FPGA based Directional control of MTB cells For Bioengineering Applications

We designed a circuit using the logic elements of FPGA for controlling MTB. The circuit is connected to a mesh of coil, where a path of magnetic field is created using FPGA. The MTB’s motility is controlled in a particular direction along this path. Then the bacterial invasion is studied highlighting how the MTB cells and mutant cells interact using the FPGA based controller

Interaction Between Nucleoside Diphosphate Kinase And Graphene Oxide And Its Impact On Cardiovascular Diseases

Here we report possibly for the first time the computational understanding of the interactions between the nanomaterial Graphene Oxide (GO) and the enzyme Nuclear Diphosphate Kinase (NDPK) and its implications. Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) were used to run simulations and analyze the interactions between NDPK and GO. The simulations have run for 100 ns, and it is observed that GO is able to block the active site of the enzyme. Graphene oxide is being used because of its excellent biocompatibility, high water dispersibility, and large surface area. NDPK has numerous roles in the body, such as activating G-proteins and transferring a phosphate from ATP to GDP (resulting in ADP and GTP). It also plays a role in cell proliferation, development, signal transduction, endocytosis, etc[2]. Normally, increased activity of NDPK yields the synthesis of the second messenger cyclic adenosine monophosphate (cAMP) . However, during heart failure, NDPK suppresses cAMP formation due to altered signal transduction pathways via G-proteins. In a healthy heart, nitric oxide (NO) is produced by the body in the endothelium that lines the walls of blood vessels so that the veins and arteries can dilate and blood can flow through the body. However, during heart failure, the endothelium lining is damaged, which inhibits the production of NO. cAMP signal transduction pathways have the potential to produce NO after the endothelium lining is in the process of being damaged . Therefore, when NDPK suppresses cAMP during heart failure, it in turn inhibits the production of nitric oxide— which is crucial for a healthy heart. Using NAMD simulations and analysis using VMD, it is observed that graphene oxide is attracted to the active site of NDPK. Strong interactive forces (van der Waals forces) exist between the primary residue of the active site of NDPK (histidine 118) and graphene oxide. Also, throughout the simulation, the structure of the enzyme is preserved. From the 100 ns worth of simulation, it is observed that the graphene oxide blocks the primary residue of the active site of NDPK and can therefore cease the enzyme’s function, lower the rate of reaction, and potentially affect heart failure

A Computational Approach for Understanding the Interactions between Graphene Oxide and Nucleoside Diphosphate Kinase with Implications for Heart Failure

During a heart failure, an increased content and activity of nucleoside diphosphate kinase (NDPK) in the sarcolemmal membrane is responsible for suppressing the formation of the second messenger cyclic adenosine monophosphate (cAMP)—a key component required for calcium ion homeostasis for the proper systolic and diastolic functions. Typically, this increased NDPK content lets the surplus NDPK react with a mutated G protein in the beta-adrenergic signal transduction pathway, thereby inhibiting cAMP synthesis. Thus, it is thus that inhibition of NDPK may cause a substantial increase in adenylate cyclase activity, which in turn may be a potential therapy for end-stage heart failure patients. However, there is little information available about the molecular events at the interface of NDPK and any prospective molecule that may potentially influence its reactive site (His118). Here we report a novel computational approach for understanding the interactions between graphene oxide (GO) and NDPK. Using molecular dynamics, it is found that GO interacts favorably with the His118 residue of NDPK to potentially prevent its binding with adenosine triphosphate (ATP), which otherwise would trigger the phosphorylation of the mutated G protein. Therefore, this will result in an increase in cAMP levels during heart failure.https://doi.org/10.3390/nano802005

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

Faculty Research Day 2018: Faculty Competitive Poster WinnerIt is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNT) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamics simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. The 3D CNT-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications

Towards Tumor Targeting via Invasive Assay Using Magnetospirillum magneticum

Magnetospirillum magneticum (AMB-1) are a species of magnetotactic bacteria (MTB) that are capable of orienting along the earth’s magnetic field lines through their organelles called magnetosomes. Many studies have shown that certain engineered bacteria can infect the tumor cells, resulting in a controlled death of a tumor. This work deals with a technique utilizing AMB-1 along a predefined path through magnetotaxis, which can pave a way for selective doping as well as isolation of the tumor cells from a group of healthy cells through a magnetic invasive assay. For such a control, a tiny mesh of vertical electrical coils each having a diameter of ∼3 mm is fabricated, which establishes the path for the bacteria to move along the magnetic field lines. The molecular dynamics (MD) simulations at the interface of the bacterial cell surface proteins (MSP-1 and flagellin) and Chinese hamster ovary (CHO) cell surface containing cytoplasmic and extracellular proteins (BSG, B2M, SDC1, AIMP1, and FOS) are shown to establish an association between the AMB-1 and the host CHO cells. It is found that the CHO protein structure is compromised, which disables the activation of its defense function, allowing the bacteria to interact and survive. The experimental demonstration involves the CHO cells’ interaction with the AMB-1 and isolation of selected CHO cells. It is found that AMB-1-integrated CHO cells successfully moved along the magnetic field lines generated by the coils. Statistical analysis performed for the assay showed that AMB-1 cells were found to be viable after co-incubating with CHO cells, and the number of viable cells post co-incubation over a period of 24 h showed a slight decrease in both cell population. Overall, 51% of AMB-1 cells and 67% of CHO cells were found viable 24 h post co-incubation. Scanning electron microscopy (SEM) along with energy-dispersive X-ray spectroscopy (EDAX) analysis revealed AMB-1/CHO cell morphology, the potential interaction between them, and the presence of magnetosomes with trace amounts of iron in the AMB-1-interacted CHO cells, confirming the successful AMB-1 integration

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamics simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. The 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications

Bacteria as Bio-Template for 3D Carbon Nanotube Architectures

Abstract It is one of the most important needs to develop renewable, scalable and multifunctional methods for the fabrication of 3D carbon architectures. Even though a lot of methods have been developed to create porous and mechanically stable 3D scaffolds, the fabrication and control over the synthesis of such architectures still remain a challenge. Here, we used Magnetospirillum magneticum (AMB-1) bacteria as a bio-template to fabricate light-weight 3D solid structure of carbon nanotubes (CNTs) with interconnected porosity. The resulting porous scaffold showed good mechanical stability and large surface area because of the excellent pore interconnection and high porosity. Steered molecular dynamics simulations were used to quantify the interactions between nanotubes and AMB-1 via the cell surface protein MSP-1 and flagellin. The 3D CNTs-AMB1 nanocomposite scaffold is further demonstrated as a potential substrate for electrodes in supercapacitor applications