Department of Biological Sciences

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https://udspace.udel.edu/handle/19716/545

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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Now showing 1 - 20 of 64

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.
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, Rita
In 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.
Alumni Newsletter 2001
(University of Delaware Department of Biological Sciences, 2001-12) Carson, Daniel; Usher, David; Smith, David; Farach-Carson, Mary C.
Alumni Newsletter 2002
(University of Delaware Department of Biological Sciences, 2002-12) Carson, Daniel; Usher, David; Karin, Norman; Smith, David; Kingston, Sherrie
Alumni Newsletter 2003
(University of Delaware Department of Biological Sciences, 2003-12) Carson, Daniel; Smith, David; Usher, David; Drumm, Marc
Alumni Newsletter 2004
(University of Delaware Department of Biological Sciences, 2004-12) Carson, Daniel; Smith, David; Drumm, Marc
Alumni Newsletter 2005
(University of Delaware Department of Biological Sciences, 2005-12) Carson, Daniel; Duncan, Melinda; Usher, David; Smith, David; Drumm, Marc
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, Marc
Alumni Newsletter 2007
(University of Delaware Department of Biological Sciences, 2007-12) Carson, Daniel; Usher, David; Duncan, Melinda; Smith, David; Skopik, Steven; Drumm, Marc
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, Hélène
Purpose: 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.
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.
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.
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.
Erythroid differentiation in mouse erythroleukemia cells depends on Tmod3-mediated regulation of actin filament assembly into the erythroblast membrane skeleton
(FASEB Journal, 2022-02-23) Ghosh, Arit; Coffin, Megan; West, Richard; Fowler, Velia M.
Erythroid differentiation (ED) is a complex cellular process entailing morphologically distinct maturation stages of erythroblasts during terminal differentiation. Studies of actin filament (F-actin) assembly and organization during terminal ED have revealed essential roles for the F-actin pointed-end capping proteins, tropomodulins (Tmod1 and Tmod3). Tmods bind tropomyosins (Tpms), which enhance Tmod capping and F-actin stabilization. Tmods can also nucleate F-actin assembly, independent of Tpms. Tmod1 is present in the red blood cell (RBC) membrane skeleton, and deletion of Tmod1 in mice leads to a mild compensated anemia due to mis-regulated F-actin lengths and membrane instability. Tmod3 is not present in RBCs, and global deletion of Tmod3 leads to embryonic lethality in mice with impaired ED. To further decipher Tmod3’s function during ED, we generated a Tmod3 knockout in a mouse erythroleukemia cell line (Mel ds19). Tmod3 knockout cells appeared normal prior to ED, but showed defects during progression of ED, characterized by a marked failure to reduce cell and nuclear size, reduced viability, and increased apoptosis. Tmod3 does not assemble with Tmod1 and Tpms into the Triton X-100 insoluble membrane skeleton during ED, and loss of Tmod3 had no effect on α1,β1-spectrin and protein 4.1R assembly into the membrane skeleton. However, F-actin, Tmod1 and Tpms failed to assemble into the membrane skeleton during ED in absence of Tmod3. We propose that Tmod3 nucleation of F-actin assembly promotes incorporation of Tmod1 and Tpms into membrane skeleton F-actin, and that this is integral to morphological maturation and cell survival during erythroid terminal differentiation.
Genome-Wide Analysis of Differentially Expressed miRNAs and Their Associated Regulatory Networks in Lenses Deficient for the Congenital Cataract-Linked Tudor Domain Containing Protein TDRD7
(Frontiers in Cell and Developmental Biology, 2021-02-16) Anand, Deepti; Al Saai, Salma; Shrestha, Sanjaya K.; Barnum, Carrie E.; Chuma, Shinichiro; Lachke, Salil A.
