Bioengineering Research Articles

Green synthesis of gold nanoparticles obtained from Punica granatum flower extract for phytochemical determination and antibacterial activity

Numerous biomedical applications such as biological detection, drug delivery, diagnostic imaging and tissue engineering, have incorporated nanotechnology. Parts of the pomegranate (Punica granatum) flower are known to have strong antibacterial properties. In this study, the anti-susceptibility test was used to look into the green synthesis of gold nanoparticles using Punica granatum and the inhibitory effect of these particles. According to the current study, prepared AuNPs were evaluated using a variety of methods including UV-visible spectrophotometry, FTIR, SEM and GC-MS to identify the phytochemicals. The bacterial and fungal species Candida albicans and Malassezia furfur that are inhibited by the synthetic colloidal gold nanoparticles made with Punica granatum flower extract include Escherichia coli, Pseudomonas, Staphylococcus, Klebsiella pneumoniae and Protea. In this work, we describe a simple, quick and reproducible method for the environmentally friendly synthesis of AuNPs without the need for expensive reducing agents. Simple incubation of a flower extract with aqueous gold ions at ambient temperature resulted in ‘medium monodisperse’ nanoparticles, suggesting that the plant extract acted as a strong reducing agent.

PhD Student Funding Patterns: Placing Biomedical, Biological, and Biosystems Engineering in the Context of Engineering Sub-disciplines, Biological Sciences, and Other STEM Disciplines

Whether doctoral students are funded primarily by fellowships, research assistantships, or teaching assistantships impacts their degree completion, time to degree, learning outcomes, and short- and long-term career outcomes. Variations in funding patterns have been studied at the broad field level but not comparing engineering sub-disciplines. We addressed two research questions: How do PhD student funding mechanisms vary across engineering sub-disciplines? And how does variation in funding mechanisms across engineering sub-disciplines map onto the larger STEM disciplinary landscape? We analyzed 103,373 engineering and computing responses to the U.S. Survey of Earned Doctorates collected between 2007 and 2016. We conducted analysis of variance with Bonferroni post hoc comparisons to examine variation in funding across sub-disciplines. Then, we conducted a k-means cluster analysis on percentage variables for fellowship, research, and teaching assistantship funding mechanism with STEM sub-discipline as the unit of analysis. A statistically significantly greater percentage of biomedical/biological engineering doctoral students were funded via a fellowship, compared to every other engineering sub-discipline. Consequently, biomedical/biological engineering had significantly lower proportions of students supported via research and teaching assistantships than nearly all other engineering sub-disciplines. We identified five clusters. The majority of engineering sub-disciplines grouped together into a cluster with high research assistantships and low teaching assistantships. Biomedical/biological engineering clustered in the high fellowships grouping with most other biological sciences but no other engineering sub-disciplines. Biomedical/biological engineering behaves much more like biological and life sciences in utilizing fellowships to fund graduate students, far more than other engineering sub-disciplines. Our study provides further evidence of the prevalence of fellowships in life sciences and how it stretches into biomedical/biological engineering. The majority of engineering sub-disciplines relied more on research assistantships to fund graduate study. The lack of uniformity provides an opportunity to diversify student experiences during their graduate programs but also necessitates an awareness to the advantages and disadvantages that different funding portfolios can bestow on students.

Design and practice of biological reaction engineering flipped classroom in applied undergraduate colleges

This study aims to explore and refine the teaching aspects of a flipped classroom approach for biological reaction engineering. The study encompasses three iterations of teaching practice, focusing on key elements such as theme content selection, implementation process, evaluation and effectiveness. By integrating relevant industry and societal topics with course's professional knowledge, students are encouraged to independently collect data, analyze and discuss findings, and present their work in group. Comprehensive literacy of students is assessed through discussion reports, defense reports, utilization of new tools, and team cooperation. Analysis of student performance reveals that the design and implementation of the flipped classroom approach significantly enhances student motivation to learn, improves scores, and supports the achievement of course objectives. Therefore, the methodology presented in this study may serve as a reference for implementing teaching reforms in core courses in applied undergraduate colleges, thereby fostering well-round individuals with strong theoretical foundation, innovative analytical skills, and excellent teamwork abilities.

