Biology subjects

Nguyen, B.

Publications and source records attributed to Nguyen, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-omics Reveals Divergent Endothelial Molecular Responses to New and Old World Hantaviruses

Hantaviruses cause vascular leakage syndromes that vary in clinical manifestation and severity. Although tissue tropism contributes to these differences, both Old and New World hantaviruses infect endothelial cells, where species-specific disease phenotypes remain poorly understood. Here we integrated time-resolved global RNA sequencing, mass spectrometry proteomics, and phosphoproteomics of human endothelial cells infected with New World Andes virus (ANDV) or Old World Hantaan virus (HTNV). Despite equivalent early viral RNA and protein levels, ANDV elicited a stronger innate immune protein response, preceding its restriction while HTNV replication continued. At later stages of infection, HTNV induced downregulation of cytoskeletal and junctional protein phosphorylation, accompanied by visual disruption of cellular actin architecture. Additionally, ANDV induced heightened activity of ERBB-family kinases, whose chemical inhibition by neratinib and afatinib reduced viral replication. Together, these data define species-specific responses in endothelial cells, identify druggable host targets, and reveal mechanisms with relevance to divergent vascular leakage symptomology.

systems biology↗

bioRxiv2026

Detection of Frustration-related Operant Behavior in Rats via Machine Learning Methods

Despite its strong link to neuropsychiatric conditions, frustration remains critically understudied in humans and animals alike. Therefore, there is an urgent need to develop tools to understand and therapeutically target frustration-related functions. Interestingly, humans and rats respond similarly during frustrative nonreward by increasing barpress durations. We previously validated barpress duration in rat operant tasks as a reliable measure of frustration-related behavior; however, it is wellknown that in addition to duration of responding, emotional states such as frustration alter other aspects of responding such as force of pressing. One-dimensional, static measures such as maximum force could miss rich information contained within operant data. Thus, the objective of this study is to apply machine learning (ML) to force/time profiles to discriminate frustration-related barpresses from non-frustration-related barpresses. Results showed an AUROC for FR1 (i.e., non-frustrated) vs. extinction (frustrated condition) for individual barpresses of 0.65 that improved to 0.84 with a chunk size of 10. The model generalized well to progressive ratio responding, a different kind of frustration procedure. We conclude that force/time profiling does provide utility beyond one dimensional measures of duration or force separately, meaning that we can indeed infer the internal state of frustration from behavior using ML techniques. Importantly, this project will also serve as proof-of-concept for applying ML to predict other internal states from barpress data.

animal behavior and cognition↗

bioRxiv2026

Life without cytoplasm: sperm sustain protein production utilizing cytoplasmic droplets and mitochondria as translational apparatuses

Sperm present a unique paradox: heavily compacted chromatin silences transcription, and loss of cytoplasm during spermiation eliminates the conventional translational apparatus, yet sperm require [~]10 days of protein-demanding epididymal maturation to acquire motility and fertilization competence. How sperm produce the necessary proteins has remained enigmatic. Here, we show that mammalian sperm sustain protein synthesis through a biphasic translational program. In testicular sperm, a residual cytoplasmic droplet retains the full complement of translational machinery, including ribosomes and intact tRNAs, and supports nascent protein synthesis. As sperm enter the epididymis, this droplet is progressively fragmented, and protein synthesis shifts to the midpiece, where mitochondrial translation machinery becomes active. Proteomic and functional analyses indicate that both systems contribute to sperm maturation. Inhibiting cytoplasmic translation in testicular sperm or mitochondrial translation in epididymal sperm abolishes motility. These findings reveal how cytoplasm-free sperm overcome transcriptional silence to complete maturation and support male fertility. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/744062v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@e4285forg.highwire.dtl.DTLVardef@11685d7org.highwire.dtl.DTLVardef@1ad1913org.highwire.dtl.DTLVardef@1495d6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Two heads are better than one: Single stranded DNA translocation of UvrD-family dimers vs. monomers

