Biology subjects

Johnson, S.

Publications and source records attributed to Johnson, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Infection of point-of-lay hens to assess the sequential events during H7N7 high-pathogenicity avian influenza emergence at a layer premises

H7N7 low-pathogenicity avian influenza virus (H7N7-LPAIV) incursions have preceded emergence of H7N7 high-pathogenicity (HP)AIV at several European layer hen outbreaks. Evidence from a UK layer H7N7-HPAIV (2008) outbreak informed in vivo modelling of sequential events, beginning with H7N7-LPAIV precursor incursion. Three groups of 17-week-old (point-of-lay) hens were inoculated with three precursor H7N7-LPAIV candidates which possessed: Group 1 - the classic LPAIV single-basic cleavage site (CS) (H7N7-SBCS); Group 2 - the dibasic CS (H7N7-DBCS) discovered at the outbreak (both represented direct H7N7-HPAIV (2008) precursors); Group 3 - a related European H7N7-LPAIV (2008) which possessed a DBCS within its haemagglutinin (HA) gene which was highly-conserved with the HA of the UK (2008) outbreak H7N7-HPAIV, but its other genetic segments differed. In Groups 1-3, initial H7N7-LPAIV exposure caused limited viral shedding, restricted H7-antibody responses and no deaths, by 14-days post-inoculation (dpi). H7N7-HPAIV challenge of all groups (n=8 per challenge group, including AIV-naive hens in Group 4) followed at 14 dpi. Prior H7N7-LPAIV inoculation protected against mortality due to H7N7-HPAIV challenge to varying degrees, with eight (100%), seven (87.5%), six (75%) and three (37.5%) survivors in Groups 1-4, respectively, by study-end (14-days post-challenge), when all 24 survivors had strongly seroconverted. Among challenge survivors belonging to Groups 1-3, 20/21 (95%) shed H7N7-HP, indicating that immunity acquired during initial H7N7-LPAIV exposure did not arrest H7N7-HPAIV replication. Despite prior H7N7-LPAIV incursion which elicited additional clinical protection against H7N7-HPAIV challenge, we showed how an emergent H7N7-HPAIV may represent a source for onward spread and further HPAIV outbreaks.

microbiology↗

bioRxiv2025

Depletion of extracellular asparagine impairs self-reactive T cells and ameliorates autoimmunity in a murine model of multiple sclerosis

Amino acids play critical roles in the activation and function of lymphocytes. Here we show that the non-essential amino acid, asparagine, is essential for optimal activation and proliferation of CD4+ T cells. We demonstrate that asparagine depletion at different time points after CD4+ T cell activation reduces mitochondrial membrane potential and function. Furthermore, asparagine depletion at specific time points during CD4+ T cell differentiation reduces cytokine production in multiple CD4+ T cell subsets. In an adoptive transfer model of experimental autoimmune encephalomyelitis (EAE), myelin oligodendrocyte-specific pathogenic T helper 17 cells differentiated under Asn-deficient conditions exhibited reduced encephalitogenic potential and attenuated EAE severity. In a model of EAE induced by active immunization, therapeutic depletion of extracellular Asn significantly reduced disease severity. These results identify asparagine as a key metabolic regulator of the pathogenicity of autoreactive CD4+ T cells and suggest that targeting asparagine metabolism may be a novel therapeutic strategy for autoimmunity.

immunology↗

bioRxiv2025

Intelectin-2 is a broad-spectrum antimicrobial lectin

Mammals regulate the localization, composition, and activity of their native microbiota at colonization sites. Lectins residing at these sites influence microbial populations, but their individual functions are often unclear. Intelectins are found in chordates at mucosal barriers, but their functions are not well characterized. We found that mouse intelectin-2 (mItln2) and human intelectin-2 (hItln2) engage and crosslink mucins via carbohydrate recognition. Moreover, both lectins recognize microbes within native microbial communities, including gram-positive and gram-negative isolates from the respiratory and gastrointestinal tracts. This ability to engage mammalian and microbial glycans arises from calcium-coordinated binding of carbohydrate residues within mucus and microbial surfaces. Microbes, but not human cells, bound by mItln2 or hItln2, suffer a loss of viability. These findings underscore the crucial antimicrobial role of mammalian intelectin-2 in mucosal defense, where it plays offensive (microbial killing) and defensive (mucus crosslinking) roles in regulating microbial colonization.

