Biology subjects

Patel, N.

Publications and source records attributed to Patel, N..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

CTx001 for geographic atrophy: a gene therapy expressing soluble, truncated complement receptor 1 (mini-CR1)

Over-activation of the complement system is strongly associated with geographic atrophy (GA), a late-stage form of age-related macular degeneration (AMD) and major cause of blindness. Here we report the development of a candidate GA treatment that is a potent complement modifier (mini-CR1) that addresses consequences of complement over-activation including membrane attack complex (MAC) formation. Mini-CR1 acts a potent cofactor for factor I driven proteolysis of C3b leading to iC3b and then C3dg formation; iC3b itself remains a potent opsonin. As well as inhibiting the alternative complement pathway, mini-CR1 acts as a cofactor for C4b degradation thereby inhibiting the classical pathway. Mini-CR1 prevents MAC formation in activated human serum with an IC50 of 125 nM. Mini-CR1 was shown to cross human Bruchs membrane ex vivo, implying the ability to cross into the choroidal space. Transduction of RPE cell lines with rAAV2-mini-CR1 (CTx001) resulted in dose-dependent transcription, and both basolateral and apical secretion of mini-CR1 by monolayers of human iPSC derived RPE cells. Mini-CR1 transduction of ARPE19 cells resulted in increased consumption of C3b and iC3b1 in activated culture media and decreased MAC formation on the cell surfaces. Subretinal injection of CTx001 in rats resulted in dose-dependent mini-CR1 production as demonstrated by solid-phase immunoassay. MAC formation following laser induced CNV in a rat model was reduced by 75% in CTx001-treated animals relative to null vector (p<0.01). This first generation of CTx001 represents a potent single administration complement modifier capable of effectively addressing pathologic complement amplification in the retina/choroid.

biochemistry↗

bioRxiv2025

Epithelial eversion, a collective rearrangement from apical-in to apical-out polarity, is initiated by α6β4 integrins and sustained by increased cell proliferation and anchorage-independence

Epithelial cells primarily segregate transmembrane proteins to apical or basal surfaces, establishing apical-basal polarity. For 3D tissues, apical proteins face inwards and basal proteins are on the outer surfaces (in contact with ECM). Apical-basal polarity can become inverted such that the apical proteins are on the outer surfaces. Originally this polarity inversion was assumed to always occur due to changes in protein trafficking. However, recent work by our group showed that increased RhoA activation causes epithelial spheroids to invert apical-basal polarity via a collective rearrangement of cells, a process we and others have termed eversion. We hypothesized that specific integrin-ECM interactions could facilitate the collective cellular migration required for eversion. Using multiple integrin knockout lines, we observed that epithelial cells lacking either 6 or {beta}4 integrins do not develop apical-out polarity in response to RhoA activation. Similarly, 6 blocking antibody or culturing spheroids in collagen (lacking laminin) also inhibited the formation apical-out polarity. These data indicate that 6{beta}4-laminin interactions are required for eversion. Next, we examined the role of cell proliferation and anchorage independence in maintaining apical-out polarity of everted spheroids. Inhibition of cell proliferation (with DNA synthesis inhibitor aphidicolin) or inhibition of anchorage-independence (with FAK inhibitor 14) were sufficient to restore apical-in polarity to RhoA treated spheroids, indicating that both proliferation and anchorage-independence maintain spheroids in an apical-out state. We also observed that apical-out spheroids can revert to apical-in polarity through apoptotic cavitation of cells located in the center of the spheroids. Lastly, through RNA sequencing we demonstrate that apical-out spheroids have unique gene expression profiles. This study provides new mechanistic insights into the biochemical and biophysical mechanisms that drive eversion and maintain apical-out polarity. This work supports the concept that changing from apical-in to apical-out polarity be an important marker for phenotypic switch in epithelial cells.

cell biology↗

bioRxiv2025

Exploring the C(2)M Cohesin Complex: Structure, Dynamics, and Ability to Facilitate Assembly of the Synaptonemal Complex

