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Black, C.

Publications and source records attributed to Black, C..

13 recordsLinked to original sources

A trait-based framework for quantifying arthropod invasion potential: Predictive modeling with Tropilaelaps mites as a case study

Over the past decade, the global rise in invasive species has accelerated at an unprecedented rate, intensifying threats to ecosystems, human health, and economies worldwide. Newly invasive taxa, such as Tropilaelaps mites, are of particular concern for apiculture and agroecosystems. Despite growing concern about the spread of Tropilaelaps mites and other arthropods, limited resources are available to assess their invasive potential. We characterized 118 invasive arthropod species using available literature to identify key biological and ecological traits associated with invasive potential. We developed predictive generalized linear mixed models (GLMMs) to determine the traits most important for predicting invasive potential (number of invaded regions), and the top-performing models were subsequently applied to Tropilaelaps mercedesae. Several traits were identified as significant predictors of invasiveness, including the degree of human association, resilience at small population sizes, diet breadth, maximum annual number of generations, altitude range, and the interaction between human association and temperature range. Notably, T. mercedesae was predicted to be capable of invading 160 regions, ranking it within the top 10% most invasive species among those evaluated (12th out of 119), ranked just below the cosmopolitan Varroa destructor mite. These findings position T. mercedesae as a high-risk, yet under-recognized, invasive threat. Collectively, this demonstrates the power of predictive trait-based modeling to inform invasion risk prior to widespread establishment and underscores the urgency of reallocating resources toward surveillance, research, and proactive management strategies rather than relying on costly, often ineffective post-establishment eradication.

ecology↗

Pre-injury subchronic stress confers sex-specific protection against pain-associated symptoms in osteoarthritic mice

Exposure to stress in adulthood alters the manifestation of persistent pain, yet its role in chronic pain vulnerability remains unclear. Here, we report that sub-chronic restraint stress experienced two weeks before unilateral osteoarthritis (OA) induction via intra-articular mono-iodoacetate (MIA) promoted the emergence of a resilient-like phenotype in adult male mice. This was evidenced by decreased MIA-induced mechanical hypersensitivity, improved gait dynamics and lower anxiety-like behaviour. In contrast, stress exposed females exhibited augmented pain-associated symptoms. In males, sub-chronic stress mitigated several MIA-induced molecular changes, including reduced adult hippocampal neurogenesis, increased glucocorticoid receptor levels in the hypothalamic paraventricular nucleus (PVN) and elevated c-Fos expression in deep spinal laminae, periaqueductal gray (PAG) and PVN. RNA sequencing suggested that restraint stress in males primed the spinal cord for an exacerbated GABAergic response post-MIA and pre-empted some pro-nociceptive MIA-induced transcriptional changes. However, the combination of stress and injury disrupted longevity-associated programs and shifted neurons toward a stress-vulnerable state. These findings reveal that prior stress exposure can modulate the long-term pain experience in osteoarthritis, with sexually dimorphic outcomes. Importantly, these results challenge the notion of stress as inherently maladaptive and underscore its potential to foster resilience to chronic pain.

neuroscience↗

SPEF1 mediates assembly of the central pair microtubule complexes in cilia of Tetrahymena.

SPEF1 is a conserved protein that reinforces the seam of central microtubules within the distal segment of motile cilia. We show that in Tetrahymena, loss of SPEF1 destabilized the central pair throughout the cilium length, producing gaps in the microtubule lattice, loss of proximal microtubule portions, and loss of lateral projections. While both central microtubules were affected, C1 suffered more damage than C2 and the defects were already apparent during ciliary assembly. Tetrahymena cells lacking SPEF1 had fewer cilia, which contained an excessively dense ciliary matrix and abnormal densities on the doublet microtubules. Although SPEF1 loss visibly affected only the central microtubules, it localized to all stable microtubules in the cell, both ciliary and non-ciliary. Within cilia, SPEF1 was enriched near the distal tip, but was also present throughout the middle segment, where it was more concentrated along the central than the outer doublet microtubules. In live cilia, SPEF1 particles were mostly stationary and turned over slowly, some diffused but none moved by IFT. We propose that SPEF1 acts as a stabilizer of central microtubules in both the middle and distal segment and its activity contributes to central microtubule assembly.

