Biology subjects

Miller, J. J.

Publications and source records attributed to Miller, J. J..

16 recordsLinked to original sources

bioRxiv2026

Single-Cell Multimodal Profiling Reveals Maternal Diabetes-Nkx2-5 Interaction in Congenital Heart Disease in a Genetic Model Recapitulating Human Embryopathies

The etiological complexity of congenital heart disease (CHD) arises from the interaction between genetic and environmental factors. We hypothesized that environmental exposure could potentiate a genetic susceptibility, leading to an increased incidence of specific cardiac defects. To test this hypothesis, we used betaV59M+ female mice exhibiting severe hyperglycemia (>28 mmol/L) without dyslipidemia, a model we characterized that faithfully recapitulates human diabetic embryopathy. These females were crossed with males haploinsufficient for Nkx2-5, a transcription factor essential for cardiac development and implicated in human CHD. Our results show that the combination of genetic susceptibility and a hyperglycemic maternal environment (GxE) leads to a higher frequency and severity of cardiac malformations, including ventricular septal defects specifically involving the muscular septum, univentricular morphologies, and dilation with thinning of the myocardium. These structural abnormalities were associated with transcriptional changes affecting the contractile identity of the chamber myocardium. Single-nucleus multiomic profiling (snRNA-seq and snATAC-seq) of the E9.5 cardiac region revealed that the interaction between maternal diabetes and Nkx2-5 haploinsufficiency profoundly reshapes transcriptional and chromatin accessibility landscapes. These changes affect not only metabolic pathways, but also cell cycle progression in second heart field (SHF) progenitors, likely contributing to the observed structural cardiac defects. Multiomic integration further identifies a disrupted indirect Nkx2-5-Aldh1a2 regulatory axis in posterior SHF progenitors, while demonstrating that maternal diabetes selectively affects a restricted subset of Nkx2-5-dependent regulatory elements associated with cardiomyocyte maturation. Our findings establish a comprehensive single-cell multiomic resource that will facilitate the integration of human GWAS and other genomic datasets, enabling the identification and functional interpretation of disease-associated loci.

developmental biology↗

bioRxiv2026

Antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces

Antibody design is a challenging task that could be improved by understanding the conformational changes accompanying affinity maturation. Antibody maturation is a critical immune system process by which antibodies gain mutations that improve affinity and specificity for antigen targets. However, how these mutations change antibody dynamics, specifically whether antibodies become more rigid as they mature, remains a contested topic. Using adaptive sampling molecular dynamics simulations and over 8.5 milliseconds of Folding@home simulations of seven lineages, we discover that affinity maturation selectively tunes the dynamics of antibody paratope regions depending on whether they contact protein residues or glycans. We find that antibody regions that contact glycans evolve to become more flexible and, consistent with other studies, antibody regions that contact protein residues on the antigen become rigid. This pattern holds regardless of whether one includes the constant region in the simulations, indicating that the computational cost of all-atom antibody MD simulations can be reduced by half without sacrificing the accuracy of the variable regions dynamics. We expect the principles identified in this study will enable precise, dynamics-based engineering of high-affinity antibodies and to inform immunogen design against challenging, glycan-shielded viral targets such as HIV. Significance StatementAntibodies are currently one of the most powerful therapeutics available. Our bodies evolve antibodies to bind a target (called an antigen) through a process called maturation. Understanding how antibody dynamics change during maturation would lead to improved antibody design strategies. Through extensive all-atom molecular dynamics simulations of multiple antibody lineages, we demonstrate that the dynamics accompanying affinity maturation are dependent on the antigen binding site. Antibody regions that contact protein residues on the antigen become rigid while regions that contact glycans gain flexibility with maturation. These findings can be leveraged for improved, dynamics-based antibody design.

biophysics↗

bioRxiv2026

Rate limiting release of product underlies concave Arrhenius break point of thermolysin with a Phe-Leu-Ala substrate

