Biology subjects

Kaplan, D.

Publications and source records attributed to Kaplan, D..

10 recordsLinked to original sources

bioRxiv2026

Limb-localized induction of regeneration reshapes brain and amputation-site transcriptional states in adult Xenopus laevis

Limb regeneration requires coordinated tissue reconstruction and nervous system reintegration, yet whether regenerative induction alters brain responses to limb loss remains unclear. We analyzed transcriptomics from the paired brains and amputation sites of adult Xenopus laevis after hindlimb amputation with or without a 24 hour exposure to localized, pro-regenerative multi-drug treatment (MDT) delivered through a wearable bioreactor device. At 24 hours post treatment (24 HPT), MDT brains showed increased vascular and basement membrane transcripts and enrichment of oxidative phosphorylation and mTORC1 programs. In the limb, an exploratory integrated stress response (ISR) score increased at 11 and 24 HPT and returned to control levels by 7 days post-treatment (7 DPT), coinciding with induction of growth differentiation factor 15 (GDF15), a cytokine responsive to mitochondrial stress. We detected no corresponding increase in brain ISR score. At 7 DPT, MDT brains showed enrichment of immune, heme metabolism and biosynthetic programs, reduced synaptic transmission gene expression, and increased gdf15.L. Relative to an external uninjured reference, MDT and amputation only brains showed concordant changes, with treatment modifying selected programs. Cross-species comparative analyses identified partial overlap with an axolotl regenerative glutamatergic signature and separation from selected mammalian injury profiles. These findings reveal cross-tissue responses to regenerative induction and identify candidate mechanisms of brain body communication in biomedically engineered vertebrate limb regeneration.

neuroscience↗

bioRxiv2026

Persistent microbial material contributes to Alzheimer disease and is targetable by vaccination

Chronic neuroinflammation is increasingly recognized as a contributor to Alzheimer disease, yet the upstream stimuli that sustain it remain poorly defined. We investigated whether persistent microbial material contributes to Alzheimer disease using the conserved microbial polysaccharide poly-N-acetylglucosamine (PNAG). PNAG-containing microbial material colocalized with amyloid plaques in human Alzheimer disease brain tissue. In fully human neuronal and three-dimensional brain models, purified PNAG and PNAG-containing microbial vesicles activated Toll-like receptor 2-dependent inflammasome signaling and promoted amyloid-{beta} and phosphorylated tau accumulation. Vaccination targeting PNAG improved cognition, reduced glial activation and amyloid pathology, remodeled amyloid processing, and preserved gut microbial community structure in APP/PS1 mice. These findings identify persistent microbial material as an upstream contributor to Alzheimer disease-associated neuroinflammation and a potential therapeutic target.

neuroscience↗

bioRxiv2024

Multi-spectral photoacoustic imaging combined with acoustic radiation force impulse imaging for applications in tissue engineering

Tissue engineering is a dynamic field focusing on the creation of advanced scaffolds for tissue and organ regeneration. These scaffolds are customized to their specific applications and are often designed to be complex, large structures to mimic tissues and organs. This study addresses the critical challenge of effectively characterizing these thick, optically opaque scaffolds that traditional imaging methods fail to fully image due to their optical limitations. We introduce a novel multi-modal imaging approach combining ultrasound, photoacoustic, and acoustic radiation force impulse imaging. This combination leverages its acoustic-based detection to overcome the limitations posed by optical imaging techniques. Ultrasound imaging is employed to monitor the scaffold structure, photoacoustic imaging is employed to monitor cell proliferation, and acoustic radiation force impulse imaging is employed to evaluate the homogeneity of scaffold stiffness. We applied this integrated imaging system to analyze melanoma cell growth within silk fibroin protein scaffolds with varying pore sizes and therefore stiffness over different cell incubation periods. Among various materials, silk fibroin was chosen for its unique combination of features including biocompatibility, tunable mechanical properties, and structural porosity which supports extensive cell proliferation. The results provide a detailed mesoscale view of the scaffolds internal structure, including cell penetration depth and biomechanical properties. Our findings demonstrate that the developed multimodal imaging technique offers comprehensive insights into the physical and biological dynamics of tissue-engineered scaffolds. As the field of tissue engineering continues to advance, the importance of non-ionizing and non-invasive imaging systems becomes increasingly evident, and by facilitating a deeper understanding and better characterization of scaffold architectures, such imaging systems are pivotal in driving the success of future tissue-engineering solutions.

bioengineering↗

bioRxiv2023

Environmental life cycle assessment of recombinant growth factor production for cultivated meat applications

