Graduate Student Publications

2020

• Shaopeng Pei, Sucharitha Parthasarathy, Ashutosh Parjuli, Jerahme Martinez, Mengxi Lv, Sida Jiang, Danielle Wu, Shuo Wei, X Lucas Lu, Mary C. Farach-Carson, Catherine B. Kirn-Safrin, Liyun Wang - Perlecan/Hspg2 deficiency impairs bone's calcium signaling and associated transcriptome in response to mechanical loading

• Daniel Halloran, Vrathasha Vrathasha, Hilary W. Durbano and Anja Nohe; Bone Morphogenetic Protein-2 Conjugated to Quantum Dot®s is Biologically Functional; Nanomaterials

• Aryal, S., Viet J., Weatherbee, B.A., Siddam A.D., Hernandez, F.G., Gautier-Courteille, C., Paillard, L., Lachke, S.A. The cataract-linked RNA-binding protein Celf1 post-transcriptionally controls the spatiotemporal expression of the key homeodomain transcription factors Pax6 and Prox1 in lens development. Human Genetics (2020).

• Halloran, D.; Durbano, H.W.; Nohe, A. Bone Morphogenetic Protein-2 in Development and Bone Homeostasis. J. Dev. Biol. 2020, 8, 19.

2019

• Weatherbee, B.A.T., Barton, J.R., Siddam, A.D., Anand, D., Lachke, S.A.* Molecular characterization of the human lens epithelium-derived cell line SRA01/04.Experimental Eye Research 2019: accepted on August 30, 2019 *Corresponding Author

• Barnum, C.E., Al Saai, S., Cheng, C., Anand, D., Patel, S.D., Dash, S., Siddam, A.D., Glazewski, L., Paglione, E., Polson, S., Chuma, S., Mason R.W., Batish, M., Fowler, V.M., Lachke, S.A.* The Tudor-domain family protein TDRD7, mutated in congenital cataract, controls the heat shock protein HSPB1 and lens fiber cell morphology. Human Molecular Genetics 2019: in revision *Corresponding Author

• "Dash, S., Brastrom, M.K., Patel, S.D., Scott, A.C., Slusarski, D.C., Lachke, S.A.* The master transcription factors SOX2, mutated in anophthalmia/microphthalmia, is regulated by the conserved RNA-binding protein RBM24 in vertebrate eye development. Human Molecular Genetics 2019: in minor revision *Corresponding Author"

• Aryal, S., Hernandez, F.G., Anand, D., Weatherbee, B.A.T., Willmarth, P., Reddy, A., David, L.L., Lachke, S.A.* MS/MS in silico subtraction-based profiling of the developing lens to facilitate cataract gene discovery.  2019: submitted *Corresponding Author

• Remsburg*, C., Konrad*, K, Sampilo*, NF. and J.L. Song (2019). Functional analysis of microRNAs. Methods in Cell Biology. Echinoderms part B, Volume 151.

• Jiejing Li, Mark Perfetto, Christopher Materna, Rebecca Li, Hong Thi Tran, Kris Vleminckx, Melinda K. Duncan and Shuo Wei (2019), A new transgenic reporter line reveals Wnt-dependent Snail2 re-expression and cranial neural crest differentiation in Xenopus bioRxiv520726; Scientific Reports; 9(1) 11191

• Mahbubul H. Shihan, Samuel G. Novo, and Melinda K. Duncan (2019) Cataract surgeon viewpoints on the need for novel preventative anti-inflammatory and anti-posterior capsular opacification therapies Current Medical Research and Opinion 35, 1971-1981

• Gregory, G.S., D.P. Morreale, M.R. Carpenter, S.S. Kalburge, and E.F. Boyd. 2019. Quorum sensing regulator OpaR controls expression of the compatible solute ectoine. Applied and Environmental Microbiology, 85:

• Regmi, A. and E.F. Boyd. 2019. Carbohydrate metabolism systems present on genomic islands that are lost and gained in Vibrio parahaemolyticus. BMC Microbiology, 19:112.