microbiology↗

bioRxiv2025

A spatially targeted metric of potential koala populations based on Bayesian Networks for conservation management

Koalas (Phascolarctos cinereus) face significant threats from habitat loss and fragmentation, with South-East Queensland (SEQ) experiencing some of the most severe population declines. Current metrics used to assess conservation impacts often lack spatial resolution, transparency, or integration of diverse data sources. We propose a novel, spatially targeted metric, Koala Population Potential (KPP), to estimate the potential number of koalas that could inhabit a given area under ideal conditions. This metric is derived from a Bayesian Network model that integrates ecological, environmental, and threat data, including satellite imagery, expert knowledge, and stakeholder input. We developed and validated the KPP within an interactive online platform, the Koala Bayesian Network Platform (KBNP), enabling stakeholders to visualise and assess the conservation impact of various management scenarios at the land-parcel scale. Application of the KPP across SEQ revealed substantial spatial variation in potential koala populations. Regional areas like Somerset and the Scenic Rim exhibited high KPP scores, while urban LGAs such as Redland City and Logan had lower scores due to elevated threat levels. Model predictions of habitat support were strongly correlated with independent habitat quality assessments (R{superscript 2} = 0.803, p < .001), supporting the validity of the approach. The KBNP provides an accessible, evidence-based decision-support tool that empowers landholders, planners, and conservation managers to evaluate and communicate the likely outcomes of their actions. While developed for koalas, this framework is adaptable to other vulnerable species requiring localised, data-driven conservation planning under uncertainty.

ecology↗

bioRxiv2025

3D Printed Nerve Guidance Conduit for Biologics-Free Nerve Regeneration and Vascular Integration

There is a clinical need for an effective nerve guidance conduit to treat peripheral nerve injuries. Many studies have explored different materials and active cues to guide neural regeneration, with some success. However, none have demonstrated a comparable or better functional recovery than the clinical standard autograft. Autografts are often insufficient for reconstruction of an injury to long nerves such as the sciatic or brachial plexus. Synthetic nerve guidance conduits (NGCs) have been investigated for these injuries to guide axonal regeneration and lead to functional recovery. We have designed a biologics-free hydrogel-based multi-channel conduit with defined microscale features to guide axonal outgrowth. To investigate extraneural vascular infiltration and its effects on functional recovery, we also designed a multi-microchannel conduit with defined regularly spaced micropores, orthogonal to the axon guidance channels. Using our custom-built Rapid Projection, Image-guided, Dynamic (RaPID) bioprinting system, we are able to fabricate each hydrogel conduit within minutes from a milliliter-volume prepolymer vat. With our state-of-the-art printing platform, we have achieved NGCs with a consistent channel wall width of 10 microns. We implanted the NGCs for 17 weeks in a murine sciatic nerve transection injury model. We assessed the functional recovery by dynamic gait analysis throughout the recovery period and by compound muscle action potential (CMAP) electrophysiology before NGC harvesting. Both the non-porous and micro-porous conduit groups led to functional nerve regeneration on par with the autograft group. Further, both conduit groups resulted in restoration of bulk motor function to pre-injury performance. Translational Impact StatementWe have developed a synthetic therapeutic that can be implanted to aid nerve regeneration after a debilitating injury that performs similarly to the current clinical standard treatment. One major hurdle to clinically translating an implantable therapeutic is needing to include biologics such as cells or active biomolecules, which increases the regulatory burden. With this in mind, we systematically developed a biologics-free synthetic hydrogel nerve guidance conduit, composed of polymer backbones that have been used in many FDA-approved applications, capable of restoring motor function.