Thermolysin, a bacterial zinc metalloprotease, has been previously been reported to exhibit a biphasic kinetic temperature dependence of kcat with a characteristic convex shape. This convex shaping is observed for almost all enzymes which display an Arrhenius break; fumarase is the exception with concave shaping. Here, thermolysin kinetics measured with the tripeptide substrate N-[3-(2-furyl)acryloyl]-Phe-Leu-Ala (FAFLA) resulted in a concave Arrhenius plot, characterized by a 30 kJ/mol increase in enthalpy and entropy of activation, in contrast to the typical 30 kJ/mol decrease. Although the shape of the Arrhenius break differs, ionic strength and macromolecular crowding both attenuate the energetic magnitude of the break point, consistent with prior work. It was hypothesized that a different step of the catalytic cycle of thermolysin was represented by kcat with FAFLA to give rise to this new behavior. A 91% dependence of kcat on viscosity and modest solvent isotope effects, both distinct from previously-characterized substrates, indicated that a physical step was responsible for the observed Arrhenius concavity. Hinge bending conformational changes of thermolysin, monitored using the phosphoramidon inhibitor (a FAFLA mimic), exhibited a fully linear temperature dependence, excluding these large-scale motions as the origin of concavity. It was therefore proposed that release of the N-[3-(2-furyl)acryloyl]-Phe product is likely rate limiting since release was proposed to involve a two-step pathway to free the product coordinated to the catalytic Zn2+ of thermolysin. These findings provide a mechanistic framework for seldom-seen concave break point behavior and insights into the contribution of dynamics of physical processes to catalysis. IMPORTANCE AND IMPACTEnzymes which display Arrhenius break behavior provide insight into how dynamics impact catalysis. Almost every enzyme thus far displays convex biphasic shape, with concave shaping often not acknowledged. Thermolysin, which previously only showed convex shaping, displayed concave behavior with a tripeptide substrate. By linking this unusual kinetic behavior to a physical, not chemical, process, this work highlights the possible origin of a rare phenomenon which can expand understanding of protein dynamics and biphasic Arrhenius behavior.

biochemistry↗

bioRxiv2026

The cellular esterase FrmB controls metabolic homeostasis and small colony variant formation in Staphylococcus aureus

Staphylococcus aureus is a gram-positive bacterium that commonly colonizes the nasal passage, axilla, groin, and gastrointestinal tract of adults and adolescents. Although frequently nonpathogenic, S. aureus can infect most tissue types with clinical outcomes ranging from mild to fatal. The ability of S. aureus to persist and infect multiple body sites is driven largely by its metabolism. S. aureus can metabolize a wide range of niche-specific carbon sources, which contributes significantly to its persistence. Specifically, the utilization of glycolytic intermediates and pyruvate are associated with S. aureus bacterial burden and survival in the host. In this study, we establish the biological role of a serine hydrolase, FrmB, and evaluate its impact on S. aureus carbon metabolism. Using targeted metabolomics on S. aureus strains with and without FrmB, we find that FrmB is required for central carbon metabolic homeostasis. Mechanistically, we find that FrmB controls the enzymatic activity of the crucial rate-limiting enzyme, pyruvate dehydrogenase, which links glycolysis to the downstream tricarboxylic acid (TCA) cycle. Importantly, we find that the metabolic derangements in the absence of FrmB impact the ability of S. aureus to utilize pyruvate as a primary carbon source and reduce fitness. Finally, we demonstrate that FrmB is important for the formation of small colony variants (SCVs), a clinically relevant metabolic transition that is associated with chronic infection and antibiotic resistance.

microbiology↗

bioRxiv2026

AI-Based Methods for Cryptic Pocket Detection Are Fast and Qualitative Compared to Quantitatively Predictive Simulations

Identifying and understanding cryptic pockets remains a compelling goal in drug discovery, as they can offer new avenues for targeting proteins that are otherwise challenging to modulate. While artificial intelligence (AI) methods for structure prediction have been revolutionary, they have not learned enough physics to characterize the rest of a proteins conformational ensemble, such as structures with cryptic pockets. This limitation has motivated the development of new AI-based methods for characterizing ensembles, or properties thereof, such as AlphaFlow, BioEmu, PocketMiner, and CryptoBank. Here, we benchmark how well these models and physics-based molecular dynamics (MD) simulations can recapitulate the thermodynamics of known cryptic pockets in Ebola VP35 and TEM {beta}-lactamase. These two pockets were chosen because the probability that they are open and the impact of point mutations have been well characterized experimentally. Multiple methods are remarkably successful at predicting whether a mutation will increase or decrease the probability of cryptic pocket opening. However, none can reliably predict the absolute probability of pocket opening. MD is very close for the two wild-type proteins but all the methods struggle for pockets with small probabilities of opening experimentally (e.g. less than 1%). BioEmu and PocketMiner capture some trends between variants with experimental populations over 1% but have systematic errors and poorer performance for rare pockets (e.g. <1% open experimentally). These results highlight the promise of AI- and simulation-based strategies for cryptic pocket characterization while pointing to the need for further improvements to achieve robust predictors.