UvrD-family Superfamily 1A helicases are processive ATP-dependent motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD-family monomers translocate along single stranded (ss) DNA with 3-to-5 directionality but must be activated by dimerization to become helicases in the absence of force or accessory factors. Mycobacterium tuberculosis (Mtb) UvrD1 helicase forms dimers via a disulfide bond between native cysteines in the 2B sub-domains of each monomer. E. coli UvrD forms non-covalent dimers using the same 2B domain interface as in Mtb UvrD1. Using both ensemble and single DNA molecule approaches we examined an E. coli UvrD variant (R421C), which forms covalent dimers with constitutive helicase activity. For the first time this has enabled us to compare the ssDNA translocation and helicase activities of covalent dimers and monomers. Crosslinked UvrD dimers exhibit much higher ssDNA translocation processivities than monomers, although with similar translocation rates. Crosslinked UvrD dimers also show highly processive DNA unwinding of thousands of base pairs, much higher than non-crosslinked UvrD dimers, while monomers show no DNA unwinding activity. DNA unwinding rates of crosslinked UvrD dimers are only [~]20% slower than ssDNA translocation rates, indicating they are "active" helicases that directly facilitate duplex destabilization.

biophysics↗

bioRxiv2026

A Conserved Mechanism for Dimerization and Activation of Superfamily 1A UvrD-family Helicases

DNA helicases are ATP-dependent motor proteins that catalyze duplex DNA unwinding and are involved in DNA repair, recombination and replication restart. Prominent members of the non-hexameric SF1A UvrD-family helicases are E. coli UvrD, Rep, B. stearothermophilus PcrA and M. tuberculosis UvrD1. SF1A monomers are processive 3 to 5 single stranded DNA translocases, but need to be activated to become DNA helicases. One mechanism of activation is dimerization. Whereas Rep, UvrD and PcrA form non-covalent dimers, the Mtb UvrD1 helicase forms a redox-dependent covalent dimer. Dimerization of Mtb UvrD1 occurs between the same regulatory domain (2B) within each subunit stabilized by a disulfide bond formed between the same cysteine (Cys451) within each subunit. Dimerization relieves an inhibitory interaction between the 2B domain and duplex DNA within the monomer-DNA complex. We show here that Rep, UvrD and PcrA dimerize using the same 2B-2B interface. By placing a Cys residue within the 2B domains of Rep, UvrD and PcrA in the structurally equivalent position occupied by Cys451 of Mtb UvrD1, all three enzymes form redox-dependent covalent dimers that are constitutively active helicases with increased processivity compared to the non-covalent dimers. Hence, the 2B domain is a general dimerization domain for UvrD-family SF1A helicases.

biochemistry↗

bioRxiv2026

Mapping Evidence Gap Between NMN and NR for Metabolic Outcomes: A Systematic Review, Transitivity Assessment, and Indirect Comparison Meta-Analysis

BackgroundNicotinamide mononucleotide (NMN) and nicotinamide riboside (NR) are NAD+ precursor supplements widely marketed for metabolic health benefits. Despite billions of dollars in annual sales, no head-to-head randomized controlled trial (RCT) has compared their effects on metabolic endpoints, and no systematic characterization of why reliable comparison is currently impossible has been published. ObjectiveTo characterize the structural heterogeneity of the NMN and NR trial evidence bases across population, dose, duration, and biomarker dimensions; to formally assess transitivity; and to estimate indirect NMN versus NR effects where methodologically feasible using the Bucher indirect comparison method. MethodsFive databases (PubMed, Embase, Scopus, Web of Science, Cochrane CENTRAL) were searched from January 2018 to May 2025. Eligible studies were RCTs of oral NMN or NR versus placebo in adults reporting metabolic outcomes. A formal transitivity assessment was conducted comparing effect modifier distributions across NMN and NR trial arms. Random-effects pairwise meta-analyses were conducted for each precursor versus placebo, and Bucher indirect comparisons estimated NMN versus NR effects through the common placebo node. Risk of bias was assessed using RoB 2 and certainty of evidence using the GRADE/CINeMA framework. ResultsFifteen studies (5 NMN, 10 NR; 740 participants) were included. The NMN and NR trial evidence bases were systematically asymmetric across every major effect modifier: NR was dosed 1.9 to 9.2 times higher than NMN on a molar basis; NMN trials were conducted predominantly in East Asian populations while NR trials were predominantly Western; and available NAD+ pharmacodynamic measures used incompatible assay matrices precluding indirect comparison. Across 14 metabolically comparable outcomes, no indirect comparison reached statistical significance and all were rated Very Low certainty by GRADE/CINeMA, consistent with the structural limitations of the evidence base. Leave-one-out sensitivity analyses showed zero pairwise significance changes and one indirect significance change (triglycerides upon exclusion of Conze 2019). ConclusionCurrent evidence is structurally insufficient to support reliable indirect comparison of NMN and NR for metabolic outcomes. The barriers are quantifiable and modifiable: future head-to-head trials should use equimolar dosing (approximately 1,150 mg NMN is molar-equivalent to 1,000 mg NR), harmonized whole-blood NAD+ assays reported in mol/L, minimum 24 weeks duration, and enrollment of metabolically at-risk populations to generate interpretable comparative evidence. RegistrationPROSPERO 2026 CRD420261330487; registered prior to data screening.

