Bioengineering, Volume 8, Issue 5 (May 2021) – 21 articles

The menisci of the knee are complex fibro-cartilaginous tissues that play important roles in load bearing, shock absorption, joint lubrication, and stabilization. The objective of this study was to evaluate the interaction between the different meniscal tissue components (i.e., the solid matrix constituents and the fluid phase) and the mechanical response according to the developmental stage of the tissue. Menisci derived from partially and fully developed pigs were analyzed. We carried out biochemical analyses to quantify glycosaminoglycan (GAG) and DNA content according to the developmental stage. These values were related to tissue mechanical properties that were measured in vitro by performing compression and tension tests on meniscal specimens. Both compression and tension protocols consisted of multi-ramp stress–relaxation tests comprised of increasing strains followed by stress–relaxation to equilibrium. To better understand the mechanical response to different directions of mechanical stimulus and to relate it to the tissue structural composition and development, we performed numerical simulations that implemented different constitutive models (poro-elasticity, viscoelasticity, transversal isotropy, or combinations of the above) using the commercial software COMSOL Multiphysics. The numerical models also allowed us to determine several mechanical parameters that cannot be directly measured by experimental tests. The results of our investigation showed that the meniscus is a non-linear, anisotropic, non-homogeneous material: mechanical parameters increase with strain, depend on the direction of load, and vary among regions (anterior, central, and posterior). Preliminary numerical results showed the predominant role of the different tissue components depending on the mechanical stimulus. The outcomes of biochemical analyses related to mechanical properties confirmed the findings of the numerical models, suggesting a specific response of meniscal cells to the regional mechanical stimuli in the knee joint. During maturation, the increase in compressive moduli could be explained by cell differentiation from fibroblasts to metabolically active chondrocytes, as indicated by the found increase in GAG/DNA ratio. The changes of tensile mechanical response during development could be related to collagen II accumulation during growth. This study provides new information on the changes of tissue structural components during maturation and the relationship between tissue composition and mechanical response. Full article

Bone marrow (BM) is a reliable source of multipotent mesenchymal stromal cells (MSCs), which have been successfully used for treating osteonecrosis. Considering the functional advantages of BM-MSCs as bone and cartilage reparatory cells and supporting angiogenesis, several donor-related factors are also essential to consider when autologous BM-MSCs are used for such regenerative therapies. Aging is one of several factors contributing to the donor-related variability and found to be associated with a reduction of BM-MSC numbers. However, even within the same age group, other factors affecting MSC quantity and function remain incompletely understood. For patients with osteonecrosis, several underlying factors have been linked to the decrease of the proliferation of BM-MSCs as well as the impairment of their differentiation, migration, angiogenesis-support and immunoregulatory functions. This review discusses the quality and quantity of BM-MSCs in relation to the etiological conditions of osteonecrosis such as sickle cell disease, Gaucher disease, alcohol, corticosteroids, Systemic Lupus Erythematosus, diabetes, chronic renal disease and chemotherapy. A clear understanding of the regenerative potential of BM-MSCs is essential to optimize the cellular therapy of osteonecrosis and other bone damage conditions. Full article

Research on human stem cells, such as pluripotent stem cells and mesenchymal stromal cells, has shown much promise in their use for regenerative medicine approaches. However, their use in patients requires large-scale expansion systems while maintaining the quality of the cells. Due to their characteristics, bioreactors have been regarded as ideal platforms to harbour stem cell biomanufacturing at a large scale. Specifically, single-use bioreactors have been recommended by regulatory agencies due to reducing the risk of product contamination, and many different systems have already been developed. This review describes single-use bioreactor platforms which have been used for human stem cell expansion and differentiation, along with their comparison with reusable systems in the development of a stem cell bioprocess for clinical applications. Full article

