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The Department of Biological Sciences is composed of 38 faculty engaged in teaching and research activities. The Department is home to many vibrant research programs and our faculty are located in state-of-the-art laboratories in Wolf and McKinly Halls as well as the Delaware Biotechnology Institute, a joint effort between the University of Delaware and area biotechnology industries.
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Item A long-term high-fat diet induces differential gene expression changes in spatially distinct adipose tissue of male mice(Physiological Genomics, 2024-11-11) Alradi, Malak; Askari, Hassan; Shaw, Mark; Bhavsar, Jaysheel D.; Kingham, Brewster F.; Polson, Shawn W.; Fancher, Ibra S.The accumulation of visceral adipose tissue (VAT) is strongly associated with cardiovascular disease and diabetes. In contrast, individuals with increased subcutaneous adipose tissue (SAT) without corresponding increases in VAT are associated with a metabolic healthy obese phenotype. These observations implicate dysfunctional VAT as a driver of disease processes, warranting investigation into obesity-induced alterations of distinct adipose depots. To determine the effects of obesity on adipose gene expression, male mice (n = 4) were fed a high-fat diet to induce obesity or a normal laboratory diet (lean controls) for 12–14 mo. Mesenteric VAT and inguinal SAT were isolated for bulk RNA sequencing. AT from lean controls served as a reference to obesity-induced changes. The long-term high-fat diet induced the expression of 169 and 814 unique genes in SAT and VAT, respectively. SAT from obese mice exhibited 308 differentially expressed genes (164 upregulated and 144 downregulated). VAT from obese mice exhibited 690 differentially expressed genes (262 genes upregulated and 428 downregulated). KEGG pathway and GO analyses revealed that metabolic pathways were upregulated in SAT versus downregulated in VAT while inflammatory signaling was upregulated in VAT. We next determined common genes that were differentially regulated between SAT and VAT in response to obesity and identified four genes that exhibited this profile: elovl6 and kcnj15 were upregulated in SAT/downregulated in VAT while trdn and hspb7 were downregulated in SAT/upregulated in VAT. We propose that these genes in particular should be further pursued to determine their roles in SAT versus VAT with respect to obesity. NEW & NOTEWORTHY A long-term high-fat diet induced the expression of more than 980 unique genes across subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT). The high-fat diet also induced the differential expression of nearly 1,000 AT genes. We identified four genes that were oppositely expressed in SAT versus VAT in response to the high-fat diet and propose that these genes in particular may serve as promising targets aimed at resolving VAT dysfunction in obesity.Item A Review of IsomiRs in Colorectal Cancer(Non-Coding RNA, 2023-06-07) Lausten, Molly A.; Boman, Bruce M.As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine.Item Adseverin, an actin-binding protein, modulates hypertrophic chondrocyte differentiation and osteoarthritis progression(Science Advances, 2023-08-04) Chan, Byron; Glogauer, Michael; Wang, Yongqiang; Wrana, Jeffrey; Chan, Kin; Beier, Frank; Bali, Supinder; Hinz, Boris; Parreno, Justin; Ashraf, Sajjad; Kandel, RitaIn osteoarthritis (OA), a disease characterized by progressive articular cartilage degradation and calcification, the articular chondrocyte phenotype changes and this correlates with actin cytoskeleton alterations suggesting that it regulates gene expression essential for proper phenotype. This study reports that OA is associated with the loss of adseverin, an actin capping and severing protein. Adseverin deletion (Adseverin−/−) in mice compromised articular chondrocyte function, by reducing F-actin and aggrecan expression and increasing apoptosis, Indian hedgehog, Runx2, MMP13, and collagen type X expression, and cell proliferation. This led to stiffer cartilage and decreased hyaline and increased calcified cartilage thickness. Together, these changes predisposed the articular cartilage to enhanced OA severity in Adseverin−/− mice who underwent surgical induction of OA. Adseverin−/− chondrocyte RNA sequencing and in vitro studies together suggests that adseverin modulates cell viability and prevents mineralization. Thus, adseverin