Bioengineering — Open Access Journal

A novel horizontally aligned single-walled carbon nanotube (CNT) Field Effect Transistor (FET)-based biosensing platform for real-time and sensitive protein detections is proposed. Aligned nanotubes were synthesized on quartz substrate using catalyst contact stamping, surface-guided morphological growth and chemical vapor deposition gas-guided growth methods. Real-time detection of prostate-specific antigen (PSA) using as-prepared FET biosensors was demonstrated. The kinetic measurements of the biosensor revealed that the drain current (I_d) decreased exponentially as the concentration of PSA increased, indicating that the proposed FET sensor is capable of quantitative protein detection within a detection window of up to 1 µM. The limit of detection (LOD) achieved by the proposed platform was demonstrated to be 84 pM, which is lower than the clinically relevant level (133 pM) of PSA in blood. Additionally, the reported aligned CNT biosensor is a uniform sensing platform that could be extended to real-time detections of various biomarkers. Full article

Biomedical signals carry valuable physiological information and many researchers have difficulty interpreting and analyzing long-term, one-dimensional, quasi-periodic biomedical signals. Traditionally, biomedical signals are analyzed and visualized using periodogram, spectrogram, and wavelet methods. However, these methods do not offer an informative visualization of main events within the processed signal. This paper attempts to provide an event-related framework to overcome the drawbacks of the traditional visualization methods and describe the main events within the biomedical signal in terms of duration and morphology. Electrocardiogram and photoplethysmogram signals are used in the analysis to demonstrate the differences between the traditional visualization methods, and their performance is compared against the proposed method, referred to as the “eventogram” in this paper. The proposed method is based on two event-related moving averages that visualizes the main time-domain events in the processed biomedical signals. The traditional visualization methods were unable to find dominant events in processed signals while the eventogram was able to visualize dominant events in signals in terms of duration and morphology. Moreover, eventogram-based detection algorithms succeeded with detecting main events in different biomedical signals with a sensitivity and positive predictivity >95%. The output of the eventogram captured unique patterns and signatures of physiological events, which could be used to visualize and identify abnormal waveforms in any quasi-periodic signal. Full article

A photoplethysmogram (PPG) is a noninvasive circulatory signal related to the pulsatile volume of blood in tissue and is typically collected by pulse oximeters. PPG signals collected via mobile devices are prone to artifacts that negatively impact measurement accuracy, which can lead to a significant number of misleading diagnoses. Given the rapidly increased use of mobile devices to collect PPG signals, developing an optimal signal quality index (SQI) is essential to classify the signal quality from these devices. Eight SQIs were developed and tested based on: perfusion, kurtosis, skewness, relative power, non-stationarity, zero crossing, entropy, and the matching of systolic wave detectors. Two independent annotators annotated all PPG data (106 recordings, 60 s each) and a third expert conducted the adjudication of differences. The independent annotators labeled each PPG signal with one of the following labels: excellent, acceptable or unfit for diagnosis. All indices were compared using Mahalanobis distance, linear discriminant analysis, quadratic discriminant analysis, and support vector machine with leave-one-out cross-validation. The skewness index outperformed the other seven indices in differentiating between excellent PPG and acceptable, acceptable combined with unfit, and unfit recordings, with overall $F_1$ scores of 86.0%, 87.2%, and 79.1%, respectively. Full article

Biological signals such as electrocardiogram (ECG) and electromyography (EMG) that can be measured at home can reveal vital information about the patient’s health. In today modern technology, the measured ECG or EMG signals at home can be monitored by medical staff from long distance through the use of internet. Biopotential electrodes are crucial in monitoring ECG, EMG, etc., signals. Applying the right type of electrode that lasts for a long time and assists in recording high signal quality is desirable in medical devices industry. Three types of electrodes (Silver/Silver Chloride (Ag/AgCl) electrodes, Orbital electrodes and Stainless steel electrodes) were tested to identify the most appropriate one for recording biological signals. The evaluation was based on determining the electrode circuit model components and having high capacitance value or high capacitor value of electrode circuit model (C_d) and low electrode-skin impedance value or low resistor value of electrode circuit model (R_d). The results revealed that Ag/AgCl is the best type of electrodes, followed by Orbital electrodes. Stainless steel electrodes had performed poorly. However, Orbital electrodes material can last longer than Ag/AgCl and hence perform similar to Ag/AgCl electrodes, which can be idle for monitoring biological signals at home without the need for medical staff to replace the electrodes in a short period of time. Full article

