Bioengineering a plant NLR immune receptor with a robust binding interface toward a conserved fungal pathogen effector.

Bioengineering of plant immune receptors has emerged as a key strategy for generating novel disease resistance traits to counteract the expanding threat of plant pathogens to global food security. However, current approaches are limited by rapid evolution of plant pathogens in the field and may lack durability when deployed. Here, we show that the rice nucleotide-binding, leucine-rich repeat (NLR) immune receptor Pik-1 can be engineered to respond to a conserved family of effectors from the multihost blast fungus pathogen Magnaporthe oryzae. We switched the effector binding and response profile of the Pik NLR from its cognate rice blast effector AVR-Pik to the host-determining factor pathogenicity toward weeping lovegrass 2 (Pwl2) by installing a putative host target, OsHIPP43, in place of the native integrated heavy metal-associated domain (generating Pikm-1OsHIPP43). This chimeric receptor also responded to other PWL alleles from diverse blast isolates. The crystal structure of the Pwl2/OsHIPP43 complex revealed a multifaceted, robust interface that cannot be easily disrupted by mutagenesis, and may therefore provide durable, broad resistance to blast isolates carrying PWL effectors in the field. Our findings highlight how the host targets of pathogen effectors can be used to bioengineer recognition specificities that have more robust properties compared to naturally evolved disease resistance genes.

HaloTag display enables quantitative single-particle characterisation and functionalisation of engineered extracellular vesicles.

Extracellular vesicles (EVs) play key roles in diverse biological processes, transport biomolecules between cells and have been engineered for therapeutic applications. A useful EV bioengineering strategy is to express engineered proteins on the EV surface to confer targeting, bioactivity and other properties. Measuring how incorporation varies across a population of EVs is important for characterising such materials and understanding their function, yet it remains challenging to quantitatively characterise the absolute number of engineered proteins incorporated at single-EV resolution. To address these needs, we developed a HaloTag-based characterisation platform in which dyes or other synthetic species can be covalently and stoichiometrically attached to engineered proteins on the EV surface. To evaluate this system, we employed several orthogonal quantification methods, including flow cytometry and fluorescence microscopy, and found that HaloTag-mediated quantification is generally robust across EV analysis methods. We compared HaloTag-labelling to antibody-labelling of EVs using single vesicle flow cytometry, enabling us to measure the substantial degree to which antibody labelling can underestimate proteins present on an EV. Finally, we demonstrate the use of HaloTag to compare between protein designs for EV bioengineering. Overall, the HaloTag system is a useful EV characterisation tool which complements and expands existing methods.

Bioengineered Nerve Conduits and Wraps.

Peripheral nerve injuries are prevalent and their treatments present significant challenges. Among the various reconstructive options, nerve conduits and wraps are popular choices. Advances in bioengineering and regenerative medicine have led to the development of new biocompatible materials and implant designs that offer the potential for enhanced neural recovery. Cost, nerve injury type, and implant size must be considered when deciding on the ideal reconstructive option.

Multifunctional Three-in-One Sensor on t-ZnO for Ultraviolet and VOC Sensing for Bioengineering Applications.

Zinc oxide (ZnO) is considered to be one of the most explored and reliable sensing materials for UV detection due to its excellent properties, like a wide band gap and high exciton energy. Our current study on a photodetector based on tetrapodal ZnO (t-ZnO) reported an extremely high UV response of ~9200 for 394 nm UV illumination at 25 °C. The t-ZnO network structure and morphology were investigated using XRD and SEM. The sensor showed a UV/visible ratio of ~12 at 25 °C for 394 nm UV illumination and 443 nm visible illumination. By increasing the temperature, monotonic decreases in response and recovery time were observed. By increasing the bias voltage, the response time was found to decrease while the recovery time was increased. The maximum responsivity shifted to higher wavelengths from 394 nm to 400 nm by increasing the operating temperature from 25 °C to 100 °C. The t-ZnO networks exhibited gas-sensing performances at temperatures above 250 °C, and a maximum response of ~1.35 was recorded at 350 °C with a good repeatability and fast recovery in 16 s for 100 ppm of n-butanol vapor. This study demonstrated that t-ZnO networks are good biosensors that can be used for diverse biomedical applications like the sensing of VOCs (volatile organic compounds) and ultraviolet detection under a wide range of temperatures, and may find new possibilities in biosensing applications.

Rodent Model of Masseter Volumetric Muscle Loss for Studying Bioengineering Materials.