Like all cells, hematopoietic stem cells (HSCs) and their offspring, the hematopoietic progenitor cells (HPCs), are highly sociable. Their capacity to interact with bone marrow niche cells and respond to environmental cytokines orchestrates the generation of the different types of blood and immune cells. The starting point for engineering hematopoiesis ex vivo is the nature of HSCs, and a longstanding premise is that they are a homogeneous population of cells. However, recent findings have shown that adult bone marrow HSCs are really a mixture of cells, with many having lineage affiliations. A second key consideration is: Do HSCs “choose” a lineage in a random and cell-intrinsic manner, or are they instructed by cytokines? Since their discovery, the hematopoietic cytokines have been viewed as survival and proliferation factors for lineage committed HPCs. Some are now known to also instruct cell lineage choice. These fundamental changes to our understanding of hematopoiesis are important for placing niche support in the right context and for fabricating an ex vivo environment to support HSC development. Full article

The left ventricle (LV) constantly changes its shape and function as a response to pathological conditions, and this process is known as remodeling. In the presence of aortic stenosis (AS), the degenerative process is not limited to the aortic valve but also involves the remodeling of LV. Statistical shape analysis (SSA) offers a powerful tool for the visualization and quantification of the geometrical and functional patterns of any anatomic changes. In this paper, a SSA method was developed to determine shape descriptors of the LV under different degrees of AS and thus to shed light on the mechanistic link between shape and function. A total of $n=86$ patients underwent computed tomography (CT) for the evaluation of valvulopathy were segmented to obtain the LV surface and then were automatically aligned to a reference template by rigid registrations and transformations. Shape modes of the anatomical LV variation induced by the degree of AS were assessed by principal component analysis (PCA). The first shape mode represented nearly 50% of the total variance of LV shape in our patient population and was mainly associated to a spherical LV geometry. At Pearson’s analysis, the first shape mode was positively correlated to both the end-diastolic volume ($p<0.01$, $R=0.814$) and end-systolic volume ($p<0.01$, and $R=0.922$), suggesting LV impairment in patients with severe AS. A predictive model built with PCA-related shape modes achieved better performance in stratifying the occurrence of adverse events with respect to a baseline model using clinical demographic data as risk predictors. This study demonstrated the potential of SSA approaches to detect the association of complex 3D shape features with functional LV parameters. Full article

Collective cell migration of epithelial tumor cells is one of the important factors for elucidating cancer metastasis and developing novel drugs for cancer treatment. Especially, new roles of E-cadherin in cancer migration and metastasis, beyond the epithelial–mesenchymal transition, have recently been unveiled. Here, we quantitatively examined cell motility using micropatterned free edge migration model with E-cadherin re-expressing EC96 cells derived from adenocarcinoma gastric (AGS) cell line. EC96 cells showed increased migration features such as the expansion of cell islands and straightforward movement compared to AGS cells. The function of tight junction proteins known to E-cadherin expression were evaluated for cell migration by knockdown using sh-RNA. Cell migration and straight movement of EC96 cells were reduced by knockdown of ZO-1 and claudin-7, to a lesser degree. Analysis of the migratory activity of boundary cells and inner cells shows that EC96 cell migration was primarily conducted by boundary cells, similar to leader cells in collective migration. Immunofluorescence analysis showed that tight junctions (TJs) of EC96 cells might play important roles in intracellular communication among boundary cells. ZO-1 is localized to the base of protruding lamellipodia and cell contact sites at the rear of cells, indicating that ZO-1 might be important for the interaction between traction and tensile forces. Overall, dynamic regulation of E-cadherin expression and localization by interaction with ZO-1 protein is one of the targets for elucidating the mechanism of collective migration of cancer metastasis. Full article

