Single-cell proteomics by mass spectrometry (MS) allows quantifying proteins with high specificity and sensitivity. To increase its throughput, we developed nPOP, a method for parallel preparation of thousands of single cells in nanoliter volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation with plexDIA demonstrates accurate quantification of about 3,000 - 3,700 proteins per human cell. The protocol is implemented on the CellenONE instrument and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 days to prepare over 3,000 single cells. We provide metrics and software for quality control that can support the robust scaling of nPOP to higher plex reagents for achieving reliable high-throughput single-cell protein analysis. less

Machine learning approaches have the potential for meaningful impact in the biomedical field. However, there are often challenges unique to biomedical data that prohibits the adoption of these innovations. For example, limited data, data volatility, and data shifts all compromise model robustness and generalizability. Without proper tuning and data management, deploying machine learning models in the presence of unaccounted for corruptions leads to reduced or misleading performance. This study explores techniques to enhance model generalizability through iterative adjustments. Specifically, we investigate a detection tasks using electron microscopy images and compare models trained with different normalization and augmentation techniques. We found that models trained with Group Normalization or texture data augmentation outperform other normalization techniques and classical data augmentation, enabling them to learn more generalized features. These improvements persist even when models are trained and tested on disjoint datasets acquired through diverse data acquisition protocols. Results hold true for transformer- and convolution-based detection architectures. The experiments show an impressive 29% boost in average precision, indicating significant enhancements in the model\'s generalizibality. This underscores the models\' capacity to effectively adapt to diverse datasets and demonstrates their increased resilience in real-world applications. less

Osteoarthritis (OA) is the most common inflammatory joint disease and currently lacks an effective curative treatment. Intra-articular injection of mesenchymal stromal cells (MSCs) has gained attention as a relevant therapeutic approach for OA treatment due to the MSC\'s ability to secrete anti-inflammatory and immunomodulatory factors. Given their limited viability post-intraarticular injection and the potential leakage of cells out of the injection site, encapsulating MSCs in hydrogels is considered a promising strategy to protect them and provide a suitable 3D microenvironment to support their biological activities. Calcium-cross-linked alginate hydrogels are commonly used for MSC encapsulation, but their long-term in vivo stability remains uncertain. On the other hand, alginate cross-linking by the strain-promoted azide-alkyne cycloaddition (SPAAC) reaction would create a network unaffected by an ionic environment. Hence, this study aimed to develop an alginate-based hydrogel cross-linked via stable and cytocompatible covalent bonds for cell encapsulation. We established for the first time the formation of covalent alginate hydrogels between two SPAAC precursors, namely alginate-BCN and alginate-N3. These hydrogels exhibited in vitro stability and enabled the diffusion of molecules of interest. We then generated alginate-based SPAAC microgels of 170 m in mean diameter, suitable for intra-articular injection. We next encapsulated human adipose MSCs (hASCs) in these alginate-based SPAAC microgels and confirmed their cytocompatibility, with over 90 % of cells remaining viable after 14 days in culture. Finally, the microencapsulated hASCs maintained their biological properties and were able to secrete anti-inflammatory factors (IDO, PGE2, and HGF) when exposed to pro-inflammatory cytokines (TNF and IFN {gamma}). In the end, human-activated lymphocytes were cultured in contact with microencapsulated hASCs, and CD3+ T cell proliferation was quantified by flow cytometry. We demonstrated that the encapsulation process did not impair the hASC immunomodulatory activity. Overall, our findings show the potential of alginate-based SPAAC hydrogels for microencapsulating hASCs for cell therapy. less