biophysics↗

bioRxiv2024

The G protein inhibitor YM-254890 is an allosteric glue

Given the prominence of G protein coupled receptors (GPCRs) as drug targets, targeting their immediate downstream effectors, G proteins, could be of immense therapeutic value. The discovery that the natural product YM-254890 (YM) can arrest uveal melanoma by specifically inhibiting constitutively active Gq/11without impacting other G protein families demonstrates the potential of this approach. However, efforts to find other G protein family-specific inhibitors have had limited success. Better understanding the mechanism of YM could facilitate efforts to develop other highly specific G protein inhibitors. We hypothesized that differences between the conformational distributions of various G proteins play an important role in determining he specificity of inhibitors like YM. To explore this hypothesis, we built Markov state models (MSMs) from molecular dynamics simulations of the G subunits of three different G proteins, as YM predominantly contacts G. We also modeled the heterotrimeric versions of these proteins where G is bound to the G{beta}{gamma} heterodimer. We find that YM-sensitive G proteins have a higher probability of adopting YM-bound-like conformations than insensitive variants. There is also strong allosteric coupling between the YM- and G{beta}{gamma}-binding interfaces of G. This allostery gives rise to positive cooperativity, wherein the presence of G{beta}{gamma} enhances preorganization for YM binding. We predict that YM acts as an "allosteric" glue that allosterically stabilizes the complex between G and G{beta}{gamma} despite the minimal contacts between YM and G{beta}{gamma}.

biophysics↗

bioRxiv2024

Prodrug activation in malaria parasites mediated by an imported erythrocyte esterase, acylpeptide hydrolase (APEH)

The continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by poor drug-like properties of lead compounds. Prodrugging temporarily masks undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin, exhibit significantly higher antimalarial potency than their parent compounds (1). However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH) is the major activating enzyme of multiple lipophilic ester prodrugs. Surprisingly, this enzyme is taken up by the malaria parasite, Plasmodium falciparum, where it localizes to the parasite cytoplasm and retains enzymatic activity. Using a novel fluorogenic ester library, we characterize the structure activity relationship of APEH, and compare it to that of P. falciparum esterases. We show that parasite-internalized APEH plays an important role in the activation of substrates with branching at the alpha carbon, in keeping with its exopeptidase activity. Our findings highlight a novel mechanism for antimicrobial prodrug activation, relying on a host-derived enzyme to yield activation at a microbial target. Mutations in prodrug activating enzymes are a common mechanism for antimicrobial drug resistance (2-4). Leveraging an internalized host enzyme would circumvent this, enabling the design of prodrugs with higher barriers to drug resistance. SignificanceRising antimalarial drug resistance threatens current gains in malaria control. New antimalarial drugs are urgently needed. Unfortunately, many drug candidates have poor drug-like properties, such as poor absorbability in the gastrointestinal tract, or poor accumulation at the site of action. This can be overcome by prodrugging, the addition of prodrug groups which mask poor drug features until they are removed by an activating enzyme. Here, we show that a red blood cell enzyme, acylpeptide hydrolase, is taken up by malaria parasites and serves as the activating enzyme for multiple lipophilic ester prodrugs. Our findings highlight a novel mechanism for prodrug activation, which could be leveraged to design novel prodrugs with high barriers to drug resistance.

microbiology↗

bioRxiv2024

Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states

Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Forster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a proteins structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a proteins dynamics. This allows us to accurately assess which timescales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (A{beta}40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in NMR, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings.

