Journal of Biological Engineering
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Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory
Journal of Biological Engineering - Tập 11 - Trang 1-9 - 2017
Electronic lab notebooks (ELNs) are better equipped than paper lab notebooks (PLNs) to handle present-day life science and engineering experiments that generate large data sets and require high levels of data integrity. But limited training and a lack of workforce with ELN knowledge have restricted the use of ELN in academic and industry research laboratories which still rely on cumbersome PLNs for recordkeeping. We used LabArchives, a cloud-based ELN in our bioprocess engineering lab course to train students in electronic record keeping, good documentation practices (GDPs), and data integrity. Implementation of ELN in the bioprocess engineering lab course, an analysis of user experiences, and our development actions to improve ELN training are presented here. ELN improved pedagogy and learning outcomes of the lab course through stream lined workflow, quick data recording and archiving, and enhanced data sharing and collaboration. It also enabled superior data integrity, simplified information exchange, and allowed real-time and remote monitoring of experiments. Several attributes related to positive user experiences of ELN improved between the two subsequent years in which ELN was offered. Student responses also indicate that ELN is better than PLN for compliance. We demonstrated that ELN can be successfully implemented in a lab course with significant benefits to pedagogy, GDP training, and data integrity. The methods and processes presented here for ELN implementation can be adapted to many types of laboratory experiments.
Optimizing the fabrication of a 3D high-resolution implant for neural stimulation
Journal of Biological Engineering - Tập 17 - Trang 1-16 - 2023
Tissue-integrated micro-electronic devices for neural stimulation hold great potential in restoring the functionality of degenerated organs, specifically, retinal prostheses, which are aimed at vision restoration. The fabrication process of 3D polymer-metal devices with high resolution and a high aspect-ratio (AR) is very complex and faces many challenges that impair its functionality. Here we describe the optimization of the fabrication process of a bio-functionalized 3D high-resolution 1mm circular subretinal implant composed of SU-8 polymer integrated with dense gold microelectrodes (23μm pitch) passivated with 3D micro-well-like structures (20μm diameter, 3μm resolution). The main challenges were overcome by step-by-step planning and optimization while utilizing a two-step bi-layer lift-off process; bio-functionalization was carried out by N2 plasma treatment and the addition of a bio-adhesion molecule. In-vitro and in-vivo investigations, including SEM and FIB cross section examinations, revealed a good structural design, as well as a good long-term integration of the device in the rat sub-retinal space and cell migration into the wells. Moreover, the feasibility of subretinal neural stimulation using the fabricated device was demonstrated in-vitro by electrical activation of rat’s retina. The reported process and optimization steps described here in detail can aid in designing and fabricating retinal prosthetic devices or similar neural implants.
Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway
Journal of Biological Engineering - Tập 13 - Trang 1-10 - 2019
The automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. To manage the design of genetic pathways, researchers have turned to modelling-based computer aided design software tools. An automated workflow has been developed for the design and build of heterologous metabolic pathways. In addition, to demonstrate the powers of electronic datasheets we have developed software which can transfer part information from a datasheet to the Design of Experiment software JMP. To this end we were able to use Design of Experiment software to rationally design and test randomised samples from the design space of a lycopene pathway in E. coli. This pathway was optimised by individually modulating the promoter strength, RBS strength, and gene order targets. The use of standardised and characterised biological parts will empower a design-oriented synthetic biology for the forward engineering of heterologous expression systems. A Design of Experiment approach streamlines the design-build-test cycle to achieve optimised solutions in biodesign. Developed automated workflows provide effective transfer of information between characterised information (in the form of datasheets) and DoE software.
An innovative lab-scale production for a novel therapeutic DNA vaccine candidate against rheumatoid arthritis
Journal of Biological Engineering - - 2024
Recent therapeutic-plasmid DNA vaccine strategies for rheumatoid arthritis (RA) have significantly improved. Our pcDNA-CCOL2A1 vaccine is the most prominent and the first antigen-specific tolerising DNA vaccine with potent therapeutic and prophylactic effects compared with methotrexate (MTX), the current “gold standard” treatment for collagen-induced arthritis (CIA). This study developed a highly efficient, cost-effective, and easy-to-operate system for the lab-scale production of endotoxin-free supercoiled plasmids with high quality and high yield. Based on optimised fermentation culture, we obtained a high yield of pcDNA-CCOL2A1 vaccine by PEG/MgCl2 precipitation and TRION-114. We then established a method for quality control of the pcDNA-CCOL2A1 vaccine. Collagen-induced arthritis (CIA) model rats were subjected to intramuscular injection of the pcDNA-CCOL2A1 vaccine (300 μg/kg) to test its biological activity. An average yield of 11.81 ± 1.03 mg purified supercoiled plasmid was obtained from 1 L of fermentation broth at 670.6 ± 57.42 mg/L, which was significantly higher than that obtained using anion exchange column chromatography and a commercial purification kit. Our supercoiled plasmid had high purity, biological activity, and yield, conforming to the international guidelines for DNA vaccines. The proposed innovative downstream process for the pcDNA-CCOL2A1 vaccine can not only provide a large-scale high-quality supercoiled plasmid DNA for preclinical research but also facilitate further pilot-scale and even industrial-scale production of pcDNA-CCOL2A1 vaccine.
