Journal of Biological Engineering

Cordyceps sobolifera (C. sobolifera) isolated from cicadae was used as the starting fungus to produce selenium-enriched C. sobolifera extracellular polysaccharide (Se-CEPS). An orthogonal experimental design based on a single-factor experiment was used to optimize the C. sobolifera fermentation conditions, including the potato juice, peptone, and KH2PO4 concentrations. Ultraviolet (UV) and infrared (IR) analyses of CEPS and Se-CEPS were conducted, as well as an in vivo anti-tumor analysis. Under optimal conditions (i.e., 40 potato juice, 0.4 KH2PO4, and 0.5 % peptone), the fermentation yield of Se-CEPS was 5.64 g/L. UV and IR spectra showed that Se-CEPS contained a characteristic absorption peak of a selenite Se = O double bond, demonstrating the successful preparation of Se-CEPS. Activity tests showed that Se-CEPS improved the immune organ index, serum cytokine content, and CD8+ and CD4+ T lymphocyte ratio in colon cancer CT26 tumor-bearing mice, thereby inhibiting tumor growth. When combined with 5-FU, Se-CEPS reduced the toxicity and enhanced the function of 5-FU. The result of these experiments indicated that orthogonal experimental design is a promising method for the optimization of Se-CEPS production, and the Se-CEPS from C. sobolifera can improve the anti-tumor capacity of mice.

Tumor numerical models have been used to quantify solute transport with a single capillary embedded in an infinite tumor expanse, but measurements from different mammalian tumors suggest that a tissue containing a single capillary with an infinite intercapillary distance assumption is not physiological. The present study aims to investigate the limits of the intercapillary distance within which nanoparticle transport resembles solute extravasation in a breast tumor model as a function of the solute size, the intercapillary separation, and the flow direction in microvessels. Solute transport is modeled in a breast tumor for different vascular configurations using mixture theory. A comparison of a single capillary configuration (SBC) with two parallel cylindrical blood vessels (2 BC) and a lymph vessel parallel to a blood vessel (BC_LC) embedded in the tissue cylinder is performed for five solute molecular weights between 0.1 kDa and 70 kDa. The effects of counter flow (CN) versus co-current flow (CO) on the solute accumulation were also investigated and the scaling of solute accumulation-decay time and concentration was explored. We found that the presence of a second capillary reduces the extravascular concentration compared to a single capillary and this reduction is enhanced by the presence of a lymph vessel. Varying the intercapillary distance with respect to vessel diameter shows a deviation of 10–30% concentration for 2 BC and 45–60% concentration for BC_LC configuration compared to the reference SBC configuration. Finally, we introduce a non-dimensional time scale that captures the concentration as a function of the transport and geometric parameters. We find that the peak solute concentration in the tissue space occurs at a non-dimensional time, $$ {T}_{peak}^{\ast } $$ = 0.027 ± 0.018, irrespective of the solute size, tissue architecture, and microvessel flow direction. This work suggests that the knowledge of such a unique non-dimensional time would allow estimation of the time window at which solute concentration in tissue peaks. Hence this can aid in the design of future therapeutic efficacy studies as an example for triggering drug release or laser excitation in the case of photothermal therapies.

Biofilters are soil-plant based passive stormwater treatment systems which demonstrate promising, although inconsistent, removal of faecal microorganisms. Antimicrobial-producing plants represent a safe, inexpensive yet under-researched biofilter design component that may enhance treatment reliability. The mechanisms underlying plant-mediated microbial removal in biofilters have not been fully elucidated, particularly with respect to antimicrobial production. The aim of this study was therefore to inform biofilter vegetation selection guidelines for optimal pathogen treatment by conducting antimicrobial screening of biofilter-suitable plant species. This involved: (1) selecting native plants suitable for biofilters (17 species) in a Victorian context (southeast Australia); and (2) conducting antimicrobial susceptibility testing of selected plant methanolic extracts (≥ 5 biological replicates/species; 86 total) against reference stormwater faecal bacteria (Salmonella enterica subsp. enterica ser. Typhimurium, Enterococcus faecalis and Escherichia coli). The present study represents the first report on the inhibitory activity of polar alcoholic extracts from multiple tested species. Extracts of plants in the Myrtaceae family, reputed for their production of antimicrobial oils, demonstrated significantly lower minimum inhibitory concentrations (MICs) than non-myrtaceous candidates (p < 0.0001). Melaleuca fulgens (median MIC: 8 mg/mL; range: [4–16 mg/mL]), Callistemon viminalis (16 mg/mL, [2–16 mg/mL]) and Leptospermum lanigerum (8 mg/mL, [4–16 mg/mL]) exhibited the strongest inhibitory activity against the selected bacteria (p < 0.05 compared to each tested non-myrtaceous candidate). In contrast, the Australian biofilter gold standard Carex appressa demonstrated eight-fold lower activity than the highest performer M. fulgens (64 mg/mL, [32–64 mg/mL]). Our results suggest that myrtaceous plants, particularly M. fulgens, may be more effective than the current vegetation gold standard in mediating antibiosis and thus improving pathogen treatment within biofilters. Further investigation of these plants in biofilter contexts is recommended to refine biofilter vegetation selection guidelines.