Streptomyces thermoviolaceus NT1, an endophytic isolate, was studied for optimization of granaticinic acid production. It is an antimicrobial metabolite active against even drug resistant bacteria. Different media, optimum glucose concentration, initial media pH, incubation temperature, incubation period, and inoculum size were among the selected parameters optimized in the one-variable-at-a-time (OVAT) approach, where glucose concentration, pH, and temperature were found to play a critical role in antibiotic production by this strain. Finally, the Box–Behnken experimental design (BBD) was employed with three key factors (selected after OVAT studies) for response surface methodological (RSM) analysis of this optimization study.RSM analysis revealed a multifactorial combination; glucose 0.38%, pH 7.02, and temperature 36.53 °C as the optimum conditions for maximum antimicrobial yield. Experimental verification of model analysis led to 3.30-fold (61.35 mg/L as compared to 18.64 mg/L produced in un-optimized condition) enhanced granaticinic acid production in ISP2 medium with 5% inoculum and a suitable incubation period of 10 days. So, the conjugated optimization study for maximum antibiotic production from Streptomyces thermoviolaceus NT1 was found to result in significantly higher yield, which might be exploited in industrial applications. Full article

Parkinson’s patients suffer from severe tremor due to an abnormality in their central oscillator. Medications used to decrease involuntary antagonistic muscles contraction can threaten their life. However, mechanical vibration absorbers can be used as an alternative treatment. The objective of this study is to provide a dynamic modeling of the human hand that describes the biodynamic response of Parkinson’s patients and to design an effective tuned vibration absorber able to suppress their pathological tremor. The hand is modeled as a three degrees-of-freedom (DOF) system describing the flexion motion at the proximal joints on the horizontal plane. Resting tremor is modeled as dual harmonic excitation due to shoulder and elbow muscle activation operating at resonance frequencies. The performance of the single dynamic vibration absorber (DVA) is studied when attached to the forearm and compared with the dual DVA tuned at both excitation frequencies. Equations of motion are derived and solved using the complex transfer function of the non-Lagrangian system. The absorber’s systems are designed as a stainless steel alloy cantilevered beam with an attached copper mass. The dual DVA was the most efficient absorber which reduces 98.3%–99.5%, 97.0%–97.3% and 97.4%–97.5% of the Parkinson’s tremor amplitude at the shoulder, elbow and wrist joint. Full article

Pepsin was used to effectively degrade chitosan in order to make it more useful in biotechnological applications. The optimal conditions of enzymolysis were investigated on the basis of the response surface methodology (RSM). The structure of the degraded product was characterized by degree of depolymerization (DD), viscosity, molecular weight, FTIR, UV-VIS, SEM and polydispersity index analyses. The mechanism of chitosan degradation was correlated with cleavage of the glycosidic bond, whereby the chain of chitosan macromolecules was broken into smaller units, resulting in decreasing viscosity. The enzymolysis by pepsin was therefore a potentially applicable technique for the production of low molecular chitosan. Additionally, the substrate degradation kinetics of chitosan were also studied over a range of initial chitosan concentrations (3.0~18.0 g/L) in order to study the characteristics of chitosan degradation. The dependence of the rate of chitosan degradation on the concentration of the chitosan can be described by Haldane’s model. In this model, the initial chitosan concentration above which the pepsin undergoes inhibition is inferred theoretically to be about 10.5 g/L. Full article

Deep drying and torrefaction compose a thermal pretreatment method where biomass is heated in the temperature range of 150–300 °C in an inert or reduced environment. The process parameters, like torrefaction temperature and residence time, have a significant impact on the proximate, ultimate, and energy properties. In this study, torrefaction experiments were conducted on 2-mm ground lodgepole pine (Pinus contorta) using a thermogravimetric analyzer. Both deep drying and torrefaction temperature (160–270 °C) and time (15–120 min) were selected. Torrefied samples were analyzed for the proximate, ultimate, and higher heating value. The results indicate that moisture content decreases with increases in torrefaction temperature and time, where at 270 °C and 120 min, the moisture content is found to be 1.15% (w.b.). Volatile content in the lodgepole pine decreased from about 80% to about 45%, and ash content increased from 0.77% to about 1.91% at 270 °C and 120 min. The hydrogen, oxygen, and sulfur content decreased to 3%, 28.24%, and 0.01%, whereas the carbon content and higher heating value increased to 68.86% and 23.67 MJ/kg at 270 °C and 120 min. Elemental ratio of hydrogen to carbon and oxygen to carbon (H/C and O/C) calculated at 270 °C and a 120-min residence time were about 0.56 and 0.47. Based on this study, it can be concluded that higher torrefaction temperatures ≥230 °C and residence time ≥15 min influence the proximate, ultimate, and energy properties of ground lodgepole pine. Full article