bioengineering↗

bioRxiv2025

Pigeons exhibit low susceptibility and poor transmission capacity for H5N1 clade 2.3.4.4b high pathogenicity avian influenza virus

The ongoing panzootic of H5N1 high pathogenicity avian influenza virus (HPAIV) has caused the deaths of over half a billion wild birds and poultry, and has led to spillover events in both wild and domestic mammals, alongside sporadic human infections. A key driver of this panzootic is the apparent high viral fitness across diverse avian species, which facilitates an increased interface between wild and domestic species. Columbiformes (pigeons and doves) are commonly found on poultry premises, yet little is known about their potential role in contemporary HPAIV disease ecology. Here we investigated the epidemiological role of pigeons (Columba livia) by determining their susceptibility using decreasing doses of clade 2.3.4.4b H5N1 HPAIV (genotype AB). We investigated infection outcomes and transmission potential between pigeons and to chickens. Following direct inoculation, pigeons did not develop clinical signs, and only those inoculated with the highest dose shed viral RNA or seroconverted to H5N1-AB, revealing a MID50 of 105 EID50. Even in the high-dose group, only low-level shedding and environmental contamination was observed, and low-level viral RNA were present in the tissues of directly inoculated pigeons, with no distinct pathological lesions. Pigeons did not transmit the virus to pigeons or chickens placed in direct contact. We observed distinct differences in sialic acid receptor distribution in the pigeon respiratory tract compared to chickens and ducks. Together, these findings suggest that pigeons have low susceptibility to clade 2.3.4.4b H5N1 HPAIV and are unlikely to contribute significantly to virus maintenance, transmission to poultry, or zoonotic infection.

microbiology↗

bioRxiv2025

Investigating Factors Driving Shifts in Subtype Dominance within H5Nx Clade 2.3.4.4b High-Pathogenicity Avian Influenza viruses

H5Nx clade 2.3.4.4b high-pathogenicity avian influenza viruses (HPAIVs) have decimated wild bird and poultry populations globally since the autumn of 2020. In the United Kingdom (UK) and in continental Europe, the H5N8 subtype predominated during the first epizootic wave of 2020/21, with few detections of H5N1. However, during the second (2021/22) and third (2022/23) epizootic waves, H5N1 was the dominant subtype. The rapid shift in dominance from H5N8 to H5N1 was likely driven by a combination of virological, immunological, and/or host-related factors. In this study, we compared viral fitness and immunological responses in ducks, a key reservoir species, using dominant genotypes of H5N1 (genotype AB) and H5N8 (genotype A) from the second wave. While viral shedding dynamics were similar for both viruses, H5N8 was more pathogenic. Antigenic analysis of post-infection duck sera revealed that the haemagglutinin (HA) protein was antigenically similar across clade 2.3.4.4b H5 HPAIVs, but neuraminidase (NA) proteins displayed different patterns of cross-reactivity. We also modelled a scenario where ducks were pre-exposed to H5N1 (genotype C) or H5N8 (genotype A) from the first wave and subsequently challenged with either homologous or heterologous subtypes from the second wave (genotype AB or A). Despite the absence of seroconversion, pre-exposure to different subtypes resulted in varying clinical outcomes following challenge. These findings indicate that both viral and immunological factors likely played significant roles in the emergence and spread of H5Nx HPAIVs in wild bird populations.

microbiology↗

bioRxiv2025

Functional Neural Connectivity of the Mouse Brain using Photoacoustic Ultrasound Imaging

Brain connectomes are insightful models that describe the connectivity of different regions throughout the brain. These connectomes are traditionally generated through temporal correlation of blood oxygen level dependent (BOLD) signals detected by functional magnetic resonance imaging (fMRI). Photoacoustic ultrasound (PAU) can also detect oxygenation levels while being more accessible and cost effective than fMRI. We propose the use of PAU to generate brain connectomes as an alternative to fMRI. In this study we successfully developed a pipeline for processing PAU data from whole brain scans of mice models and found that the connectomes it produced were comparable to those generated by fMRI, particularly, in detecting connections previously documented in the literature. Our findings suggest that PAU is a promising alternative to fMRI for mapping brain connectome, offering advantages in sensitivity and accessibility, making it a valuable tool for future research on brain connectivity.