A theoretical fluid mechanical model is proposed for the investigation of myocardial perfusion in healthy and stenotic conditions. The model hinges on Terzaghi’s consolidation theory and reformulates the related unsteady flow equation for the simulation of the swelling–drainage alternation characterizing the diastolic–systolic phases. When compared with the outcome of experimental in vivo observations in terms of left ventricle transmural perfusion ratio (T.P.R.), the analytical solution provided by the present study for the time-dependent blood pressure and flow rate across the ventricle wall proves to consistently reproduce the basic mechanisms of both healthy and ischemic perfusion. Therefore, it could constitute a useful interpretative support to improve the comprehension of the basic hemodynamic mechanisms leading to the most common cardiac diseases. Additionally, it could represent the mathematical basis for the application of inverse methods aimed at estimating the characteristic parameters of ischemic perfusion (i.e., location and severity of coronary stenoses) via downstream ventricular measurements, possibly inspiring their assessment via non-invasive myocardial imaging techniques. Full article

Normal wound healing progresses through inflammatory, proliferative and remodeling phases in response to tissue injury. Collagen, a key component of the extracellular matrix, plays critical roles in the regulation of the phases of wound healing either in its native, fibrillar conformation or as soluble components in the wound milieu. Impairments in any of these phases stall the wound in a chronic, non-healing state that typically requires some form of intervention to guide the process back to completion. Key factors in the hostile environment of a chronic wound are persistent inflammation, increased destruction of ECM components caused by elevated metalloproteinases and other enzymes and improper activation of soluble mediators of the wound healing process. Collagen, being central in the regulation of several of these processes, has been utilized as an adjunct wound therapy to promote healing. In this work the significance of collagen in different biological processes relevant to wound healing are reviewed and a summary of the current literature on the use of collagen-based products in wound care is provided. Full article

Chronic leg ulcers (CLUs) are full thickness wounds that usually occur between the ankle and knee, fail to heal after 3 months of standard treatment, or are not entirely healed at 12 months. CLUs present a considerable burden on patients, subjecting them to severe pain and distress, while healthcare systems suffer immense costs and loss of resources. The poor healing outcome of the standard treatment of CLUs generates an urgent clinical need to find effective solutions for these wounds. Tissue Engineering and Biomaterials Science offer exciting prospects for the treatment of CLUs, using a broad range of skin substitutes or scaffolds, and dressings. In this review, we summarize and discuss the various types of scaffolds used clinically in the treatment of CLUs. Their structure and therapeutic effects are described, and for each scaffold type representative examples are discussed, supported by clinical trials. Silver dressings are also reviewed due to their reported benefits in the healing of leg ulcers, as well as recent studies on new dermal scaffolds, reporting on clinical results where available. We conclude by arguing there is a further need for tissue-engineered products specifically designed and bioengineered to treat these wounds and we propose a series of properties that a biomaterial for CLUs should possess, with the intention of focusing efforts on finding an effective treatment. Full article

Uncoordinated carbon-nitrogen ratio in raw materials will lead to excessive contents of higher alcohols in alcoholic beverages. The effect of GAT1 gene, the GATA transcription activator, on higher alcohol biosynthesis was investigated to clarify the mechanism of Saccharomyces cerevisiae regulating higher alcohol metabolism under high concentrations of free amino nitrogen (FAN). The availability of FAN by strain SDT1K with a GAT1 double-copy deletion was 28.31% lower than that of parent strain S17, and the yield of higher alcohols was 33.91% lower. The transcript levels of the downstream target genes of GAT1 and higher alcohol production in the double-copy deletion mutant suggested that a part of the effect of GAT1 deletion on higher alcohol production was the downregulation of GAP1, ARO9, and ARO10. This study shows that GATA factors can effectively regulate the metabolism of higher alcohols in S. cerevisiae and provides valuable insights into higher alcohol biosynthesis, showing great significance for the wheat beer industry. Full article

