Binary Research Group

Dr. Chen received his Ph.D. from the University of Maryland, USA in 1998. The BINARY lab (Biology, Information science and Nanotechnology Applications and Research laboratorY) was founded in Spring 2003. The mission is to provide a cross-disciplinary research environment for exploring new nanoscale device & circuit designs and nanotechnology for bio-medical applications. Our primary research focuses include:

  1. Developing a pulsed-wave technology platform to stimulate cell growth (with the applications in cell therapy, tissue engineering, mental health and antibody productions), and microorganism growth (with the applications in increasing renewable biofuel /algal oil, antibiotics, omega-3, and wine/beverage productions);
  2. Building functional nanomaterials for water filtration (removing microorganisms, organic chemicals and heavy metals), gene transformation of agricultural products, targeted cancer imaging and treatment, gene/peptide/microRNA delivery (especially across the blood-brain-barrier);
  3. Designing portable impedance-based point-of-care devices for detecting metabolic biomarkers, monitoring environmental toxins, sensing plant infections at an earlier stage, and screening pathogens for food safety.
  4. Developing smart-phone Apps incorporating artificial intelligence methods to diagnose depression, especially postpartum syndrome, and invoke clinical intervention if needed. Making low-intensity pulsed ultrasound wearable devices for treatment.

The University of Alberta is home to cutting edge facilities such as the National Institute for Nanotechnology, as well as having the interdisciplinary expertise to be an epicentre for new waves of innovation in Biomedical Engineering. The University of Alberta was ranked 46th in the world for the impact of its engineering publications.


"Classification of cannabis strains in the Canadian market with discriminant analysis of principle components using genome-wide single nucleotide polymorphisms" was accepted    (06/06/2021)

"Classification of cannabis strains in the Canadian market with discriminant analysis of principle components using genome-wide single nucleotide polymorphisms" by Dan Jin, Philippe Henry, Jacqueline Shan, Jie Chen was accepted by PLOS ONE AbstractThe cannabis community typically uses the terms "Sativa" and "Indica" to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a reference genome, and, after filtering for minor allele frequency of 10%, identified 137,858 single nucleotide polymorphisms (SNPs). Discriminant analysis of principal components (DAPC) was applied to these SNPs and further identified 344 structural SNPs, wh [ ... ]

"High-resolution Metabolomic Biomarkers for Lung Cancer Diagnosis and Prognosis" was accepted    (06/06/2021)

"High-resolution Metabolomic Biomarkers for Lung Cancer Diagnosis and Prognosis" by Shi-ang Qi, Qian Wu, Zhenpu Chen, Wei Zhang1, Yongchun Zhou, Kaining Mao, Jia Li, Yuanyuan Li, Jie Chen, Youguang Huang, Yunchao Huang was accepted by Scientific Reports. Abstract Lung cancer is the leading cause of human cancer mortality due to the lack of early diagnosis technology. The low-dose computed tomography scan (LDCT) is one of the main techniques to screen cancers. However, LDCT still has a risk of radiation exposure and it is not suitable for the general public. In this study, plasma metabolic profiles of lung cancer were performed using a comprehensive metabolomic method with different liquid chromatography methods coupled with a Q-Exactive high-resolution mass spectrometer. Metabolites with different polarities (amino acids, fatty acids, and acylcarnitines) can be detected and identified as differential metabolites of lung cancer in small volumes of plasma. Logistic regression models were further developed to identify cancer stages and types using those significant biomarkers. Using the Variable Importance in Projection (VIP) and the area under the curve (AUC) scores, we have successfully identified the top 5, 10, and 20 metabolites that can be used to differentiate lung cancer stages and types. The discrimination accuracy and AUC score can be as high as 0.829 and 0.869 using the five most significant metabolites. This study demonstrated that using 5+ metabolites (Palmitic aci [ ... ]

"Exploratory Study on Neurochemical Effects of Low Intensity Pulsed Ultrasound in Brains of Mice" was accepted    (13/03/2021)

