United States

The mission of the Bioinformatics Core Facility at UD’s Center for Bioinformatics and Computational Biology (CBCB) is to provide scientific expertise, training, and infrastructure support in bioinformatics and data science for the Delaware life science and biomedical research and education community. Drawing on the combined resources of CBCB, the Delaware Biotechnology Institute (DBI), the Data Science Institute (DSI), and the Protein Information Resource (PIR), the Core provides both computing infrastructure and knowledgeable staff with significant expertise across various specialties in bioinformatics, data science, and related fields. The Core is further supported by the Delaware Biotechnology Institute’s BioIT team providing support for systems administration and high performance computing support. A special focus of the Core has been omics data analysis, and pipelines and support are available under fee-for-service models to support investigators. The facility also has substantial capabilities built upon its close relationship with the Protein Information Resource (PIR) that have been successfully applied to a number of research projects including proteomic analysis using tools such as iProXpress and literature and data mining capabilities of iProLINK. These combined omics analysis and data integration pipelines form the nucleus of a bioinformatics framework to provide a user portal for dynamic analysis and visualization of genomic, transcriptomic, and proteomic data to its users at UD. Consultation, advice, and training offerings are also available to help support researchers in analysis and interpretation of data. The Core also works with investigators to design and host web portals and databases to store, organize, and share scientific data and findings. The Center’s in-house High-Performance Computational hardware include the Biomix cluster (freely accessible to members of Delaware INBRE partner institutions), as well as development and production web/database servers and data storage options including a triple redundancy Hadoop data archiving system.

Delaware Neuroscience Symposium 2021

CBCB Bioinformatics Core Facility

This annual event showcases and celebrates the neuroscience research in Delaware.  Posters and talks highlight neuroscience research carried out by graduate students, undergraduate students, and research staff at all of Delaware’s research and education institutions. The Lounge section of the symposium allows real-time interactions and networking among attendees.  New this year is an expo of research core facilities in Delaware.  Check them out in the Research Cores section of our poster session, or see the logos below.

poster

The relationship between gut microbiota and host brain health has seen a surge in recent scientific investigation, specifically the causal link between gut imbalance and neuropsychiatric disorders. To increase our understanding of the gut-brain axis, we investigate the molecular interactions of a common bacterial fragment in the gut and its influence in the brain on a cellular level. This study uses primary neural cells in culture as well as an adult rat model to observe the fate of bacteria in the brain and peripheral organs. Cultured neural samples and adult rats were treated with Muramyl dipeptide (MDP), a common bacterial fragment. Relative gene expression was evaluated with rt-PCR across a zero to 24-hr time course post-treatment. Cells and adult rat brain tissues were fixed and stained using immunochemistry to detect the presence and location of the MDP molecule. Using confocal microscopy, we can visualize the time course of interactions between this bacterial fragment and microglia, the innate immune cells of the brain. Early results indicate that microglia will phagocytose these bacterial fragments that travel from the gut to the brain.

Tracking a labeled bacterial cell wall fragment throughout the body and the brain to determine their specific cellular and molecular interactions

Animals living in groups frequently interact with conspecifics and use social feedback to modify their behavior. While social status strongly influences how individuals modify their behavior in groups, other factors may also impact group dynamics. In particular, the role that an animal's current behavioral state plays in future interactions with other group members is less clear. To explore this question, we recorded unrestricted social interactions for 5 hours in mixed-sex groups (n = 11; two males and two females in each group) of adult mice (13-21 weeks old; B6.CAST-Cdh23Ahl+/Kjn) and automatically extracted distinct behaviors using a machine-based learning system (Kabra et al., 2013). For every recording, we computed an aggression score based on the number of aggressive behaviors performed by each male, with scores ranging from 0.02 to 0.97. The overall level of a male's aggression did not affect the number or duration of male-female interactions (Mann-Whitney, all p values > 0.05). However, we found that a male’s aggressive state profoundly influenced subsequent male-female interactions. Surprisingly, animals in a submissive state interacted with a female more frequently, for shorter durations, and sooner after the aggressive encounter than animals in an aggressive state (Mann Whitney, all p values < 0.04). In contrast, the number, duration, and temporal delay of interactions with a female were similar between males after non-social or non-aggressive behaviors (Mann-Whitney, all p’s > 0.05). When looking at the movement patterns across different post-aggression behavioral sequences, the kinematics were strikingly different between males in submissive and aggressive states (Mann-Whitney, p < 0.05). The movement patterns of males with higher or lower aggression levels were similar (Mann-Whitney, p > 0.05), suggesting that a male's role in aggressive behavior strongly influenced subsequent male-female interactions. Additionally, movement patterns were highly predictive of a male’s aggressive state and subsequent social engagement (Z-test, p < 0.01). Our results demonstrate that mice rapidly update their behavior in response to changes in aggressive social contexts, indicating that an animal’s behavioral state influences overall group dynamics.

