Biology subjects

Prakash, P.

Publications and source records attributed to Prakash, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Assessment of antimicrobial potential of cell-free supernatant from Lacticaseibacillus paracasei SRG isolated from the vaginal microbiota of healthy women against uropathogens

Among women, urinary tract infection (UTI) represents a major health concern. Approximately 50% of the adult female population experienced an episode of UTI at least once. UTI and recurrent UTIs caused by resistant bacteria are very common in clinical settings. The treatment and management of UTI is becoming more challenging because of the rise in antibiotic-resistant bacteria. Lactobacillus spp are the dominant bacterial genus in urinary and vaginal microbiota, which are also used as probiotics. In this study, Lacticaseibacillus paracasei SRG isolated from the vagina of healthy women were evaluated for its probiotic-associated properties and cell-free supernatant (CFS)-mediated antibacterial activity against eight uropathogens. The antibacterial activity of CFS was concentration- and pH-dependent, which was significantly evident at CFS/2 and CFS/4 concentrations and acidic pH values of 4 and 5. The antibacterial activity in CFS remains unaltered even after heat and proteinase K treatment, which suggests the role of heat- and protease-resistant metabolites beside the contributions from acidic conditions. L. paracasei SRG showed strong autoaggregation (85.32%) and cell-surface hydrophobicity (55.60%). In addition, it also exhibits co-aggregation with all indicator strains, suggesting substantial interaction with diverse pathogenic bacteria. These observations highlighted the L. paracasei SRG as a potential probiotic candidate developed from indigenous vaginal microbiota.

microbiology↗

bioRxiv2026

Toward A Whole-Brain Interface Enabled by High-Resolution Surface Electrophysiology

The goal of building a whole-brain interface - capable of generating a real-time digital representation of the state of the entire central nervous system - has long been framed as a hardware challenge of recording simultaneously from ever-larger numbers of microelectrodes. Advances in high-resolution neural interfaces now enable electrophysiologic interaction with the human nervous system at spatial and temporal resolutions previously unattainable without disrupting tissue architecture or physiology. These capabilities create new opportunities for mechanistic neuroscience, neuroprosthetics, and precision-guided neurosurgery. With the advent of modern microelectrode array technology, however, the whole-brain interface has also become a data challenge. Rather than pursuing large-scale human brain recording purely through a single device placed in a single patient, we demonstrate here that systematic multi-subject aggregation, across brain regions and behavioral paradigms, in a common anatomical framework, can achieve something functionally similar to a whole-brain interface. Here we present an approach to a functional atlas of the human central nervous system derived from high-resolution surface electrophysiology recordings obtained in the first 70 patients implanted with an anatomically conformal, thin-film neural interface positioned in more than 100 locations. The atlas comprises >100,000 electrode deployments and catalogs placement across a broad range of neuroanatomic targets spanning the motor, sensory, language, auditory, and associative domains, as well as brainstem and spinal cord structures that have historically been difficult to access at high electrophysiologic resolution. Across participants, aggregated recordings reveal somatotopic organization, including digit representations that follow a lateral-to-medial ordering consistent with classical homuncular maps, with transitions between adjacent representations occurring over spatial scales of approximately 0.8 - 2.0 mm; canonical frequency-band signatures, such as movement-related beta-band suppression and focal high-gamma (70 - 200 Hz) increases during motor and speech behaviors; and task-modulated population dynamics in both evoked and spontaneous activity across cortical, brainstem, and spinal cord regions. These findings yield insight into patterns of mesoscale electrophysiological dynamics conserved across the entire human central nervous system, suggesting that fine-scale functional organization is preserved across individuals when aligned to common anatomical landmarks. We further demonstrate several applications of these high-resolution recordings, including real-time neural decoding from upper extremity motor cortex to enable real-time neuroprosthetic control, and from ventrolateral cortex to decode cortical correlates of spoken language, facial movements, and complex facial expressions of emotion, supporting initial feasibility of combined verbal and nonverbal communication interfaces. Together, these results establish a paradigm for approaching large-scale interfaces with the human brain, as well as a starting point for a scalable, extensible atlas of human electrophysiologic function designed to accelerate discovery across basic neuroscience, translational research, and clinical neurotechnology.

neuroscience↗

bioRxiv2026

Retention, not flux: endpoint confounding caps computational prediction of peptide skin penetration, with a delivery-aware reframing