A Metabolic Biofuel Cell: Conversion of Human Leukocyte Metabolic Activity to Electrical Currents
Journal of Biological Engineering - Tập 5 - Trang 1-10 - 2011
An investigation of the electrochemical activity of human white blood cells (WBC) for biofuel cell (BFC) applications is described. WBCs isolated from whole human blood were suspended in PBS and introduced into the anode compartment of a proton exchange membrane (PEM) fuel cell. The cathode compartment contained a 50 mM potassium ferricyanide solution. Average current densities between 0.9 and 1.6 μA cm-2 and open circuit potentials (Voc) between 83 and 102 mV were obtained, which were both higher than control values. Cyclic voltammetry was used to investigate the electrochemical activity of the activated WBCs in an attempt to elucidate the mechanism of electron transfer between the cells and electrode. Voltammograms were obtained for the WBCs, including peripheral blood mononuclear cells (PBMCs - a lymphocyte-monocyte mixture isolated on a Ficoll gradient), a B lymphoblastoid cell line (BLCL), and two leukemia cell lines, namely K562 and Jurkat. An oxidation peak at about 363 mV vs. SCE for the PMA (phorbol ester) activated primary cells, with a notable absence of a reduction peak was observed. Oxidation peaks were not observed for the BLCL, K562 or Jurkat cell lines. HPLC confirmed the release of serotonin (5-HT) from the PMA activated primary cells. It is believed that serotonin, among other biochemical species released by the activated cells, contributes to the observed BFC currents.
Label-free multimodal electro-thermo-mechanical (ETM) phenotyping as a novel biomarker to differentiate between normal, benign, and cancerous breast biopsy tissues
Journal of Biological Engineering - Tập 17 Số 1 - Trang 1-17 - 2023
Technologies for quick and label-free diagnosis of malignancies from breast tissues have the potential to be a significant adjunct to routine diagnostics. The biophysical phenotypes of breast tissues, such as its electrical, thermal, and mechanical properties (ETM), have the potential to serve as novel markers to differentiate between normal, benign, and malignant tissue. We report a system-of-biochips (SoB) integrated into a semi-automated mechatronic system that can characterize breast biopsy tissues using electro-thermo-mechanical sensing. The SoB, fabricated on silicon using microfabrication techniques, can measure the electrical impedance (Z), thermal conductivity (K), mechanical stiffness (k), and viscoelastic stress relaxation (%R) of the samples. The key sensing elements of the biochips include interdigitated electrodes, resistance temperature detectors, microheaters, and a micromachined diaphragm with piezoresistive bridges. Multi-modal ETM measurements performed on formalin-fixed tumour and adjacent normal breast biopsy samples from N = 14 subjects were able to differentiate between invasive ductal carcinoma (malignant), fibroadenoma (benign), and adjacent normal (healthy) tissues with a root mean square error of 0.2419 using a Gaussian process classifier. Carcinoma tissues were observed to have the highest mean impedance (110018.8 ± 20293.8 Ω) and stiffness (0.076 ± 0.009 kNm−1) and the lowest thermal conductivity (0.189 ± 0.019 Wm−1 K−1) amongst the three groups, while the fibroadenoma samples had the highest percentage relaxation in normalized load (47.8 ± 5.12%). The work presents a novel strategy to characterize the multi-modal biophysical phenotype of breast biopsy tissues to aid in cancer diagnosis from small-sized tumour samples. The methodology envisions to supplement the existing technology gap in the analysis of breast tissue samples in the pathology laboratories to aid the diagnostic workflow.