cell biology↗

Global stress response in Pseudomonas aeruginosa upon malonate utilization

Versatility in carbon source utilization assists Pseudomonas aeruginosa in its adaptation to various niches. Recently, we characterized the role of malonate, an understudied carbon source, in quorum sensing regulation, antibiotic resistance, and virulence factor production in P. aeruginosa. These results indicate that global responses to malonate metabolism remain to be uncovered. We leveraged a publicly available metabolomic dataset on human airway and found malonate to be as abundant as glycerol, a common airway metabolite and carbon source for P. aeruginosa. Here, we explored and compared adaptations of P. aeruginosa UCBPP-PA14 (PA14) in response to malonate or glycerol as a sole carbon source using transcriptomics and phenotypic assays. Malonate utilization activated glyoxylate and methylcitrate cycles and induced several stress responses, including oxidative, anaerobic, and metal stress responses associated with increases in intracellular aluminum and strontium. Some induced genes were required for optimal growth of P. aeruginosa in malonate. To assess the conservation of malonate-associated responses among P. aeruginosa strains, we compared our findings in strain PA14 with other lab strains and cystic fibrosis isolates of P. aeruginosa. Most strains grew on malonate as a sole carbon source as efficiently as or better than glycerol. While not all responses to malonate were conserved among strains, formation of biomineralized biofilm-like aggregates, increased tolerance to kanamycin, and increased susceptibility to norfloxacin were the most frequently observed phenotypes. Our findings reveal global remodeling of P. aeruginosa gene expression during its growth on malonate as a sole carbon source that is accompanied by several important phenotypic changes. These findings add to accumulating literature highlighting the role of different carbon sources in the physiology of P. aeruginosa and its niche adaptation. ImportancePseudomonas aeruginosa is a notorious pathogen that causes local and systemic infections in immunocompromised individuals. Different carbon sources can uniquely modulate metabolic and virulence pathways in P. aeruginosa, highlighting the importance of the environment that the pathogen occupies. In this work, we used a combination of transcriptomic analysis and phenotypic assays to determine how malonate utilization impacts P. aeruginosa, as recent evidence indicates this carbon source may be relevant to certain niches associated within the human host. We found that malonate utilization can induce global stress responses, alter metabolic circuits, and influence various phenotypes of P. aeruginosa that could influence host colonization. Investigating the metabolism of malonate provides insight into P. aeruginosa adaptations to specific niches where this substrate is abundant, and how it can be leveraged in the development of much-needed antimicrobial agents or identification of new therapeutic targets of this difficult-to-eradicate pathogen.

microbiology↗

Comparing physiological impacts of positive pressure ventilation versus self-breathing via a versatile cardiopulmonary model incorporating a novel alveoli opening mechanism

Mathematical models can be used to generate high-fidelity simulations of the cardiopulmonary system. Such models, when applied to real patients, can provide valuable insights into underlying physiological processes that are hard for clinicians to observe directly. In this work, we propose a novel modelling strategy capable of generating scenario-specific cardiopulmonary simulations to replicate the vital physiological signals clinicians use to determine the state of a patient. This model is composed of a tree-like pulmonary system that features a novel, non-linear alveoli opening strategy, based on the dynamics of balloon inflation, that interacts with the cardiovascular system via the thorax. A baseline simulation of the model is performed to measure the response of the system during spontaneous breathing which is subsequently compared to the same system under mechanical ventilation. To test the new lung opening mechanics and systematic recruitment of alveolar units, a positive end-expiratory pressure (PEEP) test is performed and its results are then compared to simulations of a deep spontaneous breath. The system displays a marked decrease in tidal volume as PEEP increases, replicating a sigmoidal curve relationship between volume and pressure. At high PEEP, cardiovascular function is shown to be visibly impaired, in contrast to the deep breath test where normal function is maintained.

physiology↗

Heterogeneity of radial spokes structural components and associated enzymes in Tetrahymena cilia