There are two meiotic cohesin pathways that regulate synaptonemal complex (SC) assembly in Drosophila. We previously proposed that C(2)M, which is required for SC assembly, is the only meiosis-specific component of a complex that includes Stromalin (SA), Nipped-B, SMC1 and SMC3. This model also predicts that specific residues within the C-terminus and N-terminus of C(2)M should interact with SMC1 and SMC3 to form a ring structure that may regulate the ability of C(2)M to facilitate SC assembly. Through mutant analysis, our results show several residues known to interact with SMC1 or SMC3 are critical for SC formation, suggesting that C(2)M may require a ring structure to perform meiosis-specific functions such as the formation of SC. We also show that SA colocalizes with and depends on C(2)M. However, the dynamics of C(2)M differ from SA and the SMCs in a way that suggests C(2)M regulates the dynamics and chromosome loading of the other cohesin proteins SMC1 and SA. Consistent with this conclusion, our results suggest that C(2)M can promote chromosome localization of the other cohesin components, and can induce SC assembly when ectopically expressed in germline mitotic cells.

genetics↗

bioRxiv2025

Molecular basis for multidrug efflux by an anaerobic RND transporter

Bacteria can resist antibiotics and toxic substances within demanding ecological settings, such as low oxygen, extreme acid, and during nutrient starvation. MdtEF, a proton motive force-driven efflux pump from the resistance-nodulation-cell division (RND) superfamily, is upregulated in these conditions but its molecular mechanism is unknown. Here, we report cryo-electron microscopy structures of Escherichia coli multidrug transporter MdtF within native-lipid nanodiscs, including a single-point mutant with an altered multidrug phenotype and associated substrate-bound form. We reveal that drug binding domain and channel conformational plasticity likely governs promiscuous substrate specificity, analogous to its closely related, constitutively expressed counterpart, AcrB. Whereas we discover distinct transmembrane state transitions within MdtF, which create a more engaged proton relay network, altered drug transport allostery and an acid-responsive increase in efflux efficiency. Physiologically, this provides means of xenobiotic and metabolite disposal within remodelled cell membranes that presage encounters with acid stresses, as endured in the gastrointestinal tract.

biochemistry↗

bioRxiv2025

StarTrace: A Multiplex Organoid Avatar Drug Testing Platform for Personalized Medicine

The goal of precision medicine is to improve clinical outcomes of cancer patients by choosing treatments most likely to work. One idea is to match tumor response to cancer-causing somatic mutations, but this strategy still faces limitations in colorectal cancer due to poorly understood genetic influences on drug resistance. We describe here a simple direct drug sensitivity assay platform applied to mixtures of patient-derived organoid avatars as a practical solution for choosing therapy, sidestepping the need for exhaustive knowledge of drug-genetic interactions. This approach rank orders individual patient organoid avatars responses to various drugs to be used to guide treatment choices. The platform multiplexes organoids using a clonal barcoding method, called StarTrace, which simultaneously tests pools of multiple patients organoid avatars for sensitivity or resistance to small molecule inhibitors. We utilized both quantitative real-time PCR-based and single-molecule sequencing assays to track the relative Darwinian fitness of each barcoded organoid within the pool. StarTrace offers a rapid, cost effective and sensitive testing platform that could be useful for either preclinical drug development or tailoring personalized therapy.