Experience dependent behavioral flexibility during social interaction

The Center for Biomedical and Brain Imaging is a core facility at the University of Delaware. We provide instruments for structural and functional imaging. We have a research-dedicated Siemens Prisma 3T MRI scanner for humans, and a Bruker 9.4T MRI scanner for small animals. Our instruments are capable of acquiring images in multiple modalities, including structural MRI, functional MRI (fMRI), DTI, spectroscopy and X-nuclei imaging. We have multiple MRI coils specialized for body and brain imaging, and a variety of peripheral devices for physiological monitoring, stimulus presentation and subject responses. In addition to the MRI scanners, we also have instruments for Transcranial Magnetic Stimulation (TMS), both inside and outside the MRI scanner, and an EEG system for simultaneous EEG/fMRI. We have three full-time staff, including a certified MRI technologist and an MRI physicist. We are available for consultation to help design your MRI experiments.

Center for Biomedical and Brain Imaging at the University of Delaware

The Nemours Biomedical Research Informatics Center (BRIC) (formerly Bioinformatics Core facility) provides consultation, training and computational resources (both hardware and software). Services offered by BRIC include experimental design of parallel, crossover, longitudinal and cross-section studies, generalized statistical analysis, EHR and PEDSnet data requests and analysis and development of special purpose software and applications. BRIC serves as the interface between PEDSnet and the Nemours Children’s Healthcare System. This includes maintaining relationships with the partner institutions, facilitating data transfer from our institution to the national pediatric database, and aiding other entities from within Nemours in participating in the PEDSnet community. As a member of the National COVID Cohort Collaborative, BRIC and the DE-CTR aid in providing COVID-related patient data to an open-source national database and serve as an ambassador for the program to the entire Nemours and DE-CTR community. BRIC maintains the Nemours distribution of REDCap. Responsibilities include aiding in project setup and management as well as maintaining hosting and compute resources for Nemours sponsored projects.

Nemours Biomedical Research Informatics Center (BRIC)

DHIN Introduction to Neuroscience Symposium 2021 April

The primary objective of the Cell Electrophysiology Core is to provide critical collaboration for neuroscience projects across University of Delaware (UD), Delaware State University (DSU) and the Nemours AI DuPont Children’s Hospital that require analysis of ion channel, synaptic, and network activity in neurons and glia. The Core is also open to outside investigators for data collection and collaboration. The Core will perform experiment design, data acquisition, data analysis and assist with result presentation for patch-clamp studies. The Core will also provide training and access to microelectrode array (MEA) system for users to perform their own experiments. The primary service of the Electrophysiology Core is to provide expert consultation and assistance with electrophysiological analyses of ion channel, synaptic, and network activity in neuronal cells and tissues with patch-clamp and MEA techniques plus optogentic stimulation and fluorescence imaging. Typically, this involves assessment of neuronal excitability and action potential firing, measurements of synaptic transmission and its plasticity, or recordings of the activity of specific ligand-gated or voltage-gated ion channels. The Core performs experiments for the User, and provides access and training in the use of certain equipment, consultation on experimental design, assistance with data analysis and publication. The experiment preparations include: • Primary cell cultures • Cell lines • Acute slices • Cultured slices The experiment types are: • Basic cell membrane properties • Action potential properties • Ion channel currents • Synaptic transmissions • Intrinsic and synaptic plasticity • Fluorescence imaging • MEA for network study • Optogenetics for network study

Cell Electrophysiology Core Facility

The current study focuses on disentangling some of the neurobiological, developmental, and relational theories and factors that affect adoptees academic performance. Specifically, we aim to differentiate the impact of age of adoption and the length of time adoptees spend in their new homes on parental perception of academic performance. Previous investigations have suggested that adopted children perform less well academically in both reading and math (Beckett, 2007). Yet, this result—children who are adopted having poorer academic performance—is not consistent across the literature (Bramlett et al., 2011). This is likely due to evidence of behavioral and neurobiological developmental delays (Grotevant & McDermott, 2014). However, this interpretation does not account for the period in which adoptees and their new families adjust to one another. A period we refer to as relational uncertainty. The present study includes participants from the National Survey of Adopted Parents (NSAP, 2007). This included 1,647 (757 male) children from adopted families ranging from 3 - 6 years old. To examine this issue, we investigated indices of parental perception of the academic performance of adopted children using a difference score, which captured the number of years between the child’s current age and the age at which the child was placed in their adoptive home. As hypothesized, we found a positive significant effect of relational uncertainty on both reading (β = .09, SE = .02, z = 5.16, p < .0001) and math (β = .07, SE = .02, z = 3.85, p < .001). This indicates the longer the child is with their adopted family the more likely the family is to perceive the adopted child as academically successful. After providing evidence for this period of relational uncertainty, we investigated the impact of factors previously found to be associated with the academic performance of adoptees.