Imitation of Life: A Search Engine for Biologically Inspired Design

Biologically Inspired Design (BID), or Biomimicry, is a problem-solving methodology that applies analogies from nature to solve engineering challenges. For example, Speedo engineers designed swimsuits based on shark skin. Finding relevant biological solutions for real-world problems poses significant challenges, both due to the limited biological knowledge engineers and designers typically possess and to the limited BID resources. Existing BID datasets are hand-curated and small, and scaling them up requires costly human annotations. In this paper, we introduce BARcode (Biological Analogy Retriever), a search engine for automatically mining bio-inspirations from the web at scale. Using advances in natural language understanding and data programming, BARcode identifies potential inspirations for engineering challenges. Our experiments demonstrate that BARcode can retrieve inspirations that are valuable to engineers and designers tackling real-world problems, as well as recover famous historical BID examples. We release data and code; we view BARcode as a step towards addressing the challenges that have historically hindered the practical application of BID to engineering innovation.

Generalised shot-noise representations of stochastic systems driven by non-Gaussian Lévy processes

Abstract We consider the problem of obtaining effective representations for the solutions of linear, vector-valued stochastic differential equations (SDEs) driven by non-Gaussian pure-jump Lévy processes, and we show how such representations lead to efficient simulation methods. The processes considered constitute a broad class of models that find application across the physical and biological sciences, mathematics, finance, and engineering. Motivated by important relevant problems in statistical inference, we derive new, generalised shot-noise simulation methods whenever a normal variance-mean (NVM) mixture representation exists for the driving Lévy process, including the generalised hyperbolic, normal-gamma, and normal tempered stable cases. Simple, explicit conditions are identified for the convergence of the residual of a truncated shot-noise representation to a Brownian motion in the case of the pure Lévy process, and to a Brownian-driven SDE in the case of the Lévy-driven SDE. These results provide Gaussian approximations to the small jumps of the process under the NVM representation. The resulting representations are of particular importance in state inference and parameter estimation for Lévy-driven SDE models, since the resulting conditionally Gaussian structures can be readily incorporated into latent variable inference methods such as Markov chain Monte Carlo, expectation-maximisation, and sequential Monte Carlo.

Theoretical investigation of MHD peristalsis of non‐Newtonian nanofluid flow under the impacts of temperature‐dependent thermal conductivity: Application to biomedical engineering

AbstractNanofluids have the tendency to improve thermal characteristics in a broader context, such as in medical processes, industrial cooling applications, the transportation industry, hybrid engines, gas temperature reduction, microelectromechanical systems, refrigerators, nuclear reactors, vehicle temperature control, pharmaceutical processes, thermal management of vehicles, microelectronics, and chillers, etc. Therefore, present study investigates the effects of a two‐dimensional magnetohydrodynamics (MHD) peristalsis of the Carreau–Yasuda nanofluid through conservation principles of energy, concentration, mass, and momentum, which is motivated by recent advances in biological engineering. The entire system is coupled through viscous dissipation, Joule heating, a heat sink/source, Brownian diffusion, a radially magnetic field, thermophoresis motion, and slip conditions in a curved geometry. Lubrication theory is employed in order to simplify governing equations. Resulting systems are nonlinear coupled differential equations whose exact solutions are difficult to obtain, therefore, numerical solutions are obtained through NDSolve in Mathematica. The key features of peristaltic movement and rates of heat transfer are disseminated in detail via graphical representations for variation of various physical parameters. According to the findings, for greater values of the Hartman number, temperature increases, and the velocity decreases. The validity of these results has been verified using the existing published articles of Hayat et al. (2018).

Tailoring deformation-induced martensitic transformation through cellular engineering in laser powder bed fusion processed 316L stainless steel

The microstructural effect of 316L stainless steel (SS) fabricated by laser powder bed fusion on deformation-induced martensitic transformation (DIMT) was investigated. Both opposing effects, i.e., disturbing/promoting DIMT were observed. While the cellular structure and low-angle grain boundaries reduce the DIMT rate by disturbing shear band formation, the high dislocation density can activate direct BCC martensite nucleation and accelerate the DIMT. This observation suggests that controlling the two competing effects is the key to cellular engineering using additive manufacturing.