Craniofacial volumetric muscle loss (VML) injuries can occur as a result of severe trauma, surgical excision, inflammation, and congenital or other acquired conditions. Treatment of craniofacial VML involves surgical, functional muscle transfer. However, these procedures are unable to restore normal function, sensation, or expression, and more commonly, these conditions go untreated. Very little research has been conducted on skeletal muscle regeneration in animal models of craniofacial VML. This manuscript describes a rat model for the study of craniofacial VML injury and a protocol for the histological evaluation of biomaterials in the treatment of these injuries. Liquid hydrogel and freeze-dried scaffolds are applied at the time of surgical VML creation, and masseters are excised at terminal time points up to 12 weeks with high retention rates and negligible complications. Hematoxylin and eosin (HE), Masson's Trichrome, and immunohistochemical analysis are used to evaluate parameters of skeletal muscle regeneration as well as biocompatibility and immunomodulation. While we demonstrate the study of a hyaluronic-acid-based hydrogel, this model provides a means for evaluating subsequent iterations of materials in VML injuries.

Emergent digital bio-computation through spatial diffusion and engineered bacteria.

Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.

Fuzzy-Based Bioengineering System for Predicting and Diagnosing Diseases of the Nervous System Triggered by the Interaction of Industrial Frequency Electromagnetic Fields.

The study aims to enhance the standard of medical care for individuals working in the electric power industry who are exposed to industrial frequency electromagnetic fields and other relevant risk factors. This enhancement is sought through the integration of fuzzy mathematical models with contemporary information and intellectual technologies. The study addresses the challenges of forecasting and diagnosing illnesses within a specific demographic characterized by a combination of poorly formalized issues with interconnected conditions. To tackle this complexity, a methodological framework was developed for synthesizing hybrid fuzzy decision rules. This approach combines clinical expertise with artificial intelligence methodologies to promote innovative problem-solving strategies. Additionally, the researchers devised an original method to evaluate the body's protective capacity, which was integrated into these decision rules to enhance the precision and efficacy of medical decision-making processes. The research findings indicate that industrial frequency electromagnetic fields contribute to illnesses of societal significance. Additionally, it highlights that these effects are worsened by other risk factors such as adverse microclimates, noise, vibration, chemical exposure, and psychological stress. Diseases of the neurological, immunological, cardiovascular, genitourinary, respiratory, and digestive systems are caused by these variables in conjunction with unique physical traits. The development of mathematical models in this study makes it possible to detect and diagnose disorders in workers exposed to electromagnetic fields early on, especially those pertaining to the autonomic nervous system and heart rhythm regulation. The results can be used in clinical practice to treat personnel in the electric power industry since expert evaluation and modeling showed high confidence levels in decision-making accuracy.

Basic immunologic study as a foundation for engineered therapeutic development.

Bioengineering and drug delivery technologies play an important role in bridging the gap between basic scientific discovery and clinical application of therapeutics. To identify the optimal treatment, the most critical stage is to diagnose the problem. Often these two may occur simultaneously or in parallel, but in this review, we focus on bottom-up approaches in understanding basic immunologic phenomena to develop targeted therapeutics. This can be observed in several fields; here, we will focus on one of the original immunotherapy targets-cancer-and one of the more recent targets-regenerative medicine. By understanding how our immune system responds in processes such as malignancies, wound healing, and medical device implantation, we can isolate therapeutic targets for pharmacologic and bioengineered interventions.

Machine learning: an advancement in biochemical engineering.

One of the most remarkable techniques recently introduced into the field of bioprocess engineering is machine learning. Bioprocess engineering has drawn much attention due to its vast application in different domains like biopharmaceuticals, fossil fuel alternatives, environmental remediation, and food and beverage industry, etc. However, due to their unpredictable mechanisms, they are very often challenging to optimize. Furthermore, biological systems are extremely complicated; hence, machine learning algorithms could potentially be utilized to improve and build new biotechnological processes. Gaining insight into the fundamental mathematical understanding of commonly used machine learning algorithms, including Support Vector Machine, Principal Component Analysis, Partial Least Squares and Reinforcement Learning, the present study aims to discuss various case studies related to the application of machine learning in bioprocess engineering. Recent advancements as well as challenges posed in this area along with their potential solutions are also presented.

Multiscale engineering of brain organoids for disease modeling.

Brain organoids hold great potential for modeling human brain development and pathogenesis. They recapitulate certain aspects of the transcriptional trajectory, cellular diversity, tissue architecture and functions of the developing brain. In this review, we explore the engineering strategies to control the molecular-, cellular- and tissue-level inputs to achieve high-fidelity brain organoids. We review the application of brain organoids in neural disorder modeling and emerging bioengineering methods to improve data collection and feature extraction at multiscale. The integration of multiscale engineering strategies and analytical methods has significant potential to advance insight into neurological disorders and accelerate drug development.

Global epistasis and the emergence of function in microbial consortia.