Patients whose lungs are compromised due to various respiratory health concerns require mechanical ventilation for support in breathing. Different mechanical ventilation settings are selected depending on the patient’s lung condition, and the selection of these parameters depends on the observed patient response and experience of the clinicians involved. To support this decision-making process for clinicians, good prediction models are always beneficial in improving the setting accuracy, reducing treatment error, and quickly weaning patients off the ventilation support. In this study, we developed a machine learning model for estimation of the mechanical ventilation parameters for lung health. The model is based on inverse mapping of artificial neural networks with the Graded Particle Swarm Optimizer. In this new variant, we introduced grouping and hierarchy in the swarm in addition to the general rules of particle swarm optimization to further improve its prediction performance of the mechanical ventilation parameters. The machine learning model was trained and tested using clinical data from canine and feline patients at the University of Georgia College of Veterinary Medicine. Our model successfully generated a range of parameter values for the mechanical ventilation applied on test data, with the average prediction values over multiple trials close to the target values. Overall, the developed machine learning model should be able to predict the mechanical ventilation settings for various respiratory conditions for patient’s survival once the relevant data are available. Full article

Sequence files formats (FASTA and FASTQ) are commonly used in bioinformatics, molecular biology and biochemistry. With the advent of next-generation sequencing (NGS) technologies, the number of FASTQ datasets produced and analyzed has grown exponentially, urging the development of dedicated software to handle, parse, and manipulate such files efficiently. Several bioinformatics packages are available to filter and manipulate FASTA and FASTQ files, yet some essential tasks remain poorly supported, leaving gaps that any workflow analysis of NGS datasets must fill with custom scripts. This can introduce harmful variability and performance bottlenecks in pivotal steps. Here we present a suite of tools, called SeqFu (Sequence Fastx utilities), that provides a broad range of commands to perform both common and specialist operations with ease and is designed to be easily implemented in high-performance analytical pipelines. SeqFu includes high-performance implementation of algorithms to interleave and deinterleave FASTQ files, merge Illumina lanes, and perform various quality controls (identification of degenerate primers, analysis of length statistics, extraction of portions of the datasets). SeqFu dereplicates sequences from multiple files keeping track of their provenance. SeqFu is developed in Nim for high-performance processing, is freely available, and can be installed with the popular package manager Miniconda. Full article

Automated biomimetic systems for the preclinical testing of drugs are of great interest. Here, an in vitro testing platform for in vivo adapted drug absorption studies is presented. It has been designed with a focus on easy handling and the usability of established cell cultivation techniques in standard well plate inserts. The platform consists of a microfluidic device, which accommodates a well plate insert with pre-cultivated cells, and provides a fluid flow with dynamic drug dilution profiles. A low-cost single-board computer with a touchscreen was used as a control unit. This provides a graphical user interface, controls the syringe pump flow rates, and records the transepithelial electrical resistance. It thereby enables automated parallel testing in multiple devices at the same time. To demonstrate functionality, an MDCK cell layer was used as a model for an epithelial barrier for drug permeation testing. This confirms the possibility of performing absorption studies on barrier tissues under conditions close to those in vivo. Therefore, a further reduction in animal experiments can be expected. Full article

Third generation biofuels and high-value bioproducts produced from microalgal biomass have been considered promising long-term sustainable alternatives for energy and/or food production, potentially decreasing greenhouse gas emissions. Microalgae as a source of biofuels have been widely studied for bioethanol/biodiesel/biogas production. However, critical research is needed in order to increase the efficiency of microalgae production from high-N agri-waste, not only for biofuels but also for bio-based products, and thus enhance its commercial viability. The growth in the poultry industry has led to increased chicken manure (CM), which are rich in ammonia, phosphate, potassium, and other trace elements. These constituents could be used as nutrients for growing microalgae. In this research, a two-stage (liquid–solid) anaerobic digester treating CM at 20 ± 1 °C was performed, and liquid digestate (leachate) obtained after the digestion process was used as a substrate to grow the microalgal strain Chlorella vulgaris CPCC 90. Considering the high-N content (NH₃-N: 5314 mg/L; TKN: 6197 mg/L) in liquid digestate, different dilutions were made, using distilled water to obtain viz. 10%, 30%, 50%, 70%, 90%, and 100% of the digestate concentrations for the microalgae cultivation. Preliminary results showed that Chlorella vulgaris CPCC 90 was able to grow and utilize nutrients from a 10% diluted CM digestate. Future research is underway to enhance microalgal growth at higher digestate concentrations and to optimize the use of microalgae/microalgae-bacteria consortia for better adaptation to high-N content wastes. An AD-microalgae coupling scenario has been proposed for the circulation bioeconomy framework. Full article