AgroClimate Indicators Web-Based Monitoring Tool

This guide introduces users to a recently developed web-based tool on AgroClimate.org that was designed to systematically monitor climate indicators and detect anomalies with the potential to affect the agricultural industry in Florida and elsewhere in the continental United States. Written by Clyde W. Fraisse, Mauricio A. Z. Karrei, and Margaret Walsh, and published by the UF/IFAS Department of Agricultural and Biological Engineering, January 2024.

Simulation of pulsatory liposome working using a linear approximation for transmembrane pore dynamics

This paper presents an analytical solution of the differential equations describing the pulsatory liposome dynamics. We consider a unilamellar liposome filled with an aqueous solution of osmotic solute inserted in a hypotonic aqueous medium. Due to the osmosis process the liposome has a cyclic evolution. The lipid vesicle swells to a critical size, at which point a transbilayer pore suddenly appears. Part of the internal solution leaks through this pore. The liposome relaxes and returns to the initial size. The swelling starts again and the liposome goes through a periodical process. The swelling of the liposome is described by a differential equation. The appearance of the pore changes the evolution of the liposome. The internal solution comes out through the pore and the liposome starts its deflation (relaxation). The evolution of the pore has two phases: first, the radius of the pore increases to its maximum value, then the radius decreases until it disappears, and the liposome reaches its initial size. During each cycle, the liposome will release a quantity (a pulse) of the solution from its interior. All the processes which contribute to the liposome relaxing and its coming back to the initial size are described by three differential equations. This system of differential equations can be integrated using numerical methods. The functions – which model our biological engine in three stages, are as follows: R(t) - the liposome radius, r(t) - the pore radius, C(t) - solute concentration, Q(t) - the osmotic solute amount inside the liposome. The graphs representing these functions contain important linear portions, which suggested a solution using analytical methods. Based on some analytical methods, we solve these equations, and their explicit solutions are validated by comparing with numerical results of previous studies.

Emerging approaches for the development of artificial islets.

The islet of Langerhans, functioning as a "mini organ", plays a vital role in regulating endocrine activities due to its intricate structure. Dysfunction in these islets is closely associated with the development of diabetes mellitus (DM). To offer valuable insights for DM research and treatment, various approaches have been proposed to create artificial islets or islet organoids with high similarity to natural islets, under the collaborative effort of biologists, clinical physicians, and biomedical engineers. This review investigates the design and fabrication of artificial islets considering both biological and tissue engineering aspects. It begins by examining the natural structures and functions of native islets and proceeds to analyze the protocols for generating islets from stem cells. The review also outlines various techniques used in crafting artificial islets, with a specific focus on hydrogel-based ones. Additionally, it provides a concise overview of the materials and devices employed in the clinical applications of artificial islets. Throughout, the primary goal is to develop artificial islets, thereby bridging the realms of developmental biology, clinical medicine, and tissue engineering.

Using senior undergraduate students as coaches in an introductory chemical engineering design course

Senior undergraduate students were hired as Teaching Assistants (TAs) in CHBE 221, an introductory bioprocess design course offered in the Department of Chemical and Biological Engineering at University of British Columbia, and the roles were recast from traditional course support, to being coaches and mentors to a small number of teams working on term-spanning design projects. This was done as a means to provide more personalized support to students working on realistic design problems early in their training, leverage the benefits of peer learning strategies, and provide professional and leadership development opportunities to the TAs ahead of graduation. At the end of the course in which this was implemented, surveys were sent to students asking them to comment on their experience with this mentorship model, and the TAs of the course were interviewed to better understand theirs. This paper presents the results of these surveys and interviews, highlights the benefits and challenges of this approach, and provides recommendations for future implementations of this student support model