• McDonald, N.D, Regmi, A., J.D. Borowski, D.P. Morreale, and Boyd, E.F. 2019. CRISPR-Cas systems are carried on mobile genetic elements in Vibrio species. BMC Genomics, 4;20(1):105. * co-first authors. *Undergraduate researcher

• Yuhao Zhang, Cristian Coarfa, Xiaoyu Dong, Weiwu Jiang, Brielle Hayward-Piatkovskyi, Jason Gleghorn, and Krithika Lingappan (2019) MicroRNA-30a as a candidate underlying sex-specific differences in neonatal hyperoxic lung injury: Implications for BPD. American Journal of Physiology-Lung Cellular and Molecular Physiology 316(1):L144-L156. doi: 10.1152/ajplung.00372.2018.

2018

• Yichen Wang, Priyha Mahesh, Yan Wang, Samuel G. Novo, Mahbubul H. Shihan, Brielle, Hayward-Piatkovskyi, and Melinda K. Duncan (2018) Spatiotemporal dynamics of canonical Wnt signaling during embryonic eye development and posterior capsular opacification (PCO). Experimental Eye Research 175, 148-158

• Kakrana, A., Yang, A., Anand, D., Djordjevic, D., Ramachandruni, S.D., Singh, A., Huang, H., Ho, J.W.K.*, Lachke, S.A.*iSyTE 2.0: a developmental expression-based database for eye gene discovery. *Corresponding authors Nucleic Acids Research 2018: 46:D875-D885. View in: Pubmed

• Budak, G., Dash, S., Srivastava, R., Lachke, S.A., Janga, S.C. Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. Experimental Eye Research 2018: 168:57-68. View in: Pubmed

• Anand, D., Agrawal, S.A., Slavotinek, A., Lachke, S.A.* Mutation update of transcription factor genes HSF4, FOXE3, MAF and PITX3 cataracts and other developmental ocular defects.  Human Mutation 2018: 39:471-494. View in: Pubmed

• Siddam, A.D., Gautier-Courteille, C., Perez-Campos, L., Anand, D., Kakrana, A., Dang, C.A., Legagneux, V., Méreau, A., Viet, J., Gross, J.M., Paillard, L.*, Lachke, S.A.* The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development. *Corresponding authors. PLoS Genetics 2018: 14(3):e1007278. View in: Pubmed

• Anand, D., Kakrana, A., Siddam, A.D., Huang, H., Saadi, I., Lachke, S.A.* RNA-sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery. Human Genetics 2018: 137:941-954. View in: Pubmed

• Sampilo*1, NF., Stepicheva*1,3, N.A., Zaidi*1, S.A.M., Wang2, L., Wu2, W.,Wikramanayake2, A., and J.L. Song1* (2018). Inhibition of microRNA suppression of Dishevelled results in Wnt pathway associated developmental defects. Development, Nov2. pii: dev.167130. doi: 10.1242/dev.167130.

• Jian Jiang, Mahbubul Shihan, Yan Wang and Melinda K. Duncan (2018) Lens epithelial cells initiate the inflammatory response following cataract surgery. Investigative Ophthalmology and Visual Sciences 59, 4986-4997. Denoted a "hot topic" in ophthalmology at the 2018 ARVO meeting

• Mc Donald, N.D., C. L. Grimes, K. Demeester, and E.F. Boyd. 2018. Structural and functional characterization of a modified legionaminic acid involved in glycosylation of the bacterial lipopolysaccharide. Journal Biological Chemistry, 7;293(49):19113-19126.

