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Baker, L.

Publications and source records attributed to Baker, L..

16 recordsLinked to original sources

Single-molecule imaging of DNA repair and cytoplasmic rigidification in intracellular bacteria

DNA damage is an important component of the antibacterial response of phagocytes, but which DNA repair mechanisms are active in intracellular bacteria remains unclear. We developed a live-cell single-molecule tracking approach to directly measure DNA repair activity in Escherichia coli within macrophages. Phagocytosis activates bacterial base excision and nucleotide excision repair pathways and increases DNA mismatch repair foci indicative of DNA replication errors. Phagocyte-generated stresses also cause a general slowdown in protein diffusion within bacteria, consistent with a transition of the cytoplasm towards a glass-like state, which is associated with reduced metabolic activity. At the single-cell level, DNA repair activity is highly heterogeneous, with metabolically inactive bacteria showing the greatest engagement of repair proteins. Together, these findings reveal how distinct DNA repair pathways are deployed during macrophage infection and link repair activity to the metabolic and biophysical states of individual intracellular bacteria.

microbiology↗

Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease

Lysogenic conversion, in which bacteriophages (viruses that infect bacteria) integrate into bacterial genomes and confer new phenotypic traits on their hosts, is a well-established mechanism for the emergence of pathogens. While this process underpins many bacterial diseases in humans and other animals, its role in coral disease remains largely unexplored. Here, we investigate the potential role of lysogenic conversion in stony coral tissue loss disease (SCTLD), which has caused unprecedented mortality of Caribbean corals since 2014 and for which the etiological agent remains unknown. Across 27 original coral samples and 178 publicly available metagenomes from the Florida Reef Tract spanning seven coral species, we detected a greater number of unique viral genomes capable of lysogeny in diseased corals or visually healthy portions of diseased corals (DD and HD, respectively) compared to visually healthy (VH) corals. SCTLD-associated bacteriophages were primarily predicted to infect bacterial taxa previously implicated in the disease, such as Vibrionales, Rhodobacterales, and Flavobacteriia, and carried abundant and widespread virulence genes with the potential to enhance bacterial colonization, competition, or direct host damage, including homologs of Tse2, Zot, RTX, pneumolysin, and cytolytic delta-endotoxin. Although causal relationships remain unresolved, our findings indicate that phages capable of lysogenic conversion have the genomic capacity to laterally transfer bacterial virulence genes in SCTLD-affected corals. The acquisition of genes via lysogenic conversion could contribute to bacterial virulence while maintaining community taxonomic profiles, helping to explain previous community profiling observations and providing a mechanistic framework for disease pathogenesis.

genomics↗

Membrane proteins retain native architecture through native ESI and soft-landing

Native MS offers a clear picture of membrane protein stoichiometry and interactions, but it lacks direct structural insights at high resolution. Here, we examine the extent to which solution-phase structure and architecture can be retained after native, soft-landing electrospray ion beam deposition (ESIBD) by interrogating several membrane-protein complexes of diverse folds and oligomeric states by cryoEM. The overall protein architectures with secondary structure motifs can be observed after gas-phase transfer, soft landing, and embedding in amorphous ice. Notably, we determined the structure of the ammonium transporter AmtB at sub-3 [A] resolution. It is nearly identical to the structure of the plunge-frozen control and even shows an extended C-terminal segment of AmtB, a dynamic region absent in the solution-phase structure. Our analysis shows that detergent adducts preserve membrane protein structure in vacuum by minimising destabilization of solvent-exposed regions and stabilization through additional polar contacts in vacuo. Molecular dynamics (MD) simulations support these results, suggesting that a monolayer shell of surfactant adducts avoids destabilization driven by unshielded polar residues and disruption of hydrogen bond networks. Overall, our findings provide a structural framework for integrating native MS with cryo-EM showing that gas-phase transfer and surfactant stabilisation preserves key architectural features and high-resolution structure of membrane proteins.

