Biology subjects

Smith, P.

Publications and source records attributed to Smith, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Exploring Differences in Functional Connectivity in Australian Rules Football Players : A Resting-State fMRI Study on the Default Mode Network

The effects of non-concussive impacts in contact-sports such as in Australian rules football (ARF) are still largely unexplored. These impacts are often but not always lower in intensity, but occur more frequently than actual concussions. Since non-concussive impacts are often asymptomatic, their significance may be underestimated. Acute or subacute measurement of non-concussive injury is challenging as the pathological response and injury is poorly described. There is therefore a need for a greater understanding of the pathological consequences of exposure. Growing evidence indicates that resting-state functional connectivity (rs-fMRI) changes in the Default Mode Network (DMN) may be an important biomarker that is sensitive to characterize these impacts. In this work, we examined functional connectivity changes within the DMN of ARF players to evaluate its potential as an early biomarker for non-concussive impacts. Based on rs-fMRI, we compare the DMN of 47 sub-elite ARF players (mean age 21.5{+/-}2.7 years [SD], males 57%) and 42 age-matched healthy controls (mean age 23.2{+/-}2.3 years [SD], males 48%) using Independent Component Analysis (ICA) and Dual Regression. This approach permits an unbiased decomposition of brain activity into networks with principled handling of statistical error. An 83% increase in DMN connectivity (as measured by the Strictly Standardized Mean Difference on values derived from Dual Regression) was observed in ARF players in the left retrosplenial cingulate cortex compared to healthy controls (FDR-corrected p-value from dual regression = 0.03, 95% CI computed via bootstrapping was 58% to 116%). The AUC for distinguishing ARF players from controls was 0.80 (95% CI; [0.71, 0.89]), equating to a PPV of 78% and a NPV of 74%. These results are preliminary; future work could investigate robustness to different random initializations of ICA and validate the findings on an independent testing set, as well as investigate longitudinal changes in ARF players over the course of a playing season.

neuroscience↗

bioRxiv2024

AMH regulates ovary size by counteracting ovarian follicle cluster effects.

Serum anti-Mullerian hormone (AMH) is the primary clinical indicator of mature oocyte counts in the ovaries, but its biological role remains poorly understood. Mammalian ovaries have a finite lifetime of oocytes that are slowly depleted as the dormant follicles housing the oocytes initiate maturation. Less than 0.1% of these follicles will reach maturity and ovulate an oocyte. Recent studies suggest that AMH is a key regulator that removes most of these follicles at early stages of follicle maturation. Most AMH is secreted as an inactive precursor protein, and we show that the required activating-enzymes are largely present outside the follicle. We then measured AMH concentrations in ovarian stroma with microdialysis showing that activity is confined to a short range from the site of secretion. To examine short-range interactions between follicles, we reconstructed the ovarian follicle positions from sheep ovaries in 3D space. This showed that most early follicles develop in proximity to more advanced follicles. Active immunisation of sheep against AMH to inhibit signalling, greatly expanded early follicle numbers, but almost entirely in proximity to large follicles. Large follicle proximity appears to greatly enhance early follicle survival, and AMH appears to attenuate this effect to prevent follicle overgrowth beyond sustainable limits.

physiology↗

bioRxiv2024

The dual activity of BBK32: Implications for simultaneous inhibition of borrelial-specific antibody-dependent complement activation and fibronectin binding