The Covid-19 pandemic caused a sudden shift towards remote learning, moving classes to online formats. Not exempt from this switch, laboratory courses traditionally taught in-person were also moved to remote methods, costing students the opportunity to learn these skills hands-on. In order for instructors to provide course materials effectively and engagingly, non-traditional methods should be explored. Virtual reality (VR) has become more accessible in recent years. VR simulations have been used for many years as educational tools in high-risk settings such as flight or medical simulations. Immersive VR videos implemented in a remote laboratory course could provide the students with an engaging and suitable learning experience. To test the effectiveness of VR videos as a tool for remote education, VR videos of the laboratory component of a Biomolecular Engineering course were provided to students. A survey was distributed for students to self-report their experience with the videos. The survey contained quantitative and qualitative ratings of VR as an educational tool. The survey showed that students (~ 89% strongly agree or agree) believed the videos provided the opportunity to work at their own pace and were an appropriate length. While ~ 74% of students said that the videos provided enough information to understand the tasks, a small percentage felt that the videos improved their retention (~ 16%) and understanding (~ 9%) of the course material. About 28% of the students responded positively when asked about how VR videos improved their engagement with the material. ~ 30% reported confidence in applying the skills learned in the videos in the future and ~ 43% believe the VR videos were an acceptable alternative to in-person labs. Two-thirds of students reported feeling some form of discomfort while viewing the VR videos and 54% reported not using the headset for the videos and using the 3D video feature instead. As many students reported the videos containing appropriate information, the content of the videos was not an issue. A combination of improved camera quality with motion stability, more comfortable headsets, and a reduction in editing issues could greatly improve the quality and effectiveness of VR videos.

Molecular rotors are a group of fluorescent molecules that form twisted intramolecular charge transfer (TICT) states upon photoexcitation. When intramolecular twisting occurs, the molecular rotor returns to the ground state either by emission of a red-shifted emission band or by nonradiative relaxation. The emission properties are strongly solvent-dependent, and the solvent viscosity is the primary determinant of the fluorescent quantum yield from the planar (non-twisted) conformation. This viscosity-sensitive behavior gives rise to applications in, for example, fluid mechanics, polymer chemistry, cell physiology, and the food sciences. However, the relationship between bulk viscosity and the molecular-scale interaction of a molecular rotor with its environment are not fully understood. This review presents the pertinent theories of the rotor-solvent interaction on the molecular level and how this interaction leads to the viscosity-sensitive behavior. Furthermore, current applications of molecular rotors as microviscosity sensors are reviewed, and engineering aspects are presented on how measurement accuracy and precision can be improved.

Synthesis of a variety of biological circuits for specific functional purposes has made a tremendous progress in recent years. The ultimate goal of combining molecular biology and engineering is to realize a functional biocomputer. To address this challenge, all previous efforts work toward building up the bio-computer as the ultimate goal. To this aim, there should be a key module, named control unit (CU), to direct a serious of logic or arithmetic operations within the processor. This research task develops a bio-CU to work with a bio-ALU, which is realized from the combination of previously developed genetic logic gates to fulfill the kernel function of CPU as those done in the silicon computer. A possible framework of the bio-CPU has demonstrated how to connect a bio-CU with a bio-ALU to conduct a fetch-decode-execute cycle of a macro instruction. It presents not only capability of 4-bit full adder but coordination of related modules in biocomputer. We have demonstrated computer simulation for applications of the genetic circuits in biocomputer construction. It’s expected to inspire follow-up study to synthesize potential configurations of the future biocomputer.