biophysics↗

Ancestral neuronal receptors are bacterial accessory toxins

Symbiosis and horizontal gene transfer events were crucial in the emergence of eukaryotic and multicellular life. A striking example is the acquisition of Teneurins, putative surface-exposed toxins in bacteria that function as cell adhesion receptors in metazoan neuronal development. Here, we demonstrate the evolutionary relationships between metazoan and bacterial Teneurins. We show that bacterial Teneurins are accessory proteins, that harbour diverse encapsulated toxins. They predominate in species with complex social behaviours, suggesting roles in both cell-to-cell competition and cooperation. Metazoan Teneurins are therefore repurposed bacterial toxins central to cell-to-cell communication in nervous systems. Their acquisition was a foundational event in the evolution of metazoans.

biochemistry↗

Transcriptomic Suppression of Immune and Regenerative Signalling in Skeletal Muscle of Patients with Chronic Kidney Disease

BackgroundChronic kidney disease (CKD) is a growing public health emergency with a global prevalence of approximately 14%. Sarcopenia is a common complication of CKD contributing to functional decline and poor outcomes. However, the molecular mechanisms driving muscle wasting in CKD remain incompletely understood. This study aimed to characterise the transcriptomic profile in individuals with CKD compared to healthy control counterparts, to identify key pathways implicated in muscle dysfunction. MethodsVastus lateralis muscle biopsy samples were obtained from n=10 people with CKD and n=9 healthy controls matched for age, sex, ethnicity and physical activity. Bulk RNA sequencing was performed on all samples. Differential gene expression was assessed using DESeq2 and pathway enrichments analyses were conducted using Gene Ontology (GO) and KEGG databases. ResultsA total of 76 genes were differentially expressed in CKD muscle (FDR < 0.05, |log2FC| [&ge;] 1), with 62 downregulated and 14 upregulated. Transcriptomic analysis revealed suppression of immune-related pathways, including leukocyte chemotaxis and macrophage-associated signalling (e.g., CD163, CXCL14, MPEG1). GO and KEGG analyses further supported downregulation of immune surveillance and inflammatory pathways. Several genes implicated in muscle regeneration (e.g., MEGF10, PODN, SOX4) were also differentially expressed, suggesting impaired regenerative signalling. Classical markers of myogenesis and protein degradation were unchanged, indicating a blunted rather than overtly inflammatory or catabolic muscle environment. ConclusionsSkeletal muscle in CKD exhibits a distinct transcriptional profile marked by suppression of immune and regenerative processes. These findings refine our understanding of CKD-associated sarcopenia and may inform the development of targeted therapeutic strategies beyond conventional exercise-based interventions.

molecular biology↗

The response of the skeletal muscle transcriptome to exercise in chronic kidney disease

BackgroundChronic kidney disease (CKD) affects approximately 14% of the UK population and is associated with significant exercise intolerance, partly due to skeletal muscle dysfunction. While exercise is a potential therapeutic strategy, the molecular response of skeletal muscle to exercise in CKD remains poorly understood. This study aimed to characterise transcriptomic changes in skeletal muscle 24 hours after aerobic (AE) or combined aerobic and resistance exercise (CE) in non-dialysis CKD. MethodsThis study utilised muscle biopsies from participants in the ExTRA CKD trial with stage 3b-4 CKDages 3b-4 (AE: 24 (15-32) ml/min/1.73m2; CE: 25 (19-31) ml/min/1.73m2). Participants (n=4 per group) were randomised to 12 weeks of thrice-weekly AE or CE. Vastus lateralis skeletal muscle biopsies were collected at baseline and 24h after the first bout of exercise. RNA was extracted for Bulk RNA sequencing. Bulk RNA sequencing was performed, and differentially expressed genes (DEGs) were identified between baseline and post-exercise samples, followed by pathway enrichment analysis. ResultsFollowing AE, 1480 genes were upregulated and 1554 downregulated. CE resulted in 556 upregulated and 115 downregulated genes. The most upregulated gene after AE was CHI3L1 (log2FC 10.7), followed by SAA2 and PTX3, all associated with inflammation. After CE, SFN (log2FC 6.8) and MT1A were among the most highly upregulated. Enrichment analysis showed strong activation of inflammatory and cellular senescence pathways, and downregulation of mitochondrial function-related processes, particularly after AE. ConclusionBoth AE and CE triggered robust inflammatory gene expression responses in CKD skeletal muscle, indicative of early repair processes. Unexpectedly, mitochondrial-related pathways were downregulated, aligning with previous findings of impaired mitochondrial adaptation in CKD. These results highlight mitochondrial dysfunction as a potential barrier to effective exercise adaptation and a possible therapeutic target in this population.