2017

• "Wang, Y., Terrell, A.M., Riggio, B.A., Anand, D., Lachke, S.A., Duncan, M.K. Beta1-integrin deletion from the lens activates cellular stress responses leading to fibrosis and apoptosis. Investigative Ophthalmology and Visual Science 2017: 58:3896-3922. View in: Pubmed"

• Srivastava, R., Budak, G., Dash, S., Lachke, S.A., Janga, S.C. Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. Scientific Reports 2017: 7:11572. View in: Pubmed

• "Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management. Langwig KE, Wargo AR, Jones DR, Viss JR, Rutan BJ, Egan NA, Sá-Guimarães P, Kim MS, Kurath G, Gomes MGM, Lipsitch M. MBio. 2017 Nov 21;8(6). pii: e00796-17. doi: 10.1128/mBio.00796-17. PMID:29162706"

• Stepicheva*, N., M. Dumas**, P. Kobi*, J. Donaldson, and J.L. Song (2017) The small GTPase Arf6 regulates sea urchin cellular morphogenesis. Differentiation. May - Jun;95:31-43. doi: 10.1016/j.diff.2017.01.003. PMID:28188999

• Mallika Pathania, Yan Wang, Vladimir N. Simirskii, and Melinda K. Duncan (2016) b1-integrin controls cell fate specification in early lens development Differentiation, 92, 133-147.

• Dylan S. Audette, David A. Scheiblin and Melinda K. Duncan (2017) The molecular mechanisms underlying lens fiber elongation. Experimental Eye Research-invited review, David Beebe memorial issue 156, 41-49.

• Carpenter, M.R., S.S. Kalburge, J.D. Borowski, M. Peters*, R.R. Colwell, and E.F. Boyd. 2017. CRISPR-Cas and contact dependent secretion systems carried on excisable pathogenicity islands with conserved recombination modules. J. Bacteriology, 25;199(10). pii: e00842-16.

• Kalburge, S.S., Carpenter, M.R., S. Rozovsky, and E.F. Boyd. 2017. Quorum sensing regulators are required for Vibrio parahaemolyticus metabolic fitness. Infection and Immunity, 23;85(3). pii: e00930-16.

2016

• Audette, D.S., Anand, D., So, T., Rubenstein, T.B., Lachke, S.A., Lovicu, F.J., Duncan, M.K.Prox1 and fibroblast growth factor receptors form a novel regulatory loop controlling lens fiber differentiation and gene expression. Development 2016: 143:318-328. View in: Pubmed

• Dash, S., Siddam, A.D., Barnum, C.E., Janga, S.C., Lachke, S.A.* RNA binding proteins in eye development and disease: implication of RNA granule components. Wiley Interdisciplinary Reviews: RNA 2016 7:527-557.*** View in: Pubmed * Corresponding Author

• Dylan S. Audette, Deepti Anand, Tammy So, Troy B. Rubenstein, Salil A. Lachke, Frank J. Lovicu and Melinda K. Duncan (2016) Prox1 and fibroblast growth factor receptors form a novel regulatory loop controlling lens fiber differentiation and gene expression Development 143, 318-328.

• Mallika Pathania, Yan Wang, Vladimir N. Simirskii, and Melinda K. Duncan (2016) b1-integrin controls cell fate specification in early lens development Differentiation, 92, 133-147.

• Melinda K. Duncan, Yichen Wang and Christopher D. Riemann (2016) Aniridia fibrosis syndrome: An infrequent but potentially very serious problem in congenital aniridia. Eye on Aniridia Newsletter, Fall 2016 edition, Aniridia Foundation International.

• McDonald, N.D., J.B. Lubin, N. Chowdhury, and E.F. Boyd. 2016. Host derived sialic acids are an important nutrient source that increases bacterial fitness in vivo. Mbio. 7(2):e02237-15.

• Carpenter, M.R., S. Rozovsky, and E.F. Boyd. 2016. Pathogenicity island cross-talk mediated by recombination directionality factors can facilitate excision from the chromosome. J. Bacteriology, 198(5):766-76.