maintains articular chondrocyte phenotype and cartilage tissue homeostasis by preventing progression to hypertrophic differentiation in vivo. Adseverin may be chondroprotective and a potential therapeutic target.Item Alumni Newsletter 2001(University of Delaware Department of Biological Sciences, 2001-12) Carson, Daniel; Usher, David; Smith, David; Farach-Carson, Mary C.Item Alumni Newsletter 2002(University of Delaware Department of Biological Sciences, 2002-12) Carson, Daniel; Usher, David; Karin, Norman; Smith, David; Kingston, SherrieItem Alumni Newsletter 2003(University of Delaware Department of Biological Sciences, 2003-12) Carson, Daniel; Smith, David; Usher, David; Drumm, MarcItem Alumni Newsletter 2004(University of Delaware Department of Biological Sciences, 2004-12) Carson, Daniel; Smith, David; Drumm, MarcItem Alumni Newsletter 2005(University of Delaware Department of Biological Sciences, 2005-12) Carson, Daniel; Duncan, Melinda; Usher, David; Smith, David; Drumm, MarcItem Alumni Newsletter 2006(University of Delaware Department of Biological Sciences, 2006-12) Carson, Daniel; Usher, David; Smith, David; Duncan, Melinda; Farach-Carson, Mary C.; Drumm, MarcItem Alumni Newsletter 2007(University of Delaware Department of Biological Sciences, 2007-12) Carson, Daniel; Usher, David; Duncan, Melinda; Smith, David; Skopik, Steven; Drumm, MarcItem Association of Behavioral and Clinical Risk Factors With Cataract: A Two-Sample Mendelian Randomization Study(Investigative Ophthalmology & Visual Science, 2023-07) Jiang, Chen; Melles, Ronald B.; Sangani, Poorab; Hoffmann, Thomas J.; Hysi, Pirro G.; Glymour, M. Maria; Jorgenson, Eric; Lachke, Salil A.; Choquet, HélènePurpose: To investigate the association of genetically determined primary open-angle glaucoma (POAG), myopic refractive error (RE), type 2 diabetes (T2D), blood pressure (BP), body mass index (BMI), cigarette smoking, and alcohol consumption with the risk of age-related cataract. Methods: To assess potential causal effects of clinical or behavioral factors on cataract risk, we conducted two-sample Mendelian randomization analyses. Genetic instruments, based on common genetic variants associated with risk factors at genome-wide significance (P < 5 × 10−8), were derived from published genome-wide association studies (GWAS). For age-related cataract, we used GWAS summary statistics from our previous GWAS conducted in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (28,092 cataract cases and 50,487 controls; all non-Hispanic whites) or in the UK Biobank (31,852 cataract cases and 428,084 controls; all European-descent individuals). We used the inverse-variance weighted (IVW) method as our primary source of Mendelian randomization estimates and conducted common sensitivity analyses. Results: We found that genetically determined POAG and mean spherical equivalent RE were significantly associated with cataract risk (IVW model: odds ratio [OR] = 1.04; 95% confidence interval [CI], 1.01–1.08; P = 0.018; per diopter more hyperopic: OR = 0.92; 95% CI, 0.89–0.93; P = 6.51 × 10−13, respectively). In contrast, genetically determined T2D, BP, BMI, cigarette smoking, or alcohol consumption were not associated with cataract risk (P > 0.05). Conclusions: Our results provide evidence that genetic risks for POAG and myopia may be causal risk factors for age-related cataract. These results are consistent with previous observational studies reporting associations of myopia with cataract risk. This information may support population cataract risk stratification and screening strategies.Item Biophysical Regulation of Chromatin Architecture Instills a Mechanical Memory in Mesenchymal Stem Cells(Nature Publishing Group, 2015-11-23) Heo, Su-Jin; Thorpe, Stephen D.; Driscoll, Tristan P.; Duncan, Randall L.; Lee, David A.; Mauck, Robert L.; Su-Jin Heo, Stephen D. Thorpe, Tristan P. Driscoll, Randall L. Duncan, David A. Lee & Robert L. Mauck; Duncan, Randall L.Mechanical cues direct the lineage commitment of mesenchymal stem cells (MSCs). In this study, we identified the operative molecular mechanisms through which dynamic tensile loading (DL) regulates changes in chromatin organization and nuclear mechanics in MSCs. Our data show that, in the absence of exogenous differentiation factors, short term DL elicits a rapid increase in chromatin condensation, mediated by acto-myosin based cellular contractility and the activity of the histone-lysine N-methyltransferase