Complement inhibition is exploited by extracellular pathogens to combat clearance. Borreliella burgdorferi, the causative agent of Lyme disease, harnesses complement evasion techniques to establish and maintain infection in mammalian hosts. B. burgdorferi encodes bbk32, a surface lipoprotein that binds extracellular matrix (ECM) components, specifically glycosoaminoglycans (GAGs) and fibronectin (Fn) within its amino terminus. In addition to its ECM-binding functions, the carboxy terminal half of BBK32 binds to the C1r protease and prevents complement activation. This classical complement inhibitory activity protects B. burgdorferi from complement-mediated killing following the addition of normal human serum. Herein we demonstrate that full length BBK32 binds both Fn and C1 concurrently, indicating that binding of these macromolecules do not sterically hinder their simultaneous interaction. Given the link of antibody dependence to the classical pathway, we tested how the presence of BBK32 would protect B. burgdorferi from antibody mediated, complement dependent killing. The presence of BBK32 provided protection against borrelial-specific antibody binding and concomitant complement activation in vitro. We also demonstrated, using both fluorescence microscopy and flow cytometry, that the presence of BBK32 was required for reduced C4 deposition on the surface of borrelial cells. This work demonstrates the potential for BBK32 to simultaneously bind to both C1r and Fn and contributes to the broader understanding of the ability of B. burgdorferi to evade antibody-dependent complement-mediated killing. We contend that these observations ostensibly provide B. burgdorferi with coincident dissemination and immune evasion activities needed for optimal survival during infection. AUTHOR SUMMARYLyme disease, caused by Borreliella burgdorferi and other related species, is the most common arthropod-borne infection in the United States. As an extracellular pathogen, B. burgdorferi is exposed to the complement system--a soluble proteolytic cascade that clears invaders. Complement is defined by three pathways known as the alternative, lectin, and classical. The classical complement cascade is activated by the binding of antibodies to a foreign or damaged cell. For B. burgdorferi, the BBK32 surface protein is known to mute the classical pathway by binding and inhibiting the initiating protease C1r. However, no studies have addressed how BBK32 protects infectious B. burgdorferi from borrelial-specific antibody binding and clearance. Here we show that native BBK32 protects infectious B. burgdorferi from antibody-dependent, complement mediated killing. Given BBK32s other activity--namely its known adherence to fibronectin--we were interested to test if BBK32 could bind the C1 complex, which contains C1r, together with fibronectin. Our results suggest that these complex macromolecules can bind BBK32 simultaneously. These observations suggest that the dual activity of BBK32, namely fibronectin binding and C1r inhibition, are not mutually exclusive and contribute to B. burgdorferis ability to establish infection and evade antibody-based host clearance, respectively.

microbiology↗

bioRxiv2024

Global mapping of the Chlamydia trachomatis conventional secreted effector-host interactome reveals CebN interacts with nucleoporins and Rae1 to impede STAT1 nuclear translocation.

To usurp host defenses and establish a replicative niche, obligate intracellular pathogens are tasked with remodeling the host cell using a comparatively small repertoire of effector proteins. For Chlamydia trachomatis (C.t), discovery of secreted proteins and their host targets has been particularly challenging due to the bacteriums historical genetic intractability. Using affinity purification-mass spectrometry, we defined host interaction partners for 21 secreted effector proteins, providing the first comprehensive type III secretion system (T3SS) effector- host interactome generated during infection. Among these, we show that the C-terminus of CebN (CT584) binds multiple nucleoporins and Rae1, host factors previously associated only with viral immune evasion. Remarkably, we shown that CebN localizes to the nuclear envelope not only in infected cells but also in uninfected bystander cells. Functionally, CebN is both necessary and sufficient to perturb STAT1 nuclear import following IFN-{gamma} stimulation and its expression is critical for C.t. survival, as evidenced by reduced bacterial replication and smaller inclusions in cells infected with a CebN mutant. Together, these finds expand our understanding of chlamydia effector biology and highlight novel bacterial strategies for manipulating host defenses at the nuclear pore. SIGNIFICANCEChlamydia trachomatis (C.t.) is a leading cause of sexually transmitted infections and blindness, yet the molecular mechanisms it uses to manipulate host defenses remain poorly defined. Unlike many pathogens, C.t. relies on a limited set of effectors to remodel the host cell and establish its niche. We identified host targets for 21 C.t. effector proteins. Focusing on CebN, we show that it binds nucleoporins and Rae1, host factors previously linked only to viral immune antagonism. CebN localizes to the nuclear envelope of both infected and bystander cells, and is critical for replication, inclusion development, and perturbation of STAT1 nuclear import following IFN-{gamma} stimulation. These findings uncover a novel strategy by which C.t. manipulates nuclear pore function to evade host defenses and establish infection.