2015

• Agrawal, S.A., Anand, D., Siddam, A.D., Kakrana, A., Schieblin, D.A., Dang, C.A., Terrell, A.M., Waters, S.M., Singh, A., Motohashi, H., Yamamoto, M., Lachke, S.A.* Compound mouse mutants of bZIP transcription factors MafG and MafK reveal a regulatory network of lens fiber cell genes in cataractogenesis. Human Genetics 2015: 134:717-735. View in: Pubmed *Corresponding Author

• Anand, D., Agrawal, S., Siddam, A., Motohashi, H., Yamamoto, M., Lachke, S.A.* An integrative approach to analyze microarray datasets for prioritization of genes relevant to lens biology and disease. Genomics Data 2015: 5:223-227. View in: Pubmed *Corresponding Author

• Dash, S., Dang, C.A., Beebe, D.C., Lachke, S.A.* Deficiency of the RNA binding protein Caprin2 causes lens defects and features of Peters anomaly. Developmental Dynamics 2015: 244:1313-1327. View in: Pubmed *Corresponding Author

• Stepicheva*, N. and J.L. Song (2015) miR-31 modulates skeletal patterning in the sea urchin embryo. Development. Sep 23. pii: dev.127969. Nov 1:142(21):3769-80. doi: 10.1242/dev.127969.PMID:26400092

• Stepicheva*, N, P.A. Nigam*, A. Siddam*, C.F. Peng, J.L. Song (2015) microRNAs regulate β-catenin of the Wnt signaling pathway in early sea urchin development. Developmental Biology. Jan 19. Pii: S0012-1606 (15)00016-0. doi:10.1016/j.ydbio.2015.01.008. PMID: 25614238.

• Boyd, E.F., M.R. Carpenter, N. Chowdhury, A.L. Cohen, B.L. Haines-Menges, J.J. Kingston, S. S. Kalburge, J.B. Lubin, S.Y. Ongagna-Yhombi, and W.B. Whitaker. 2015. Postgenomic analysis of the evolutionary history of Vibrio. Microbiology Spectrum, 3 (5).

• Lubin, J.B., W.G. Lewis, N.M Gilbert, S. Almagro-Moreno, E.F. Boyd, and A.L. Lewis. 2015. Host-like carbohydrates promote bloodstream survival of Vibrio vulnificus in vivo. Infection and Immunity, 83(8):3126-36.

• Yhombi-Ongagna, S.Y., N. D. McDonald, and E.F. Boyd. 2015. Deciphering the role of multiple BCCT compatible solute transporters from Vibrio parahaemolyticus. Applied and Environmental Microbiology, 81(1):351-63.

• Haines-Menges, B.L., Whitaker, W.B., J.B. Lubin, and E.F. Boyd. 2015. Host Sialic acids: a delicacy for the pathogen with discerning taste. Microbiology Spectrum, 3 (4).

2014

• Stepicheva*, N. and J.L. Song (2014) High throughput microinjections of sea urchin zygotes. Journal of Visualized Experiments. Jan 21;(83):e50841. doi: 10.3791/50841. PMID: 24473085

• Abby L. Manthey, Salil A. Lachke, Paul G. FitzGerald, Robert W. Mason, David A. Scheiblin, John H. McDonald, and Melinda K. Duncan (2014) Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development Mechanisms of Development, 131, 86-110.

• Fahmy A. Mamuya, Yan Wang, Victoria H. Roop, David A. Scheiblin, Jocelyn C. Zajac and Melinda K. Duncan (2014) The Roles of αV Integrin in Lens EMT and Posterior Capsular Opacification Journal of Cellular and Molecular Medicine, 18, 656-670.

• Mallika Pathania, Elena V. Semina, and Melinda K. Duncan (2014) Lens extrusion from Laminin alpha 1 mutant zebrafish The Scientific World Journal-Developmental Biology, 524929. doi: 10.1155/2014/524929. eCollection 2014

• David A. Scheiblin, Junyuan Gao, Jeffrey L. Caplan, Vladimir N. Simirskii, Kirk J. Czymmek, Richard T. Mathias  and Melinda K. Duncan (2014) Beta-1 integrin is important for the structural maintenance and homeostasis of differentiating fiber cells International Journal of Biochemistry and Cell Biology,50, 132-145.