Attention deficit hyperactivity disorder (ADHD) is a pervasive condition affecting persons across all age groups, although it is primarily diagnosed in children. This neurological condition affects behavior, learning, and social adjustment and requires specific symptomatic criteria to be fulfilled for diagnosis. ADHD may be treated with a combination of psychological or psychiatric therapeutic interventions, but it often goes unattended. People with ADHD face societal bias challenges that impact how they manage the disorder and how they view themselves. This paper summarizes the present state of understanding of this disorder, with particular attention to early diagnosis and innovative therapeutic intervention. Contemporary understanding of the mind–brain duality allows for innovative therapeutic interventions based on neurological stimulation. This paper introduces the concept of neurostimulation as a therapeutic intervention for ADHD and poses the question of the relationship between patient adherence to self-administered therapy and the aesthetic design features of the neurostimulation device. By fabricating devices that go beyond safety and efficacy to embrace the aesthetic preferences of the patient, it is proposed that there will be improvements in patient adherence to a device intended to address ADHD. Full article

The increasing use of chemical fertilizers causes the loss of natural biological nitrogen fixation in soils, water eutrophication and emits more than 300 Mton CO₂ per year. It also limits the success of external bacterial inoculation in the soil. Nitrogen fixing bacteria can be inhibited by the presence of ammonia as its presence can inhibit biological nitrogen fixation. Two aerobic sludges from wastewater treatment plants (WWTP) were exposed to high ammonium salts concentrations (>450 mg L⁻¹ and >2 dS m⁻¹). Microbial analysis after treatment through 16S pyrosequencing showed the presence of Fluviicola sp. (17.70%), a genus of the Clostridiaceae family (11.17%), and Azospirillum sp. (10.42%), which were present at the beginning with lower abundance. Denaturing gradient gel electrophoresis (DGGE) analysis based on nifH genes did not show changes in the nitrogen-fixing population. Nitrogen-Fixing Bacteria (NFB) were identified and associated with other microorganisms involved in the nitrogen cycle, presumably for survival at extreme conditions. The potential use of aerobic sludges enriched with NFB is proposed as an alternative to chemical fertilizer as this bacteria could supplement nitrogen to the plant showing competitive results with chemical fertilization. Full article

After the initiation of the current outbreak, humans’ lives have been profoundly impacted by COVID-19. During the first months, no rapid and reliable detecting tool was readily available to sufficiently respond to the requirement of massive testing. In this situation, when the development of an effective vaccine requires at least a few months, it is crucial to be prepared by developing and commercializing affordable, accurate, rapid and adaptable biosensors not only to fight Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but also to be armed to avoid the pandemic in the earliest stages in the future. The COVID-19 diagnostic tools are categorized into two main groups of Nucleic Acid (NA)-based and protein-based tests. To date, nucleic acid-based detection has been announced as the gold-standard strategy for coronavirus detection; however, protein-based tests are promising alternatives for rapid and large-scale screening of susceptible groups. In this review, we discuss the current protein-based biosensing tools, the research advances and the potential protein-detecting strategies for COVID-19 detection. This narrative review aims to highlight the importance of the diagnostic tests, encourage the academic research groups and the companies to eliminate the shortcomings of the current techniques and step forward to mass-producing reliable point-of-care (POC) and point-of-need (PON) adaptable diagnostic tools for large-scale screening in the future outbreaks. Full article