biophysics↗

bioRxiv2024

Modulating Cardiac Energetics in Cardio-Metabolic Syndromes: A mechanistic, hyperpolarized MR Trial of Ninerafaxstat Treatment

BackgroundType 2 diabetes (T2D) and obesity are key contributors for heart failure (HF)- development, especially for HF with a preserved ejection fraction (HFpEF). On a molecular basis, excessive use of fatty acids (FA) induces lipotoxicity which in turn promotes inflammation, reduces mitochondrial pyruvate dehydrogenase (PDH) activity and impairs myocardial energetics and -function. Harnessing in-vivo, real time measurement of cellular metabolism via hyperpolarized pyruvate MR, we aimed to assess the effects of ninerafaxstat, a selective FA oxidation inhibitor, on cardiac energetics, metabolism & diastolic function in patients with cardio-metabolic syndromes. MethodsIMPROVE-DiCE was an open-label, mechanistic phase 2a trial. 21 participants received 200mg ninerafaxstat twice daily for four (n=5) or eight weeks (n=16). Myocardial energetics (phosphocreatine to adenosine triphosphate ratio, PCr/ATP), metabolism and function were assessed pre-& post-treatment using magnetic resonance imaging (MRI), 31P- and 1H-MR spectroscopy (MRS). We utilised hyperpolarized [1-13C]pyruvate MRS to assess in-vivo PDH-flux (n=9) and plasma metabolomics and proteomics to assess whole body metabolism. ResultsPatients presented with impaired PCr/ATP, (median 1.6 [IQR 1.4, 2.1]), myocardial steatosis (2.2 % [IQR 1.5, 3.2]) and LV diastolic dysfunction (peak circumferential diastolic strain rate 0.86/s [IQR 0.82, 1.06]) at baseline. Ninerafaxstat treatment improved myocardial energetics by 32% (p<0.01), reduced myocardial triglyceride content by 34% (p=0.03) and showed a trend towards improved PDH-flux (mean 45% increase, p=0.08). Diastolic function was significantly improved post-treatment (peak diastolic strain rate by 10%, peak LV filling rate by 11%, both p<0.05). ConclusionsMetabolic modulation with ninerafaxstat significantly improved myocardial energetics, reduced myocardial steatosis and improved LV diastolic filling. Combining hyperpolarized MRS and metabolomics, is a powerful approach to examine the mechanism of action of novel metabolic modulators. REGISTRATIONURL: https://clinicaltrials.gov; Unique identifier: NCT04826159 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/591019v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@86fae1org.highwire.dtl.DTLVardef@1c1037eorg.highwire.dtl.DTLVardef@cc5ca9org.highwire.dtl.DTLVardef@d789d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

A nepenthesin insert allosterically controls catalysis in the malaria parasite protease plasmepsin V

Plasmepsin V (PM V) is a pepsin-like aspartic protease essential for growth of the malaria parasite Plasmodium falciparum. Previous work has shown PM V to be an ER-resident protease that processes parasite proteins destined for export into the host cell. Depletion or inhibition of the enzyme is lethal during asexual replication within red blood cells, as well as during the formation of sexual stage gametocytes. The structure of the P. vivax PM V has been characterized by x-ray crystallography, revealing a canonical pepsin fold punctuated by structural features uncommon to secretory aspartic proteases. Here we use parasite genetics to probe these structural features by attempting to rescue lethal PM V depletion with various mutant enzymes. We find an unusual nepenthesin 1-type insert to be essential for parasite growth and PM V activity. Mutagenesis of the nepenthesin insert suggests that both its amino acid sequence and one of the two disulfide bonds that undergird its structure are required for the nepenthesin inserts role in PM V function. Molecular dynamics simulations paired with Markov state modelling suggest that the nepenthesin insert allosterically controls PM V catalysis through multiple mechanisms.

microbiology↗

bioRxiv2022

Apolipoprotein E4 has extensive conformational heterogeneity in lipid free and bound forms