During advanced biological wastewater treatment, a huge amount of sludge is produced as a by-product of the treatment process. Hence, reuse and recovery of resources and energy from the sludge is a big technological challenge. The processing of sludge produced by Wastewater Treatment Plants (WWTPs) is massive, which takes up a big part of the overall operational costs. In this regard, anaerobic digestion (AD) of sewage sludge continues to be an attractive option to produce biogas that could contribute to the wastewater management cost reduction and foster the sustainability of those WWTPs. At the same time, AD reduces sludge amounts and that again contributes to the reduction of the sludge disposal costs. However, sludge volume minimization remains, a challenge thus improvement of dewatering efficiency is an inevitable part of WWTP operation. As a result, AD parameters could have significant impact on sludge properties. One of the most important operational parameters influencing the AD process is temperature. Consequently, the thermophilic and the mesophilic modes of sludge AD are compared for their pros and cons by many researchers. However, most comparisons are more focused on biogas yield, process speed and stability. Regarding the biogas yield, thermophilic sludge AD is preferred over the mesophilic one because of its faster biochemical reaction rate. Equally important but not studied sufficiently until now was the influence of temperature on the digestate quality, which is expressed mainly by the sludge dewateringability, and the reject water quality (chemical oxygen demand, ammonia nitrogen, and pH). In the field of comparison of thermophilic and mesophilic digestion process, few and often inconclusive research, unfortunately, has been published so far. Hence, recommendations for optimized technologies have not yet been done. The review presented provides a comparison of existing sludge AD technologies and the gaps that need to be filled so as to optimize the connection between the two systems. In addition, many other relevant AD process parameters, including sludge rheology, which need to be addressed, are also reviewed and presented. Full article

In this study, Aspergillus niger ADM110 fungi was gamma irradiated to produce lipase enzyme and then immobilized onto magnetic barium ferrite nanoparticles (BFN) for biodiesel production. BFN were prepared by the citrate sol-gel auto-combustion method and characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR) and scanning electron microscopy with energy dispersive analysis of X-ray (SEM/EDAX) analysis. The activities of free and immobilized lipase were measured at various pH and temperature values. The results indicate that BFN–Lipase (5%) can be reused in biodiesel production without any treatment with 17% loss of activity after five cycles and 66% loss in activity in the sixth cycle. The optimum reaction conditions for biodiesel production from waste cooking oil (WCO) using lipase immobilized onto BFN as a catalyst were 45 °C, 4 h and 400 rpm. Acid values of WCO and fatty acid methyl esters (FAMEs) were 1.90 and 0.182 (mg KOH/g oil), respectively. The measured flash point, calorific value and cetane number were 188 °C, 43.1 MJ/Kg and 59.5, respectively. The cloud point (−3 °C), pour point (−9 °C), water content (0.091%) and sulfur content (0.050%), were estimated as well. Full article

Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites. In most applications, the regulatory network structure is unknown, and has to be reverse engineered from experimental data consisting of expression levels of the genes usually measured as messenger RNA concentrations in microarray experiments. Steady-state gene expression data are obtained from measurements of the variations in expression activity following the application of small perturbations to equilibrium states in genetic perturbation experiments. In this paper, the least absolute shrinkage and selection operator-vector autoregressive (LASSO-VAR) originally proposed for the analysis of economic time series data is adapted to include a stability constraint for the recovery of a sparse and stable regulatory network that describes data obtained from noisy perturbation experiments. The approach is applied to real experimental data obtained for the SOS pathway in Escherichia coli and the cell cycle pathway for yeast Saccharomyces cerevisiae. Significant features of this method are the ability to recover networks without inputting prior knowledge of the network topology, and the ability to be efficiently applied to large scale networks due to the convex nature of the method. Full article