Why death and aging ? All memories are imperfect

Recent papers have emphasized the primary role of cellular information management in biological and evolutionary development. In this framework, intelligent cells collectively measure environmental cues to improve informational validity to support natural cellular engineering as collaborative decision-making and problem-solving in confrontation with environmental stresses. These collective actions are crucially dependent on cell-based memories as acquired patterns of response to environmental stressors. Notably, in a cellular self-referential framework, all biological information is ambiguous. This conditional requirement imposes a previously unexplored derivative. All cellular memories are imperfect. From this atypical background, a novel theory of aging and death is proposed. Since cellular decision-making is memory-dependent and biology is a continuous natural learning system, the accumulation of previously acquired imperfect memories eventually overwhelms the flexibility cells require to react adroitly to contemporaneous stresses to support continued cellular homeorhetic balance. The result is a gradual breakdown of the critical ability to efficiently measure environmental information and effect cell-cell communication. This age-dependent accretion governs senescence, ultimately ending in death as an organism-wide failure of cellular networking. This approach to aging and death is compatible with all prior theories. Each earlier approach illuminates different pertinent cellular signatures of this ongoing, obliged, living process.

Transcriptomic Insights into Metabolism-Dependent Biosynthesis of Bacterial Nanocellulose.

Bacterial nanocellulose (BNC) is an attractive green-synthesized biomaterial for biomedical applications and various other applications. However, effective engineering of BNC production has been limited by our poor knowledge of the related metabolic processes. In contrast to the traditional perception that genome critically determines biosynthesis behaviors, here we discover that the glucose metabolism could also drastically affect the BNC synthesis in Gluconacetobacter hansenii. The transcriptomic profiles of two model BNC-producing strains, G. hansenii ATCC 53582 and ATCC 23769, which have highly similar genomes but drastically different BNC yields, were compared. The results show that their BNC synthesis capacities were highly related to metabolic activities such as ATP synthesis, ion transport protein assembly, and carbohydrate metabolic processes, confirming an important role of metabolism-related transcriptomes in governing the BNC yield. Our findings provide insights into the microbial biosynthesis behaviors from a transcriptome perspective, potentially guiding cellular engineering for biomaterial synthesis.

Specific codons control cellular resources and fitness.

As cellular engineering progresses from simply overexpressing proteins to imparting complex phenotypes through multigene expression, judicious appropriation of cellular resources is essential. Since codon use is degenerate and biased, codons may control cellular resources at a translational level. We investigate how partitioning transfer RNA (tRNA) resources by incorporating dissimilar codon usage can drastically alter interdependence of expression level and burden on the host. By isolating the effect of individual codons' use during translation elongation while eliminating confounding factors, we show that codon choice can trans-regulate fitness of the host and expression of other heterologous or native genes. We correlate specific codon usage patterns with host fitness and derive a coding scheme for multigene expression called the Codon Health Index (CHI, χ). This empirically derived coding scheme (χ) enables the design of multigene expression systems that avoid catastrophic cellular burden and is robust across several proteins and conditions.

Inaugural Editorial

It is a great pleasure for me to provide an editorial commentary for the first edition of the recently established Journal of Optics and Photonics Research (JOPR). Greetings and salutations to all of you on the inaugural issue of JOPR, a new and exciting portfolio journal from Bon View Publishing, which focuses on cutting-edge research trends in optics and photonics. The journal features international peer-reviewed multidisciplinary papers that provide new and original insights to the field, while maintaining accuracy in theory and technology. We are committed to ensuring that every accepted article meets these standards. Being the Editor-in-Chief of JOPR is an honor and a source of great gratitude for me. The fields of optics and photonics are primarily concerned with the study of light, its creation, and manipulation, as well as its interactions with gases, plasmas, molecules, and solids, including micro- and nanostructures. The optical domain of ultraviolet, visible, and infrared light is much surpassed by the electromagnetic spectrum covered by optics and photonics. Researchers from physics, chemical and biological engineering, electronic and electrical engineering, and other fields are involved in this highly multidisciplinary topic. JOPR draws on both theoretical and practical results in the field of optical science and engineering, without being limited to any one discipline. It is committed to a wide spectrum of fundamental and applied optical research and brings scientists from many domains together. We encourage authors to conduct interdisciplinary research through the application of reasonable modeling or computational methods and experimental analysis. My goal for JOPR is to create a premier, open-access, highly peer-reviewed platform whose goal is to publish the most significant research in photonics and optics. I'm appreciative of the community's tremendous support in assisting us in achieving this objective.