"Exploratory Study on Neurochemical Effects of Low-Intensity Pulsed Ultrasound in Brains of Mice" was accepted for publication Abstract Background. There is now a relatively large body of evidence suggesting a relationship between dysfunction of myelin and oligodendrocytes and the etiology of several neuropsychiatric disorders, including depression and schizophrenia, and also suggesting that ultrasound methods may alleviate some of the symptoms of depression. Methods. We have applied low-intensity pulsed ultrasound (LIPUS) to the brains of mice treated with the demyelinating drug cuprizone, a drug that has been used as the basis for a rodent model relevant to a number of psychiatric and neurologic disorders including depression, schizophrenia, and multiple sclerosis. Prior to conducting the studies in mice, preliminary studies were carried out on the effects of LIPUS in vitro in neuron-like SH-SY5Y cells and primary glial cells. In subsequent studies in mice, female C57BL/6 mice were restrained in plastic tubes for 20 minutes daily with the ultrasound transducer near the end of the tube directly above the mouse's head. LIPUS was used at an intensity of 25mW/cm2 once daily for 22 days in control mice and in mice undergoing daily repetitive restraint stress (RRS). Behavioral or neurochemical studies were done on the mice or the brain tissue obtained from them. Results. The studies in vitro indicated that LIPUS stimulation at an intensity of 15 mW/cm2 delivered for 5 min daily [ ... ]

American Institute for Medical and Biological Engineering (AIMBE) College of Fellows    (07/03/2021)

Dr. Chen, Congratulations! You have been elected to the American Institute for Medical and Biological Engineering (AIMBE) College of Fellows. You have been peer-nominated, peer-reviewed, and peer-elected into this prestigious group.  AIMBE is a non-profit, honorific society of the most accomplished individuals in the fields of medical and biological engineering. AIMBE's mission is to advocate for biomedical engineering innovation through public policy initiatives. No other organization brings together academia, industry, government, and scientific societies into a highly influential community in medical and biological engineering. 
Your election to the College of Fellows is more than just another accolade. Being part of the AIMBE College of Fellows enables intimate networking and public policy engagement among trailblazers at the pinnacle of their careers. As a leader in the field, AIMBE provides opportunities for you to give back to the community that has shaped your transformative career.    Among AIMBE's most important work includes advocacy for medical and biological engineering. This includes arranging personal meetings for our Fellows with their Members of Congress, as well as a host of initiatives educating Congress on the importance of federal funding for basic research and medical innovation. We are proud to host annual congressional tours of NIH and FDA, congressional lunch briefings, and scientific exhibitions for Congress. 
 [ ... ]

"Identification of phenotypic characteristics in three chemotype categories in the genus Cannabis" was accepted by Hortscience    (15/02/2021)

"Identification of phenotypic characteristics in three chemotype categories in the genus Cannabis" was accepted by Hortscience Abstract: Modern Cannabis cultivars are morphologically distinguished by their leaflet shapes (wide for “Indica” and narrow for “Sativa”) by users and breeders. However, there are no scientific bases or references for determining the shape of these leaflets. In addition, these two categories contained mostly THC dominant (high THC) cultivars while excluded CBD dominant (high CBD) and intermediate (intermediate level of both THC and CBD) cultivars. This study investigated the phenotypic variation in 21 Cannabis cultivars covering three chemical phenotypes, referred to as chemotypes, grown in a commercial greenhouse. Thirty morphological traits were measured in the vegetative, flowering, and harvest stages on live plants and harvested inflorescences. The collected data were subjected to correlation analysis, hierarchical clustering, principal component analysis, and canonical correlation analysis with preassigned chemotypes. Canonical correlation analysis assigned individual plants to their chemotypes with 92.9% accuracy. Significant morphological differences were identified. Traits usable as phenotype markers for CBD dominant cultivars included light-green and narrow leaflets, a greater number of primary and secondary serrations, loose inflorescences, dense and resinous trichomes, and Botrytis cinerea resistance. Traits for intermediate culti [ ... ]

"Impact of Low-intensity Pulsed Ultrasound on the Growth of Schizochytrium sp. for Omega-3 Production" was published in Biotechnology and Bioengineering    (18/10/2020)

Impact of Low-intensity Pulsed Ultrasound on the Growth of Schizochytrium sp. for Omega-3 Production by  Oleksandra Savchenko, Jida Xing, Mark Burrell, Robert Burrell and Jie Chen
was published in Biotechnology and Bioengineering
Abstract Schizochytrium sp. is a microalga that is known for its high content of oils or lipids. It has a high percentage of polyunsaturated fatty acids in the accumulated oil, especially docosahexaenoic acid (DHA). DHA is an important additive for the human diet. Large-scale production of Schizochytrium sp. can serve as an alternative source of DHA for humans as well as for fish feed, decreasing the burden on aqua systems. Therefore, research on improving the productivity of Schizochytrium attracts a lot of attention. We studied the potential of using low-intensity pulsed ultrasound (LIPUS) in the growth cycle of Schizochytrium sp. in shake flasks. Different intensities and treatment durations were tested. A positive effect of LIPUS on biomass accumulation was observed in the Schizochytrium sp. culture. Specifically, LIPUS stimulation at the ultrasound intensity of 400 mW/cm2 with 20 minutes per treatment 10 times a day with equal intervals of 2.4 hours between the treatments was found to enhance the growth of Schizochytrium biomass most effectively (by up to 20%). Due to the nature of cell division in Schizochytrium sp. which occurs via zoospore formation, LIPUS stimulation was inefficient if applied continuously during  [ ... ]