microbiology↗

bioRxiv2024

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1

Lineage plasticity is a recognized hallmark of cancer progression that can shape therapy outcomes. The underlying cellular and molecular mechanisms mediating lineage plasticity remain poorly understood. Here, we describe a versatile in vivo platform to identify and interrogate the molecular determinants of neuroendocrine lineage transformation at different stages of prostate cancer progression. Adenocarcinomas reliably develop following orthotopic transplantation of primary mouse prostate organoids acutely engineered with human-relevant driver alterations (e.g., Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+), but only those with Rb1 deletion progress to ASCL1+ neuroendocrine prostate cancer (NEPC), a highly aggressive, androgen receptor signaling inhibitor (ARSI)-resistant tumor. Importantly, we show this lineage transition requires a native in vivo microenvironment not replicated by conventional organoid culture. By integrating multiplexed immunofluorescence, spatial transcriptomics and PrismSpot to identify cell type-specific spatial gene modules, we reveal that ASCL1+ cells arise from KRT8+ luminal epithelial cells that progressively acquire transcriptional heterogeneity, producing large ASCL1+;KRT8- NEPC clusters. Ascl1 loss in established NEPC results in transient tumor regression followed by recurrence; however, Ascl1 deletion prior to transplantation completely abrogates lineage plasticity, yielding adenocarcinomas with elevated AR expression and marked sensitivity to castration. The dynamic feature of this model reveals the importance of timing of therapies focused on lineage plasticity and offers a platform for identification of additional lineage plasticity drivers.

cell biology↗

bioRxiv2024

Metabolic Reprogramming by Mutant GNAS Creates an Actionable Dependency in Intraductal Papillary Mucinous Neoplasms of the Pancreas

ObjectiveOncogenic "hotspot" mutations of KRAS and GNAS are two major driver alterations in Intraductal Papillary Mucinous Neoplasms (IPMNs), which are bona fide precursors to pancreatic ductal adenocarcinoma. We previously reported that pancreas-specific KrasG12D and GnasR201C co-expression in p48Cre; KrasLSL-G12D; Rosa26LSL-rtTA; Tg (TetO-GnasR201C) mice ("Kras;Gnas" mice) caused development of cystic lesions recapitulating IPMNs. Here, we aim to unveil the consequences of mutant GnasR201C expression on phenotype, transcriptomic profile, and genomic dependencies. DesignWe performed multimodal transcriptional profiling (bulk RNA sequencing, single cell RNA sequencing, and spatial transcriptomics) in the "Kras;Gnas" autochthonous model and tumor-derived cell lines (Kras;Gnas cells), where GnasR201C expression is inducible. A genome-wide CRISPR/Cas9 screen was conducted to identify potential vulnerabilities in KrasG12D;GnasR201Cco-expressing cells. ResultsInduction of GnasR201C - and resulting G(s)alpha signaling - leads to the emergence of a gene signature of gastric (pyloric type) metaplasia in pancreatic neoplastic epithelial cells. CRISPR screening identified the synthetic essentiality of glycolysis-related genes Gpi1 and Slc2a1 in KrasG12D;GnasR201C co-expressing cells. Real-time metabolic analyses in Kras;Gnas cells and autochthonous Kras;Gnas model confirmed enhanced glycolysis upon GnasR201C induction. Induction of GnasR201C made KrasG12D expressing cells more dependent on glycolysis for their survival. Protein kinase A-dependent phosphorylation of the glycolytic intermediate enzyme PFKFB3 was a driver of increased glycolysis upon GnasR201C induction. ConclusionMultiple orthogonal approaches demonstrate that KrasG12D and GnasR201C co-expression results in a gene signature of gastric pyloric metaplasia and glycolytic dependency during IPMN pathogenesis. The observed metabolic reprogramming may provide a potential target for therapeutics and interception of IPMNs. SUMMARYO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIActivating "hotspot" mutations of KRAS and GNAS are found in a majority of Intraductal Papillary Mucinous Neoplasms (IPMNs). C_LIO_LIExpression of mutant KRAS and GNAS drives development of IPMN-like cystic lesions in the murine pancreas that eventually progress to pancreatic ductal adenocarcinoma (PDAC). C_LI What this study addsO_LIMutant GNAS and the resulting aberrant G(s)alpha signaling drives a transcriptional signature of gastric (pyloric type) metaplasia in IPMNs with mucin production. C_LIO_LIAberrant G(s)alpha signaling enhances glycolysis via protein kinase A-dependent phosphorylation of the glycolytic enzyme PFKFB3. C_LIO_LIEnhanced glycolysis in KRAS;GNAS-mutated IPMN cells is validated via multiple orthogonal approaches in vitro and in vivo and represents an actionable metabolic vulnerability. C_LI How this study might affect research, practice or policyO_LIThe present study provides mechanistic insight into how aberrant G(s)alpha signaling alters the biology of Kras-mutant pancreatic epithelial neoplasia through metaplastic and metabolic reprogramming. C_LIO_LITargeting glycolysis in IPMNs may represent both a therapeutic avenue as well as an opportunity for intercepting progression to invasive cancer. C_LI