We report the controlled release of an antimicrobial peptide using enzyme-activatable prodrugs to treat and detect Candida albicans and Porphyromonas gingivalis. Our motivation lies in the prevalence of these microorganisms in the subgingival area where the frequency of fungal colonization increases with periodontal disease. This work is based on an antimicrobial peptide that is both therapeutic and induces a color change in a nanoparticle reporter. This antimicrobial peptide was then built into a zwitterionic prodrug that quenches its activity until activation by a protease inherent to these pathogens of interest: SAP9 or RgpB for C. albicans and P. gingivalis, respectively. We first confirmed that the intact zwitterionic prodrug has negligible toxicity to fungal, bacterial, and mammalian cells absent a protease trigger. Next, the therapeutic impact was assessed via disk diffusion and viability assays and showed a minimum inhibitory concentration of 3.1 - 16 /mL, which is comparable to the antimicrobial peptide alone (absent integration into prodrug). Finally, the zwitterionic design was exploited for colorimetric detection of C. albicans and P. gingivalis proteases. When the prodrugs were cleaved, the plasmonic nanoparticles aggregated causing a color change with a limit of detection of 10 nM with gold nanoparticles and 3 nM with silver nanoparticles. This approach has value as a convenient and selective protease sensing and protease-induced treatment mechanism based on bioinspired antimicrobial peptides. less

Force-driven cellular interactions are known to play a critical role in cancer cell invasion, but have remained largely unexplored in the context of vascular abnormalities, partly due to a lack of suitable genetic and cellular models. One such vascular abnormality, cerebral cavernous malformation (CCM) is characterized by leaky, tumor-like vessels in the brain, where CCM mutant cells recruit wild-type cells from the surrounding endothelium to form mosaic lesions and promote lesion growth; however the mechanisms underlying this recruitment remain poorly understood. Here, we use 3D traction force microscopy in a in-vitro model of early angiogenic invasion to reveal that hyper-angiogenic CCM2-silenced endothelial cells enhance angiogenic invasion of neighboring wild-type cells through force and extracellular matrix-guided mechanisms. We show that mechanically hyperactive CCM2-silenced tips guide wild-type cells by exerting and transmitting pulling forces and by leaving degraded paths in the matrix as cues promoting invasion in a ROCKs-dependent manner. This transmission of forces is associated with a reinforcement of beta1 integrin-dependent adhesive sites and actin cytoskeleton in the wild-type followers. We also show that during this process wild-type cells are reprogrammed into stalk cells through activation of matrisome and DNA replication programs, eventually leading to cell proliferation. These observations unveil a novel vascular lesion growth mechanism where CCM2 mutants hijack the function of wild-type cells to fuel CCM lesion growth. By integrating biophysical computational methodologies to quantify cellular forces with advanced molecular techniques, we provide new insights in the etiology of vascular malformations, and open up avenues to study the role of cell mechanics in tissue heterogeneity and disease progression. less

The mechanisms responsible for increased walking metabolic cost among older adults are poorly understood. We recently proposed a theoretical premise by which age-related reductions in Achilles tendon stiffness (kAT) can disrupt the neuromechanics of calf muscle behavior and contribute to faster rates of oxygen consumption during walking. The purpose of this study was to objectively evaluate this premise. We quantified kAT at a range of matched activations prescribed using electromyographic biofeedback and walking metabolic cost in a group of 15 younger (age: 23{+/-}4 yrs) and 15 older adults (age: 72{+/-}5 yrs). Older adults averaged 44% less kAT than younger adults at matched triceps surae activations (p=0.046). This effect appeared to arise not only from altered tendon length-tension relations with age, but also from differences in the operating region of those length-tension relations between younger and older adults. Older adults also walked with a 17% higher net metabolic power than younger adults (p=0.017). In addition, we discovered empirical evidence that lesser kAT exacts a metabolic penalty and was positively correlated with higher net metabolic power during walking (r=-0.365, p=0.048). These results pave the way for interventions focused on restoring ankle muscle-tendon unit structural stiffness to improve walking energetics in aging. less

Industrial biotechnology uses Design-Build-Test-Learn (DBTL) cycles to accelerate the development of microbial cell factories, required for the transition to a bio-based economy. To use them effectively, appropriate connections between each phase of the cycle are crucial. Using p-coumaric acid production in Saccharomyces cerevisiae as case study, we propose the use of one-pot library generation, random screening, targeted sequencing and machine learning (ML) as links during DBTL cycles. We showed that the robustness and flexibility of ML models strongly enable pathway optimization, and propose feature importance and SHAP values as a guide to expand the design space of original libraries. This approach led to a 68% increased production of p-coumaric acid within two DBTL cycles. less