molecular biology↗

bioRxiv2025

The molecular basis of arthropod appendage diversity

Arthropods have an incredible diversity of limbs that are modified for walking, chewing, cleaning, mating, grasping, sensing, and more. Understanding the relationships and evolutionary histories of different limbs is a central task, but their sheer diversity makes this a daunting if not impossible task using morphology alone. Here, the in situ expression patterns and CRISPR-Cas9 phenotypes for the five best-studied leg-patterning genes - Distal-less, Sp6-9, dachshund, extradenticle, and homothorax - are described for all limbs of the crustacean Parhyale. Crustaceans are well-suited for this task because their limbs are more diverse than those of other arthropods, and each individual possesses a wide range of limb types that are relevant to many other arthropods, living and extinct. These results will a) provide a template for understanding the genetic basis of limb construction in arthropods more generally based on the strong phenotypes that can be obtained with CRISPR-Cas9, and b) contribute to our understanding of the evolution and affinities of highly modified legs like mouthparts and genitalia using molecular methods to complement previous morphological and embryological approaches.

developmental biology↗

bioRxiv2024

Goliath clades and in vivo tracking of clonal dynamics show three phases of UV-induced skin carcinogenesis

While the genetic paradigm of cancer etiology has proven powerful, it remains incomplete as evidenced by the widening spectrum of non-cancer cell-autonomous "hallmarks" of cancer. Studies have demonstrated the commonplace presence of high oncogenic mutational burdens in homeostatically-stable epithelia. Hence, the presence of driver mutations alone does not result in cancer. Here, we reveal additional forces governing the eco-evolutionary dynamics of carcinogenesis. Using a UV-driven mouse model of cutaneous squamous cell carcinoma, we tested our central hypothesis that cancer initiation occurs in three phases: 1) tissue disruption and the emergence of unusually large "goliath" clades (ecological driver), 2) clonal selection within a subset of these goliaths as evidenced by the presence of areas of unusually high local densities of cells (termed "micro-lumps") with higher mutational burdens (evolutionary driver), and 3) emergence of macroscopic lesions. We tracked these tissue level ecological and evolutionary drivers of cancer initiation via in-vivo serial imaging and 3-D reconstruction of fluorescently labeled keratinocyte clades, yielding 25,085 clade measurements from 14 mice over 3 months, and 14,525 clades from 4 of these mice over 6 months. While median and mean clade sizes differed little between UV and non-UV exposure (cc. 65,000 {micro}m3), our ecological survey revealed the emergence of large goliath clades (> cc. 4.2x106 {micro}m3), almost exclusively within UV-exposed skin. Goliath clades emerged by month 2, increased dramatically in number by months 3-4, and plateaued between months 5-6. Goliath clades arose as serpentine structures, intercalating between adjacent keratinocytes. Unexpectedly, targeted DNA sequencing revealed mutations with very low variant allele frequencies within clades, but substantial differences among clades, suggesting that positive selection for these mutations is superfluous to the development of goliaths early in carcinogenesis. scRNAseq analysis of both bulk skin and sorted clades revealed epidermal de-differentiation and immune suppression as early events. By month 7, mutational burdens were significantly larger in goliath clades, particularly for those with micro-lumps. Finally, lesions began to emerge between months 6 and 7, only in UV-exposed skin. To confirm that goliath clades are orders of magnitude more likely to spawn lesions, we randomly selected 21 goliath clades at months 6-7, prior to the time of the emergence of detectable lesions, and followed them over time. Remarkably, 2 of these developed into macroscopic lesions. Our adaptation of the Drake equation estimated the probability of this to be <10-6. Taken together, our results support the presence of three phases of cancer initiation, the earliest of which presage the acquisition of driver mutations and also explains why cancers are relatively rare in relation to the degree of somatic mosaicism present in UV-exposed skin.

cancer biology↗

bioRxiv2024

Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines

Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing platforms requires an in-depth understanding of the antigenic and immunogenic properties of available vaccines. Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping (EMPEM) of serum from immunized non-human primates (NHPs) and clinical trial donors. Both vaccines induce diverse polyclonal antibody (pAb) responses to the N-terminal domain (NTD) in addition to the receptor-binding domain (RBD) of the Spike protein, with the NTD supersite being an immunodominant epitope. High-resolution cryo-EMPEM studies revealed extensive pAb responses to and around the supersite with unique angles of approach and engagement. NTD supersite pAbs were also the most susceptible to variant mutations compared to other specificities, indicating that ongoing Spike ectodomain-based vaccine design strategies should consider immuno-masking this site to prevent induction of these strain-specific responses.