cancer biology↗

bioRxiv2023

SCF cyclin F - EXO1 axis controls cell cycle dependent execution of double strand break repair

Ubiquitination is a crucial post-translational modification required for the proper repair of DNA double-strand breaks (DSBs) induced by ionising radiation (IR). DSBs are mainly repaired through homologous recombination (HR) when template DNA is present and non-homologous end joining (NHEJ) in its absence. Additionally, microhomology-mediated end joining (MMEJ) and single strand annealing (SSA) provide back-up DSBs repair pathways. However, the mechanisms controlling their use remain poorly understood. By employing a high-resolution CRISPR screen of the ubiquitin system after IR, we systematically uncover genes required for cell survival and elucidate a critical role of the E3 ubiquitin ligase SCFcyclin F in cell cycle-dependent DSB repair. We show that SCFcyclin F -mediated EXO1 degradation prevents DNA end resection in mitosis, allowing MMEJ to take place. Moreover, we identify a conserved cyclin F recognition motif, distinct from the one used by other cyclins, with broad implications in cyclin specificity for cell cycle control.

cell biology↗

bioRxiv2023

Middle-schoolers' reading and processing depth in response to digital and print media: An N400 study

We report the first use of ERP measures to identify text engagement differences when reading digitally or in print. Depth of semantic encoding is key for reading comprehension, and we predicted that deeper reading of expository texts would facilitate stronger associations with subsequently-presented related words, resulting in enhanced N400 responses to unrelated probe words and a graded attenuation of the N400 to related and moderately related words. In contrast, shallow reading would produce weaker associations between probe words and text passages, resulting in enhanced N400 responses to both moderately related and unrelated words, and an attenuated response to related words. Behavioral research has shown deeper semantic encoding of text from paper than from a screen. Hence, we predicted that the N400 would index deeper reading of text passages that were presented in print, and shallower reading of texts presented digitally. Middle-school students (n = 59) read passages in digital and print formats and high-density EEG was recorded while participants completed single-word semantic judgment tasks after each passage. Following digital text reading, the N400 response pattern anticipated for shallow reading was observed. Following print reading, the N400 response pattern expected for deeper reading was observed for related and unrelated words, although mean amplitude differences between related and moderately related probe words did not reach significance. These findings provide evidence of differences in brain responses to texts presented in print and digital media, including deeper semantic encoding for print than digital texts.