EZH2. The resulting change in chromatin condensation stiffened the MSC nucleus, making it less deformable when stretch was applied to the cell. We also identified stretch induced ATP release and purinergic calcium signaling as a central mediator of this chromatin condensation process. Further, we showed that DL, through differential stabilization of the condensed chromatin state, established a ‘mechanical memory’ in these cells. That is, increasing strain levels and number of loading events led to a greater degree of chromatin condensation that persisted for longer periods of time after the cessation of loading. These data indicate that, with mechanical perturbation, MSCs develop a mechanical memory encoded in structural changes in the nucleus which may sensitize them to future mechanical loading events and define the trajectory and persistence of their lineage specification.Item Chicken intestinal organoids: a novel method to measure the mode of action of feed additives(Frontiers in Immunology, 2024-05-20) Mitchell, Jordan; Sutton, Kate; Elango, Jeyashree Nathan; Borowska, Dominika; Perry, Famatta; Lahaye, Ludovic; Santin, Elizabeth; Arsenault, Ryan J.; Vervelde, LonnekeThere is a rapidly growing interest in how the avian intestine is affected by dietary components and feed additives. The paucity of physiologically relevant models has limited research in this field of poultry gut health and led to an over-reliance on the use of live birds for experiments. The development of complex 3D intestinal organoids or “mini-guts” has created ample opportunities for poultry research in this field. A major advantage of the floating chicken intestinal organoids is the combination of a complex cell system with an easily accessible apical-out orientation grown in a simple culture medium without an extracellular matrix. The objective was to investigate the impact of a commercial proprietary blend of organic acids and essential oils (OA+EO) on the innate immune responses and kinome of chicken intestinal organoids in a Salmonella challenge model. To mimic the in vivo prolonged exposure of the intestine to the product, the intestinal organoids were treated for 2 days with 0.5 or 0.25 mg/mL OA+EO and either uninfected or infected with Salmonella and bacterial load in the organoids was quantified at 3 hours post infection. The bacteria were also treated with OA+EO for 1 day prior to challenge of the organoids to mimic intestinal exposure. The treatment of the organoids with OA+EO resulted in a significant decrease in the bacterial load compared to untreated infected organoids. The expression of 88 innate immune genes was investigated using a high throughput qPCR array, measuring the expression of 88 innate immune genes. Salmonella invasion of the untreated intestinal organoids resulted in a significant increase in the expression of inflammatory cytokine and chemokines as well as genes involved in intracellular signaling. In contrast, when the organoids were treated with OA+EO and challenged with Salmonella, the inflammatory responses were significantly downregulated. The kinome array data suggested decreased phosphorylation elicited by the OA+EO with Salmonella in agreement with the gene expression data sets. This study demonstrates that the in vitro chicken intestinal organoids are a new tool to measure the effect of the feed additives in a bacterial challenge model by measuring innate immune and protein kinases responses.Item Clinicians’ Perspectives on Proactive Patient Safety Behaviors in the Perioperative Environment(Jama Network Open, 2023-04-11) Duffy, Caoimhe; Menon, Neil; Horak, David; Bass, Geoffrey D.; Talwar, Ruchika; Lorenzi, Cara; Vo, Christina Taing; Chiang, Chienhui; Ziemba, Justin B.Importance The perioperative environment is hazardous, but patients remain safe with a successful outcome during their care due to staff adaptability and resiliency. The behaviors that support this adaptability and resilience have yet to be defined or analyzed. One Safe Act (OSA), a tool and activity developed to capture self-reported proactive safety behaviors that staff use in their daily practice to promote individual and team-based safe patient care, may allow for improved definition and analysis of these behaviors. Objective To thematically analyze staff behaviors using OSA to understand what may serve as the basis for proactive safety in the perioperative environment. Design, Setting, and Participants This qualitative thematic