Nanoemulsions have been widely used for pharmaceutic applications. However, there remains a significant challenge to functionalize available pharmaceutical surfactants with targeting or reporter moieties to generate next-generation drug delivery systems. Herein, a designed biosurfactant platform technology, based on our library of -helical peptide AM1 derivatives, was used to prepare multifunctional magnetic nanoemulsion drug delivery systems. Key factors such as electrostatic and steric stabilization of the nanoemulsions were determined using this peptide library. Stabilization of the nanoemulsion was achieved by controlled and tunable loading of PEG-functionalized biosurfactant at the oil-water interface. A model drug and iron oxide nanoparticles were incorporated into the oil core to prepare multifunctional nanoemulsions. In vitro cell uptake experiments using an external magnetic field demonstrated controlled rapid uptake of iron oxide loaded nanoemulsions by SKOV3 cancer and RAW 264.7 macrophage cells. SKOV3 cells demonstrated a slower rate of uptake under a magnetic field when compared to RAW 264.7 cells. This work demonstrates a highly adaptable hierarchical nanoemulsion system that can provide a platform to develop effective multifunctional nanomedicines and tools for biomedical insights. less

Slip and fall incidents are a serious health care concern globally. Previous research describes a backwards loss of balance during a slip incident, however hip fractures only occur if individuals fall on their side. Therefore, this study is investigating and quantifying the trunk motion in the sagittal and frontal plane. 13 healthy young participants trunk kinematics were analyzed during a slip incident. Peak trunk angle of the trunk in the sagittal and frontal plane were calculated. There was no significant difference between sagittal and frontal plane peak trunk angles suggesting that there is frontal plane motion during an overground slip incident. Our findings suggest research should investigate frontal plane mechanics during a slip incident as there is trunk frontal plane motion which if uncontrolled can result in falling on the femoral neck. Understanding and preventing falls based upon frontal plane mechanics may be more useful for preventing hip fractures from a slip incident. Lastly, the findings of this study are confirmatory results as the frontal plane trunk motion was quantified and reported in 2008. less

Traditionally, biological barriers are assessed in vitro by measuring trans-endothelial/epithelial electrical resistance (TEER) across a monolayer using handheld chopstick electrodes. Implementation of TEER into organ-on-chip (OOC) setups is a challenge however, due to non-uniform current distribution and interference from biomaterials typically found in such systems. In this work, we address the pitfalls of standard TEER measurement through the application of porous membrane electrical cell-substrate impedance sensing (PM-ECIS) to an OOC setup. Gold leaf electrodes (working electrode diameters = 250, 500, 750 m) were incorporated onto porous membranes and combined with biocompatible tape to assemble microfluidic devices. PM-ECIS resistance at 4 kHz was not influenced by presence of collagen hydrogel in bottom channels, compared to TEER measurements in same devices, which showed a difference of 1723 {+/-} 381.8 Ohms; (p=0.006) between control and hydrogel conditions. A proof of concept, multi-day co-culture model of the blood-brain barrier was also demonstrated in these devices. PM-ECIS measurements were robust to fluid shear (5 dyn/cm2) in cell-free devices, yet were highly sensitive to flow-induced changes in an endothelial barrier model. Initiation of perfusion (0.06 dyn/cm2) in HUVEC-seeded devices corresponded to significant decreases in impedance at 40 kHz (p<0.01 for 750 and 500 m electrodes) and resistance at 4 kHz (p<0.05 for all electrode sizes) relative to static control cultures, with minimum values reached at 6.5 to 9.5 hours after induction of flow. Our microfluidic PM-ECIS platform enables sensitive, non-invasive, real-time measurements of barrier function in setups integrating critical OOC features like 3D co-culture, biomaterials and shear stress. less