Bioactive peptides are now central to cosmetic and dermatological actives, yet predicting whether a given sequence will reach its site of action in skin remains unsolved. We contend that the dominant framing, predicting a single binary "skin permeability" label from sequence, is ill-posed, and that this, rather than a shortage of modelling power, explains the fields stalled predictive performance. The scope of the claim is narrow: barrier-crossing propensity is a legitimate, learnable function of molecular structure, whereas the vehicle- and endpoint-agnostic binary label that the literature supplies is not. We support this with a first-principles analysis and a study of public-source data. First, the experimental endpoint most commonly reported, transdermal flux into a diffusion-cell receptor compartment (OECD Test Guideline 428), conflates two opposite outcomes (genuine deep delivery and undesired systemic transport) and is, for a cosmetic active, frequently a failure signal rather than a success signal. That receptor flux is an imperfect measure of cutaneous bioavailability is long established in dermatopharmacokinetics; our contribution is to show that the same confound, inherited through scraped labels, is what caps machine learning from sequence. Second, reported "permeability" is a property of the sequence x delivery-vehicle x measurement-compartment triad, two terms of which are usually unrecorded. Third, on public-source data, a physicochemical intrinsic-permeability estimate (Potts-Guy) carries no positive predictive signal for scraped penetration labels (grouped AUC 0.45, 95% CI 0.40-0.51); sequence-only classifiers plateau in the mid-0.70s with diminishing returns as labels accumulate (AUC 0.70-0.77); and the same descriptor pipeline on a clean single-endpoint membrane dataset scores materially higher (AUC 0.83, non-overlapping CI). Our proposed reframing separates barrier-crossing (data-driven, sequence-level) from depth-and-retention (physics-driven, delivery-aware) and treats intrinsic transdermal flux as a regulatory risk axis; we close by proposing a triad-annotated reporting schema and a seed benchmark.

bioinformatics↗

bioRxiv2026

A comparative analysis of urinary microbiome identifies putative probiotics

Urinary tract infections (UTIs) are the most prevalent bacterial infections globally, and their management increasingly challenged by antimicrobial resistance (AMR). Probiotics offer a promising approach to mitigate AMR by competitively excluding uropathogens and enhancing host immunity by producing immune modulators. Despite being potential, key gaps persist between the discovery of uroprotective probiotic strains and optimization of formulations for urinary tract delivery. Here, we analyzed the urinary microbiome of UTI patients and healthy individuals to identify potential probiotic candidates for the prevention and management of UTIs. Publicly available 16S rRNA amplicon sequencing data of the urinary tract were processed using a standardized pipeline for sequence quality assessment, taxonomic assignment, and microbial function prediction. Comparative analysis showed a significant shift in microbial composition between UTI patients and healthy controls. The dominated phyla identified included Acidobacteriota, Actinobacteriota, Bacteroidota, Campylobacterota, Cyanobacteria, Firmicutes, Fusobacteriota, Patescibacteria, Proteobacteria, and Synergistota. Overall differential abundance analysis revealed Escherichia coli as the predominant UTI-associated species, while Lactobacillus crispatus was enriched in healthy samples. Additionally, predictive functional analysis indicated that metabolic pathways associated with beneficial microbes were enriched in the healthy group. Overall, the study highlights the association of distinct urinary microbiome signatures with infection status, which supports L. crispatus as the most promising probiotic for UTI prevention and control.

bioinformatics↗

bioRxiv2026

Constrained Evolutionary Design of Matrixyl Analogs: Balancing Permeability and Functional Preservation Through Computational Optimization

Matrixyl (palmitoyl pentapeptide-4, KTTKS core) is a collagen-stimulating peptide used in topical anti-ageing products, but its in-use efficacy is limited by poor permeation through the stratum corneum. We describe a deterministic computational workflow that combines a tournament genetic algorithm and NSGA-II with exact RDKit molecular descriptors to search the fixed-length, edit-distance-2 neighbourhood of KTTKS (3,706 candidate sequences) for analogs with descriptors more favourable for passive transdermal diffusion. The search returns a 9-member Pareto frontier that quantifies the trade-off between predicted permeability and motif preservation. Five of the nine frontier members carry the same substitution, lysine to proline at position 4 (K4P). This single change lowers the topological polar surface area by 25.6%, removes the +1 charge contributed by lysine, and reduces the functional-preservation score from 1.00 (KTTKS) to 0.67. The frontier ranking is unchanged by {+/-}30% perturbations to the TPSA and Mw penalty weights and by a 30% increase in the LogP penalty; only a 30% reduction in the LogP penalty produces rank movement. The frontier matches the ground-truth Pareto set obtained by exhaustive enumeration of all 3,706 candidates (precision and recall both 100%). On the basis of these results we recommend three sequences for experimental validation: PTTPS (largest predicted gain), KTTPS (single-mutation, conservative), and KTTPP (backup). All code, results, and figures are released under MIT and CC BY 4.0.