Accounting for Climate Change in Rainfall Intensity-Duration-Frequency (IDF) Curves for Stormwater Management

This publication is meant to describe three major approaches to account for climate change in rainfall intensity-duration-frequency (IDF) curves and the pros and cons of each approach. This document aims to provide information to practicing engineers, Extension agents, and others interested in how projected changes in rainfall patterns can be considered for water resources management. Written by Christopher J. Martinez, Young Gu Her, and Eban Bean, and published by the UF/IFAS Department of Agricultural and Biological Engineering, January 2024.

WebODM: An Open-Source Alternative to Commercial Image Stitching Software for Uncrewed Aerial Systems

This publication aims to help UAS operators become familiar with advanced data processing tools integrated into the WebODM FOSS. The central aim of this publication is to underscore the process and sequence involved in producing data and outcomes by acquainting users with the fundamental features of WebODM. Written by Sahaj Patel, Jesse Chintanadilok, Brittany Hall-Scharf, Yilin Zhuang, Joseph Strickland, and Aditya Singh, and published by the UF/IFAS Department of Agricultural and Biological Engineering, February 2024.

Buckling behavior of soft spherical shells with patterned surface under indentation

A well understanding of instability mechanics of soft shell structures is key issue due to its important implications in functional shape morphing, flexible electronics, soft robotics, nanotechnology, biological engineering, etc. Despite abundant studies, buckling analysis of flexible shells with patterned surface under indentation is rare, primarily because of the complexities of high nonlinearities in geometry, material, and surface contact. In this paper, buckling behavior of spherical shells with patterned surface under indentation is comprehensively investigated by using experimental, numerical and theoretical analyses. It is found shells with stripes show similar variation in the force-displacement curves and post-buckling morphologies like perfect shells. Unlike perfect ones, shells with discontinuous protrusions exhibit multiple snap-through due to local buckling under indentation. What is more, mechanical response and buckling morphology can be well controlled by tuning shell thickness as well as positions and sizes of protrusions. These results can not only deepen understanding of mechanism of spherical shell buckling under local loads, but also provide a designing guidance for flexible electronics, soft robotics, and other future devices.

RETRACTED: Cellular functions of spermatogonial stem cells in relation to JAK/STAT signaling pathway

This manuscript comprehensively reviews the interrelationship between spermatogonial stem cells (SSCs) and the JAK/STAT signaling pathway. Spermatogonial stem cells in the testes of male mammals, characterized by their self-renewal and pluripotential differentiation capabilities, are essential for tissue regeneration, immunomodulation, and advancements in regenerative medicine. This review delves into the historical background and biological characteristics of SSCs, with a particular emphasis on the pivotal role of the JAK/STAT signaling pathway in their proliferation, maturation, and differentiation processes. Research indicates that the JAK/STAT pathway extensively influences various functionalities of spermatogonial stem cells, encompassing immunomodulation, tissue differentiation, homing, and adaptation to the microenvironment. Herein, we collate and dissect related studies, shedding light on the intricate dynamics between SSCs and the JAK/STAT signaling pathway, and examine the implications of these interactions on the biological attributes and functionalities of SSCs. Furthermore, the review discusses the profound implications of these findings for preclinical research and the domain of cellular engineering. It is acknowledged that, despite advancements in the research of SSCs and the JAK/STAT signaling pathway, investigations in humans and larger mammals remain inadequate, necessitating more in-depth exploration to establish a comprehensive theoretical framework. Overall, this review offers an invaluable reference for deciphering the mechanisms of the spermatogonial stem cell signaling pathways and establishes a theoretical groundwork for related preclinical research.

Roadway Safety: Logging Truck-Related Crashes in Florida

This report summarizes logging truck-related crashes in Florida. It discusses crash characteristics, vehicles, traffic violations, injuries, key findings, and recommendations for safety. Written by Serap Gorucu, Madison Moore, and Nikolay Bliznyuk, and published by the UF/IFAS Department of Agricultural and Biological Engineering, February 2024.