analysis included a convenience sample of perioperative staff at a single-center, tertiary care academic medical center who participated in an OSA activity during a 6-month period in 2021. All perioperative staff were eligible for inclusion. A combined deductive approach, based on a human factor analysis and classification framework, as well as an inductive approach was used to develop themes and analyze the self-reported staff safety behaviors. Exposures Those selected to participate were asked to join an OSA activity, which was conducted in-person by a facilitator. Participants were to self-reflect about their OSA (proactive safety behavior) and record their experience as free text in an online survey tool. Main Outcome and Measures The primary outcome was the development and application of a set of themes to describe proactive safety behaviors in the perioperative environment. Results A total of 140 participants (33 nurses [23.6%] and 18 trainee physicians [12.9%]), which represented 21.3% of the 657 total perioperative department full-time staff, described 147 behaviors. A total of 8 non–mutually exclusive themes emerged with the following categories and frequency of behaviors: (1) routine-based adaptations (46 responses [31%]); (2) resource availability and assessment adaptations (31 responses [21%]); (3) communication and coordination adaptation (23 responses [16%]); (4) environmental ergonomics adaptation (17 responses [12%]); (5) situational awareness adaptation (12 responses [8%]); (6) personal or team readiness adaptation (8 responses [5%]); (7) education adaptation (5 responses [3%]); and (8) social awareness adaptation (5 responses [3%]). Conclusions and Relevance The OSA activity elicited and captured proactive safety behaviors performed by staff. A set of behavioral themes were identified that may serve as the basis for individual practices of resilience and adaptability that promote patient safety.Item Coupling Novel Probes with Molecular Localization Microscopy Reveals Cell Wall Homeostatic Mechanisms in Staphylococcus aureus(ACS Chemical Biology, 2022-11-22) Lund, Victoria A.; Gangotra, Haneesh; Zhao, Zhen; Sutton, Joshua A. F.; Wacnik, Katarzyna; DeMeester, Kristen; Liang, Hai; Santiago, Cintia; Grimes, Catherine Leimkuhler; Jones, Simon; Foster, Simon J.Bacterial cell wall peptidoglycan is essential for viability, and its synthesis is targeted by antibiotics, including penicillin. To determine how peptidoglycan homeostasis controls cell architecture, growth, and division, we have developed novel labeling approaches. These are compatible with super-resolution fluorescence microscopy to examine peptidoglycan synthesis, hydrolysis, and the localization of the enzymes required for its biosynthesis (penicillin binding proteins (PBPs)). Synthesis of a cephalosporin-based fluorescent probe revealed a pattern of PBPs at the septum during division, supporting a model of dispersed peptidoglycan synthesis. Metabolic and hydroxylamine-based probes respectively enabled the synthesis of glycan strands and associated reducing termini of the peptidoglycan to be mapped. Foci and arcs of reducing termini appear as a result of both synthesis of glycan strands and glucosaminidase activity of the major peptidoglycan hydrolase, SagB. Our studies provide molecular level details of how essential peptidoglycan dynamics are controlled during growth and division.Item Cultural Competence in Pediatrics: Health Care Provider Knowledge, Awareness, and Skills(MDPI AG, 2015-12-15) Dabney, Kirk; McClarin, Lavisha; Romano, Emily; Fitzgerald, Diane; Bayne, Lynn; Oceanic, Patricia; Nettles, Arie L.; Holmes, Laurens Jr.; Kirk Dabney, Lavisha McClarin, Emily Romano, Diane Fitzgerald, Lynn Bayne, Patricia Oceanic, Arie L. Nettles and Laurens Holmes Jr.; Holmes, Laurens Jr.The purpose of this study was to assess the effects of a cultural competence training (CCT) program on pediatric health care providers’ self-reported ability to provide culturally competent care to a diverse pediatric patient population. This quantitative, nested ecologic level study design used a repeated measure in the form of pre-test and post-test data to assess percent change in providers’ cultural awareness, experience working or learning about different cultures, and preparedness and skills in working with different cultures before and after CCT. The study was conducted between 2011 and 2012 in a pediatric hospital and associated outpatient