physiology↗

Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar

Native mass spectrometry (native MS) is a powerful technique that provides information on stoichiometry, interactions, homogeneity and shape of protein complexes. However, the extent of deviation between protein structures in the mass spectrometer and in solution remains a matter of debate. Here, we uncover the gas-phase structure of {beta}-galactosidase using single particle electron cryomicroscopy (cryo-EM) down to 2.6 [A] resolution, enabled by soft-landing of mass-selected protein complexes onto cold TEM grids and in-situ ice coating. We find that large parts of the secondary and tertiary structure are retained from solution, with dehydration-driven subunit reorientation leading to consistent compaction in the gas phase. Our work enables visualizing the structure of gas-phase protein com-plexes from numerous experimental scenarios at side-chain resolution and demonstrates the possibility of more controlled cryo-EM sample preparation. One Sentence SummaryElectrospray ion-beam deposition on cold grids and in-vacuum ice growth enable cryo-EM of mass-selected proteins at 2.6 [A].

biochemistry↗

High Maternal Adiposity During Pregnancy Programs an Imbalance in the Lipidome and Predisposes to Diet-induced Hepatosteatosis in the Offspring

BackgroundExposure to high maternal adiposity in utero is a significant risk factor for the later-life development of metabolic syndrome (MetS), including non-alcoholic fatty liver disease (NAFLD). We have previously shown that high pre-pregnancy adiposity programs adipose tissue dysfunction in the offspring, leading to spillover of fatty acids into the circulation, a key pathogenic event in obesity-associated MetS. Herein, we hypothesized that programming of adipose tissue dysfunction in offspring born to overweight dams increases the risk for developing NAFLD. ResultsFemales heterozygous for leptin receptor deficiency (Hetdb) were used as a model of high pre-pregnancy adiposity. Wild-type (Wt) offspring born to Hetdb pregnancies gained significantly more body fat following high fat/fructose diet (HFFD) compared to Wt offspring born to Wt dams. HFFD increased circulating free fatty acids (FFA) in male offspring of control dams, while FFA levels were similar in HFFD-fed offspring from Wt dams compared to CD or HFFD-Wt offspring from Hetdb dams. Despite female-specific protection from diet-induced FFA spillover, both male and female offspring from Hetdb. dams were more susceptible to diet-induced hepatosteatosis. Lipidomic analysis revealed that CD-offspring of overweight dams had decreased hepatic PUFA levels compared to control offspring. Changes to saturated fatty acids (SFA) and the de novo lipogenic (DNL) index were diet driven; however, there was a significant effect of the intrauterine environment on FA elongation and {Delta}9 desaturase activity. ConclusionHigh maternal adiposity during pregnancy programs a susceptibility to diet-induced hepatosteatosis.

developmental biology↗

Exploring oxidative stress and endothelial dysfunction as a mechanism linking bisphenol S exposure to vascular disease in human umbilical vein endothelial cells and a mouse model of postnatal exposure.