Screening and obtaining a novel high activity cellulase and its producing microbe strain is the most important and essential way to improve the utilization of crop straw. In this paper, we devoted our efforts to isolating a novel microbe strain which could produce high activity cellulase. A novel strain Trichoderma virens ZY-01 was isolated from a cropland where straw is rich and decomposed, by using the soil dilution plate method with cellulose and Congo red. The strain has been licensed with a patent numbered ZL 201210295819.6. The cellulase activity in the cultivation broth could reach up to 7.4 IU/mL at a non-optimized fermentation condition with the newly isolated T. virens ZY-01. The cellulase was separated and purified from the T. virens culture broth through (NH₄)₂SO₄ fractional precipitation, anion-exchange chromatography and gel filtration chromatography. With the separation process, the CMC specific activity increased from 0.88 IU/mg to 31.5 IU/mg with 35.8 purification fold and 47.04% yield. Furthermore, the enzymatic properties of the cellulase were investigated. The optimum temperature and pH is 50 °C and pH 5.0 and it has good thermal stability. Zn²⁺, Ca²⁺ and Mn²⁺ could remarkably promote the enzyme activity. Conversely, Cu²⁺ and Co²⁺ could inhibit the enzymatic activity. This work provides a new highly efficient T. virens strain for cellulase production and shows good prospects in practical application. Full article

The study of brain dynamics currently utilizes the new features of nanobiotechnology and bioengineering. New geometric and analytical approaches appear very promising in all scientific areas, particularly in the study of brain processes. Efforts to engage in deep comprehension lead to a change in the inner brain parameters, in order to mimic the external transformation by the proper use of sensors and effectors. This paper highlights some crossing research areas of natural computing, nanotechnology, and brain modeling and considers two interesting theoretical approaches related to brain dynamics: (a) the memory in neural network, not as a passive element for storing information, but integrated in the neural parameters as synaptic conductances; and (b) a new transport model based on analytical expressions of the most important transport parameters, which works from sub-pico-level to macro-level, able both to understand existing data and to give new predictions. Complex biological systems are highly dependent on the context, which suggests a “more nature-oriented” computational philosophy. Full article

Enterohemorrhagic Escherichia coli (EHEC) are responsible for large outbreaks of hemorrhagic colitis, which can progress to life-threatening hemolytic uremic syndrome (HUS) due to the release of Shiga-like toxins (Stx). The presence of a functional nitric oxide (NO·) reductase (NorV), which protects EHEC from NO· produced by immune cells, was previously found to correlate with high HUS incidence, and it was shown that NorV activity enabled prolonged EHEC survival and increased Stx production within macrophages. To enable quantitative study of EHEC NO· defenses and facilitate the development of NO·-potentiating therapeutics, we translated an existing kinetic model of the E. coli K-12 NO· response to an EHEC O157:H7 strain. To do this, we trained uncertain model parameters on measurements of [NO·] and [O₂] in EHEC cultures, assessed parametric and prediction uncertainty with the use of a Markov chain Monte Carlo approach, and confirmed the predictive accuracy of the model with experimental data from genetic mutants lacking NorV or Hmp (NO· dioxygenase). Collectively, these results establish a methodology for the translation of quantitative models of NO· stress in model organisms to pathogenic sub-species, which is a critical step toward the application of these models for the study of infectious disease. Full article

Co-utilization of carbon sources in microbes is an important topic in metabolic engineering research. It is not only a way to reduce microbial production costs but also an attempt for either improving the yields of target products or decreasing the formation of byproducts. However, there are barriers in co-utilization of carbon sources in microbes, such as carbon catabolite repression. To overcome the barriers, different metabolic engineering strategies have been developed, such as inactivation of the phosphotransferase system and rewiring carbon assimilation pathways. This review summarizes the most recent developments of different strategies that support microbes to utilize two or more carbon sources simultaneously. The main content focuses on the co-utilization of glucose and pentoses, major sugars in lignocellulose. Full article

Five institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on physical and chemical lysis with excellent extraction efficiency yielded highly reproducible results among the partners and clearly outperformed a traditional CTAB/chloroform/isoamylalcohol based method. Analytical purpose, sample texture, consistency and upstream pretreatment steps determine the modifications that should be applied to achieve maximum efficiency in the trade-off between extract purity and nucleic acid recovery rate. RNA extraction was much more variable, and the destination of the extract determines the method to be used. RNA stabilization with quaternary ammonium salts was an as satisfactory approach as flash freezing in liquid N₂. Due to co-eluted impurities, spectrophotometry proved to be of limited value for nucleic acid qualification and quantification in extracts obtained with the kit, and picoGreen^® based quantification was more trustworthy. Absorbance at 230 nm can be extremely high in the presence of certain chaotropic guanidine salts, but guanidinium isothiocyanate does not affect (q)PCR. Absolute quantification by qPCR requires application of a reliable internal standard for which correct PCR efficiency and Y-intercept values are important and must be reported. Full article