biochemistry↗

bioRxiv2026

VesSynth: Tubes Are All You Need for Robust Cross-Scale Cross-Modal 3D Vessel Segmentation

The cerebral vasculature is central to brain function, with alterations linked to numerous cerebrovascular and neurological disorders. Yet, no single imaging modality can capture the entire cerebral vascular network in humans. Instead, an array of techniques are sensitized to different spatial scales, while trading off resolution for coverage. Magnetic Resonance Imaging (MRI) typically resolves only large pial vessels, while high-resolution microscopy allows micrometer-scale vessels to be mapped over limited spatial extents. These techniques must therefore be combined to obtain a complete mapping of the cerebral angioarchitecture, which underscores the need for automatic, cross-modal vessel segmentation. Here, we introduce VesSynth, a flexible vessel segmentation framework that achieves state-of-the-art accuracy across multiple modalities and spatial resolutions (MR, optical and X-ray imaging), despite being trained entirely on synthetic data. By enabling consistent vascular mapping across scales, this framework paves the way to comprehensive investigation of cerebrovascular organization and its role in health and disease.

bioengineering↗

bioRxiv2025

Functional Characterization of 123 Genes from Mycobacteriophage LeBron Uncovers Cytotoxic Gene Families in Cluster L1

Bacteriophages represent a vast reservoir of genetic diversity however, functional annotation remains a major challenge, as most predicted gene products lack detectable similarity to characterized gene families. Experimental approaches such as systematic overexpression screens provide an avenue for identifying phage genes that influence bacterial physiology. Here, we report an overexpression screen of all 123 predicted protein-coding genes from Cluster L1 mycobacteriophage LeBron, the first representative of this cluster to undergo genome-wide functional analysis. Expression assays in Mycobacterium smegmatis revealed that 39 genes (32%) impaired host growth, with nineteen of these toxic genes (49%) assigned no known function. The proportion of cytotoxic genes observed in LeBron is comparable to findings from Clusters K and F, despite minimal sequence conservation across clusters. Interestingly, a subset of LeBrons toxic genes appear to be functionally analogous to previously identified toxic genes in other clusters, suggesting conserved biological activities carried out by non-homologous proteins. Additionally, this analysis uncovered several novel gene families that elicit strong cytotoxic effects, expanding the known catalog of phage-derived bacterial growth inhibitors. These results provide new insights into phage gene functions and demonstrate the value of genome-wide expression screening for uncovering conserved and cluster-specific interactions between bacteriophages and their hosts.