bioengineering↗

bioRxiv2025

Characterization of the intraspecies chimeric mouse brain at embryonic day 12.5

Incidence of neurodegenerative diseases such as Alzheimers, Parkinsons, Huntingtons, and amyotrophic lateral sclerosis have increased dramatically as life expectancy at birth has risen year-over-year and the population ages. Neurological changes within the central nervous system, specifically the brain, include cell loss and deterioration that impact motor function, memory, executive function, and mood. Available treatments are limited and often only address symptomatic manifestations of the disease rather than disease progression. Cell transplantation therapy has shown promise for treating neurodegenerative diseases, but a source of autologous cells is required. Blastocyst complementation provides an innovative method for generating those autologous neural cells. By injecting mouse induced pluripotent stem cells (iPSCs) into a wild type (WT) mouse blastocyst, we generated a chimeric mouse brain derived of both donor and host neuronal and non-neuronal cells. An embryonic day 12.5 (E12.5), automated image analysis of mouse-mouse chimeric brains showed the presence of GFP-labeled donor-derived dopaminergic and serotonergic neuronal precursors. GFP-labeled donor-derived cholinergic precursor neurons and non-neuronal microglia-like and macrophage-like cells were also observed using more conventional imaging analysis software. This work demonstrates that the generation of mouse-mouse chimeric neural cells is possible; and that characterization of early neuronal and non-neuronal precursors provides a first step towards utilizing these cells for cell transplantation therapies for neurodegenerative diseases.

developmental biology↗

bioRxiv2025

Shear stress targeted delivery of nitroglycerin to brain collaterals improves ischaemic stroke outcome

In patients with ischaemic stroke, retrograde perfusion of the penumbra by the leptomeningeal collateral vessels (LMCs) is a strong predictor of clinical outcome, thus raising the possibility that enhancing LMC flow could offer a novel therapeutic approach. Here, using computational modelling we show that LMCs experience elevated fluid shear stress that is significantly higher than that in other blood vessels during ischaemic stroke in animals and humans. We take advantage of this to selectively enhance flow in LMCs using shear-activated nanoparticle aggregates carrying the vasodilator nitroglycerin (NG-NPAs) that specifically release drug in regions of vessels with high shear stress ([≥]100 dyne/cm2). The NG-NPAs significantly increased LMC-mediated penumbral perfusion, decreased infarct volume, and reduced neurological deficit without altering systemic blood pressure in a rat ischaemic stroke model. The NG-NPAs also did not cause known common side effects of systemic nitrate administration, such as systemic hypotension, cerebral vascular steal, cortical vein dilation, or intracranial pressure elevation. Systemic administration of free NG at the maximal tolerated dose, which was ten times higher than the dose of NG used in the NG-NPAs, did not enhance LMC perfusion and dropped blood pressure. Thus, packaging NG within shear-activated NPAs can potentially enable this widely available vasodilator to become a highly effective therapeutic for ischaemic stroke.

physiology↗

bioRxiv2025

12/15-Lipoxygenase orchestrates murine wound healing via PPARg-activating oxylipins acting holistically to dampen inflammation.