The many functions of microbial communities emerge from a complex web of interactions between organisms and their environment. This poses a significant obstacle to engineering microbial consortia, hindering our ability to harness the potential of microorganisms for biotechnological applications. In this study, we demonstrate that the collective effect of ecological interactions between microbes in a community can be captured by simple statistical models that predict how adding a new species to a community will affect its function. These predictive models mirror the patterns of global epistasis reported in genetics, and they can be quantitatively interpreted in terms of pairwise interactions between community members. Our results illuminate an unexplored path to quantitatively predicting the function of microbial consortia from their composition, paving the way to optimizing desirable community properties and bringing the tasks of predicting biological function at the genetic, organismal, and ecological scales under the same quantitative formalism.

Bioengineered models of cardiovascular diseases.

Age-associated cardiovascular diseases (CVDs), predominantly resulting from artery-related disorders such as atherosclerosis, stand as a leading cause of morbidity and mortality among the elderly population. Consequently, there is a growing interest in the development of clinically relevant bioengineered models of CVDs. Recent developments in bioengineering and material sciences have paved the way for the creation of intricate models that closely mimic the structure and surroundings of native cardiac tissues and blood vessels. These models can be utilized for basic research purposes and for identifying pharmaceutical interventions and facilitating drug discovery. The advancement of vessel-on-a-chip technologies and the development of bioengineered and humanized in vitro models of the cardiovascular system have the potential to revolutionize CVD disease modelling. These technologies offer pathophysiologically relevant models at a fraction of the cost and time required for traditional experimentation required in vivo. This progress signifies a significant advancement in the field, transitioning from conventional 2D cell culture models to advanced 3D organoid and vessel-on-a-chip models. These innovative models are specifically designed to explore the complexities of vascular aging and stiffening, crucial factors in the development of cardiovascular diseases. This review summarizes the recent progress of various bioengineered in vitro platforms developed for investigating the pathophysiology of human cardiovascular system with more focus on advanced 3D vascular platforms.

Bioengineered vascular grafts with a pathogenic TGFBR1 variant model aneurysm formation in vivo and reveal underlying collagen defects.

Thoracic aortic aneurysm (TAA) is a life-threatening vascular disease frequently associated with underlying genetic causes. An inadequate understanding of human TAA pathogenesis highlights the need for better disease models. Here, we established a functional human TAA model in an animal host by combining human induced pluripotent stem cells (hiPSCs), bioengineered vascular grafts (BVGs), and gene editing. We generated BVGs from isogenic control hiPSC-derived vascular smooth muscle cells (SMCs) and mutant SMCs gene-edited to carry a Loeys-Dietz syndrome (LDS)-associated pathogenic variant (TGFBR1A230T). We also generated hiPSC-derived BVGs using cells from a patient with LDS (PatientA230T/+) and using genetically corrected cells (Patient+/+). Control and experimental BVGs were then implanted into the common carotid arteries of nude rats. The TGFBR1A230T variant led to impaired mechanical properties of BVGs, resulting in lower burst pressure and suture retention strength. BVGs carrying the variant dilated over time in vivo, resembling human TAA formation. Spatial transcriptomics profiling revealed defective expression of extracellular matrix (ECM) formation genes in PatientA230T/+ BVGs compared with Patient+/+ BVGs. Histological analysis and protein assays validated quantitative and qualitative ECM defects in PatientA230T/+ BVGs and patient tissue, including decreased collagen hydroxylation. SMC organization was also impaired in PatientA230T/+ BVGs as confirmed by vascular contraction testing. Silencing of collagen-modifying enzymes with small interfering RNAs reduced collagen proline hydroxylation in SMC-derived tissue constructs. These studies demonstrated the utility of BVGs to model human TAA formation in an animal host and highlighted the role of reduced collagen modifying enzyme activity in human TAA formation.

Bioengineering methods for vascularizing organoids.

Organoids, self-organizing three-dimensional (3D) structures derived from stem cells, offer unique advantages for studying organ development, modeling diseases, and screening potential therapeutics. However, their translational potential and ability to mimic complex in vivo functions are often hindered by the lack of an integrated vascular network. To address this critical limitation, bioengineering strategies are rapidly advancing to enable efficient vascularization of organoids. These methods encompass co-culturing organoids with various vascular cell types, co-culturing lineage-specific organoids with vascular organoids, co-differentiating stem cells into organ-specific and vascular lineages, using organoid-on-a-chip technology to integrate perfusable vasculature within organoids, and using 3D bioprinting to also create perfusable organoids. This review explores the field of organoid vascularization, examining the biological principles that inform bioengineering approaches. Additionally, this review envisions how the converging disciplines of stem cell biology, biomaterials, and advanced fabrication technologies will propel the creation of increasingly sophisticated organoid models, ultimately accelerating biomedical discoveries and innovations.