microbiology↗

bioRxiv2025

The Connectome Modulates Critical Brain Dynamics Across Local and Global Scales

Neuronal activity in the brain has been hypothesized to operate near criticality-a dynamical regime poised between order and disorder that maximizes information processing, adaptability, and dynamic range. While criticality has been extensively studied at local scales (within neuronal populations) and at global scales (across interacting brain regions), the interplay between these levels remains poorly understood. Here, we propose a multiscale computational framework that bridges local and global criticality within a single, mechanistic model. At the mesoscopic level, individual brain regions are represented by neural mass models tuned near the transition between asynchronous and synchronous regimes. These regions are then coupled via an empirically derived mouse connectome to investigate how structural connectivity shapes the emergence of large-scale coordination. We show that (i) local near critical dynamics for an isolated brain region can be faithfully reproduced within a mean-field model framework, (ii) local distance to criticality is modulated by long-range coupling, (iii) whole-brain simulations reveal non-linear gradients of timescales and heterogeneous shifts towards/away from local criticality, and (iv) global criticality, manifested in scale-free avalanche distributions and optimal functional connectivity, emerges when local populations are locally tuned near criticality and coupled within an optimal range. These results demonstrate that local and global criticality are dynamically intertwined but not directly aligned, and that their relationship depends on the underlying structural connectivity. Our multiscale modeling framework provides a tractable tool for generating testable hypotheses on how brain criticality co-arises across scales and how it may be modulated in health and disease.

neuroscience↗

bioRxiv2025

Integration of artificial intelligence and high-content screening enabled identification of drugs for long-term treatment of cerebral cavernous malformation disease

BackgroundAdults and children with cerebral cavernous malformations (CCMs) are at risk of experiencing lifelong complications such as hemorrhagic strokes, neurological deficits, and epileptic seizures. These complications can severely reduce quality of life. At present, there is no safe or effective therapeutic option for the long-term treatment of CCMs. MethodsUsing advanced artificial intelligence (AI) and machine learning models, powered by the Benevolent Platform, we aimed to identify therapeutic drug targets for CCM pathology (e.g., CCM1, CCM2, CCM3). An AI integrative approach utilized various data types from biomedical entities, including diseases, genes, tissues, and biological mechanisms, together with CCM transcriptomic experimental data. High-throughput drug screening of AI-selected FDA-approved medications, analyses of mitochondrial morphology, and studies on pharmacokinetics, pharmacodynamics, and toxicology were conducted in CCM animal models to identify drugs that could potentially be repurposed for the long-term treatment of CCM disease. ResultsAI predicted the AMPK (AMP-activated protein kinase) and mTOR (mammalian target of rapamycin) pathways as potential therapeutic targets that contribute to CCM pathology. High-content screening validation revealed that the FDA-approved drug metformin, which acts as an AMPK agonist and mTOR inhibitor, can reverse changes in cell-cell junction organization and increase KLF4 expression, a marker for CCM, in human CCM endothelial cells in cultured assays. In addition, pharmacodynamic markers of metformin were observed in CCM mouse models (Slco1c1-iCreERT2;Krit1fl/fl;Ptenfl/wt and Slco1c1-iCreERT2;Pdcd10fl/fl) including reduced S6 kinase or ribosomal protein phosphorylation, a marker of decrease mTOR signaling, and increased AMPK phosphorylation, a marker of AMPK activation, that corresponded to reduced lesion burden. Pharmacokinetic and toxicological studies in CCM animal models showed that that metformin penetrates the brain and long-term administration has a favorable safety profile. We also demonstrated that brain endothelial cells in chronic CCM mouse models exhibit increased levels of the inflammatory marker VCAM-1, which is associated with altered mitochondrial phenotypes, as observed by immunofluorescence, MITO-tagging, and electron microscopy analysis. Additionally, we discovered that metformin and a potent AMPK activator, PF-06409577, can reverse mitochondrial phenotypic changes in brain endothelial cells and reduce the elevation of VCAM-1 expression associated with chronic CCM disease. Therefore, metformin can provide cytoprotection and may reverse the CCM endothelial phenotype by activating AMPK. ConclusionsPredictions using AI technology and high-throughput drug screening, combined with pharmacokinetic, pharmacodynamic, and toxicological studies in CCM animal models, identified metformin as a promising drug candidate for repurposing for the long-term treatment of CCM disease. We propose that metformin enhances metabolic adaptation to brain vascular malformations by activating AMPK, which helps reverse mitochondrial fragmentation in brain endothelial cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/693036v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@17bfadforg.highwire.dtl.DTLVardef@936708org.highwire.dtl.DTLVardef@15171ceorg.highwire.dtl.DTLVardef@69029_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Exploring the Effect of LED-to-Photodetector Spacing on Subcutaneous Photoplethysmography for Continuous Blood Pressure Measurement