offices. The sample consisted of pediatric health care providers from various departments, mainly physicians and nurses (n = 69). Participants completed a pre-intervention cultural competence assessment and then were subjected to a cultural competence-training program, after which they completed the assessment a second time. The baseline and post-intervention data were collected in the form of Likert scales and transformed into a quintile or quartile scale as appropriate. Data were assessed using paired t-tests or Wilcoxon’s signed-rank tests. Providers indicated a 13% increase in knowledge (53.9% vs. 66.7%, t = 3.4, p = 0.001), 8.7% increase in awareness (46.7% vs. 55.4%, t = 3.0, p = 0.002), and 8% statistically marginal increase in skills (66.4% vs. 74.5%, z = 1.8, p = 0.06). Culturally competent training in a pediatric environment significantly enhances knowledge, awareness and to some extent skills in providing care to culturally diverse patient population.Item Development of an efficient, effective, and economical technology for proteome analysis(Cell Reports: Methods, 2024-06-11) Martin, Katherine R.; Le, Ha T.; Abdelgawad, Ahmed; Yang, Canyuan; Lu, Guotao; Keffer, Jessica L.; Zhang, Xiaohui; Zhuang, Zhihao; Asare-Okai, Papa Nii; Chan, Clara S.; Batish, Mona; Yu, YanbaoHighlights • Rapid, robust, and cost-effective alternative to proteomics sample preparation • Versatile filter devices can meet a wide range of proteomics analysis needs • On-filter in-cell digestion facilitates low-input proteomics • Ready-to-go E3 and E4 filter devices are available Motivation Conventional proteomics sample processing methods often have high technical barriers to broad biomedical scientists, leading to difficulties for quick adoption and standardization. Existing protocols are also typically associated with costly reagents and accessories, making them less feasible for resource-limited settings as well as for clinical proteomics and/or core facilities where large numbers of samples are usually processed. Thus, there is a strong unmet need for an easy-to-use, reliable, and low-cost approach for general proteomics sample preparation. Summary We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. Graphical abstract available at: https://doi.org/10.1016/j.crmeth.2024.100796Item Discovery of Power-Law Growth in the Self- Renewal of Heterogeneous Glioma Stem Cell Populations(PLOS (Public Library of Science), 2015-08-18) Sugimori, Michiya; Hayakawa, Yumiko; Boman, Bruce M.; Fields, Jeremy Z.; Awaji, Miharu; Kozano, Hiroko; Tamura, Ryoi; Yamamoto, Seiji; Ogata, Toru; Yamada, Mitsuhiko; Endo, Shunro; Kurimoto, Masanori; Kuroda, Satoshi; Michiya Sugimori, Yumiko Hayakawa, Bruce M. Boman, Jeremy Z. Fields, Miharu Awaji, Hiroko Kozano, Ryoi Tamura, Seiji Yamamoto, Toru Ogata, Mitsuhiko Yamada, Shunro Endo, Masanori Kurimoto, Satoshi Kuroda; Boman, Bruce M.BACKGROUND Accumulating evidence indicates that cancer stem cells (CSCs) drive tumorigenesis. This suggests that CSCs should make ideal therapeutic targets. However, because CSC populations in tumors appear heterogeneous, it remains unclear how CSCs might be effectively targeted. To investigate the mechanisms by which CSC populations maintain heterogeneity during self-renewal, we established a glioma sphere (GS) forming model, to generate a population in which glioma stem cells (GSCs) become enriched. We hypothesized, based on the clonal evolution concept, that with each passage in culture, heterogeneous clonal sublines of GSs are generated that progressively show increased proliferative ability. METHODOLOGY/PRINCIPAL FINDINGS To test this hypothesis, we determined whether, with each passage, glioma neurosphere culture generated from four different glioma cell lines become progressively proliferative (i.e., enriched in large spheres). Rather than monitoring self-renewal, we measured heterogeneity based on neurosphere clone sizes (#cells/clone). Log-log plots of distributions of clone sizes yielded a good fit (r>0.90) to a straight line (log(% total clones) = k*log(#cells/ clone)) indicating that the system follows a power-law (y = xk) with a specific degree exponent (k = −1.42). Repeated passaging of the total GS population showed that the same power-law was maintained over six passages (CV = −1.01 to −1.17). Surprisingly, passage of either isolated small or large subclones generated fully heterogeneous populations that retained the original power-law-dependent heterogeneity. The