immunology↗

bioRxiv2024

Single-dose avian influenza A(H5N1) Clade 2.3.4.4b hemagglutinin-Matrix-M nanoparticle vaccine induces neutralizing responses in nonhuman primates

With the recent rise in cases of highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b infection in humans and animals, there is an associated increase in the risk of human-to-human transmission. In this study, we characterize recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b vaccine. Purified recombinant A/AW/SC/2021 HA trimers upon formulation with Matrix-M adjuvant, saponin-cholesterol-phospholipid icosahedral particles, non-covalently anchored to the vertices of the Matrix-M forming A(H5N1) HA-Matrix-M nanoparticles (H5-MNPs). In naive mice, two intranasal (IN) or intramuscular (IM) doses of A/AW/SC/2021 H5-MNP vaccine induced robust antibody- and cell-mediated immune responses, including neutralizing antibodies against A(H5N1). In non-human primates (NHPs) primed with seasonal influenza vaccine, a single IM or IN dose of the A/AW/SC/2021 H5-MNP vaccine induced geometric mean serum A(H5N1) clade 2.3.4.4b pseudovirus neutralizing titers of 1:1160 and 1:54, respectively; above the generally accepted seroconverting neutralizing titer of 1:40. Immunization with H5-MNP vaccine induced antibody responses against conserved epitopes in the A(H5N1) HA stem, vestigial esterase subdomain, and receptor binding site. This novel A(H5N1) H5-MNP IN and IM vaccine was immunogenic in rodents and NHPs as a potential A(H5N1) pandemic single-dose vaccine.

microbiology↗

bioRxiv2024

Altered systemic bioenergetic reserve in chronic kidney disease predisposes hearts to worse functional outcomes

BackgroundCardiovascular mortality in chronic kidney disease (CKD) remains disproportionately high, yet the mechanisms linking renal dysfunction to cardiac vulnerability are incompletely understood. Uraemic cardiomyopathy is increasingly recognised as a systemic metabolic disease, but the contribution of multi-organ bioenergetic failure in cardiac dysfunction is poorly defined. HypothesisCKD induces metabolic remodelling across peripheral organs (liver, skeletal muscle, and kidneys) depleting systemic bioenergetic reserve, compromising cardiometabolic flexibility and stress resilience. MethodsUsing CKD models of different aetiologies in rats (glomerulosclerosis by partial nephrectomy and interstitial fibrosis by adenine diet) we investigated cardiac and systemic metabolic remodelling. ResultsIrrespective of aetiology, renal insufficiency resulted in cardiac dysfunction including impaired functional recovery after 25-minutes ischaemia. 1H NMR metabolomic analysis revealed perturbations of systemic metabolism in CKD were more severe than cardiometabolic changes with alterations of skeletal muscle, liver, and kidney metabolism indicating reduced systemic bioenergetic reserve. This pre-clinical observation was recapitulated in human CKD patients where phosphorus magnetic resonance spectroscopy assessment of exercising lower leg muscle identified bioenergetic deficiencies preventing maximal force generation. Thus, both heart and skeletal muscles in CKD have impaired response to metabolic stress. ConclusionsCKD induces multi-organ metabolic failure that limits the hearts ability to meet energetic demands under stress. This study identifies systemic bioenergetic collapse as a contributing factor to uraemic cardiomyopathy, thus targeting peripheral organ metabolism may represent a novel therapeutic strategy to improve cardiac outcomes in CKD. Key learning pointsO_ST_ABSWhat Was KnownC_ST_ABSCKD significantly increases cardiovascular risk, but the cause of heart failure in these patients is largely attributed to cardiac pathology alone whilst the potential contribution of systemic metabolic dysfunction remains unexplored. What This Study AddsUtilising clinical and pre-clinical approach we show that CKD triggers widespread metabolic dysfunction in the liver, skeletal muscle, and kidney, depleting the systemic bioenergetic reserve and impairing the hearts ability to handle metabolic stress. Potential ImpactThese findings show uraemic cardiomyopathy is a multi-organ metabolic disease and targeting peripheral metabolic dysfunction could offer a new therapeutic strategy to enhance cardiac resilience by restoring systemic energy balance.