Towards an integrated systems-based modelling framework for drug transport and its effect on tumour cells
Journal of Biological Engineering - Tập 8 - Trang 1-19 - 2014
A systematic understanding of chemotherapeutic influence on solid tumours is highly challenging and complex as it encompasses the interplay of phenomena occurring at multiple scales. It is desirable to have a multiscale systems framework capable of disentangling the individual roles of multiple contributing factors, such as transport and extracellular factors, and purely intracellular factors, as well as the interactions among these factors. Based on a recently developed systems-based modelling framework, we have developed a coupled system in order to further elucidate the role of drug transport, and its interplay with cellular signalling by incorporating intra- and extra-vascular drug transport in tumour, dynamic descriptions of intracellular signalling and tumour cell density dynamics. Different aspects of the interaction between transport and cell signalling and the effects of transport parameters have been investigated in silico. Limited drug penetration is found to be a major constraint in inducing drug effect; many aspects of the interaction of transport with cell signalling are independent of the details of cell signalling. A sensitivity analysis indicates that the effect of drug diffusivity depends on the balance between interstitial drug transport and the specific requirement for triggering apoptosis (governed by highly nonlinear signalling networks), suggesting that the effect of drug diffusivity in such cases must be considered in conjunction with descriptions of cellular dynamics. The modelling framework developed in this study provides qualitative and mechanistic insights into the effect of drug on tumour cells. It provides an in silico experimental platform to investigate the interplay between extracellular factors (e.g. transport) and intracellular factors. Such a platform is essential to understanding the individual and combined effects of transport and cellular factors in solid tumour.
Hệ thống phân phối thuốc dựa trên dendrimer: lịch sử, thách thức và những phát triển mới nhất Dịch bởi AI Tóm tắt
Journal of Biological Engineering - Tập 16 Số 1 - 2022
Kể từ khi dendrimer đầu tiên được báo cáo vào năm 1978 bởi Fritz Vögtle, nghiên cứu về dendrimer đã phát triển mạnh mẽ, từ tổng hợp đến ứng dụng trong bốn thập kỷ qua. Các đặc điểm cấu trúc riêng biệt của dendrimer bao gồm kích thước nano, bề mặt đa chức năng, nhánh cao, cấu trúc rỗng bên trong, và nhiều đặc điểm khác, làm cho dendrimer trở thành những phương tiện phân phối thuốc lý tưởng. Bài viết tổng quan ngắn này cung cấp một cái nhìn tổng quan về lịch sử và tính chất của dendrimer cũng như những phát triển mới nhất về dendrimer với vai trò là hệ thống phân phối thuốc. Bài viết tập trung vào những tiến bộ gần đây trong các ứng dụng của dendrimer như các chất mang thuốc và gen, bao gồm 1) chiến lược giải phóng thuốc chủ động để phân giải thuốc/ gen từ dendrimer đáp ứng với kích thích; 2) hệ thống phân phối dendrimer thay đổi kích thước và đảo ngược điện tích có thể tận dụng tốt hơn kích thước và tính chất bề mặt của dendrimer; 3) hệ thống phân phối gel dendrimer khối lượng và vi mô/nano. Những tiến bộ gần đây trong công thức dendrimer có thể dẫn đến việc tạo ra các sản phẩm thuốc và gen mới cũng như cho phép phát triển các liệu pháp phối hợp mới.
#dendrimers #drug delivery #gene carriers #drug release strategies #formulation advancements
Ma trận nhạy cảm sinh học trong việc phân phối thuốc Dịch bởi AI Tóm tắt
Journal of Biological Engineering - - 2010
Trong nhiều năm qua, lĩnh vực phân phối thuốc đã tập trung vào (1) kiểm soát sự giải phóng của một liệu pháp và (2) nhắm mục tiêu liệu pháp đến một loại tế bào cụ thể. Những nỗ lực nghiên cứu này chủ yếu tập trung vào việc phát triển các polyme phân hủy mới và các phương tiện phân phối thuốc có gắn phân tử. Sự quan tâm gần đây đối với các vật liệu sinh học phản ứng với môi trường đã mở ra những phương pháp mới để kích hoạt sự giải phóng thuốc và định vị liệu pháp tại một vị trí cụ thể. Những vật liệu sinh học mới này, thường được gọi là "thông minh" hoặc "thông dụng", có khả năng phân phối một tác nhân liệu pháp dựa trên các tín hiệu từ môi trường hoặc kích thích từ xa. Các vật liệu nhạy cảm với kích thích có thể tạo ra một liều liệu pháp có hiệu quả mà không có tác dụng phụ không mong muốn. Các polyme phản ứng với các kích thích khác nhau, chẳng hạn như pH, ánh sáng, nhiệt độ, siêu âm, từ tính, hoặc các phân tử sinh học đã được nghiên cứu như là những phương tiện tiềm năng cho việc phân phối thuốc. Bài đánh giá này mô tả những tiến bộ gần đây nhất trong các hệ thống phân phối thuốc "thông minh" phản ứng với một hoặc nhiều kích thích.
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