Growth factors are critical components of current serum-supplemented and serum-free media formulations for cultivated meat production. However, growth factors have been excluded, estimated using proxies, or modeled using proprietary data in existing environmental assessments of cultivated meat products. Cell culture media has been identified as a hotspot in such studies, therefore it is important to accurately quantify the environmental impacts of growth factor supplementation. To address this gap, this study applied life cycle assessment (LCA) methodology to comparatively assess the environmental impacts of recombinant growth factor production for cultivated meat applications. Life cycle inventories were developed for four recombinant growth factors (IGF-1, FGF, TGF-{beta}, and PDGF) produced using a novel bench- scale process. The functional unit of the product output was selected as 1 mg of produced growth factor. The results indicate that recombinant growth factors can have significant environmental impacts within cultivated meat systems, despite being used in very small quantities. For example, the global warming potential of production of 1 mg of IGF-1, FGF, TGF-{beta}, and PDGF was estimated to be 0.1, 0.04, 0.2 and 0.2 kg CO2 eq, respectively. Future research should explore the sustainability of producing these growth factors at scale to meet the needs of the expanding cultivated meat industry or identifying alternatives to these growth factors that have a lower impact on the environment. Nomenclature O_TBL View this table: org.highwire.dtl.DTLVardef@1f0c19org.highwire.dtl.DTLVardef@534179org.highwire.dtl.DTLVardef@1ef86b1org.highwire.dtl.DTLVardef@73fd9eorg.highwire.dtl.DTLVardef@10fb642_HPS_FORMAT_FIGEXP M_TBL C_TBL

ecology↗

bioRxiv2022

A 3D bioengineered neural tissue model generated from patient-derived iPSCs develops Alzheimer's disease-related phenotypes

BackgroundCurrent models to study Alzheimers disease (AD) include cell cultures and animal models. Human diseases, however, are often poorly reproduced in animal models. Developing techniques to differentiate human brain cells from induced pluripotent stem cells (iPSCs) provides a novel approach to studying AD. Three-dimensional (3D) cultures to model AD are represented by organoids, neurospheroids, and scaffold-based cultures. Some AD-related phenotypes have been identified across 3D models [1]. However, to our knowledge, none of these studies could recapitulate several AD-related hallmarks in one single model and establish a temporal relation among them. Furthermore, to date, the transcriptomic features of these 3D models have not been compared with those of human AD brains. These data are, in our opinion, key to understanding the pertinency of these models for studying AD-related pathomechanisms over time. MethodsWe developed a 3D bioengineered model of iPSC-derived neural tissue that combines a porous scaffold composed of silk fibroin protein with an intercalated collagen hydrogel to support the growth of neurons and glial cells into complex and functional networks. This biomaterial scaffold, designed to match the mechanical properties of brain tissue, can support 3D neural cultures for an extended time without necrosis, a fundamental requisite for aging studies. We have optimized our protocol by seeding neural precursor cells (NPCs) into these scaffolds. NPC-derived cultures were generated from iPSC lines obtained from two subjects carrying the familial AD (FAD) APP London mutation, two well-studied control lines, and an isogenic control. Cultures were analyzed at 2 and 4.5 months. ResultsAn elevated A{beta}42/40 ratio was detected in conditioned media from FAD cultures at both time points, as previously reported in 2D cultures derived from the same FAD lines. However, extracellular A{beta}42 deposition and enhanced neuronal excitability were observed in FAD culture only at 4.5 months. The increased excitability of FAD cultures correlated with extracellular A{beta}42 deposition but not with soluble A{beta}42/40 ratio levels, as they were similar at both time points. These data suggest that extracellular A{beta} deposition may trigger enhanced network activity. Notably, neuronal hyperexcitability has been described in AD patients early in the disease. Transcriptomic analysis revealed the deregulation of multiple gene sets in FAD samples. Notably, such alterations were similar to those observed in human AD brains in a large study that performed a co-expression meta-analysis of harmonized data from Accelerating Medicines Partnership for Alzheimers Disease (AMP-AD) across three independent cohorts. ConclusionsOur 3D tissue model supports the differentiation of healthy iPSC-derived cultures in a porous silk-collagen composite sponge with an optically clear central region. This design facilitates nutrient delivery to meet the metabolic demand of long-term cultures. These data provide evidence that our bioengineered model from patient-derived FAD iPSCs develops time-dependent AD-related phenotypes and establishes a temporal relation among them. Furthermore, FAD iPSC-derived neuronal tissue recapitulates transcriptomic features of AD patients. Thus, our bioengineered neural tissue represents a unique tool to model AD-related pathomechanisms over time, with several advantages compared to the existing models.

neuroscience↗

bioRxiv2020

Transarterial embolization modulates the immune response within target and non-target hepatocellular carcinomas.