BackgroundStructural analogues used to replace bisphenol A (BPA) since the introduction of new regulatory restrictions are considered emerging environmental toxicants and remain understudied with respect to their biological actions and health effects. Studies reveal a link between BPA exposure and vascular disease in human populations, whereas the vascular effects of BPA substitutes remain largely unknown. ObjectivesTo determine the effect of BPS, a commonly used BPA substitute, on redox balance, nitric oxide (NO) availability and microvascular NO-dependent dilation. MethodsIn human umbilical vein endothelial cells (HUVEC), production of reactive oxygen species (ROS) and NO after exposure to BPS was measured using fluorescent probes for DCFDA and DAF-FM diacetate, respectively. The contribution of endothelial NO synthase (eNOS) uncoupling to ROS generation was determined by measuring ROS in the presence or absence of an eNOS inhibitor (L-NAME) or eNOS co-factor, BH4, while the contribution of mitochondria-derived ROS was determined by treating cells with mitochondria-specific antioxidants prior to BPS exposure. Bioenergetic profiles were assessed using Seahorse extracellular flux analysis and mitochondria membrane polarization was measured with TMRE and JC-1 assays. In a mouse model of low dose BPS exposure, NO-mediated endothelial function was assessed in pressurized microvessels by inducing endothelium-dependent dilation in the presence or absence of L-NAME. ResultsBPS exposure ([&ge;] 25 nM) reduced NO and increased ROS production in HUVEC, the latter corrected by treating cells with L-NAME or BH4. BPS exposure led to a loss of mitochondria membrane potential but had no impact on bioenergetic parameters except for a decrease in the spare respiratory capacity. Treatment of HUVEC with mitochondria-specific antioxidants abolished the effect of BPS on NO and ROS. NO-mediated vasodilation was impaired in male mice exposed to BPS. DiscussionExposure to BPS may promote cardiovascular disease by perturbing NO-mediated vascular homeostasis through the induction of oxidative stress.

physiology↗

Decreased miRNA-148a-3p expression in skeletal muscle of patients with chronic kidney disease

IntroductionSkeletal muscle wasting is a common complication of chronic kidney disease which leads to a loss of muscle function. The pathogenesis of skeletal muscle wasting is incompletely understood, which is preventing the development of targeted therapeutics. Recent evidence implicates miRNAs in the of skeletal muscle wasting. Our aim was to firstly examine miRNA profiles of CKD human skeletal muscle for the identification of aberrant expression patterns compared to a healthy control (HC) cohort, and secondly, investigate the role these miRNAs may play in inducing or promoting skeletal muscle atrophy using a novel human primary skeletal muscle cell model of CKD skeletal muscle. MethodsFor the comparison between CKD and HC populations, skeletal muscle biopsies were collected from the vastus lateralis of n=15 non-dialysis dependent CKD patients stage 3b-5 CKD patients, and n=15 healthy controls matched for age, gender and physical activity. n=5 biopsies from each group underwent next generation sequencing to obtain complete microRNA profiles in CKD vs HC cohorts, which were then validated in a separate cohort by PCR (N=10 in each group). A causative role in muscle wasting was determined by transfection of key microRNAs into a primary culture model of CKD skeletal muscle and changes in protein degradation determined by L-[3H]- phenylalanine release into the media. ResultsNext Generation Sequencing identified differential expression of 16 miRNAs in skeletal muscle of CKD patients versus controls, and PCR validation confirmed miRNA-148a-3p expression was significantly decreased in CKD patients. The reduced miRNA-148a-3p expression was also maintained in the primary culture model. Upon overexpression of miRNA-148a-3p in CKD myotubes, protein degradation rates were decreased non-significantly (p=0.28) by 16.3% compared to un-transfected CKD cells. ConclusionCKD was associated with a significant reduction in miRNA-148a-3p expression in skeletal muscle compared to non-CKD controls which was retained in our in vitro model. Overexpression of miRNA-148a-3p in primary skeletal myotubes non-significantly decreased muscle protein degradation by 16.3%. In order to determine the importance of miRNA-148a-regulation of protein degradation, a deeper understanding of miRNA-148a-3p targets and their associated pathways with respect to those dysregulated in skeletal muscle wasting is required.

molecular biology↗

Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition

Electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA) have revolutionized structure determination of homogeneous proteins. However, obtaining high-resolution structures from heterogeneous samples remains a major challenge, as the various protein states embedded in thin films of vitreous ice may be classified incorrectly, resulting in detrimental averaging of features. Here we present native electrospray ion-beam deposition (native ES-IBD) for the preparation of extremely high-purity cryo-EM samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, mass-filtered, and gently deposited on cryo-EM grids, and subsequently frozen in liquid nitrogen. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected proteins and protein assemblies. SPA reveals that they remain structurally intact, but variations in secondary and tertiary structure are currently limiting information in 2D classes and 3D EM density maps. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM structure determination.