physiology↗

bioRxiv2024

Polymorphisms in rs2069845 are associated with IL-6 and soluble IL-6 receptor levels during total joint replacement

As the number of patients undergoing total joint replacement (TJR) surgery increases, so does the number of revision surgeries. One driver of implant failure and subsequent revision surgery is peri-implant osteolysis, which is driven by inflammation-mediated bone loss. IL-6 is an inflammatory marker that is elevated during the peri-operative period. Early elevations in IL-6 levels have been linked to osteolysis development. The current study asked whether there is genetic contribution to the IL-6-related peri-operative inflammatory reaction to TJR surgery. Patients undergoing primary TJR (total hip or total knee) provided pre-operative and post-operative blood samples for measurement of the circulating levels of IL-6 and the soluble IL-6 receptor (sIL-6r) and evaluation of allele status of three single nucleotide polymorphisms (SNPs) linked to IL-6 or sIL-6r levels - rs2069845, rs228145, and rs4537545. Circulating sIL-6r levels were associated with allele status in the rs2228145 SNP. More interestingly, allele status in the rs2069845 SNP was associated with the change in circulating IL-6 levels following TJR surgery. Specifically, patients with the A,A allele had increasing levels of IL-6, while those harboring the G,A allele had decreasing levels of IL-6. Although the study was not designed to follow implant survival, due to the critical role of IL-6 in driving peri-implant osteolysis development, the results may suggest that the rs2069845 allele has a role in the success of orthopedic implants. rs2069845 polymorphisms may be a useful patient-specific marker of inflammatory response to TJR surgery.

genetics↗

bioRxiv2024

Zebrafish glial-vascular interactions progressively expand over the course of brain development

Glial-vascular interactions are critical for the formation and maintenance of brain blood vessels and the blood-brain barrier (BBB) in mammals, but their role in zebrafish is not well understood. Our previous work has detailed the timeline of BBB functional maturation in zebrafish, revealing a conserved mechanism of BBB induction through the suppression of endothelial transcytosis. Yet, as opposed to extensive research on glial-vascular interactions in rodents, such interactions remain largely overlooked in the zebrafish model system. Here, we focus on glial-vascular development in the zebrafish brain, leveraging three glial gene promoters: gfap (glial fibrillary acidic protein), glast (an astrocyte-specific glutamate transporter), and glastini (a new, shortened, equally effective version of the Glast promoter). Using these glial promoters, sparse labeling revealed fewer glial-vascular interactions during early larval stages, with both glial coverage and contact area increasing as the zebrafish brain matured. We then generated stable transgenic lines for both the Glast and Glastini promoters and observed similar increases in glial coverage during larval development, starting at [~]30% coverage at 3 days post-fertilization (dpf) and peaking at [~]60% at 10 dpf. Ultrastructural assessment of glial-vascular interactions using electron microscopy (EM) confirmed a progressive increase in glial coverage over larval development, with maximal coverage reaching [~]70% in adult zebrafish, significantly lower than the nearly 100% coverage observed in mammals. Finally, immunogold-EM labeling confirmed that cells identified as glia in aforementioned morphological analyses were indeed Glast-positive. Taken together, our results identify the temporal profile of glial-vascular maturation in the zebrafish brain.

developmental biology↗

bioRxiv2024

Multi-omics identification of extracellular components of the fetal monkey and human neocortex.