Photoplethysmography (PPG) is widely used to measure heart rate, blood oxygenation, and more recently, blood pressure. Implanted PPG systems offer the possibility to measure similar real-time measures of cardiovascular health, however, the detection method may vary due to a lack of capillary vessels for PPG sensors to observe in muscle tissue. To improve volumetric blood detection in large muscles, without relying on the capillary density of skin, a flexible PPG sensor was developed. The sensor included multiple spacing of illuminating infrared (IR) light emitting diodes (LEDs) and a single IR photodetector. This arrangement was expected to enable detection of blood volume changes at variable distances from the sensor face, potentially at much longer depths then feasible with skin-mounted PPG devices. IR bench phantoms simulating a large blood vessel embedded in IR absorbing, tissue-mimicking rubber were developed and used to determine the sensor performance in vitro. A preliminary in vivo test used an adult rabbit to provide additional performance validation. Test results reveal an observed trend of increased SNR for deeper vessel depths for the farthest LED to detector spacing which is aligned with our initial prediction. However, ANOVA and post-hoc tests reveal that these trends did not reach statistical significance. The in vivo test showed a relationship consistent with relevant literature. Future experiments are required to improve the phantoms representation of the biological setting and to confirm a reduced SNR variation for the farthest spacing. Clinical RelevanceDevelopment of a subcutaneous, continuous blood pressure sensor may provide benefits towards monitoring autonomic dysreflexia and hypertension for people affected by spinal cord injury.

bioengineering↗

bioRxiv2025

CD11b Activation Reduces Myeloid Brain Infiltration and Mitigates Synucleinopathy in a Model of Parkinson's Disease

The pathology of Parkinsons disease is defined by -synuclein (-syn) aggregation into neuronal Lewy bodies, which may lead to chronic neuroinflammation and dopaminergic neurodegeneration. Misfolded -syn activates Toll-like receptor signaling in microglia, leading to downstream activation of NF-{kappa}B and subsequent release of pro-inflammatory cytokines. These cytokines recruit pro-inflammatory myeloid cells from circulation, thereby amplifying neuroinflammation. Thus, reducing microglial activation and myeloid cell infiltration has the potential to reduce neuroinflammation and PD pathology. Here, we investigated a targeted immunomodulatory strategy using LA1, a novel, small-molecule agonist of CD11b, a {beta}2 integrin receptor highly and selectively expressed on myeloid cells and microglia. CD11b has key roles in cell adhesion, migration, and phagocytosis. Previous work has demonstrated that CD11b agonism via LA1 transiently enhances integrin-mediated adhesion that limits immune cell transmigration and tissue infiltration. CD11b agonism also suppresses TLR-driven inflammatory signaling and myeloid cell activation. To evaluate its efficacy in vivo, we utilized pre-clinical Parkinsons disease model by stereotaxically delivering AAV2-SYN to induce -synuclein overexpression in the murine midbrain. Mice were treated with oral LA1 for four or eight weeks and analyzed. LA1 treatment significantly reduced microglial activation and decreased brain infiltration of peripheral immune cells, thereby attenuating -synuclein-induced neuroinflammation. These findings suggest that CD11b agonism may offer a dual-action therapeutic approach in Parkinsons disease by dampening pro-inflammatory responses by central and peripheral myeloid cells.