anti-GSC agent Temozolomide, which is well known as a standard therapy for glioblastoma multiforme (GBM), suppressed the self-renewal of clones, but it never disrupted the power-law behavior of a GS population. CONCLUSIONS/SIGNIFICANCE Although the data above did not support the stated hypothesis, they did strongly suggest a novel mechanism that underlies CSC heterogeneity. They indicate that power-law growth governs the self-renewal of heterogeneous glioma stem cell populations. That the data always fit a power-law suggests that: (i) clone sizes follow continuous, non-random, and scale-free hierarchy; (ii) precise biologic rules that reflect self-organizing emergent behaviors govern the generation of neurospheres. That the power-law behavior and the original GS heterogeneity are maintained over multiple passages indicates that these rules are invariant. These self-organizing mechanisms very likely underlie tumor heterogeneity during tumor growth. Discovery of this power-law behavior provides a mechanism that could be targeted in the development of new, more effective, anti-cancer agents. IntroductionItem Dynamic bioinspired coculture model for probing ER+ breast cancer dormancy in the bone marrow niche(Science Advances, 2023-03-08) Pradhan, Lina; Moore, DeVonte; Ovadia, Elisa M.; Swedzinski, Samantha L.; Cossette, Travis; Sikes, Robert A.; van Golen, Kenneth; Kloxin, April M.Late recurrences of breast cancer are hypothesized to arise from disseminated tumor cells (DTCs) that reactivate after dormancy and occur most frequently with estrogen receptor–positive (ER+) breast cancer cells (BCCs) in bone marrow (BM). Interactions between the BM niche and BCCs are thought to play a pivotal role in recurrence, and relevant model systems are needed for mechanistic insights and improved treatments. We examined dormant DTCs in vivo and observed DTCs near bone lining cells and exhibiting autophagy. To study underlying cell-cell interactions, we established a well-defined, bioinspired dynamic indirect coculture model of ER+ BCCs with BM niche cells, human mesenchymal stem cells (hMSCs) and fetal osteoblasts (hFOBs). hMSCs promoted BCC growth, whereas hFOBs promoted dormancy and autophagy, regulated in part by tumor necrosis factor–α and monocyte chemoattractant protein 1 receptor signaling. This dormancy was reversible by dynamically changing the microenvironment or inhibiting autophagy, presenting further opportunities for mechanistic and targeting studies to prevent late recurrence.Item Dynamic Change and Target Prediction of Axon-Specific MicroRNAs in Regenerating Sciatic Nerve(PLOS (Public Library of Science), 2015-09-02) Phay, Monichan; Kim, Hak Hee; Yoo, Soonmoon; Monichan Phay, Hak Hee Kim, Soonmoon Yoo; Phay, MonichanInjury to axons in the peripheral nervous system induces rapid and local regenerative responses to form a new growth cone, and to generate a retrogradely transporting injury signal. The evidence for essential roles of intra-axonal protein synthesis during regeneration is now compelling. MicroRNA (miRNA) has recently been recognized as a prominent player in post-transcriptional regulation of axonal protein synthesis. Here, we directly contrast temporal changes of miRNA levels in the sciatic nerve following injury, as compared to those in an uninjured nerve using deep sequencing. Small RNAs (<200 nucleotides in length) were fractionated from the proximal nerve stumps to improve the representation of differential miRNA levels. Of 141 axoplasmic miRNAs annotated, 63 rat miRNAs showed significantly differential levels at five time points following injury, compared to an uninjured nerve. The differential changes in miRNA levels responding to injury were processed for hierarchical clustering analyses, and used to predict target mRNAs by Targetscan and miRanda. By overlapping these predicted targets with 2,924 axonally localizing transcripts previously reported, the overlapping set of 214 transcripts was further analyzed by the Gene Ontology enrichment and Ingenuity Pathway Analyses. These results suggest the possibility that the potential targets for these miRNAs play key roles in numerous neurological functions involved in ER stress response, cytoskeleton dynamics, vesicle formation, and neurodegeneration and-regeneration. Finally, our results suggest that miRNAs could play a direct role in regenerative response and may be manipulated to promote regenerative ability of injured nerves. Introduction