Radial spokes, RS1-RS2-RS3, are T-shaped, multiprotein complexes that transmit regulatory signals from central apparatus to outer doublet dyneins. RSs, especially RS3, differ in morphology, protein composition, and RS base-docked IDAs. Spokes defects alter cilia beating frequency, waveform, and amplitude leading, in humans, to primary ciliary dyskinesia and infertility. In contrast to RS1 and RS2, the protein composition of RS3 is partly resolved. Moreover, the role of particular spokes is unclear. Ciliate Tetrahymena thermophila has three Rsp3 paralogs and two or three paralogs of some other RSPs. Using multiple complementary approaches, we showed that Tetrahymena forms RS1 and RS2 subtypes having core composed of various Rsp3 paralogs and one type of Rsp3-less RS3. We elucidated proteomes of RS subtypes and identified novel RS-associated proteins, including enzymatic proteins involved in local regulation of the ADP/ATP levels and protein phosphorylation, whose presence further diversifies RSs properties and likely functions. In briefRadial spokes differ in their protein composition and architecture. Studies in a ciliate Tetrahymena revealed Rsp3 paralogs-dependent RS1 and RS2 subtypes, Rsp3-less RS3, and diversity of the RSP3 mutants phenotype. Known RS components and newly identified structural and enzymatic proteins were assigned to particular RSs.

cell biology↗

Molecular architecture of the ciliary tip revealed by cryo-electron tomography

Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show the microtubules in the tip are highly cross-linked with each other and stabilised by luminal proteins, plugs and cap proteins at the plus ends. In the tip region, the central pair lacks the typical projections and twists significantly. By analysing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explain potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and inform about the mechanisms of ciliary assembly and length regulation.

cell biology↗

Development of a polymicrobial checkerboard assay as a tool for determining combinatorial antibiotic effectiveness in polymicrobial communities

AIMSTo establish a methodology for identifying the effects of combinatorial antibiotic treatment on individual members of a polymicrobial community. METHODS AND RESULTSBoth gentamicin and ceftazidime were diluted to concentrations ranging from 0.06 g ml-1 to 128 g ml-1. An equal ratio polymicrobial community of Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, and Acinetobacter baumannii was inoculated into the combined antibiotics in the checkerboard and incubated for 18 hours in static conditions. After incubation, visible turbidity of the overall community was recorded, and bacteria from the wells were diluted to 10-3 and then spot plated on selective and differential media. After 24 hours, colony-forming unit (CFU) counts were obtained for each species. CONCLUSIONSVisible turbidity is not truly indicative of cell viability, and the polymicrobial community can decrease the antibiotic susceptibility of P. aeruginosa, rendering the clinically-established beneficial combination of gentamicin and ceftazidime ineffective. SIGNIFICANCEPrevious checkerboard methodology which focuses on using visible turbidity to determine monomicrobial antibiotic susceptibility fails to account for polymicrobial cooperation that has been shown to reduce antibiotic efficacy. Our new methodology could be implemented in clinical microbiology laboratories with minimal impact on the overall time for diagnosis.

microbiology↗

Cryo-EM structure of the Agrobacterium tumefaciens T-pilus reveals the importance of positive charges in the lumen

Agrobacterium tumefaciens is a natural genetic engineer that transfers DNA into plants and this is the most frequently applied process for the generation of genetically modified plants. DNA transfer is mediated by a type IV secretion system localized in the cell envelope and extracellular T-pili. We here report the cryo-electron microscopic structures of the T-pilus at 3.2[A] resolution and that of the related plasmid pKM101-determined N-pilus at 3[A] resolution. Both pili contain a main pilus protein (VirB2 in A. tumefaciens and TraM in pKM101) and phospholipids arranged in a 5-start helical assembly. They contain positively charged amino acids in the pilus lumen and the lipids are positively charged in the T-pilus (phosphatidylcholine) conferring overall positive charge to the lumen. Mutagenesis of the lumen-exposed Arg91 residue in VirB2 resulted in protein destabilization and loss of pilus formation. Our results reveal that different phospholipids can be incorporated into type IV secretion system pili and that the charge of the lumen is of functional importance.

biochemistry↗

Nonlinear micro finite element models based on digital volume correlation measurements predict early microdamage in newly formed bone