bioinformatics↗

bioRxiv2025

Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions

The interplay between transcription factors (TFs) and nucleosomes is central to gene regulation, yet most studies adopt a protein-centric perspective that largely overlooks DNA sequence contributions. Here, we identify four distinct nucleosomal DNA classes, including the canonical WW/SS pattern (W = A/T, S = G/C). All four nucleosome types are widespread across the human genome both in vivo and in vitro. Nucleosomes sharing the same pattern are rotationally in phase, whereas different patterns exhibit specific rotational offsets, revealing distinct DNA-encoded codes for nucleosome positioning. Analysis of 747 TFs across eukaryotes shows that the WW/SS and anti-WW/SS patterns are strongly associated with TF binding in chromatin. Differences in the proportions of these two patterns, quantified as {Delta}NPS values, correlate closely with in vitro nucleosome occupancy. Integrating {Delta}NPS with in vivo nucleosome occupancy uncovers four distinct modes of nucleosome-TF interaction and provides new insight into nucleosome-depleted regions around TF binding sites.

bioinformatics↗

bioRxiv2025

Machine-learning-based determination of sex-related bladder cancer biomarkers

Bladder cancer exhibits sex-specific behavior, occurring more frequently in males but progressing to advanced stages more commonly in females. The activation of sex hormone receptors may explain these differences, but the exact genetic drivers remain poorly understood. Furthermore, current bladder cancer biomarkers have inconsistent sensitivities and specificities in practice, making early diagnosis a challenge. This study approaches bladder cancer biomarker discovery through machine learning techniques on gender and disease-stratified RNA-seq data. Training sets limited to differentially expressed genes were subjected to four different feature selection methods: differential gene expression analysis adjusted p-value, recursive feature elimination with support vector machine, logistic regression, and an optimized random forest procedure. Gene panels were compared and aggregated across selection strategies and cross-validation folds to identify robust biomarkers for sex-specific bladder cancer development and progression. When applied to unseen datasets and limited to 50 genes or less, male and female-specific panels achieved areas under the receiver operating characteristic curve of 0.932 and 0.914, respectively, in distinguishing bladder cancer samples from non-tumor controls. Genes such as PRAC1 and PCDH11Y were identified as high-impact predictors related to sex hormones or chromosomes for male tumor development. In the female-specific panel, genes related to aberrant androgen signaling across tumor types like AR, PLXNA1, USP54, and PMEPA1 were influential. These results offer potential targets for further in vivo/vitro experimentation and provide a framework for constructing generalizable, high-performance gene panels for bladder cancer diagnosis and prognosis.

bioinformatics↗

bioRxiv2025

TagF coordinates spike-loading as an intermediate checkpoint in Type VI Secretion System assembly

Diderm bacteria use contact-dependent Type VI secretion systems (T6SS) to gain a competitive advantage within bacterial communities and during infection. Whereas the structural core assembly of T6SS is well characterized, the role of diverse accessory proteins during assembly remains under investigation. One well-conserved accessory protein is TagF, a post-translational inhibitor of T6SS dynamics, which was previously characterized in the context of a kinase-phosphatase signaling relay. Here, we identify a subset of T6SS clusters in which TagF occurs in a distinct regulatory context and without known binding partners. Investigating the role of TagF in the constitutively active Acinetobacter baylyi T6SS, we show that though TagF can suppress assembly dynamics, it primarily acts as an assembly coordinator. Using structured illumination microscopy, we show that TagF coordinates the transition from baseplate assembly to sheath elongation by preventing premature and nonproductive sheath assembly in absence of the VgrG spike. Direct interactions with the conserved T6SS tube protein Hcp suggested that TagF blocks sheath elongation by binding and disrupting Hcp hexamers and thus preventing tube formation. Finally, we show that TagF activity depends on crosstalk with TagZ, a previously uncharacterized membrane-associated accessory protein that recruits TagF to the cell periphery, and demonstrate that this interaction can be specifically disrupted by expression of an artificial TagF-binding protein. Together, our findings establish a novel role of TagF as a checkpoint protein that controls for spike-insertion into the baseplate to ensure effective T6SS assembly.