12/15-lipoxygenase (12/15-LOX, Alox15) generates bioactive oxygenated lipids during inflammation, however its homeostatic role(s) in normal healing are unclear. Here, the role of 12/15-LOX in resolving skin wounds was elucidated, focusing on how its lipids act together in physiologically relevant amounts. In mice, wounding caused acute appearance of 12/15-LOX-expressing macrophages and stem cells, coupled to early generation of [~]12 monohydroxy-oxylipins and enzymatically oxygenated phospholipids (eoxPL). Alox15 deletion increased -smooth muscle actin, collagen deposition, stem cell/fibroblast proliferation, IL6/pSTAT3, pSMAD3, and IFN-{gamma} levels. Conversely, CD206 expression, F480+ cells, MMP9 and MMP2 activities were reduced. Alox15-/- skin was deficient in PPAR{gamma}/adiponectin activity. Furthermore, while pro-inflammatory genes were upregulated as normal during wounding, many including Il6, Il1b, ccl4, Cd14, Cd274, Clec4d, Clec4e, Csf3, and Cxcl2 failed to revert to baseline during healing, indicating disruption of an anti-inflammatory brake. Reconstituting Alox15-/- wounds with a physiological mixture of Alox15-derived primary oxylipins generated by healing wounds restored MMP and dampened collagen deposition. The oxylipin mixture activated PPAR{gamma} in vitro, while in vivo, the PPAR{gamma} co-activator, Helz2, was significantly upregulated. Additional inflammatory and proliferative gene networks impacted by Alox15-/-included Elf4, Cebpb and Tcf3, with many of their associated genes significantly dysregulated. In summary, the impact of 12/15-LOX is ascribed to the deficiency of abundantly generated monohydroxy oxylipins acting together via PPAR{gamma}/adiponectin. The identification of multiple gene alterations reveals several new targets for treatment of non-healing wounds. Our studies demonstrate that abundant 12/15-LOX oxylipins act together, dampening inflammation in vivo, revealing a need to consider lipid signaling holistically. Significance statementDefective wound healing is a significant global clinical problem. Macrophage 12/15-lipoxygenase (12/15-LOX, Alox15) generates abundant lipid mediators termed oxylipins during inflammation. However, its physiological role during resolving wound healing is unclear, with studies so far assessing the bioactivity of individual lipids pharmacologically, rather than holistically in physiological amounts. Here, we report that Alox15 deficiency in mice caused a fibrotic response with failure to dampen inflammation, due to a dysregulated PPAR{gamma}/adiponectin axis. Treatment of Alox15-/- wounds with physiological mixtures of PPAR{gamma}-activating 12/15-LOX primary monohydroxy products restored the phenotype. Several transcriptional networks (Elf4, Cebpb and Tcf3) controlled by Alox15 were uncovered, identifying new targets for promoting physiological wound healing.

pharmacology and toxicology↗

bioRxiv2025

Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid-base catalysis upon loop closure. These enzymes also have a conserved phosphate binding loop that is typically highly rigid and forms a well-defined anion binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTPs high sequence similarity to its natural counterparts, ShufPTP presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active site cysteine, mechanistic promiscuity, and most notably, hyperthermostability, with a denaturation temperature likely >130 {degrees}C (>8 {degrees}C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme, and showcase the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/645524v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@186bfccorg.highwire.dtl.DTLVardef@19a265borg.highwire.dtl.DTLVardef@14c526corg.highwire.dtl.DTLVardef@1b75920_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Evaluation of Aggregate Oral Fluid Sampling for Early Detection of African Swine Fever Virus Infection