Recent successes in the field of immuno-oncology have generated considerable interest in the investigation of approaches that combine standard of care treatments with immunotherapies. Transarterial embolization (TAE) represents an attractive candidate for this approach given the potential for immune system stimulation, however little is known about the influence of TAE on the tumor immunoenvironment. The purpose of this study was to perform a cellular analysis of tumor infiltrating lymphocytes (TILs) and PD-L1 expression following TAE in a translational rat model of hepatocellular carcinoma (HCC) and to identify factors that influence this response. We show that TAE causes dynamic changes in immune cell populations, with variable increases in CD3, CD4, and CD8 cells within embolized tumors over time. We also show that TAE alters the immunobiology of distant, non-target tumors as demonstrated by an increased number of CD4, CD8, and Foxp3+ cells within the intratumoral compartment of non-target tumors. We demonstrate that, in response to TAE, tumor cells up-regulate expression of PD-L1. Finally, we demonstrate marked differences in terms of the foreign body reactions induced by two commonly used embolic particles, and show changes in lymphocyte and macrophage recruitment that depend on the type of embolic particles and their propensity to extravasate beyond the vasculature and into the tumor parenchyma. These findings hold important implications for the on-going development of novel therapeutic strategies combining locoregional therapy with immunomodulators, as well as for the development of techniques and materials that can further leverage the unique modulation of the tumor immune microenvironment.

immunology↗

bioRxiv2020

Primary Human Hepatocytes Maintain Long-term Functions in Porous Silk Scaffolds Containing Extracellular Matrix Proteins

The shortage of donor organs for transplantation has prompted the development of alternative implantable human liver tissues; however, the need for a clinically viable liver tissue that can be fabricated using physiologically-relevant primary human hepatocytes (PHHs) is unmet. Purified silk proteins provide desirable features for generating implantable tissues, such as sustainable sourcing from insects/arachnids, biocompatibility, tunable mechanical properties and degradation rates, and low immunogenicity upon implantation; however, the utility of such scaffolds to generate human liver tissues using PHHs remains unclear. Here, we show that the incorporation of type I collagen during the fabrication and/or autoclaving of silk scaffolds was necessary to enable robust PHH attachment/function. Scaffolds with small pores (73 +/- 25 {micro}m) promoted higher PHH functions than large pores (235 +/- 84 {micro}m). Further incorporation of growth-arrested 3T3-J2 fibroblasts into scaffolds enhanced PHH functions up to 5-fold for 5 months in culture, an unprecedented longevity, and functions were better retained than 2D configurations. Lastly, encapsulating PHHs within Matrigel while housed in the silk/collagen scaffold led to higher functions than Matrigel or silk/collagen alone. In conclusion, porous silk scaffolds are useful for generating long-term PHH +/- fibroblast tissues which may ultimately find applications in regenerative medicine and drug development.

bioengineering↗

bioRxiv2019

Inoculation with a microbe isolated from the Negev Desert enhances corn growth

Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960s and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinensis, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans (a test for virulence) in response to D. cinnamea 55. We also looked for genes for potential virulence determinants as well as for growth promotion.

plant biology↗

bioRxiv2019

Defined extracellular ionic solutions to study and manipulate the cellular resting membrane potential

All cells possess an electric potential across their plasma membranes. While familiar in the context of excitable cells such as neurons, healthy non-excitable cells are also able to generate and receive bioelectric signals. The cellular resting membrane potential (RMP) regulates many factors in cell homeostasis, such as cell proliferation, differentiation and apoptosis. It is therefore critical to develop simple strategies to measure, manipulate and characterize this feature. Current studies to evaluate RMP rely on the patch clamp approach, which is technically challenging, low-throughput and not widely available to the scientific community. Here, we present a relatively simple methodology to functionally study the role of RMP in non-excitable cells by modulating it pharmacologically, and using a voltage-sensitive dye to characterize the contribution of individual ions to the RMP. Specifically, we define protocols for using extracellular solutions in which permeable ions (Na+, Cl- and K+) are substituted with non-permeable ions (N-Methyl-D-glucamine (NMDG), gluconate, choline, SO42-) to study and manipulate RMP in vitro. The resulting RMP modifications were assessed with both patch clamp and a voltage sensitive dye. Using an epithelial and cancer cell line, we demonstrate that the proposed ionic solutions can determine the relative contribution of ionic species in setting the RMP and be used to actively and selectively modify the RMP. The proposed method is simple and reproducible and will make the study of bioelectricity more readily available to the cell biology community by enabling functional modulation of RMP in most cellular assays.\n\nAuthor Disclosure StatementsNo competing financial interests exist.

cell biology↗

bioRxiv2017

Decoding The Brain: Neural Representation And The Limits Of Multivariate Pattern Analysis In Cognitive Neuroscience

Since its introduction, multivariate pattern analysis (MVPA), or \"neural decoding\", has transformed the field of cognitive neuroscience. Underlying its influence is a crucial inference, which we call the Decoders Dictum: if information can be decoded from patterns of neural activity, then this provides strong evidence about what information those patterns represent. Although the Dictum is a widely held and well-motivated principle in decoding research, it has received scant philosophical attention. We critically evaluate the Dictum, arguing that it is false: decodability is a poor guide for revealing the content of neural representations. However, we also suggest how the Dictum can be improved on, in order to better justify inferences about neural representation using MVPA.

neuroscience↗