neuroscience↗

bioRxiv2025

A new component of the DNA damage response biofilm axis is a TetR-like DNA damage response regulator in Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen that employs two main strategies to evade antibiotic treatment: developing antibiotic resistant through the DNA damage response (DDR), and forming biofilms, which are protective bacterial multicellular communities. Previously, we demonstrated that RecA, a key regulator of the DDR, connects the DDR and biofilm formation, with RecA levels inversely correlated with biofilm formation. In this study, we identify another DDR regulator, EppR-- a recently characterized TetR-family transcriptional repressor-- as also playing a role in biofilm formation. We show that an eppR-deficient strain is unable to form biofilms due to reduced expression of genes encoding adhesive pili. This occurs because EppR influences intracellular RecA levels. Our findings provide further insight into RecA regulation and the link between the DDR and biofilms.

microbiology↗

bioRxiv2025

The Current Landscape of Plasma Proteomics: Technical Advances, Biological Insights, and Biomarker Discovery

Plasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of plasma proteome profiling in recent years. Despite widespread adoption, few studies have directly compared different plasma proteomics platforms, particularly those using mass spectrometry. Our study provides a comprehensive comparison of seven platforms across three leading technologies - SomaLogic, Olink, and Mass Spectrometry (MS) - including affinity-based approaches and various MS techniques, covering over 13,000 proteins. By applying these methods to the same cohort, we assess their performance, revealing key differences and complementary strengths. Our findings offer valuable insights for researchers, highlighting trade-offs in coverage and their implications for biomarker discovery and clinical applications. This study serves as an essential resource, offering both technical evaluation and biological insights to support the development of novel diagnostics and therapeutics through plasma proteomics.

bioinformatics↗

bioRxiv2024

Structural and Mechanistic Bases for Resistance of the M66I Capsid Variant to Lenacapavir

Lenacapavir (LEN) is the first in class viral capsid protein (CA) targeting antiretroviral for treating multi-drug-resistant HIV-1 infection. Clinical trials and cell culture experiments have identified resistance associated mutations (RAMs) in the vicinity of the hydrophobic CA pocket targeted by LEN. The M66I substitution conferred by far the highest level of resistance to the inhibitor compared to other RAMs. Here we investigated structural and mechanistic bases for how the M66I change affects LEN binding to CA and viral replication. The high-resolution X-ray structure of the CA(M66I) hexamer revealed that the {beta}-branched side chain of Ile66 induces steric hindrance specifically to LEN thereby markedly reducing the inhibitor binding affinity. By contrast, the M66I substitution did not affect binding of Phe-Gly (FG)-motif-containing cellular cofactors CPSF6, NUP153, or SEC24C, which engage the same hydrophobic pocket of CA. In cell culture the M66I variant did not acquire compensatory mutations or replicate in the presence of LEN. Analysis of viral replication intermediates revealed that HIV-1(M66I CA) predominantly formed correctly matured viral cores, which were more stable than their wildtype counterparts. The mutant cores stably bound to the nuclear envelope but failed to penetrate inside the nucleus. Furthermore, the M66I substitution markedly altered HIV-1 integration targeting. Taken together, our findings elucidate mechanistic insights for how the M66I change confers remarkable resistance to LEN and affects HIV-1 replication. Moreover, our structural findings provide powerful means for future medicinal chemistry efforts to rationally develop second generation inhibitors with a higher barrier to resistance. IMPORTANCELenacapavir (LEN) is a highly potent and long-acting antiretroviral that works by a unique mechanism of targeting the viral capsid protein. The inhibitor is used in combination with other antiretrovirals to treat multi-drug-resistant HIV-1 infection in heavily treatment-experienced adults. Furthermore, LEN is in clinical trials for preexposure prophylaxis (PrEP) with interim results indicating 100 % efficacy to prevent HIV-1 infections. However, one notable shortcoming is a relatively low barrier of viral resistance to LEN. Clinical trials and cell culture experiments identified emergent resistance mutations near the inhibitor binding site on capsid. The M66I variant was the most prevalent capsid substitution identified in patients receiving LEN to treat muti-drug resistant HIV-1 infections. The studies described here elucidate the underlying mechanism by which the M66I substitution confers a marked resistance to the inhibitor. Furthermore, our structural findings will aid future efforts to develop the next generation of capsid inhibitors with enhanced barriers to resistance.