Bone regeneration in critical-sized defects is a clinical challenge, with biomaterials under constant development aiming at enhancing the natural bone healing process. The delivery of bone morphogenetic proteins (BMPs) in appropriate carriers represents a promising strategy for bone defect treatment but optimisation of the spatial-temporal release is still needed for the regeneration of bone with biological, structural, and mechanical properties comparable to the native tissue. Nonlinear micro finite element (FE) models can address some of these challenges by providing a tool able to predict the biomechanical strength and microdamage onset in newly formed bone when subjected to physiological or supraphysiological loads. Yet, these models need to be validated against experimental data. In this study, experimental local displacements in newly formed bone induced by osteoinductive biomaterials subjected to in situ X-ray computed tomography compression in the apparent elastic regime and measured using digital volume correlation (DVC) were used to validate FE models. Displacement predictions from homogeneous linear FE models were highly correlated to DVC-measured local displacements, while tissue heterogeneity capturing mineralisation differences showed negligible effects. Nonlinear FE models improved the correlation and showed that tissue microdamage occurs at low apparent strains. Microdamage seemed to occur next to large cavities or in biomaterial-induced thin trabeculae, independent of the mineralisation. While localisation of plastic strain accumulation was similar, the amount of damage accumulated in these locations was slightly higher when including material heterogeneity. These results demonstrate the ability of the nonlinear FE model to capture local microdamage in newly formed bone tissue and can be exploited to improve the current understanding of healing bone and mechanical competence. This will ultimately aid the development of BMPs delivery systems for bone defect treatment able to regenerate bone with optimal biological, mechanical, and structural properties.

bioengineering↗

Remodeling and activation mechanisms of outer arm dynein revealed by cryo-electron microscopy

Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryoelectron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with molecular dynamics simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.

cell biology↗

Crystal structure of human PACRG in complex with MEIG1

In human, the Parkin Co-Regulated Gene (PACRG) shares a bidirectional promoter with Parkin, a gene involved in Parkinsons disease, mitochondrial quality control and inflammation. The PACRG protein is essential to the formation of the inner junction between doublet microtubules of the axoneme, a structure found in flagella and cilia. PACRG interacts with tubulin as well as the meiosis expressed gene 1 (MEIG1) protein, which is essential for spermiogenesis in mice. However, the 3D structure of human PACRG is unknown. Here, we report the crystal structure of the C-terminal domain of human PACRG in complex with MEIG1 at 2.1 [A] resolution. PACRG adopts an -helical structure with a loop insertion that mediates a conserved network of interactions with MEIG1. Using the cryo-electron tomography structure of the axonemal doublet microtubule from the flagellated protozoan Chlamydomonas reinhardtii, we generate a model of a mammalian microtubule doublet inner junction, which reveals how PACRG interacts with tubulin subunits in both the A- and B-tubules. Furthermore, the model shows that MEIG1 interacts with {beta}-tubulin on the outer surface of the B-tubule, facing towards the central pair of the axoneme. We also model the PACRG-like protein (PACRGL), a homolog of PACRG with potential roles in microtubule remodelling and axonemal inner junction formation. Finally, we explore the evolution of the PACRG and Parkin head-to-head gene structure and analyze the tissue distribution of their transcripts. Our work establishes a framework to assess the function of the PACRG family of proteins and its adaptor proteins in the function of motile and non-motile cilia.

cell biology↗

The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

Microtubules are cytoskeletal structures involved in structural support, microtubule-based transport and the organization of organelles in the cells. The building blocks of the microtubule, the - and {beta}-tubulin heterodimers, polymerize into protofilaments, that associate laterally to form the hollow microtubule. There exists a specific type of microtubule structures in the cilia, termed doublet microtubules, where high stability is required for ciliary beating and function. The doublet microtubule, consisting of a complete A-tubule and a partial B-tubule maintains its stability through unique interactions at its outer and inner junctions, where the A- and B-tubules meet.\n\nUsing cryo-electron microscopy, we present the answer to the long-standing question regarding the identities, localizations and structures of the Chlamydomonas doublet microtubule inner junction proteins. Using a combination of sequence bioinformatics and mass spectrometry, we identified two new inner junction proteins, FAP276 and FAP106, and an inner junction associated protein FAP126. We show that inner junction proteins PACRG and FAP20, together with FAP52, previously unidentified FAP276, FAP106 and FAP126, form an interaction hub at the inner junction, which involves tubulin sites for post-translational modifications. We further compare the Chlamydomonas and Tetrahymena doublet microtubule structures to understand the common and species-specific features of the inner junction.

biophysics↗