molecular biology↗

Association between vitamin D deficiency and exercise capacity in patients with CKD, a cross-sectional analysis

Evidence is growing for a role of vitamin D in regulating skeletal muscle mass, strength and functional capacity. Given the role the kidneys play in activating total vitamin D, and the high prevalence of vitamin D deficiency in Chronic Kidney Disease (CKD), it is possible that deficiency contributes to the low levels of physical function and muscle mass in these patients. This is a secondary cross-sectional analysis of previously published interventional study, with ex vivo follow up work. 34 CKD patients at stages G3b-5 (eGFR 25.5 {+/-} 8.3ml/min/1.73m2; age 61 {+/-} 12 years) were recruited, with a sub-group (n=20) also donating a muscle biopsy. Vitamin D and associated metabolites were analysed in plasma by liquid chromatography tandem-mass spectroscopy and correlated to a range of physiological tests of muscle size, function, exercise capacity and body composition. The effects of 1,25(OH)2D3 supplementation on myogenesis and myotube size was investigated in primary skeletal muscle cells from vitamin D deficient donors. In vivo, there was no association between total or active vitamin D and muscle size or strength, but a significant correlation with [Formula] was seen with the total form. Ex vivo, 1,25(OH)2D3 supplementation reduced IL-6 mRNA expression, but had no effect upon proliferation, differentiation or myotube diameter. This early preliminary work suggests that vitamin D deficiency is not a prominent factor driving the loss of muscle mass in CKD, but may play a role in reduced exercise capacity.

cell biology↗

A Novel Therapeutic Approach to Corneal Alkaline Burn Model by Targeting Fidgetin-like 2, a Microtubule Regulator

Purpose To determine the efficacy of nanoparticle-encapsulated FL2 siRNA (FL2-NPsi), a novel therapeutic agent targeting the Fidgetin-like 2 (FL2) gene, for the treatment of corneal alkaline chemical injury.Methods Eighty 12-week-old, male Sprague-Dawley rats were divided evenly into 8 treatment groups: prednisolone, empty nanoparticles, control-NPsi (1 μM, 10 μM, 20 μM) and FL2-NPsi (1 μM, 10 μM, 20 μM). An alkaline burn was induced onto the cornea of each rat, which was then treated for 14 days according to group assignment. Clinical (N=10 per group), histopathologic (N=6 per group), and immunohistochemical (N=4 per group) analyses were conducted to assess for wound healing. FL2-NPsi-mediated knockdown of FL2 was confirmed by in vitro qPCR. Toxicity assays were performed to assess for apoptosis (TUNEL assay, N=3 per group) and nerve damage (whole mount immunochemical staining, N=2 per group). Statistical analyses were performed using student’s t-test and ANOVA.Results Compared to controls, FL2-NPsi-treated groups demonstrated enhanced corneal wound healing, with the 10 and 20 μM FL2-NPsi-treated groups demonstrating maximum rates of corneal re-epithelialization (p=0.0003 at Day 4 and p<0.0001 at Day 8) as assessed by ImageJ software, enhanced corneal transparency, and improved stromal organization on histology. Immunohistochemical analysis of vascular endothelial cells, macrophages, and neutrophils did not show significant differences between treatment groups. FL2-NPsi was not found to be toxic to nerves or induce apoptosis (p=0.917).Conclusion Dose-response studies found both 10 and 20 μM FL2-NPsi to be efficacious in this rat model. FL2-NPsi may offer a novel treatment for corneal alkaline chemical injuries.Competing Interest StatementDr. Wang, Dr. Kramer, Dr. Baker, and Dr. Dey are employees of MicroCures, Inc. Dr. Sharp is co-founder and Chief Scientific Officer for MicroCures, Inc and is the inventor of U.S. Patent #20130022667 entitled "Fidgetin-like 2 as a target to enhance wound healing,” which has been licensed by MicroCures. Dr. Chuck is a scientific advisor for MicroCures, Inc. Dr. Friedman holds stock in MicroCures. No other author has a conflict of interest.View Full Text