microbiology↗

bioRxiv2024

Microfluidic Modulation of Microvasculature in Microdissected Tumors

The microvasculature within the tumor microenvironment (TME) plays an essential role in cancer signaling beyond nutrient delivery. However, it has been challenging to control the generation and/or maintenance of microvasculature in ex vivo systems, a critical step for establishing cancer models of high clinical biomimicry. There have been great successes in engineering tissues incorporating microvasculature de novo (e.g., organoids and organs-on-chip), but these reconstituted tissues are formed with non-native cellular and molecular components that can skew certain outcomes such as drug efficacy. Microdissected tumors, on the other hand, show promise in preserving the TME, which is key for creating cancer models that can bridge the gap between bench and bedside. However, microdissected tumors are challenging to perfuse. Here, we developed a microfluidic platform that allows for perfusing the microvasculature of microdissected tumors. We demonstrate that, compared to diffusive transport, microfluidically perfused tissues feature larger and longer microvascular structures, with a better expression of CD31, a marker for endothelial cells, as analyzed by 3D imaging. This study also explores the effects of nitric oxide pathway-related drugs on endothelial cells, which are sensitive to shear stress and can activate endothelial nitric oxide synthase, producing nitric oxide. Our findings highlight the critical role of controlled perfusion and biochemical modulation in preserving tumor microvasculature, offering valuable insights for developing more effective cancer treatments.

bioengineering↗

bioRxiv2024

Optimization of rearing Transeius montdorensis under laboratory conditions

The global application of Transeius montdorensis (Acari: Phytoseiidae) as a biological control agent across various protected crops has proven effective against a range of insect pests like thrips and whiteflies, as well as pest mites like broad mites and russet mites. Optimization of rearing T. montdorensis under laboratory conditions is crucial for further studies of this species to improve their application in Integrated Pest Management (IPM) programs. Here, we evaluated the development and reproduction of T. montdorensis when fed on four different diets, including cattail pollen (Typha latifolia), living dried fruit mites (Carpoglyphus lactis), frozen C. lactis eggs, and a mixed diet of frozen C. lactis eggs and T. latifolia pollen. Females consuming the mixed diet exhibited superior total fecundity and daily oviposition rate, along with the highest intrinsic rate of increase (rm) and net productive rate (R0) among all diets tested. The immature period was significantly longer for mites on a diet of living C. lactis compared to those on other diets. Importantly, utilizing frozen C. lactis eggs and T. latifolia pollen mitigates the risk of infestation and contamination from the living dried fruit mites, which is important for laboratory and field settings when releasing the predator colonies. Our findings not only present an optimized rearing method for predatory mites under laboratory conditions but also suggest potential broader applications for enhancing the effectiveness and sustainability of biological control strategies across various agroecosystems and reducing dependency on chemical pesticides.

zoology↗

bioRxiv2024

Structural Basis for Dimerization and Activation of UvrD-family Helicases

UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single stranded (ss) DNA but need to be activated by dimerization to unwind DNA in the absence of force or accessory factors. However, prior structural studies have only revealed monomeric complexes. Here, we report the first structures of a dimeric UvrD-family helicase, Mycobacterium tuberculosis UvrD1, both free and bound to a DNA junction. In each structure, the dimer interface occurs between the 2B subdomains of each subunit. The apo UvrD1 dimer is observed in symmetric compact and extended forms indicating substantial flexibility. This symmetry is broken in the DNA-bound dimer complex with leading and trailing subunits adopting distinct conformations. Biochemical experiments reveal that the E. coli UvrD dimer shares the same 2B-2B interface. In contrast to the dimeric structures, an inactive, auto-inhibited UvrD1 DNA-bound monomer structure reveals 2B subdomain-DNA contacts that are likely inhibitory. The major re-orientation of the 2B subdomains that occurs upon UvrD1 dimerization prevents these duplex DNA interactions, thus relieving the auto-inhibition. These structures reveal that the 2B subdomain serves a major regulatory role rather than participating directly in DNA unwinding.

biochemistry↗