microbiology↗

bioRxiv2025

Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism

Human retrotransposon insertions are often associated with diseases. In the case of the neurodegenerative X-Linked Dystonia-Parkinsonism disease, a human-specific SINE-VNTR-Alu subfamily F retrotransposon was inserted in intron 32 of the TAF1 gene. Here, we genomically rewrote a portion of the mouse Taf1 allele with the corresponding 78-kb XDP patient derived TAF1 allele. In mESCs, the presence of the intronic SVAs--rather than the hybrid gene structure--reduces hyTAF1 levels. This leads to transcriptional downregulation of genes with TATA box enriched in their promoters and triggering apoptosis. Chromatin and transcriptome profiling revealed that intronic SVAs are actively transcribed, forming barriers that likely impede transcription elongation. In mice, neuronal lineage TAF1 humanization resulted lethality of male progeny within two months. XDP male mice had severe atrophy centered on the striatum--the same affected brain region in XDP patients. Lastly, CRISPRa-mediated activation of hyTAF1 restored mESC viability, suggesting boosting TAF1 transcription as a therapeutic approach.

genetics↗

bioRxiv2025

Myelin pathology is a key feature of X-linked Dystonia Parkinsonism

X-linked Dystonia-Parkinsonism (XDP) is a progressive, adult-onset neurodegenerative movement disorder that predominantly affects males of Filipino descent1-3. The disease is caused by the insertion of a SINE-VNTR-Alu subfamily F (SVA_F) retrotransposon within an intron of the TATA-box binding protein-associated factor 1 (TAF1) gene4. A major barrier to understanding the pathophysiology of XDP has been the lack of relevant animal models. Here, we introduce a novel conditional humanized XDP mouse model harboring a hybrid mouse-human Taf1/TAF1 gene (hyTAF1) containing the pathogenic SVA_F insertion. We activated the hyTAF1 in Nestin+ neural progenitor cells and found that the resulting XDP male mice recapitulate features of the human disease including severe motor impairment, striatal atrophy, and reactive gliosis. Transcriptomic, histological, and electron microscopy analysis revealed a dramatic reduction in oligodendrocyte lineage cells and widespread myelin disruption. Consistent with these findings, postmortem brain tissue from XDP patients revealed similar myelin pathology, including near-complete loss of myelin in parts of the medial prefrontal cortex. Together, these results identify oligodendrocyte dysfunction and myelin loss as previously unrecognized contributors to XDP pathogenesis, providing new mechanistic insight into this debilitating disorder.

neuroscience↗

bioRxiv2025

CPSF6 Promotes HIV-1 Preintegration Complex Function

Cleavage and polyadenylation specificity factor 6 (CPSF6) is part of the cellular cleavage factor I mammalian (CFIm) complex that regulates mRNA processing and polyadenylation. CPSF6 also functions as a HIV-1 capsid (CA) binding host factor and promotes viral DNA integration targeting into gene dense regions of the host genome. However, the effects of CPSF6 on the activity of the HIV-1 preintegration complex (PIC) - the machinery that carries out viral DNA integration to establish infection - is unknown. To study CPSF6s role in HIV-1 PIC function, we extracted PICs from cells depleted of CPSF6 or expressing a CPSF6 mutant that cannot bind to CA. These PICs exhibited significantly lower integration activity when compared to the control PICs. Addition of recombinant CPSF6 restored the integration activity of PICs extracted from the mutant cells, suggesting a direct role of CPSF6 in PIC function. To solidify CPSF6s effect on PIC function, we inoculated CPSF6-depleted and CPSF6-mutant cells with HIV-1 particles and measured viral DNA integration into the host genome. A significant reduction in viral integration in these cells was detected and this defect was not a consequence of reduced reverse transcription or nuclear entry. Additionally, mutant viruses deficient in CA-CPSF6 binding showed no integration defect in CPSF6 mutant cells. Finally, sequencing analysis revealed that HIV-1 integration in the CPSF6 mutant cells was significantly redirected from the gene dense regions of the host genome. Collectively, these results suggest that CPSF6-CA interaction regulates PIC function both in vitro and in infected cells. IMPORTANCEHIV-1 infection is dependent on the interaction of the virus with host factors. However, the molecular details of virus-host factor interactions are not fully understood. For instance, HIV-1 capsid provides binding interfaces for several host factors. CPSF6 is one such capsid-binding host factor, whose cellular function is to regulate mRNA processing and polyadenylation. Initial work identified a truncated cytosolic form of CPSF6 that restricted HIV infection by blocking viral nuclear entry. However, it is now established that the full-length CPSF6 primarily promotes integration targeting into gene dense regions of the host genome. Here we report that CPSF6-CA interaction promotes the activity of HIV-1 preintegration complexes (PICs). We also observed that disruption of CPSF6-CA binding in target cells significantly reduced viral integration and directed integration targeting away from gene-dense regions. These findings demonstrate a critical role for the CPSF6-CA interaction in PIC function and integration targeting.