neuroscience↗

bioRxiv2023

The Antitumor Activities of Anti-CD47 Antibodies Require Fc-FcγR interactions

While anti-CD47 antibodies hold promise for cancer immunotherapy, early phase clinical trials have shown limited signs of clinical benefit, suggesting that blockade of CD47 alone may not be sufficient for effective tumor control. Here, we investigate the contributions of the Fc domain of anti-CD47 antibodies required for optimal in vivo antitumor activity across multiple species-matched models, providing new insights into the mechanisms underlying the efficacy of this emerging class of therapeutic antibodies. Using a novel mouse model humanized for CD47, SIRP and Fc{gamma}Rs, we demonstrate that local administration of an Fc-engineered anti-CD47 antibody with enhanced binding to activating Fc{gamma}Rs modulates myeloid and T-cell subsets in the tumor microenvironment, resulting in improved long-term systemic antitumor immunity and minimal on-target off-tumor toxicity. Our results highlight the importance of Fc optimization in the development of effective anti-CD47 therapies and provide a novel approach for enhancing the antitumor activity of this promising immunotherapy. Highlights- Engagement of activating Fc{gamma}Rs augments the in vivo antitumor activity of CD47 blocking antibodies - Humanized mice for CD47, SIRP and Fc{gamma}Rs allow assessment of hFc{gamma}Rs contribution to the activity of anti-hCD47 Abs - Fc-optimized anti-hCD47 ab promotes systemic antitumor immunity with abscopal effect and minimal on-target toxicity Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/547082v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1c25202org.highwire.dtl.DTLVardef@960e84org.highwire.dtl.DTLVardef@1930edforg.highwire.dtl.DTLVardef@1b58fcd_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Oxidation of hemoproteins by Streptococcus pneumoniae collapses the cell cytoskeleton and disrupts mitochondrial respiration leading to cytotoxicity of human lung cells

Streptococcus pneumoniae (Spn) causes pneumonia that kills millions through acute toxicity and invasion of the lung parenchyma. During aerobic respiration, Spn releases hydrogen peroxide (Spn-H2O2), as a by-product of enzymes SpxB and LctO, and causes cell death with signs of both apoptosis and pyroptosis by oxidizing unknown cell targets. Hemoproteins are molecules essential for life and prone to oxidation by H2O2. We recently demonstrated that during infection-mimicking conditions, Spn-H2O2 oxidizes the hemoprotein hemoglobin (Hb), releasing toxic heme. In this study, we investigated details of the molecular mechanism(s) by which the oxidation of hemoproteins by Spn-H2O2 causes human lung cell death. Spn strains, but not H2O2-deficient Spn{Delta}spxB{Delta}lctO strains caused time-dependent cell cytotoxicity characterized by the rearrangement of the actin, the loss of the microtubule cytoskeleton and nuclear contraction. Disruption of the cell cytoskeleton correlated with the presence of invasive pneumococci and an increase of intracellular reactive oxygen species. In cell culture, the oxidation of Hb or cytochrome c (Cytc) caused DNA degradation and mitochondrial dysfunction from inhibition of complex I-driven respiration, which was cytotoxic to human alveolar cells. Oxidation of hemoproteins resulted in the creation of a radical, which was identified as a protein derived side chain tyrosyl radical by using electron paramagnetic resonance (EPR). Thus, we demonstrate that Spn invades lung cells, releasing H2O2 that oxidizes hemoproteins, including Cytc, catalyzing the formation of a tyrosyl side chain radical on Hb and causing mitochondrial disruption, that ultimately leads to the collapse of the cell cytoskeleton.

microbiology↗

bioRxiv2023

IL-15 synergizes with CD40 agonist antibodies to induce durable immunity against bladder cancer