How does parental perception of adoptive children’s academic performance change

Parkinson’s Disease (PD) is the second most common neurodegenerative disorder in which dopaminergic neurons are lost. The cause of PD is still unknown; however, it is believed that environmental factors may contribute to the development of PD. Rotenone is a pesticide that blocks mitochondrial respiration in the Electron Transport Chain by inhibiting Complex I. Rotenone is an environmental risk factor for sporadic PD. Here we intend to develop strategies that can lead to the development of potential preventative measures against PD. In this project, Rotenone will be mixed in fly food to analyze its effects in adult Drosophila melanogaster in terms of behavior and longevity. Dacarbazine is a possible anti-PD drug that is known for its use in chemotherapy for skin cancer. We hypothesize that Dacarbazine can help ameliorate or reverse the effects of Rotenone in Drosophila. We will set up a study to analyze the effect of Rotenone, Dacarbazine, and a mixture of the two. There will also be a control group that we will use to compare our findings to. The compounds will be mixed in the fly food and fly activity will be under observation. Ultimately, we plan to establish research that shows that Dacarbazine is a potential neuroprotective chemical against a model of PD.

Ameliorating the effects of an environmental toxin in a Drosophila model of Parkinson’s Disease

Parkinson’s Disease (PD) is a progressive neurodegenerative disorder affecting more than 10 million of people worldwide mostly over the age of 60 years. There is irreversible loss of dopaminergic neurons for PD patients, mostly in the Substantia Nigra (SN) region of the midbrain. This irreparable loss reduces the availability of dopamine, a molecule closely connected to mobility and decision making. PD patients experience tremors, difficulty in normal mobility, changes in mood and even appetite. Histological evidence shows that there is a presence of protein aggregates, known as Lewy Bodies in the SN of PD patients. Phosphorylated form of α-synuclein protein(p-α-synuclein) is also detected to be elevated in the protein aggregates. Therefore, p-α-synuclein could be one of the indicators for the dopaminergic neuronal death. The currently available and widely used therapeutics such as L-DOPA only help in alleviating the symptoms by providing the necessary amount of bioavailable dopamine in the body, however, this causes side-effects in long-term use. That is why we need to develop therapeutics that can halt protein aggregation (Lewy Bodies) and prevent dopaminergic neuronal loss for maintaining the normal level of dopamine in the body. In this study we assessed a selected novel compound from AptaBio Therapeutics (C-6) in PD mouse models. We gavaged the compound at 2 different doses to the PD symptoms-displaying transgenic mice for 2 weeks and found their improved mobility in behavioral tests, such as pole-test, hindlimb clasping, crossbeam, rotarod, as well as nesting test. Further, we confirmed that the compound reduced the level of protein aggregation in immunohistochemistry and the accumulation of p-α-synuclein in Western blot. In conclusion, the Comp-6 significantly alleviates the PD-like symptoms in the transgenic mice (L-61) and is promising to move on to next step for IND.

Testing a Novel Compound from AptaBio As A Parkinson’s Disease Therapeutic

Spatial working memory (SWM), the ability to encode, temporally maintain, and retrieve visuospatial information, is necessary for goal-directed navigation. Within a SWM T-maze task, rats need to accurately retrieve information about a previous trial in order to make an informed choice about their next trajectory. When faced with these decisions at the choice point, rats will occasionally exhibit complex behaviors, such as pausing and sweeping their head back and forth. These behaviors, called vicarious trial and error (VTE), are thought to be a behavioral manifestation of deliberation (Redish, 2016). However, when rats perform a delayed non-match to position (DNMP) task, a paradigm that experimentally separates memory encoding and retrieval into ‘sample’ and ‘choice’ phases, rats sometimes exhibit similarly complex behaviors during the cue-guided sample phase. These pause-and-reorient behaviors are typically comprised of rats hesitating and inspecting the sample-phase barrier. This study is the first to quantify and analyze these behaviors, which we hypothesize may be a behavioral manifestation of cue-specific encoding. Here, we use commonly employed methods to extract choice phase VTEs (cVTE) (Redish, 2016), and find that sample phase VTEs (sVTE) can be readily extracted from sample-phase traversals. To examine whether sVTE behaviors are linked to cue-guided encoding, our research will determine if there is a relationship between sVTEs and choice accuracy. In addition, we intend to analyze neural activity recorded from the hippocampus and prefrontal cortex, two regions critical for SWM, in order to understand if and how sVTEs may modulate neural representations of the task. By defining, quantifying, and analyzing novel sVTE behaviors, this study will expand current knowledge on the underlying strategies used to make accurate decisions during SWM-dependent tasks.

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Tracking a labeled bacterial cell wall fragment throughout the body and the brain to determine their specific cellular and molecular interactions

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