biochemistry↗

bioRxiv2024

Adrenocortical Cancer Cell uptake of Iron Oxide Nanoparticles

Adrenocortical carcinoma (ACC) is a rare cancer with poor prognosis, treated primarily through surgery and chemotherapy. Other treatments like radiation or thermal ablation for metastases have limited success, and recurrence is common. More effective management options are needed. Magnetic iron oxide nanoparticles (IONP) show promise in cancer treatment due to their ability to be modified for selective uptake by cancer cells. This study investigated IONP uptake in ACC cell lines (H295R, HAC-15, MUC-1) using a multicellular model with endothelial cells (HUVEC) and monocytes. IONP uptake was concentration- and time-dependent, with optimal uptake at 10 {micro}g/mL. IONP were found in the cytoplasm and intracellular vesicles of ACC cells. However, endothelial cells and monocytes also absorbed IONP, reducing uptake by ACC cells. These findings suggest ACC cells actively take up IONP, but better targeting is needed to enhance uptake specificity and efficiency.

pharmacology and toxicology↗

bioRxiv2024

Unbounding fish: Assessing vulnerability to overexploitation for transboundary fish populations

SummeryGlobally coastal fisheries are managed according to political jurisdictions of nations and their provinces. This practice often results in multiple states/provinces managing a single genetically distinct fish population autonomously and without coordination. In multi-species, decentralized and data poor fisheries such management lead to poor assessment and eventually overharvest of fish. To assess overexploitation risk for such interjurisdictional populations, we propose a risk indicator IRIIS which incorporates 1) species-specific vulnerability 2) distribution of genetically-distinct populations with respect to jurisdictional boundaries and 3) differences in management practices across jurisdictions. As a case study we evaluated overexploitation risk for individual populations of nine commonly caught fish species spanning across multiple jurisdictions along Indias west coast. Our results indicate that interjurisdictional differences in management alters innate biological susceptibility. IRIIS is also sensitive to population-level differences and policy changes. Our analyses emphasize the need for population-level assessments and interjurisdictional cooperation to achieve sustainable fisheries. Science and society statementCoastal fisheries worldwide are managed through politically defined maritime jurisdictions, while fish populations are structured by biological processes such as dispersal, ocean currents, and natural barriers. This fundamental mismatch between biological population boundaries and jurisdictional management boundaries often results in the same population being exploited under multiple, uncoordinated governance regimes. In the context of the global overfishing crisis, such governance fragmentation can lead to inaccurate stock assessments and heightened risk of local population collapse. This challenge is particularly acute in developing and tropical countries, where fisheries are multispecies, data-limited, and increasingly decentralized to support community-based governance. While decentralization promotes social justice, it can inadvertently intensify the misalignment between biological and administrative boundaries, complicating sustainable management. In this manuscript, we introduce a robust framework -- the Integrative Risk Indicator for Interjurisdictional Stocks (IRIIS) -- which has a high applicability for multispecies, data-poor, and decentralized fisheries. Building on, and extending beyond, species-level Productivity Susceptibility Analysis (PSA), IRIIS integrates population genomics to delineate biologically meaningful population boundaries and combines these with fisheries policies and regulations across jurisdictions to quantify management-associated risks of overexploitation at the population level. We apply IRIIS to case studies of nine commercially important fish species harvested along the west coast of India. Our results demonstrate that the framework can (i) distinguish differential vulnerability among populations of the same species, (ii) explicitly capture management disparities across jurisdictions exploiting shared populations, and (iii) detect sensitivity to temporal changes in fisheries policies. By linking genomics, governance, and risk assessment, IRIIS provides a practical framework for identifying interjurisdictional management gaps and actionable entry points for policy coordination. This approach is particularly relevant for the Global South, where reconciling social equity objectives with ecological sustainability is both essential and challenging.