"Ultrasound-assisted Magnetic Nanoparticle-based Gene Delivery" was accepted by PLOS ONE    (13/09/2020)

"ULTRASOUND-ASSISTED MAGNETIC NANOPARTICLE-BASED GENE DELIVERY" was accepted by PLOS One Abstract Targeted gene delivery is important in biomedical research and applications. In this paper, we synergistically combine non-viral chemical materials, magnetic nanoparticles (MNPs), and a physical technique, low-intensity pulsed ultrasound (LIPUS), to achieve efficiently and targeted gene delivery. The MNPs are iron oxide super-paramagnetic nanoparticles, coated with polyethyleneimine (PEI), which makes a high positive surface charge and is favorable for the binding of genetic materials. Due to the paramagnetic properties of the MNPs, the application of an external magnetic field increases transfection efficiency while LIPUS stimulation enhances cell viability and permeability. We found that stimulation at the intensity of 30 mW/cm2 for 10 minutes yields optimal results with a minimal adverse effect on the cells. By combining the effect of the external magnetic field and LIPUS, the genetic material (GFP or Cherry Red plasmid) can enter the cells. The flow cytometry results showed that by using just a magnetic field to direct the genetic material, the transfection efficiency on HEK 293 cells that were treated by our MNPs was 56.1%. Coupled with LIPUS stimulation, it increased to 61.5% or 19% higher than the positive control (Lipofectamine 2000). Besides, compared with the positive control, our method showed less toxicity. Cell viability after transfection was 63.61%, whic [ ... ]

Single Ascospore Detection for the Forecasting of Sclerotinia Stem Rot of Canola was accepted by Lab-on-a-Chip    (31/08/2020)

"Single Ascospore Detection for the Forecasting of Sclerotinia Stem Rot of Canola"  was accepted by Lab-on-a-Chip (impact factor: 6.914) by Pedro A. Duarte, Lukas Menze, Gaser N. Abdelrasoul, Shari Yosinski, Zak Kobos, Riley Stuermer, Mark Reed, Jian Yang, Xiujie S. Li and Jie Chen  Abstract—Smart-agriculture technologies comprise a set of management systems designed to sustainably increase the efficiency and productivity of farming. In this paper, we present a lab-on-a-chip device that can be employed as a plant disease forecasting tool for canola crop. Our device can be employed as a platform to forecast potential outbreaks of one of the most devastating diseases of canola and other crops, Sclerotinia stem rot. The system consists of a microfluidic chip capable of detecting single airborne Sclerotinia sclerotiorum ascospores. Target ascospores are injected in the chip and selectively captured by dielectrophoresis, while others spores in the sample are flushed away. Afterward, captured ascospores are released into the flow stream of the channel and are detected employing electrochemical impedance spectroscopy and coplanar microelectrodes. Our device provides a design for a low-cost, miniaturized, and automated platform technology for airborne spore detection and disease prevention. 

Overcoming the sensitivity vs. throughput tradeoff in Coulter counters: a novel side counter design was accepted by Biosensors and Bioelectronics    (09/08/2020)

 "Overcoming the sensitivity vs. throughput tradeoff in Coulter counters: a novel side counter design"
Daniel T. Bacheschi, William Polsky, Zachary Kobos, Shari Yosinski, Lukas Menze, Jie Chen, and Mark A. Reed
was accepted by Biosensors and Bioelectronics (impact factor: 10.257)
Abstract: Microfabricated Coulter counters are attractive for point of care (POC) applications since they are label freeand compact. However, these approaches inherently suffer from a trade off between sample throughput and sensitivity. The counter measures a change in impedance due to displaced fluid volume by passing cells, and thus the counter’s signal increases with the fraction of the sensing volume displaced. Reducing the size of the sensing region requires reductions in volumetric throughput in the absence of increased hydraulic pressure and sensor bandwidth. The risk of mechanical clog formation, rendering the counter inoperable, increases markedly with reductions in the size of the constriction aperture. We present here a microfluidic coplanar Coulter counter device design that overcomes the problem of constriction clogging while capable of operating in microfluidic channels filled entirely with highly conductive sample. The device utilizes microfabricated planar electrodes projecting into one side of the microfluidic channel and is easily integrated with upstream electronic, hydrodynamic, or other focusing units to produce efficient counting which could allow for d [ ... ]

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Dr. Jie Chen