CD40 is a central co-stimulatory receptor implicated in the development of productive anti-tumor immune responses across multiple cancers, including bladder cancer. Despite strong preclinical rationale, systemic administration of therapeutic agonistic antibodies targeting the CD40 pathway have demonstrated dose limiting toxicities with minimal clinical activity to date, emphasizing an important need for optimized CD40-targeted approaches, including rational combination therapy strategies. Here, we describe an important role for the endogenous IL-15 pathway in contributing to the therapeutic activity of CD40 agonism in orthotopic bladder tumors, with upregulation of trans-presented IL-15/IL-15R surface complexes, particularly by cross-presenting cDC1s, and associated enrichment of activated CD8 T cells within the bladder tumor microenvironment. In bladder cancer patient samples, we identify DCs as the primary source of IL-15, however, they lack high levels of IL-15R at baseline. Using humanized immunocompetent orthotopic bladder tumor models, we demonstrate the ability to therapeutically augment this interaction through combined treatment with anti-CD40 agonist antibodies and exogenous IL-15, including the fully-human Fc-optimized antibody 2141-V11 currently in clinical development for the treatment of bladder cancer. Combination therapy enhances the crosstalk between Batf3-dependent cDC1s and CD8 T cells, driving robust primary anti-tumor activity and further stimulating long-term systemic anti-tumor memory responses associated with circulating memory-phenotype T and NK cell populations. Collectively, these data reveal an important role for IL-15 in mediating anti-tumor CD40 agonist responses in bladder cancer and provide key proof-of-concept for combined use of Fc-optimized anti-CD40 agonist antibodies and agents targeting the IL-15 pathway. These data support expansion of ongoing clinical studies evaluating anti-CD40 agonist antibodies and IL-15-based approaches to evaluate combinations of these promising therapeutics for the treatment of patients with bladder cancer.

immunology↗

bioRxiv2023

Engineering and characterization of carbohydrate-binding modules to enable real-time imaging of cellulose fibrils biosynthesis in plant protoplasts

O_LICarbohydrate binding modules (CBMs) are non-catalytic domains associated with cell wall degrading carbohydrate-active enzymes (CAZymes) that are often present in nature tethered to distinct catalytic domains (CD). Fluorescently labeled CBMs have been also used to visualize the presence of specific polysaccharides present in the cell wall of plant cells and tissues. C_LIO_LIPrevious studies have provided a qualitative analysis of CBM-polysaccharide interactions, with limited characterization of optimal CBM designs for recognizing specific plant cell wall glycans. Furthermore, CBMs also have not been used to study cell wall regeneration in plant protoplasts. C_LIO_LIHere, we examine the dynamic interactions of engineered type-A CBMs (from families 3a and 64) with crystalline cellulose-I and phosphoric acid swollen cellulose (PASC). We generated tandem CBM designs to determine their binding parameters and reversibility towards cellulose-I using equilibrium binding assays. Kinetic parameters - adsorption (kon) and desorption (koff) rate constants-for CBMs towards nanocrystalline cellulose were determined using quartz crystal microbalance with dissipation (QCM-D). Our results indicate that tandem CBM3a exhibits a five-fold increased adsorption rate to cellulose compared to single CBM3a, making tandem CBM3a suitable for live-cell imaging applications. We next used engineered CBMs to visualize Arabidopsis thaliana protoplasts with regenerated cell walls using wide-field fluorescence and confocal laser scanning microscopy (CLSM). C_LIO_LIIn summary, tandem CBMs offer a novel polysaccharide labeling probe for real-time visualization of growing cellulose chains in living Arabidopsis protoplasts. C_LI

plant biology↗

bioRxiv2022

GlobalUsefulNativeTrees, a database of 14,014 tree species and their uses, supports synergies between biodiversity recovery and local livelihoods in landscape restoration

Tree planting has the potential to improve the livelihoods of millions of people as well as to support environmental services such as biodiversity preservation. Planting however needs to be executed wisely if benefits are to be achieved. We have developed the GlobalUsefulNativeTrees (GlobUNT) database to directly support the principles advocated by the golden rules for reforestation, including planting tree mixtures that maximize the benefits to local livelihoods and the diversity of native trees. Developed primarily by combining data from GlobalTreeSearch with the World Checklist of Useful Plant Species, GlobUNT includes 14,014 tree species that can be filtered for ten major use categories, across 242 countries and territories. In a subcontinental comparison GlobUNT revealed that Malesia had the highest useful tree species richness (3,349) and was also richest for materials (2,723), medicines (1,533), human food (958), fuel (734), environmental uses (632), social uses (614), animal food (443), poisons (322) and invertebrate food (266).