ecology↗

bioRxiv2024

Structural Characterization of DNA Binding Domain of Essential Mammalian Protein TTF 1

Transcription termination factor 1 (TTF1), being multifunctional in nature, is involved in a wide range of critical processes that make it essential for survival of the mammalian cells. TTF1 protein comprises three functional domains: the N-terminal (regulatory/inhibitory) domain, trans-activation domain, and C-terminal domain. The Myb domain is responsible for DNA-binding function of this protein and spans 550 to 732 amino acids (183 residues long). Despite the essential role of TTF1 in multiple cellular processes, there is no physical structure available to date. Purification of the functional full-length protein has been unsuccessful so far. Hence, we moved forward towards characterizing the Myb domain of this essential protein. We first constructed a three-dimensional model of the Myb domain using Robetta server and determined its stability through MD simulation in an explicit solvent. To validate the model, upon codon optimization we cloned this domain into a bacterial expression vector. The protein was then purified to homogeneity and its DNA-binding activity was checked by electro-mobility shift assay. We then proceeded to CD spectroscopy and Raman spectroscopy for secondary structure characterization. The results validated the computational model, concluding that this domain is predominantly helical in nature. The confidence built by this study now pushes us to move ahead in order to solve the atomic structure of this critical domain by crystallography or NMR spectroscopy, which in turn will decipher the exact mechanism by which this essential protein engages DNA to cater to various functions.

biochemistry↗

bioRxiv2024

Feeders and Expellers, Two Types of Animalcules With Outboard Cilia, Have Distinct Surface Interactions

Within biological fluid dynamics, it is conventional to distinguish between "puller" and "pusher" microswimmers on the basis of the forward or aft location of the flagella relative to the cell body: typically, bacteria are pushers and algae are pullers. Here we note that since many pullers have "outboard" cilia or flagella displaced laterally from the cell centerline on both sides of the organism, there are two important subclasses whose far-field is that of a stresslet, but whose near field is qualitatively more complex. The ciliary beat creates not only a propulsive force but also swirling flows that can be represented by paired rotlets with two possible senses of rotation, either "feeders" that sweep fluid toward the cell apex, or "expellers" that push fluid away. Experimental studies of the rotifer Brachionus plicatilis in combination with earlier work on the green algae Chlamydomonas reinhardtii show that the two classes have markedly different interactions with surfaces. When swimming near a surface, expellers such as C. reinhardtii scatter from the wall, whereas a feeder like B. plicatilis stably attaches. This results in a stochastic "run-and-stick" locomotion, with periods of ballistic motion parallel to the surface interrupted by trapping at the surface.

biophysics↗

bioRxiv2024

Cyclophilin A Facilitates HIV-1 DNA Integration

Cyclophilin A (CypA) promotes HIV-1 infection by facilitating reverse transcription, nuclear entry and by countering the antiviral activity of TRIM5. These multifunctional roles of CypA are driven by its binding to the viral capsid. Interestingly, recent studies suggest that the HIV-1 capsid lattice enters the nucleus of an infected cell and uncoats just before integration. Therefore, we tested whether CypA-capsid interaction regulates post-nuclear entry steps of infection, particularly integration. First, we challenged CypA-expressing (CypA+/+) and CypA-depleted (CypA-/-) cells with HIV-1 particles and quantified the resulting levels of provirus. Surprisingly, CypA-depletion significantly reduced integration, an effect that was independent of CypAs effect on reverse transcription, nuclear entry, and the presence or absence of TRIM5. Additionally, cyclosporin A, an inhibitor that disrupts CypA-capsid binding, inhibited HIV-1 integration in CypA+/+ cells but not in CypA-/- cells. Accordingly, HIV-1 capsid mutants (G89V and P90A) deficient in CypA binding were also blocked at integration in CypA+/+ cells but not in CypA-/- cells. Then, to understand the mechanism, we assessed the integration activity of HIV-1 preintegration complexes (PICs) extracted from infected cells. The PICs from CypA-/- cells had lower activity in vitro compared to those from CypA+/+ cells. PICs from cells depleted for CypA and TRIM5 also had lower activity, suggesting that CypAs effect on PIC activity is independent of TRIM5. Finally, addition of CypA protein significantly stimulated the integration activity of PICs extracted from both CypA+/+ and CypA-/-cells. Collectively, these results suggest that CypA promotes HIV-1 integration, a previously unknown role of this host factor. ImportanceHIV-1 capsid interaction with host cellular factors is essential for establishing a productive infection. However, the molecular details of such virus-host interactions are not fully understood. Cyclophilin A (CypA) is the first host protein identified to specifically bind to the HIV-1 capsid. Now it is established that CypA promotes reverse transcription and nuclear entry steps of HIV-1 infection. In this report, we show that CypA promotes HIV-1 integration by binding to the viral capsid. Specifically, our results demonstrate that CypA promotes HIV-1 integration by stimulating the activity of the viral preintegration complex and identifies a novel role of CypA during HIV-1 infection. This new knowledge is important because recent reports suggest that an operationally intact HIV-1 capsid enters the nucleus of an infected cell.