African swine fever (ASF) is a highly infectious viral disease that poses significant threat to the United States and global pig industries. Given the lack of effective vaccines, control and prevention of the spread of African swine fever virus (ASFV) is dependent on enhanced surveillance and early disease detection. Commercial swine operations in the US are characterized by comparatively large number of pigs, and sampling individual pigs, which represents the main strategy for current ASF surveillance, is both costly and labor intensive. The major objective of this study was to estimate the diagnostic sensitivity of pen-based aggregate oral fluid testing for ASFV in infected pigs in a pen of 30 animals and evaluate its utility as a tool to support surveillance of ASF in the United States. The study was performed in three phases: (i) Virus (Ghana ASFV24) amplification in a target host species to generate the challenge inoculum, (ii) Titration of the inoculum (10% spleen homogenate) in target host species to determine the minimum dose inducing acute ASF in pigs with survival up to 5 - 6 days post-inoculation (dpi), and (iii) The main study involving 186 pigs consisting of 6 replicates of 30 pigs per pen and one seeder pig inoculated with the Ghana ASFV24 per pen. Daily sampling of aggregate oral fluids, uncoagulated blood, oropharyngeal swabs, fecal and water nipple swabs, and recording of rectal temperatures and clinical observations, was carried out. The seeder pigs were each inoculated intramuscularly with 0.5 ml of the 10% spleen homogenate which induced the desired clinical course of ASF in the pigs with survival of up to 6 dpi. ASFV DNA could be detected in the seeder pigs as early as 1 dpi and 2 dpi in the blood and oropharyngeal swabs, respectively. Transmission of ASFV from the seeder pigs to the contact pig population was detected via positive amplification of ASFV DNA in aggregate oral fluid samples at 3 days post-contact (dpc) in 4 out of 6 pens, and in all 6 pens at 4 dpc. Testing of oropharyngeal swabs and blood samples from individual pigs revealed variable number of ASFV positive pigs between 3 and 5 dpc, with detection of 100% positivity between 6 and 18 dpc, the study endpoint. These findings demonstrate the potential utility of aggregate oral fluid sampling for sensitive and early detection of ASFV incursion into naive swine herds. It also demonstrates that testing of environmental samples from the premises could further enhance overall ASF early detection and surveillance strategy. Author summaryEarly detection of ASFV in swine farms requires robust passive surveillance using sample types and sampling methods that allow sensitive and timely detection. Commercial swine operations in the US or North America are characterized by comparatively large number of pigs, and sampling individual pigs, which represents the current strategy for ASF surveillance, is both costly and labor-intensive. Oral fluid has been shown to be an acceptable sample type for detection of ASFV in individual infected pigs. For the first time on such a scale, we conducted a study enrolling 186 pigs, with daily sampling, in six experimental replicates at 3.2% pen prevalence using a highly virulent ASFV (Ghana ASFV24) to evaluate the utility of aggregate oral fluids for early detection of ASFV. Whole genome sequencing and characterization confirmed grouping of the virus with those in the p72 genotype II cluster. We demonstrate that intramuscular inoculation of the seeder pigs induces acute ASF and transmission to the contact pigs which is detectable in aggregate oral fluids as early as 3 - 4 dpc. We have shown that ASFV DNA detections in aggregate oral fluids correlate with the oropharyngeal swabs of individual pigs. In comparison, ASFV DNA in individual blood samples is detected 1-3 days later. The study demonstrates the potential utility of aggregate oral fluid sampling for enhanced surveillance of ASFV in large commercial swine operations.

microbiology↗

bioRxiv2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme-biosynthetic inhibitor complexes

With the goal of accelerating the discovery of small molecule-protein complexes, we leverage fast, low-dose, event based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach resolves structures of the epoxide-based cysteine protease inhibitor, and natural product, E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. The combined structural power of MicroED and the analytical capabilities of native mass spectrometry (ED-MS) allows assignment of papain structures bound to E-64-like ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors, and crude biosynthetic reactions. ED-MS further discriminates the highest-affinity ligand soaked into microcrystals from a broad inhibitor cocktail, and identifies multiple similarly high-affinity ligands soaked into microcrystals simultaneously. This extends to libraries of printed ligands dispensed directly onto TEM grids and later soaked with papain microcrystal slurries. ED-MS identifies papain binding to its preferred natural products, by showing that two analogues of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analogue from crude biosynthetic reactions, without purification. This illustrates the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets.