Needle-free, painless and localized drug delivery has been a coveted technology in the area of biomedical research. We present an innovative way of trans-dermal vaccine delivery using a miniature detonation-driven shock tube device. This device utilizes~2.5 bar of in situ generated oxyhydrogen mixture to produce a strong shockwave that accelerates liquid jets to velocities of about 94 m/s. Oxyhydrogen driven shock tube was optimized for efficiently delivering vaccines in the intradermal region in vivo. Efficiency of vaccination was evaluated by pathogen challenge and host immune response. Expression levels of molecular markers were checked by qRT-PCR. High efficiency vaccination was achieved using the device. Post pathogen challenge with Mycobacterium tuberculosis, 100% survival was observed in vaccinated animals. Immune response to vaccination was significantly higher in the animals vaccinated using the device as compared to conventional route of vaccination. A novel device was developed and optimized for intra dermal vaccine delivery in murine model. Conventional as well in-house developed vaccine strains were used to test the system. It was found that the vaccine delivery and immune response was at par with the conventional routes of vaccination. Thus, the device reported can be used for delivering live attenuated vaccines in the future.

More than five million Americans suffer from heart valve disease annually, a condition that worsens cardiac function and gradually leads to heart failure if appropriate treatment is not performed on time. Currently no medication can cure heart valve disease, leaving surgical intervention as the only viable option for patients at late stages of cardiac valve disease. Tremendous efforts have been undertaken to elucidate how resident cells in the valves respond to pathological stimulation as well as the underlying mechanisms that regulate these responses, to identify potential therapeutic targets for non-surgical treatment of valvular heart disease. Cardiac valve interstitial cells (VICs) naturally reside in a complex three-dimensional environment under varying hemodynamics, which is difficult to replicate in vitro. As a result, most cell signaling studies in the field have traditionally been conducted on two-dimensional models or in the absence of hemodynamic forces. Previously, we reported the fabrication of a hydrogel scaffold that could be used to culture valve cells under dynamic mechanical stimulation in a valve-mimetic environment. This model, therefore appeared to be suitable for VIC signaling studies as it provided cells a three-dimensional environment with the ability to incorporate mechanical stretching stimulation. Utilizing this model, we investigated the possible role of fibroblast growth factor 1 and 2 (FGF1 and FGF2) via FGFR1 receptor signaling in regulating valve cell activation under physiological (10% stretch) and pathological (20% stretch) mechanical conditions as well as in mediating cell proliferation and metabolism via the Akt/mTOR pathways. We reported that 1) FGF1 and FGF2 treatment was able to maintain the quiescent phenotype of VICs; 2) Cells increased proliferation as determined by optical redox ratios under elevated cyclic stretch via Akt/mTOR pathways; and 3) FGF1 and 2 signaling via the FGFR1 reduced VIC proliferation and activation under elevated cyclic stretch conditions. Overall, these results suggested that targeting FGFR1 receptor signaling may represent a possible therapeutic strategy for preventing heart valve disease progression.

Biotechnological screening processes are performed since more than 8 decades in small scale shaken bioreactors like shake flasks or microtiter plates. One of the major issues of such reactors is the sufficient oxygen supply of suspended microorganisms. Oxygen transfer into the bulk liquid can in general be increased by introducing suitable baffles at the reactor wall. However, a comprehensive and systematic characterization of baffled shaken bioreactors has never been carried out so far. Baffles often differ in number, size and shape. The exact geometry of baffles in glass lab ware like shake flasks is very difficult to reproduce from piece to piece due to the hard to control flow behavior of molten glass during manufacturing. Thus, reproducibility of the maximum oxygen transfer capacity in such baffled shake flasks is hardly given. As a first step to systematically elucidate the general effect of different baffle geometries on shaken bioreactor performance, the maximum oxygen transfer capacity (OTRmax) in baffled 48-well microtiter plates as shaken model reactor was characterized. This type of bioreactor made of plastic material was chosen, as the exact geometry of the baffles can be fabricated by highly reproducible laser cutting. As a result, thirty different geometries were investigated regarding their maximum oxygen transfer capacity (OTRmax) and liquid distribution during shaking. The relative perimeter of the cross-section area as new fundamental geometric key parameter is introduced. An empirical correlation for the OTRmax as function of the relative perimeter, shaking frequency and filling volume is derived. For the first time, this correlation allows a systematic description of the maximum oxygen transfer capacity in baffled microtiter plates. Calculated and experimentally determined OTRmax values agree within ± 30% accuracy. Furthermore, undesired out-of-phase operating conditions can be identified by using the relative perimeter as key parameter. Finally, an optimum well geometry characterized by an increased perimeter of 10% compared to the unbaffled round geometry is identified. This study may also assist to comprehensively describe and optimize the baffles of shake flasks in future.

Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.