During development, precursor cells are continuously and intimately interacting with their extracellular environment, which guides their ability to generate functional tissues and organs. Much is known about the development of the neocortex in mammals. This information has largely been derived from histological analyses, heterochronic cell transplants, and genetic manipulations in mice, and to a lesser extent from transcriptomic and histological analyses in humans. However, these approaches have not led to a characterization of the extracellular composition of the developing neocortex in any species. Here, using a combination of single-cell transcriptomic analyses from published datasets, and our proteomics and immunohistofluorescence analyses, we provide a more comprehensive and unbiased picture of the early developing fetal neocortex in humans and non-human primates. Our findings provide a starting point for further hypothesis-driven studies on structural and signaling components in the developing cortex that had previously not been identified.

neuroscience↗

bioRxiv2024

Increased burden of rare risk variants across gene expression networks predisposes to sporadic Parkinson's disease

Alpha-synuclein (Syn) is an intrinsically disordered protein that accumulates in the brains of patients with Parkinsons disease and forms intraneuronal inclusions called Lewy Bodies. While the mechanism underlying the dysregulation of Syn in Parkinsons disease is unclear, it is thought that prionoid cell-to-cell propagation of Syn has an important role. Through a high throughput screen, we recently identified 38 genes whose knock down modulates Syn propagation. Follow up experiments were undertaken for two of those genes, TAX1BP1 and ADAMTS19, to study the mechanism with which they regulate Syn homeostasis. We used a recently developed M17D neuroblastoma cell line expressing triple mutant (E35K+E46K+E61K) "3K" Syn under doxycycline induction. 3K Syn spontaneously forms inclusions that show ultrastructural similarities to Lewy Bodies. Experiments using that cell line showed that TAX1BP1 and ADAMTS19 regulate how Syn interacts with lipids and phase separates into inclusions, respectively, adding to the growing body of evidence implicating those processes in Parkinsons disease. Through RNA sequencing, we identified several genes that are differentially expressed after knock-down of TAX1BP1 or ADAMTS19. Burden analysis revealed that those differentially expressed genes (DEGs) carry an increased frequency of rare risk variants in Parkinsons disease patients versus healthy controls, an effect that was independently replicated across two separate cohorts (GP2 and AMP-PD). Weighted gene co-expression network analysis (WGCNA) showed that the DEGs cluster within modules in regions of the brain that develop high degrees of Syn pathology (basal ganglia, cortex). We propose a novel model for the genetic architecture of sporadic Parkinsons disease: increased burden of risk variants across genetic networks dysregulates pathways underlying Syn homeostasis, thereby leading to pathology and neurodegeneration.

cell biology↗

bioRxiv2024

Phthalate exposure influences mating behavior and sperm morphology in an aquatic ecotoxicology model system

Phthalates are a group of chemicals used to make plastics more durable, found in applications from cosmetics, lubricating oils, and flooring to soap, shampoo, and hairspray (CDC, 2021). Phthalates are also now known to be endocrine disruptors with connections to adverse reproductive outcomes in animals, including humans. Here, we evaluate the potential effects of a widely used phthalate ester, dimethyl phthalate (DMP), on male reproduction in a freshwater snail. DMP is found in industrial applications like solid rocket propellant as well as consumer products such as insect repellents and plastics. While there is some evidence that DMP negatively affects reproduction, especially in females, we still know very little about potential DMP effects on males. We addressed this important knowledge gap by testing the effects of DMP on Potamopyrgus antipodarum, a prosobranch snail native to New Zealand. These snails are very sensitive to water conditions and environmental chemicals, including endocrine-disrupting compounds, and are thus rising in prominence as water-quality sentinels and ecotoxicology models. We exposed experimental groups of male P. antipodarum to one of three different concentrations of DMP and characterized mating behavior and sperm morphology as a function of DMP exposure. Differences in these traits were primarily observed between the males in the control versus the High (10-6 M) DMP concentration group. As DMP exposure levels increased, we found that mating frequency ultimately decreased by more than 69% and that sperm morphology was increasingly altered relative to control males. Altogether, study outcomes suggest DMP exposure in male animals could have negative effects on reproduction, with particular relevance in aquatic and marine environments that are especially likely to harbor leached endocrine-disrupting chemicals.