ecology↗

bioRxiv2022

Molecular landscape and functional characterization of centrosome amplification in ovarian cancer

High grade serous ovarian carcinoma (HGSOC) is characterised by poor outcome and extreme chromosome instability (CIN). Therapies targeting centrosome amplification (CA), a key mediator of chromosome missegregation and CIN, may have significant clinical utility in HGSOC. However, the prevalence of CA in HGSOC, its relationship to genomic biomarkers of CIN and its potential impact on therapeutic response have not been defined. Using high-throughput multi-regional microscopy on 287 clinical HGSOC tumour tissues and 73 ovarian cancer cell lines, we show that CA through centriole overduplication is a highly recurrent and heterogeneous feature of HGSOC and is strongly associated with CIN and genome subclonality. Cell-based studies showed that high prevalence CA is phenocopied in ovarian cancer cell lines, and that high CA is associated with increased multi-treatment resistance; most notably to paclitaxel which is the most common treatment used in HGSOC. CA in HGSOC may therefore present a potential driver of tumour evolution and a powerful biomarker for response to standard-of-care treatment.

cancer biology↗

bioRxiv2022

Recent O-antigen diversification masks highly pathogenic STEC O104:H4

Shiga toxin-producing E. coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic condition, hemolytic uremic syndrome (HUS). Although STEC O157:H7 is the serotype most frequently associated with HUS, a major outbreak of HUS occurred in 2011 in Germany, and was caused by a rare serotype, STEC O104:H4. Prior to 2011 and since the outbreak, STEC O104:H4 strains have only rarely been associated with human infections. From 2012 to 2020 intensified STEC surveillance was performed in Germany where subtyping of [~]8,000 clinical isolates by molecular methods including whole genome sequencing was carried out. A rare STEC serotype O181:H4 associated with HUS was identified and, like the STEC O104:H4 outbreak strain, this strain belongs to sequence type (ST) 678. Genomic and virulence comparisons revealed that the two strains are phylogenetically related and differ principally in the gene cluster encoding their respective lipopolysaccharide O-antigens but exhibit similar virulence phenotypes. In addition, five other serotypes belonging to ST678 from human clinical infection, such as OX13:H4, O127:H4, OgN-RKI9:H4, O131:H4, and O69:H4, were identified from diverse locations worldwide. ImportanceOur data suggest the high virulence ensemble of the STEC O104:H4 outbreak strain remains a global threat because genomically similar strains cause disease worldwide, but that horizontal acquisition of O-antigen gene clusters has diversified the O-antigens of strains belonging to ST678. Thus, identification of these highly pathogenic strains is masked by diverse and rare O-antigens, thereby confounding the interpretation of their potential risk.

microbiology↗

bioRxiv2022

Oxidative reactions catalyzed by hydrogen peroxide produced by Streptococcus pneumoniae and other Streptococci Cause the Release and Degradation of Heme from Hemoglobin