This article provides additional knowledge for cord blood platelet gel (CBPG) production. Recently, it has been shown that CBPG exerts beneficial properties in wound healing applications. CBPG is produced after a two-step centrifugation process, following the addition of calcium gluconate. Clinical-grade CBPG can be produced in public cord blood banks, worldwide. However, standardization of the CBPG production process must be established in order to reduce discrepancies that occurred due to different platelet gel preparations. This article aims to provide an update regarding the selection criteria of cord blood units (CBUs), and to provide evidence for the improvement of the CBPG production process. (Comment on “Short Term Results of Fibrin Gel Obtained from Cord Blood Units: A Preliminary in Vitro Study” Bioengineering 2019, 6, 66). Full article

Aim: to investigate the factors implied in the development of postoperative complications in both self-expandable and balloon-expandable transcatheter heart valves by means of finite element analysis (FEA). Materials and methods: FEA was integrated into CT scans to investigate two cases of postoperative device failure for valve thrombosis after the successful implantation of a CoreValve and a Sapien 3 valve. Data were then compared with two patients who had undergone uncomplicated transcatheter heart valve replacement (TAVR) with the same types of valves. Results: Computational biomechanical modeling showed calcifications persisting after device expansion, not visible on the CT scan. These calcifications determined geometrical distortion and elliptical deformation of the valve predisposing to hemodynamic disturbances and potential thrombosis. Increased regional stress was also identified in correspondence to the areas of distortion with the associated paravalvular leak. Conclusion: the use of FEA as an adjunct to preoperative imaging might assist patient selection and procedure planning as well as help in the detection and prevention of TAVR complications. Full article

Macromolecular components of the vascular extracellular matrix (ECM), particularly elastic fibers and collagen fibers, are critical for the proper physiological function of arteries. When the unique biomechanical combination of these fibers is disrupted, or in the ultimate extreme where fibers are completely lost, arterial disease can emerge. Bioengineers in the realms of vascular tissue engineering and regenerative medicine must therefore ideally consider how to create tissue engineered vascular grafts containing the right balance of these fibers and how to develop regenerative treatments for situations such as an aneurysm where fibers have been lost. Previous work has demonstrated that the primary cells responsible for vascular ECM production during development, arterial smooth muscle cells (SMCs), can be induced to make new elastic fibers when exposed to secreted factors from adipose-derived stromal cells. To further dissect how this signal is transmitted, in this study, the factors were partitioned into extracellular vesicle (EV)-rich and EV-depleted fractions as well as unseparated controls. EVs were validated using electron microscopy, dynamic light scattering, and protein quantification before testing for biological effects on SMCs. In 2D culture, EVs promoted SMC proliferation and migration. After 30 days of 3D fibrin construct culture, EVs promoted SMC transcription of the elastic microfibril gene FBN1 as well as SMC deposition of insoluble elastin and collagen. Uniaxial biomechanical properties of strand fibrin constructs were no different after 30 days of EV treatment versus controls. In summary, it is apparent that some of the positive effects of adipose-derived stromal cells on SMC elastogenesis are mediated by EVs, indicating a potential use for these EVs in a regenerative therapy to restore the biomechanical function of vascular ECM in arterial disease. Full article

The recapitulation of the stem cell microenvironment is an emerging area of research that has grown significantly in the last 10 to 15 years. Being able to understand the underlying mechanisms that relate stem cell behavior to the physical environment in which stem cells reside is currently a challenge that many groups are trying to unravel. Several approaches have attempted to mimic the biological components that constitute the native stem cell niche, however, this is a very intricate environment and, although promising advances have been made recently, it becomes clear that new strategies need to be explored to ensure a better understanding of the stem cell niche behavior. The second strand in stem cell niche research focuses on the use of manufacturing techniques to build simple but functional models; these models aim to mimic the physical features of the niche environment which have also been demonstrated to play a big role in directing cell responses. This second strand has involved a more engineering approach in which a wide set of microfabrication techniques have been explored in detail. This review aims to summarize the use of these microfabrication techniques and how they have approached the challenge of mimicking the native stem cell niche. Full article