ecology↗

bioRxiv2024

Performance effects from different shutdown methods of three electrode materials for the power-to-gas application with electromethanogenesis

Industrial applications of microbial electrochemical systems will require regular maintenance shutdowns, involving inspections and component replacements to extend the lifespan of the system. Here, we examined the impact of such shutdowns on the performance of three electrode materials (i.e., platinized titanium, graphite, and nickel) as cathodes in a microbial electrochemical system that would be used for electromethanogenesis in power-to-gas applications. We focused on methane (CH4) production from hydrogen (H2) and carbon dioxide (CO2) using Methanothermobacter thermautotrophicus. We showed that the platinized titanium cathode resulted in high volumetric CH4 production rates and Coulombic efficiencies. Using a graphite cathode would be more cost-effective than using the platinized titanium cathode in microbial electrochemical systems but showed an inferior performance. The microbial electrochemical system with the nickel cathode showed improvements compared to the graphite cathode. Additionally, this system with a nickel cathode demonstrated the fastest recovery during a shutdown experiment compared to the other two cathodes. Fluctuations in pH and nickel concentrations in the catholyte during power interruptions affected CH4 production recovery in the system with the nickel cathode. This research enhances understanding of the integration of biological and electrochemical processes in microbial electrochemical systems, providing insights into electrode selection and operating strategies for effective and sustainable CH4 production.

bioengineering↗

bioRxiv2024

Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases

Short AbstractThe intricate process of -synuclein aggregation and fibrillization hold pivotal roles in Parkinsons disease (PD) and multiple system atrophy (MSA). While mouse -synuclein can fibrillize in vitro, whether these fibrils commonly used in research to induce this process or form can reproduce structures in the human brain remains unknown. Here we report the first atomic structure of mouse -synuclein fibrils, which was solved in parallel by two independent teams. The structure shows striking similarity to MSA-amplified and PD-associated E46K fibrils. However, mouse -synuclein fibrils display altered packing arrangements, reduced hydrophobicity, heightened fragmentation sensitivity, and evoke only weak immunological responses. Furthermore, mouse -synuclein fibrils exhibit exacerbated pathological spread in neurons and humanized -synuclein mice. These findings provide new insights into the structural underpinnings of -synuclein pathogenicity and emphasize a need to reassess the role of mouse -synuclein fibrils in the development of related diagnostic probes and therapeutic interventions.

neuroscience↗

bioRxiv2024

Flexible Cell Modeling Using Frequency Modulation

Computational models of the cell can be used to study the impact of drugs and assess pathological risks. Typically, computational models are computationally demanding or difficult to implement in dedicated hardware for real-time emulation. A new Frequency Modulation (FM) model is proposed to address these limitations. This new model utilizes a single sine generator with constant amplitude, but phase/frequency is modulated to emulate an action potential (AP). The crucial element of this model is the identification of the modulating signal. Focusing on FPGA implementation, we have utilized a piecewise linear polynomial with a fixed number of breakpoints to serve as a modulating signal. The ability to adapt this modulating signal permits the emulation of dynamic properties and coupling of cells. We have introduced a state controller that handles both of these requirements. The building blocks of the FM model have direct integer equivalents and are amenable to implementation on digital platforms like Field Programming Gate Arrays (FPGA). We have demonstrated wavefront propagation of our model in 1-D and 2-D models of a tissue. Various parameters were used to quantify the wavefront propagation in 2-D tissues. We also emulate some cellular dysfunctions. The FM model can replicate any detailed cell model and emulate its corresponding tissue model. Overall, the results depict that the FM model has the potency for real-time cell and tissue emulation on an FPGA.

bioengineering↗