physiology↗

Local rabies transmission and regional spatial coupling in European foxes

Infectious diseases are often transmitted through local interactions. Yet, both surveillance and control measures are implemented within administrative units. Capturing local transmission processes and spatial coupling between regions from aggregate level data is therefore a technical challenge that can shed light on both theoretical questions and practical decisions.\n\nFox rabies has been eliminated from much of Europe through oral rabies vaccination (ORV) programmes. The European Union (EU) co-finances ORV to maintain rabies freedom in EU member and border states via a cordon sanitaire. Models to capture local transmission dynamics and spatial coupling have immediate application to the planning of these ORV campaigns and to other parts of the world considering oral vaccination.\n\nWe fitted a hierarchical Bayesian state-space model to data on three decades of fox rabies cases and ORV campaigns from Eastern Germany. Specifically, we find that (i) combining regional spatial coupling and heterogeneous local transmission allows us to capture regional rabies dynamics; (ii) incursions from other regions account for less than 1% of cases, but allow for re-emergence of disease; (iii) herd immunity achieved through bi-annual vaccination campaigns is short-lived due to population turnover. Together, these findings highlight the need for regular and sustained vaccination efforts and our modelling approach can be used to provide strategic guidance for ORV delivery. Moreover, we show that biological understanding can be gained from inference from partially observed data on wildlife disease.

ecology↗

Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays

For future food security it is important that wheat, one of the most widely consumed crops in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. For trait discovery, it is necessary that each introgression is homozygous and hence stable. Breeding programs rely on efficient genotyping platforms for marker-assisted selection (MAS). Recently, single nucleotide polymorphism (SNP) based markers have been made available on high-throughput Axiom(R) SNP genotyping arrays. However, these arrays are inflexible in their design and sample numbers, making their use unsuitable for long-term MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP) assays which are comparatively cost-effective and efficient for low-density genotyping of introgression lines. However, due to the polyploid nature of wheat, KASP assays for homoeologous SNPs can have difficulty in distinguishing between heterozygous and homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that can differentiate between heterozygotes and homozygotes, we PCR-amplified and sequenced genomic DNA from potential single-copy regions of the wheat genome and compared them to orthologous copies from different wild relatives. A panel of 620 chromosome-specific KASP assays have been developed that allow rapid detection of wild relative segments and provide information on their homozygosity and site of introgression in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that can be used for genotyping introgression lines. These multipurpose KASP assays represent a powerful tool for wheat breeders worldwide.

plant biology↗

Id proteins promote a cancer stem cell phenotype in triple negative breast cancer via Robo1-dependent c-Myc activation

Breast cancers display phenotypic and functional heterogeneity and several lines of evidence support the existence of cancer stem cells (CSCs) in certain breast cancers, a minor population of cells capable of tumor initiation and metastatic dissemination. Identifying factors that regulate the CSC phenotype is therefore important for developing strategies to treat metastatic disease. The Inhibitor of Differentiation Protein 1 (Id1) and its closely related family member Inhibitor of Differentiation 3 (Id3) (collectively termed Id) are expressed by a diversity of stem cells and are required for metastatic dissemination in experimental models of breast cancer. In this study, we show that ID1 is expressed in rare neoplastic cells within ER-negative breast cancers. To address the function of Id1 expressing cells within tumors, we developed two independent murine models of Triple Negative Breast Cancer (TNBC) in which a genetic reporter permitted the prospective isolation of Id1+ cells. Id1+ cells are enriched for self-renewal in tumorsphere assays in vitro and for tumor initiation in vivo. Conversely, depletion of Id1 and Id3 in the 4T1 murine model of TNBC demonstrates that Id1/3 are required for cell proliferation and self-renewal in vitro, as well as primary tumor growth and metastatic colonization of the lung in vivo. Using combined bioinformatic analysis, we have defined a novel mechanism of Id protein function via negative regulation of the Roundabout Axon Guidance Receptor Homolog 1 (Robo1) leading to activation of a Myc transcriptional programme.

cancer biology↗