Mutations/deficiency of TDRD7, encoding a tudor domain protein involved in post-transcriptional gene expression control, causes early onset cataract in humans. While Tdrd7 is implicated in the control of key lens mRNAs, the impact of Tdrd7 deficiency on microRNAs (miRNAs) and how this contributes to transcriptome misexpression and to cataracts, is undefined. We address this critical knowledge-gap by investigating Tdrd7-targeted knockout (Tdrd7-/-) mice that exhibit fully penetrant juvenile cataracts. We performed Affymetrix miRNA 3.0 microarray analysis on Tdrd7-/- mouse lenses at postnatal day (P) 4, a stage preceding cataract formation. This analysis identifies 22 miRNAs [14 over-expressed (miR-15a, miR-19a, miR-138, miR-328, miR-339, miR-345, miR-378b, miR-384, miR-467a, miR-1224, miR-1935, miR-1946a, miR-3102, miR-3107), 8 reduced (let-7b, miR-34c, miR-298, miR-382, miR-409, miR-1198, miR-1947, miR-3092)] to be significantly misexpressed (fold-change ≥ ± 1.2, p-value < 0.05) in Tdrd7-/- lenses. To understand how these misexpressed miRNAs impact Tdrd7-/- cataract, we predicted their mRNA targets and examined their misexpression upon Tdrd7-deficiency by performing comparative transcriptomics analysis on P4 and P30 Tdrd7-/- lens. To prioritize these target mRNAs, we used various stringency filters (e.g., fold-change in Tdrd7-/- lens, iSyTE-based lens-enriched expression) and identified 98 reduced and 89 elevated mRNA targets for overexpressed and reduced miRNAs, respectively, which were classified as “top-priority” “high-priority,” and “promising” candidates. For Tdrd7-/- lens overexpressed miRNAs, this approach identified 18 top-priority reduced target mRNAs: Alad, Ankrd46, Ceacam10, Dgat2, Ednrb, H2-Eb1, Klhl22, Lin7a, Loxl1, Lpin1, Npc1, Olfm1, Ppm1e, Ppp1r1a, Rgs8, Shisa4, Snx22 and Wnk2. Majority of these targets were also altered in other gene-specific perturbation mouse models (e.g., Brg1, E2f1/E2f2/E2f3, Foxe3, Hsf4, Klf4, Mafg/Mafk, Notch) of lens defects/cataract, suggesting their importance to lens biology. Gene ontology (GO) provided further insight into their relevance to lens pathology. For example, the Tdrd7-deficient lens capsule defect may be explained by reduced mRNA targets (e.g., Col4a3, Loxl1, Timp2, Timp3) associated with “basement membrane”. GO analysis also identified new genes (e.g., Casz1, Rasgrp1) recently linked to lens biology/pathology. Together, these analyses define a new Tdrd7-downstream miRNA-mRNA network, in turn, uncovering several new mRNA targets and their associated pathways relevant to lens biology and offering molecular insights into the pathology of congenital cataract.
Harnessing the Power of Induced Pluripotent Stem Cells and Gene Editing Technology: Therapeutic Implications in Hematological Malignancies
(Cells, 2021-10-09) Sidhu, Ishnoor; Barwe, Sonali P.; Pillai, Raju K.; Gopalakrishnapillai, Anilkumar
In vitro modeling of hematological malignancies not only provides insights into the influence of genetic aberrations on cellular and molecular mechanisms involved in disease progression but also aids development and evaluation of therapeutic agents. Owing to their self-renewal and differentiation capacity, induced pluripotent stem cells (iPSCs) have emerged as a potential source of short in supply disease-specific human cells of the hematopoietic lineage. Patient-derived iPSCs can recapitulate the disease severity and spectrum of prognosis dictated by the genetic variation among patients and can be used for drug screening and studying clonal evolution. However, this approach lacks the ability to model the early phases of the disease leading to cancer. The advent of genetic editing technology has promoted the generation of precise isogenic iPSC disease models to address questions regarding the underlying genetic mechanism of disease initiation and progression. In this review, we discuss the use of iPSC disease modeling in hematological diseases, where there is lack of patient sample availability and/or difficulty of engraftment to generate animal models. Furthermore, we describe the power of combining iPSC and precise gene editing to elucidate the underlying mechanism of initiation and progression of various hematological malignancies. Finally, we discuss the power of iPSC disease modeling in developing and testing novel therapies in a high throughput setting.
In the Spotlight: 30 Years of McKinly Lab
(University of Delaware Department of Biological Sciences, 2007-10) Drumm, Marc
In The Spotlight: Cell Biologist, Ulhas P. Naik, Ph.D.
(University of Delaware Department of Biological Sciences, 2000-11) Drumm, Marc
In The Spotlight: Class of 2002 Honors
(University of Delaware Department of Biological Sciences, 2002-05) Usher, David
In The Spotlight: Class of 2004 Honors
(University of Delaware Department of Biological Sciences, 2004-05) Usher, David

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