The {varepsilon}4-allele variant of Apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimers disease, though it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of pathogenicity remain undetermined due to limited structural information. We apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically-detailed model of monomeric ApoE4 and probe the effect of lipid association. Our data reveal that ApoE4 is far more disordered than previously thought and retains significant conformational heterogeneity after binding lipids. In particular, the behavior of the hinge region and C-terminal domain of ApoE4 differs substantially from that proposed in previous models and provides a crucial foundation for understanding how ApoE4 differs from non-pathogenic and protective variants of the protein.

biophysics↗

bioRxiv2021

Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria parasites

The malaria parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of GPI anchor biosynthesis, the putative phosphomannomutase (EC 5.4.2.8) of the parasites, HAD5 (PF3D7_1017400). We confirm the phosphomannomutase and phosphoglucomutase activity of purified recombinant HAD5. By regulating expression of HAD5 in transgenic parasites, we demonstrate that HAD5 is required for malaria parasite egress and erythrocyte reinvasion. Finally, we determine the three-dimensional crystal structure of HAD5 and identify a substrate analog that specifically inhibits HAD5, compared to orthologous human phosphomannomutases. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition, and that HAD5 has potential as a multi-stage antimalarial target.

microbiology↗

bioRxiv2020

Maternal iron deficiency perturbs embryonic cardiovascular development

Congenital heart disease (CHD) is the most common type of birth defect, with a global prevalence of 0.9% of live births1. Most research in the last 30 years has focused on finding genetic causes of CHD. However, despite the association of over 100 genes with CHD, mutations in these genes only explain ~30% of cases2. Many of the remaining cases of CHD are caused by in utero exposure to environmental factors3. Here we have identified a completely new environmental teratogen causing CHD: maternal iron deficiency. In humans, iron deficiency anaemia is a major global health problem. 38% of pregnant women worldwide are anaemic4, and at least half of these are due to iron deficiency, the most prevalent micronutrient deficiency. We describe a mouse model of maternal iron deficiency anaemia that causes severe cardiovascular defects in her offspring. We show that these defects likely arise from increased retinoic acid signalling in iron deficient embryos, probably due to reduced activity of the iron-dependent retinoic acid catabolic CYP26 enzymes. The defects can be prevented by maternal iron administration early in pregnancy, and are also greatly reduced in offspring of mothers deficient in both iron and the retinoic acid precursor vitamin A. Finally, one puzzling feature of many genetic forms of CHD in humans is the considerable variation in penetrance and severity of defects. We show that maternal iron deficiency acts as a significant modifier of heart and craniofacial phenotype in a mouse model of Down syndrome. Given the high incidence of maternal iron deficiency, peri-conceptional iron monitoring and supplementation could be a viable strategy to reduce the prevalence and severity of CHD in human populations worldwide.

developmental biology↗

bioRxiv2020

Antimicrobial prodrug activation by the staphylococcal glyoxalase GloB

With the rising prevalence of multidrug-resistance, there is an urgent need to develop novel antibiotics. Many putative antibiotics demonstrate promising in vitro potency but fail in vivo due to poor drug-like qualities (e.g. serum half-life, oral absorption, solubility, toxicity). These drug-like properties can be modified through the addition of chemical protecting groups, creating "prodrugs" that are activated prior to target inhibition. Lipophilic prodrugging techniques, including the attachment of a pivaloyloxymethyl group, have garnered attention for their ability to increase cellular permeability by masking charged residues and the relative ease of the chemical prodrugging process. Unfortunately, pivaloyloxymethyl prodrugs are rapidly activated by human sera, rendering any membrane permeability qualities absent during clinical treatment. Identification of the bacterial prodrug activation pathway(s) will allow for the development of host-stable and microbe-targeted prodrug therapies. Here, we use two zoonotic staphylococcal species, S. schleiferi and S. pseudintermedius, to establish the mechanism of carboxy ester prodrug activation. Using a forward genetic screen, we identify a conserved locus in both species encoding the enzyme hydroxyacylglutathione hydrolase (GloB), whose loss-of-function confers resistance to carboxy ester prodrugs. We enzymatically characterize GloB and demonstrate that it is a functional glyoxalase II enzyme, which has the capacity to activate carboxy ester prodrugs. As GloB homologs are both widespread and diverse in sequence, our findings suggest that GloB may be a useful mechanism for developing species-or genus-level prodrug targeting strategies.