In vitro models for studying implant-associated biofilms - A review from the perspective of bioengineering 3D microenvironments.

Biofilm research has grown exponentially over the last decades, arguably due to their contribution to hospital acquired infections when they form on foreign body surfaces such as catheters and implants. Yet, translation of the knowledge acquired in the laboratory to the clinic has been slow and/or often it is not attempted by research teams to walk the talk of what is defined as 'bench to bedside'. We therefore reviewed the biofilm literature to better understand this gap. Our search revealed substantial development with respect to adapting surfaces and media used in models to mimic the clinical settings, however many of the in vitro models were too simplistic, often discounting the composition and properties of the host microenvironment and overlooking the biofilm-implant-host interactions. Failure to capture the physiological growth conditions of biofilms in vivo results in major differences between lab-grown- and clinically-relevant biofilms, particularly with respect to phenotypic profiles, virulence, and antimicrobial resistance, and they essentially impede bench-to-bedside translatability. In this review, we describe the complexity of the biological processes at the biofilm-implant-host interfaces, discuss the prerequisite for the development and characterization of biofilm models that better mimic the clinical scenario, and propose an interdisciplinary outlook of how to bioengineer biofilms in vitro by converging tissue engineering concepts and tools.

The bioengineering application of hyaluronic acid in tissue regeneration and repair.

The multifaceted role of hyaluronic acid (HA) across diverse biomedical disciplines underscores its versatility in tissue regeneration and repair. HA hydrogels employ different crosslinking including chemical (chitosan, collagen), photo- initiation (riboflavin, LAP), enzymatic (HRP/H2O2), and physical interactions (hydrogen bonds, metal coordination). In biophysics and biochemistry, HA's signaling pathways, primarily through CD44 and RHAMM receptors, modulate cell behavior (cell migration; internalization of HA), inflammation, and wound healing. Particularly, smaller HA fragments stimulate inflammatory responses through toll-like receptors, impacting macrophages and cytokine expression. HA's implications in oncology highlight its involvement in tumor progression, metastasis, and treatment. Elevated HA in tumor stroma impacts apoptosis resistance and promotes tumor growth, presenting potential therapeutic targets to halt tumor progression. In orthopedics, HA's presence in synovial fluid aids in osteoarthritis management, as its supplementation alleviates pain, enhances synovial fluid's viscoelastic properties, and promotes cartilage integrity. In ophthalmology, HA's application in dry eye syndrome addresses symptoms by moisturizing the eyes, replenishing tear film deficiencies, and facilitating wound healing. Intravitreal injections and hydrogel-based systems offer versatile approaches for drug delivery and vitreous humor replacement. For skin regeneration and wound healing, HA hydrogel dressings exhibit exceptional properties by promoting moist wound healing and facilitating tissue repair. Integration of advanced regenerative tools like stem cells and solubilized amnion membranes into HA-based systems accelerates wound closure and tissue recovery. Overall, HA's unique properties and interactions render it a promising candidate across diverse biomedical domains, showcasing immense potentials in tissue regeneration and therapeutic interventions. Nevertheless, many detailed cellular and molecular mechanisms of HA and its applications remain unexplored and warrant further investigation.

The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis.

Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.

Engineering is evolution: a perspective on design processes to engineer biology.

Careful consideration of how we approach design is crucial to all areas of biotechnology. However, choosing or developing an effective design methodology is not always easy as biology, unlike most areas of engineering, is able to adapt and evolve. Here, we put forward that design and evolution follow a similar cyclic process and therefore all design methods, including traditional design, directed evolution, and even random trial and error, exist within an evolutionary design spectrum. This contrasts with conventional views that often place these methods at odds and provides a valuable framework for unifying engineering approaches for challenging biological design problems.

Controllable and reusable seesaw circuit based on nicking endonucleases.

Seesaw circuits are essential for molecular computing and biosensing. However, a notable limitation of seesaw circuits lies in the irreversible depletion of components, precluding the attainment of system recovery and rendering nucleic acid circuits non-reusable. We developed a brand-new method for creating controllable and reusable seesaw circuits. By using the nicking endonucleases Nt.BbvCI and Nt.Alwi, we removed "functional components" while keeping the "skeletal components" for recurrent usage. T-inputs were introduced, increasing the signal-to-noise ratio of AND logic from 2.68 to 11.33 and demonstrating compatibility. We identified the logic switching feature and verified that it does not impair circuit performance. We also built intricate logic circuits, such as OR-AND gate, to demonstrate the versatility of our methodology. This controllable reusability extends the applications of nanotechnology and bioengineering, enhancing the practicality and efficiency of these circuits across various domains.