microbiology↗

bioRxiv2024

Characterization of a Biochemical Mouse Model of Primary Aldosteronism for Thermal Therapies

IntroductionAldosterone-producing adenoma (APA) is the most common cause of endocrine-related hypertension but surgery is not always feasible. Current medical interventions are associated with significant side effects and poor patient compliance. New APA animal models that replicate basic characteristics of APA and give physical and biochemical feedback are needed to test new non-surgical treatment methods, such as image-guided thermal ablation, MethodsA model of APA was developed in nude mice using HAC15 cells, a human adrenal carcinoma cell line. Tumor growth, aldosterone production, and sensitivity to angiotensin II were characterized in the model. The utility of the model was validated via treatment with microwave ablation and characterization of the resulting physical and biochemical changes in the tumor. ResultsThe APA model showed rapid and relatively homogeneous growth. The tumors produced aldosterone and steroid precursors in response to angiotensin II challenge, and plasma aldosterone levels were significantly higher in tumor bearing mice two hours after challenge verses non-tumor bearing mice. The model was useful for testing microwave ablation therapy, reducing aldosterone production by 80% in treated mice. ConclusionThe HAC15 model is a useful tumor model to study and develop localized treatment methods for APA.

cancer biology↗

bioRxiv2024

Assessment of thermochromic phantoms for characterizing microwave ablation devices

Background and PurposeThermochromic gel phantoms provide a controlled medium for visual assessment of thermal ablation device performance. However, there are limited studies reporting on the comparative assessment of ablation profiles assessed in thermochromic gel phantoms against those in ex vivo tissue. The objective of this study was to compare microwave ablation zones in a thermochromic tissue mimicking gel phantom and ex vivo bovine liver, and to report on measurements of the temperature dependent dielectric and thermal properties of the phantom. MethodsThermochromic polyacrylamide phantoms were fabricated following a previously reported protocol. Phantom samples were heated to temperatures in the range of 20 - 90 {degrees}C in a temperature-controlled water bath, and colorimetric analysis of images of the phantom taken after heating were used to develop a calibration between color changes and temperature to which the phantom was heated. Using a custom, 2.45 GHz water-cooled microwave ablation antenna, ablations were performed in fresh ex vivo liver and phantoms using 65 W applied for 5 min or 10 min (n = 3 samples in each medium for each power/time combination). Broadband (500 MHz - 6 GHz) temperature-dependent dielectric and thermal properties of the phantom were measured over the temperature range 22 - 100 {degrees}C. ResultsColorimetric analysis showed that the sharp change in gel phantom color commences at a temperature of 57 {degrees}C. Short and long axes of the ablation zone in the phantom (as assessed by the 57 {degrees}C isotherm) for 65 W, 5 min ablations were aligned with extents of the ablation zone observed in ex vivo bovine liver. However, for the 65 W, 10 min setting, ablations in the phantom were on average 23.7% smaller in short axis and 7.4 % smaller in long axis than those observed in ex vivo liver. Measurements of the temperature dependent relative permittivity, thermal conductivity, and volumetric heat capacity of the phantom largely followed similar trends to published values for ex vivo liver tissue. ConclusionThermochromic tissue mimicking phantoms provide a controlled, and reproducible medium for comparative assessment of microwave ablation devices and energy delivery settings, though ablation zone size and shapes may not accurately represent ablation sizes and shapes observed in ex vivo liver tissue under similar conditions.

bioengineering↗