Streptococcus pneumoniae (Spn) strains cause pneumonia that kills millions every year worldwide. Spn produces Ply, a hemolysin that lyses erythrocytes releasing hemoglobin and also produces the pro-oxidant hydrogen peroxide (Spn-H2O2) during growth. The hallmark of the pathophysiology of hemolytic diseases is the oxidation of hemoglobin but oxidative reactions catalyzed by Spn-H2O2 has been poorly studied. We characterized the oxidation of hemoglobin by Spn-H2O2. We prepared a series of single ({Delta}spxB, or {Delta}lctO), double mutant ({Delta}spxB{Delta}lctO) and complemented strains in TIGR4, D39 and EF3030. We then utilized an in vitro model with oxy-hemoglobin to demonstrate that oxy-hemoglobin was oxidized rapidly, within 30 min of incubation, by Spn-H2O2 to met-hemoglobin and that the main source of Spn-H2O2 was pyruvate oxidase (SpxB). Moreover, extended incubation caused the release and the degradation of heme. We then assessed oxidation of hemoglobin and heme degradation by other bacteria inhabitants of the respiratory tract. All hydrogen peroxide-producing streptococci tested caused the oxidation of hemoglobin and heme degradation whereas those bacterial species that produce <1 M H2O2, neither oxidized hemoglobin nor degraded heme. An ex vivo bacteremia model confirmed that oxidation of hemoglobin and heme degradation occurred concurrently with hemoglobin that was released from erythrocytes by Ply. Finally, gene expression studies demonstrated that heme, but not red blood cells or hemoglobin induced an upregulated transcription of the spxB gene. Oxidation of hemoglobin may be important for pathogenesis and for the symbiosis of hydrogen peroxide-producing bacteria with other species by providing nutrients such as iron.

microbiology↗

bioRxiv2022

Automated prediction of site and sequence of protein modification with ATRP initiators

One of the most straightforward and commonly used chemical modifications of proteins is to react surface amino groups (lysine residues) with activated esters. This chemistry has been used to generate protein-polymer conjugates, many of which are now approved therapeutics. Similar conjugates have also been generated by reacting activated ester atom transfer polymerization initiators with lysine residues to create biomacromolecular initiators for polymerization reactions. The reaction between activated esters and lysine amino groups is rapid and has been consistently described in almost every publication on the topic as a "random reaction". A random reaction implies that every accessible lysine amino group on a protein molecule is equally reactive, and as a result, that the reaction is indiscriminate. Nonetheless, the literature contradicts itself by also suggesting that some lysine amino groups are more reactive than others (as a function of pKa, surface accessibility, temperature, and local environment). If the latter assumption is correct, then the outcome of these reactions cannot be random at all, and we should be able to predict the outcome from the structure of the protein. Predicting the non-random outcome of a reaction between surface lysines and reactive esters could transform the speed at which active bioconjugates can be developed and engineered. Herein, we describe a robust integrated tool that predicts the activated ester reactivity of every lysine in a protein, thereby allowing us to calculate the non-random sequence of reaction as a function of reaction conditions. Specifically, we have predicted the intrinsic reactivity of each lysine in multiple proteins with a bromine-functionalised N-hydroxysuccinimide initiator molecule. We have also shown that the model applied to PEGylation. The rules-based analysis has been coupled together in a single Python program that can bypass tedious trial and error experiments usually needed in protein-polymer conjugate design and synthesis.

bioinformatics↗

bioRxiv2021

Modelling the future distribution of rare bryophytes in Scotland: is inclusion of habitat loss important?

Species distribution models (SDMs) have been widely used to predict species ranges and their future distribution under climate change scenarios. In this study we applied Maxent, one of the most used SDMs, to project the distribution of some rare bryophyte species in Scotland in the 2050s. Most of these species are strongly linked to the blanket bog habitat, which is threatened by climate change in the near future. To assess the extent to which changes in habitat distribution leads to a different modelled distribution of the selected bryophytes, blanket bog distribution was included in the model as one of the explanatory variables for some species, and Maxent was run for three 2050s scenarios: once with the current blanket bog distribution and two other runs using the blanket bog distribution derived from two bioclimatic models (Lindsay modified and Blanket Bog Tree model) under the same climate change scenario. For seven out of nine of our studied bryophyte species, the modelled distribution in Scotland was predicted to decline, with some species retreating towards the north-west and other species almost disappearing. When the change in blanket bog distribution was also accounted for, further areas in the north/centre east of Scotland and in the south were predicted to be unfavourable for many of the species considered. Our findings suggest that when modelling species distributions, habitat distribution also needs to be considered, especially when there is a strong relationship between the species and a particular habitat.

ecology↗