction in IL-17 and TNF- in LBN males may serve as a compensatory mechanism to lower BP. This study provides insights into sex differences in BP for adults who experienced childhood poverty.

physiology↗

bioRxiv2025

Fear, anxiety, and the extended amygdala- Absence of evidence for strict functional segregation

Since the time of Freud, the distinction between fear and anxiety has been a hallmark of influential models of emotion and emotional illness, including the Diagnostic and Statistical Manual of Mental Disorders (DSM) and Research Domain Criteria (RDoC). Fear and anxiety disorders are common, debilitating, and challenging to treat, underscoring the importance of developing accurate models of the underlying neurobiology. Although there is consensus that the extended amygdala (EA) plays a central role in orchestrating responses to threat, the respective contributions of its two major subdivisions--the central nucleus of the amygdala (Ce) and bed nucleus of the stria terminalis (BST)--remain contentious. To help adjudicate this debate, we performed a harmonized mega-analysis of fMRI data acquired from 295 adults as they completed a well-established threat-anticipation paradigm. Contrary to popular double-dissociation models, results demonstrated that the Ce responds to temporally uncertain threat and the BST responds to certain threat. In direct comparisons, the two regions showed statistically indistinguishable responses, with strong Bayesian evidence of regional equivalence. In contrast, frontocortical regions responded preferentially to uncertain-threat anticipation. Together, these observations underscore the need to reformulate conceptual models that posit a strict segregation of temporally certain and uncertain threat processing in the EA.

neuroscience↗

bioRxiv2025

FAVABEAN and FALAPhyl: Open-Source Pipelines for Scalable 16s rRNA Microbiome Data Processing and Visualization

Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows--FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)--to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, including primer averaging when samples are sequenced with multiple primers. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyls integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.

bioinformatics↗

bioRxiv2025

Mycobiome analysis of electronic cigarettes reveals a reservoir of pathogenic yeasts

Research on the health impacts of e-cigarettes has focused on non-infectious manifestations. Given their enclosed plastic design and temperature fluctuations, we hypothesized that e-cigarettes are colonized by pathogenic microbes, thereby contributing to lung disease in users. Using sequencing and culture techniques of the devices and mouthwash of 25 users, we found only a small subset of mouthpieces to contain bacteria, whereas most were abundantly colonized with fungi that were distinct from the oral mycobiota, including the genera Rhodotorula, Aureobasidium, Cystobasidium, and Meyerozyma. Chronic exposure to the most frequently isolated pathogen, Cystobasidium minutum, resulted in mucus hypersecretion and obstructive lung disease in mice, characteristics of chronic bronchitis. We conclude that e-cigarettes are frequently colonized with fungal organisms capable of causing lung disease.

molecular biology↗

bioRxiv2025

An Enantioselective Chemical Probe for Chikungunya nsP2 Helicase with Antialphaviral Activity

Chikungunya virus (CHIKV) replication relies on the multifunctional nsP2 protein, making it an attractive target for antiviral drug discovery. Here, we report the resolution of oxaspiropiperidine 1, a first-in-class inhibitor of the CHIKV nsP2 RNA helicase (nsP2hel), into its constitutive enantiomers and characterization of their antiviral activity. The enantiomer (R)-1 exhibited potent inhibition of viral replication, nsP2hel ATPase activity, and dsRNA unwinding, while the (S)-1 enantiomer was >100-fold less active. The (R)-1 enantiomer also demonstrated high selectivity for CHIKV over other RNA viruses and for nsP2hel over other RNA helicases. Direct binding of (R)-1 to nsP2hel protein was confirmed by 19F NMR. Biophysical and structural studies revealed conformational polymorphism in the spirocyclic scaffold of (R)-1, suggesting a potential role of thermal mobility of the ligand in allosteric inhibition of nsP2hel. Collectively, these findings designate (R)-1 (RA-NSP2-1) as a high-quality chemical probe and (S)-1 (RA-NSP2-1N) as a negative control for probing the biology of alphavirus RNA helicases.

pharmacology and toxicology↗

bioRxiv2025

Rapid sexual reproduction in a mixotrophic dinoflagellate revealed through temporal partitioning of cellular processes

Dinophysis are specialist mixotrophs that must balance prey capture, cell division, and sexual recombination during blooms, yet relatively little is known about the occurrence and role of sex in their ecology. Here, mating was investigated in D. acuminata through continuous automated microscopy of cells in culture and during natural blooms. Both in culture and in situ, vegetative division and mating were phased on a diel timescale, occurring primarily at night and near dawn, regardless of prey availability. When prey were available, feeding occurred primarily during daylight hours. The sequencing of division and mating phases, the correlation of their daily amplitudes, and the timing of their establishment after a two-day light block suggests linkage of these processes. Mating, though frequent (up to 14% day-1 in culture), was also not associated with zygote accumulation or resting stage formation but rapid cell reproduction via meiosis. Confinement of division and mating to nighttime and early morning may minimize conflict with photosynthesis-related metabolism and/or predator exposure. Sexual reproduction was the dominant mode of proliferation during the observed blooms, accounting for 71% and 64% of new cell production in 2015 and 2021, respectively. Because it is dependent on encounter of a compatible gamete, sexual reproduction is increasingly accessible as blooms intensify. This sexual mode of proliferation may also alleviate populations susceptibility to pathogens, parasites, and other threats via genetic recombination, an example of Red Queen dynamics.

ecology↗

bioRxiv2025

Characterisation of the Avascular Mesenchyme during Digit Outgrowth

The avascular mesenchyme at the tip of the developing digit contributes to digit outgrowth and patterning, however, it has been poorly characterised. Using newly developed fate mapping approaches, tissue manipulation and single-cell mRNA sequencing data, we explore the transcriptional nature and developmental potential of this tissue. We find that the avascular mesenchyme is essential to normal segmental patterning of the digit and has a distinct transcriptional identity. In addition, we uncover an unexpected relationship between the unspecified tissue of the avascular mesenchyme and the committed phalanx forming region, which controls patterning, but not outgrowth of the digit. This multifaceted approach provides insights into the mechanics and genetic pathways that regulate digit outgrowth and patterning. HighlightsO_LIThe Avascular Mesenchyme of the developing digit contains a population of uncommitted cells, with a unique transcriptional identity. C_LIO_LIThe AVM is critical to the normal outgrowth and patterning of digits. C_LIO_LIHMGA1 expression is associated with the Avascular Mesenchyme C_LI

developmental biology↗