microbiology↗

bioRxiv2019

Potent, specific MEPicides for treatment of zoonotic staphylococci

Coagulase-positive staphylococci, which frequently colonize the mucosal surfaces of animals, also cause a spectrum of opportunistic infections including skin and soft tissue infections, urinary tract infections, pneumonia, and bacteremia. However, recent advances in bacterial identification have revealed that these common veterinary pathogens are in fact, zoonoses that cause serious infections in human patients. The global spread of multidrug-resistant zoonotic staphylococci, in particular the emergence of methicillin-resistant organisms, is now a serious threat to both animal and human welfare. Accordingly, new therapeutic targets that can be exploited to combat staphylococcal infections are urgently needed. Enzymes of the methylerythritol phosphate pathway (MEP) of isoprenoid biosynthesis represent potential targets for treating zoonotic staphylococci. Here we demonstrate that fosmidomycin (FSM) inhibits the first step of the isoprenoid biosynthetic pathway catalyzed by deoxyxylulose phosphate reductoisomerase (DXR) in staphylococci. In addition, we have both enzymatically and structurally determined the mechanism by which FSM elicits its effect. Using a forward genetic screen, the glycerol-3-phosphate transporter GlpT that facilitates FSM uptake was identified in two zoonotic staphylococci, Staphylococcus schleiferi and Staphylococcus pseudintermedius. A series of lipophilic ester prodrugs (termed MEPicides) structurally related to FSM were synthesized, and data indicate that the presence of the prodrug moiety not only substantially increased potency of the inhibitors against staphylococci, but also bypassed the need for GlpT-mediated cellular transport. Collectively, our data indicate that the prodrug MEPicides selectively and robustly inhibit DXR in zoonotic staphylococci, and further, DXR represents a promising, druggable target for future development.\n\nAuthor SummaryThe proliferation of microbial pathogens resistant to the current pool of antibiotics is a major threat to public health. Drug resistance is pervasive in staphylococci, including several species that can cause serious zoonotic infections in humans. Thus, new antimicrobial agents are urgently need to combat these life-threatening, resistant infections. Here we establish the MEP pathway as a promising new target against zoonotic staphylococci. We determine that fosmidomycin (FSM) selectively targets the isoprenoid biosynthesis pathway in zoonotic staphylococci, and use forward genetics to identify the transporter that facilitates phosphonate antibiotic uptake. Employing this knowledge, we synthesized a series of potent antibacterial prodrugs that circumvent the transporter. Together, these novel prodrug inhibitors represent promising leads for further drug development against zoonotic staphylococci.

microbiology↗

bioRxiv2019

Altered structural hub connectivity and its clinical relevance in glioma

Background and PurposeStructural network analysis of diffusion imaging is increasingly used to study neurological disease, its pathophysiology and symptoms. We therefore evaluate structural hub connectivity in glioma patients and its association with molecular subtype and clinical status.\n\nMaterials and MethodsUsing retrospective diffusion imaging, structural connectivity was investigated in 65 newly diagnosed glioma patients (36 males; mean age 52 {+/-} 14 years) and 60 healthy controls (23 males; mean age 50 {+/-} 7 years). Probabilistic tractography was performed between 39 cortical nodes per hemisphere. In patients, tumors were drawn in to exclude each tumor-containing voxel from analysis. As previous connectomic research in glioma and other neurological diseases has shown particular importance of hub nodes and connections, the numbers of connections between hubs, hubs and non-hubs, and non-hubs were calculated for each hemisphere separately. Clinical and molecular characteristics were assessed as part of routine clinical care. Group differences in connectivity and its associations with performance and molecular subtypes were tested non-parametrically through Mann-Whitney U-tests, corrected for multiple comparisons.\n\nResultsGlioma patients had more hub-related connections in the hemisphere contralateral to the tumor (hub-hub P = 0.002, hub-non-hub P = 0.005), despite being comparable to controls in terms of total and ipsilateral connections. Within patients, hub-related connectivity related to performance status (P = 0.009) and molecular subtype (P = 0.045).\n\nConclusionWe present experimental evidence for the relevance of structural connectomics as a tool to pick up on the clinical impact of glioma on the rest of the brain.

cancer biology↗