biophysics↗

bioRxiv2025

Sequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization

The use of genetically modified non-conventional yeast provides significant potential for the bioeconomy by diversifying the tools available for the development of sustainable and novel products. In this study, we sequenced and annotated the genome of Kluyveromyces marxianus Y-1190 to establish it as a platform for lactose valorization. The strain was chosen for rapid growth on lactose-rich dairy permeate, high transformation efficiency, and ease of culturing in bioreactors. Genomic sequencing revealed that K. marxianus Y-1190 possesses single nucleotide polymorphisms associated with efficient lactose metabolism. The strain is diploid with notable genomic heterogeneity, which appears to be critical for its robust growth and acid tolerance. To further exploit this platform strain, we developed protocols for gene and chromosome manipulation using CRISPR editing, constructed and validated a series of promoters compatible with MoClo vectors, and designed synthetically inducible promoters for K. marxianus. These tools enable precise control over gene expression, allowing for the tailored optimization of metabolic pathways and production processes. The synthetic promoters provide flexibility for dynamic expression tuning, while the CRISPR-based editing protocols facilitate targeted genetic modifications with high efficiency. Together, these advancements significantly enhance the genetic toolbox for K. marxianus, positioning it as a versatile platform for industrial biotechnology. These tools open new opportunities for the sustainable production of bio-based chemicals, fuels, and high-value products, leveraging lactose-rich feedstocks to contribute to a circular economy.

synthetic biology↗

bioRxiv2025

Kinesin-8/Kip3 requires β-tubulin tail for depolymerase activity

Carboxy-terminal tails (CTTs) of tubulin proteins are sites of regulating microtubule function. We previously conducted a genetic interaction screen and identified Kip3, a kinesin-8 motor, as potentially requiring the {beta}-tubulin CTT ({beta}-CTT) for function. Here we use budding yeast to define how {beta}-CTT promotes Kip3 function and the features of {beta}-CTT that are important for this mechanism. We find that {beta}-CTT is necessary for Kip3 depolymerase activity, but not for microtubule binding and motility. Mutant yeast cells lacking {beta}-CTT show increased accumulation of Kip3 at plus ends and along microtubules, but no increase in catastrophe when Kip3 is overexpressed. In vitro experiments show that the {beta}-CTT is necessary for Kip3 to form a tight complex with soluble tubulin but is unnecessary for Kip3 to bind tubulin in the microtubule lattice. These results suggest a model in which {beta}-CTT promotes Kip3 depolymerase activity by supporting a Kip3-tubulin binding state that is only accessible at the microtubule plus end or in solution.

cell biology↗

bioRxiv2025

Rising temperatures favour parasite virulence and parallel molecular evolution following a host jump

Climate change is facilitating the poleward emergence of parasites, increasing the risk of jumping into new animal species, including humans. Whether more virulent or transmissible variants will spread during these climate-driven outbreaks is unclear. We experimentally evolved a wild parasitic bacterium, across the thermal range (20-30{degrees}C) and extremes (35{degrees}C) of Cape Verde - the site of field collection - in a novel, temperate animal host. At the parasites typical warm environmental temperature, we found that virulence escalated across evolutionary time. Parasites evolved at hot temperatures, towards the limit of host-parasite survival, displayed a cryptic virulence boost, deadlier once infecting animals at cooler temperatures. Patterns of molecular evolution were constrained to parallel changes in fewer loci at extreme temperatures. Our findings suggest that rising temperatures will leave predictable phenotypic and genomic signatures on evolving parasites as they emerge with climate change.

evolutionary biology↗

bioRxiv2024

NOTCH1 S2513 is critical for the regulation of NICD levels impacting the segmentation clock in hiPSC-derived PSM cells and somitoids

The segmentation clock is a molecular oscillator that regulates the timing of somite formation in the developing vertebrate embryo. NOTCH signalling is one of the key pathways required for proper functioning of the segmentation clock. Aberrant NOTCH signalling results in developmental abnormalities such as congenital scoliosis as well as diseases such as T-cell acute lymphoblastic lymphoma (T-ALL). In this study we analyse the effects of a mutation detected in T-ALL patients on somitogenesis using human iPS derived PSM cells and somitoids. Mutation of NOTCH1 Serine 2513 into Alanine compromises the interaction of Notch intracellular domain (NICD) with the F-box protein FBXW7 and consequently increases NICD stability and NICD levels in PSM cells. Moreover, the mutation impairs several aspects of clock gene oscillations and restricts the ability of somitoids to polarise, elongate and form paired somites. The data suggest a mechanism by which post-translational modification of a key segmentation clock component plays a crucial role in vertebrate axis segmentation.

developmental biology↗