Gene expression patterns following unilateral traumatic brain injury reveals a local pro-inflammatory and remote anti-inflammatory response.

BackgroundTraumatic brain injury (TBI) results in irreversible damage at the site of impact and initiates cellular and molecular processes that lead to secondary neural injury in the surrounding tissue. We used microarray analysis to determine which genes, pathways and networks were significantly altered using a rat model of TBI. Adult rats received a unilateral controlled cortical impact (CCI) and were sacrificed 24 h post-injury. The ipsilateral hemi-brain tissue at the site of the injury, the corresponding contralateral hemi-brain tissue, and naïve (control) brain tissue were used for microarray analysis. Ingenuity Pathway Analysis (IPA) software was used to identify molecular pathways and networks that were associated with the altered gene expression in brain tissues following TBI.ResultsInspection of the top fifteen biological functions in IPA associated with TBI in the ipsilateral tissues revealed that all had an inflammatory component. IPA analysis also indicated that inflammatory genes were altered on the contralateral side, but many of the genes were inversely expressed compared to the ipsilateral side. The contralateral gene expression pattern suggests a remote anti-inflammatory molecular response. We created a network of the inversely expressed common (i.e., same gene changed on both sides of the brain) inflammatory response (IR) genes and those IR genes included in pathways and networks identified by IPA that changed on only one side. We ranked the genes by the number of direct connections each had in the network, creating a gene interaction hierarchy (GIH). Two well characterized signaling pathways, toll-like receptor/NF-kappaB signaling and JAK/STAT signaling, were prominent in our GIH.ConclusionsBioinformatic analysis of microarray data following TBI identified key molecular pathways and networks associated with neural injury following TBI. The GIH created here provides a starting point for investigating therapeutic targets in a ranked order that is somewhat different than what has been presented previously. In addition to being a vehicle for identifying potential targets for post-TBI therapeutic strategies, our findings can also provide a context for evaluating the potential of therapeutic agents currently in development

PROBLEM-BASED LEARNING IN BIOMEDICAL ENGINEERING CURRICULA

Abstract ⎯ Problem-based Learning (PBL) anchors learning and instruction in concrete problems. We believe that PBL is well suited to educating undergraduate and graduate students within the interdisciplinary field of biomedical engineering (BME). BME draws upon many traditional disciplines to address a range of problems, from biotechnology to clinical medicine. A challenge for BME educators is to balance this broad base of fundamentals with the analytical, in depth problem solving necessary to be successful bioengineers. The ability to adapt, be innovative, and acquire and integrate relevant information is not efficiently learned in a lecture format, but rather in a small group setting that encourages self-directed learning, such as PBL. We have developed a graduate BME program with PBL as one of the pivotal components and are embarking on the introduction of this methodology to undergraduate sections. We have found PBL to be an effective vehicle for instruction, retention of material, and introduction of topics necessary for professional development

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identifica-tion of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classi-fying features in 2-D and merging these classifications into 3-D objects, the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the plat-form provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological com-plexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥ 95%. We demonstrated the robustness of these algorithms in a more complex are-na through the automated segmentation of neural cells in ex vivo brain slices. The novel methods surpass previous research improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions

Lipidome Alterations following Mild Traumatic Brain Injury in the Rat

Traumatic brain injury (TBI) poses a major health challenge, with tens of millions of new cases reported globally every year. Brain damage resulting from TBI can vary significantly due to factors including injury severity, injury mechanism and exposure to repeated injury events. Therefore, there is need for robust blood biomarkers. Serum from Sprague Dawley rats was collected at several timepoints within 24 h of mild single or repeat closed head impacts. Serum samples were analyzed via ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in positive and negative ion modes. Known lipid species were identified through matching to in-house tandem MS databases. Lipid biomarkers have a unique potential to serve as objective molecular measures of injury response as they may be liberated to circulation more readily than larger protein markers. Machine learning and feature selection approaches were used to construct lipid panels capable of distinguishing serum from injured and uninjured rats. The best multivariate lipid panels had over 90% cross-validated sensitivity, selectivity, and accuracy. These mapped onto sphingolipid signaling, autophagy, necroptosis and glycerophospholipid metabolism pathways, with Benjamini adjusted p-values less than 0.05. The novel lipid biomarker candidates identified provide insight into the metabolic pathways altered within 24 h of mild TBI

Clinical Study Randomized, Placebo-Controlled, Double-Blind Pilot Study of D-Cycloserine in Chronic Stroke

Stroke is a leading cause of death and disability in the USA. Up to 60% of patients do not fully recover despite intensive physical therapy treatment. N-Methyl-D-aspartate receptors (NMDA-R) have been shown to play a role in synaptic plasticity when activated. D-Cycloserine promotes NMDA receptor function by binding to receptors with unoccupied glycine sites. These receptors are involved in learning and memory. We hypothesized that D-cycloserine, when combined with robotic-assisted physiotherapy (RAP), would result in greater gains compared with placebo + RAP in stroke survivors. Participants ( = 14) were randomized to Dcycloserine plus RAP or placebo plus RAP. Functional, cognitive, and quality-of-life measures were used to assess recovery. There was significant improvement in grip strength of the affected hand within both groups from baseline to 3 weeks (95% confidence interval for mean change, 3.95 ± 2.96 to 4.90 ± 3.56 N for D-cycloserine and 5.72 ± 3.98 to 8.44 ± 4.90 N for control). SIS mood domain showed improvement for both groups (95% confidence interval for mean change, 72.6 ± 16.3 to 82.9 ± 10.9 for D-cycloserine and 82.9 ± 13.5 to 90.3 ± 9.9 for control). This preliminary study does not provide evidence that D-cycloserine can provide greater gains in learning compared with placebo for stroke survivors

ARTICLE Shear-Induced Intracellular Loading of Cells With Molecules by Controlled Microfluidics

ABSTRACT: This study tested the hypothesis that controlled flow through microchannels can cause shear-induced intracellular loading of cells with molecules. The overall goal was to design a simple device to expose cells to fluid shear stress and thereby increase plasma membrane permeability. DU145 prostate cancer cells were exposed to fluid shear stress in the presence of fluorescent cell-impermeant molecules by using a cone-and-plate shearing device or high-velocity flow through microchannels. Using a syringe pump, cell suspensions were flowed through microchannels of 50-300 mm diameter drilled through Mylar 1 sheets using an excimer laser. As quantified by flow cytometry, intracellular uptake and loss of viability correlated with the average shear stress. Optimal results were observed when exposing the cells to high shear stress for short durations in conical channels, which yielded uptake to over one-third of cells while maintaining viability at approximately 80%. This method was capable of loading cells with molecules including calcein (0.62 kDa), large molecule weight dextrans (150-2,000 kDa), and bovine serum albumin (66 kDa). These results supported the hypothesis that shear-induced intracellular uptake could be generated by flow of cell suspensions through microchannels and further led to the design of a simple, inexpensive, and effective device to deliver molecules into cells. Such a device could benefit biological research and the biotechnology industry