Biomass and cell-specific metabolic rates usually change dynamically over time, making the “feed according to need” strategy difficult to realize in a commercial fed-batch process. We here demonstrate a novel feeding strategy which is designed to hold a particular metabolic state in a fed-batch process by adaptive feeding in real time. The feed rate is calculated with a transferable biomass model based on capacitance, which changes the nutrient flow stoichiometrically in real time. A limited glucose environment was used to confine the cell in a particular metabolic state. In order to cope with uncertainty, two strategies were tested to change the adaptive feed rate and prevent starvation while in limitation: (i) inline pH and online glucose concentration measurement or (ii) inline pH alone, which was shown to be sufficient for the problem statement. In this contribution, we achieved metabolic control within a defined target range. The direct benefit was two-fold: the lactic acid profile was improved and pH could be kept stable. Multivariate Data Analysis (MVDA) has shown that pH influenced lactic acid production or consumption in historical data sets. We demonstrate that a low pH (around 6.8) is not required for our strategy, as glucose availability is already limiting the flux. On the contrary, we boosted glycolytic flux in glucose limitation by setting the pH to 7.4. This new approach led to a yield of lactic acid/glucose (Y L/G) around zero for the whole process time and high titers in our labs. We hypothesize that a higher carbon flux, resulting from a higher pH, may lead to more cells which produce more product. The relevance of this work aims at feeding mammalian cell cultures safely in limitation with a desired metabolic flux range. This resulted in extremely stable, low glucose levels, very robust pH profiles without acid/base interventions and a metabolic state in which lactic acid was consumed instead of being produced from day 1. With this contribution, we wish to extend the basic repertoire of available process control strategies, which will open up new avenues in automation technology and radically improve process robustness in both process development and manufacturing. Full article

Although most fractures heal, critical defects in bone fail due to aberrant differentiation of mesenchymal stem cells towards fibrosis rather than osteogenesis. While conventional bioengineering solutions to this problem have focused on enhancing angiogenesis, which is required for bone formation, recent studies have shown that fibrotic non-unions are associated with arteriogenesis in the center of the defect and accumulation of mast cells around large blood vessels. Recently, recombinant parathyroid hormone (rPTH; teriparatide; Forteo) therapy have shown to have anti-fibrotic effects on non-unions and critical bone defects due to inhibition of arteriogenesis and mast cell numbers within the healing bone. As this new direction holds great promise towards a solution for significant clinical hurdles in craniofacial reconstruction and limb salvage procedures, this work reviews the current state of the field, and provides insights as to how teriparatide therapy could be used as an adjuvant for healing critical defects in bone. Finally, as teriparatide therapy is contraindicated in the setting of cancer, which constitutes a large subset of these patients, we describe early findings of adjuvant therapies that may present future promise by directly inhibiting arteriogenesis and mast cell accumulation at the defect site. Full article

Patients with acute lung injury, airway and other pulmonary diseases often require Mechanical Ventilation (MV). Knowledge of the stress/strain environment in lung airway tissues is very important in order to avoid lung injuries for patients undergoing MV. Airway tissue strains responsible for stressing the lung’s fiber network and rupturing the lung due to compliant airways are very difficult to measure experimentally. Multi-level modeling is adopted to investigate the transient mechanical response of the tissue under MV. First, airflow through a lung airway bifurcation (Generation 4–6) is modeled using Computational Fluid Dynamics (CFD) to obtain air pressure during 2 seconds of MV breathing. Next, the transient air pressure was used in structural analysis to obtain mechanical strain experienced by the airway tissue wall. Structural analysis showed that airway tissue from Generation 5 in one bifurcation can stretch eight times that of airway tissue of the same generation number but with different bifurcation. The results suggest sensitivity of load to geometrical features. Furthermore, the results of strain levels obtained from the tissue analysis are very important because these strains at the cellular-level can create inflammatory responses, thus damaging the airway tissues. Full article