• Abby L. Manthey, Anne M. Terrell, Yan Wang, Jennifer R. Taube, Alisha R. Yallowitz, and Melinda K. Duncan (2014) The Zeb proteins, dEF1 and Sip1, may have distinct functions in lens cells following cataract surgery Investigative Ophthalmology and Visual Sciences, 55, 5445-5455.

• Abby L. Manthey, Anne M. Terrell, Salil A. Lachke, Shawn W. Polson, and Melinda K. Duncan (2014) Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis Genomics Data; Data in Brief 2, 369-374.

• Chowdhury, N., J.J. Kingston, W.B. Whitaker, M.R. Carpenter, A.L. Cohen, and E.F. Boyd. 2014. Sequence and expression divergence in an ancient gene duplication of the chaperonins groELgroES in Vibrio species. Microbiology, 160(Pt 9):1953-63.

• Haines-Menges, B.L., Whitaker, W.B., and E.F. Boyd. 2014. The extracytoplasmic sigma factor RpoE is essential for Vibrio parahaemolyticus cell envelope stress response and intestinal colonization. Infection and Immunity, 82(9):3667-77.

• Kalburge, S.S., S. Polson, K. Boyd Crotty, L. Katz, C.L. Tarr, J. Martinez-Urtaza, and E.F. Boyd. 2014. Complete genome sequence of Vibrio parahaemolyticus UCM V492. Genome Announcements, 13;2(2).

• Whitaker, W.B., G.P. Richards, and E.F. Boyd. 2014. Lack of the sigma factor RpoN increases colonization proficiency of Vibrio parahaemolyticus in an adult mouse model. Infection and Immunity, 82(2):544-56.

2012

• Apostolidis, P. A., D. S. Woulfe, M. Chavez, W. M. Miller and E. T. Papoutsakis. 2012. Role of tumor suppressor p53 in megakaryopoiesis and platelet function. Exp Hematol 40: 131-42 e4.

• Aravindan, R. G., V. P. Fomin, U. P. Naik, M. J. Modelski, M. U. Naik, D. S. Galileo, R. L. Duncan and P. A. Martin-Deleon. 2012. CASK interacts with PMCA4b and JAM-A on the mouse sperm flagellum to regulate Ca(2+) homeostasis and motility. J Cell Physiol 227: 3138-50.

• Ben-Yaakov, K., S. Y. Dagan, Y. Segal-Ruder, O. Shalem, D. Vuppalanchi, D. E. Willis, D. Yudin, I. Rishal, F. Rother, M. Bader, A. Blesch, Y. Pilpel, J. L. Twiss and M. Fainzilber. 2012. Axonal transcription factors signal retrogradely in lesioned peripheral nerve. Embo J 31: 1350-63.

• Bonor, J., E. L. Adams, B. Bragdon, O. Moseychuk, K. J. Czymmek and A. Nohe. 2012. Initiation of BMP2 signaling in domains on the plasma membrane. J Cell Physiol 227: 2880-8.

• Chatterjee, S. and U. P. Naik. 2012. Pericyte-endothelial cell interaction: A survival mechanism for the tumor vasculature. Cell Adh Migr 6.

• Hillyer, R. L., P. Sirinvasin, M. Joglekar, R. A. Sikes, K. L. van Golen and A. Nohe. 2012. Differential effects of vitamin D treatment on inflammatory and non-inflammatory breast cancer cell lines. Clin Exp Metastasis.

• Jansson, K. H., J. E. Lynch, N. Lepori-Bui, K. J. Czymmek, R. L. Duncan and R. A. Sikes. 2012. Overexpression of the VSSC-associated CAM, beta-2, enhances LNCaP cell metastasis associated behavior. Prostate 72: 1080-92.

• Kostyak, J. C., M. U. Naik and U. P. Naik. 2012. Calcium- and integrin-binding protein 1 regulates megakaryocyte ploidy, adhesion, and migration. Blood 119: 838-46.

• Lubin, J. B., J. J. Kingston, N. Chowdhury and E. F. Boyd. 2012. Sialic acid catabolism and transport gene clusters are lineage specific in Vibrio vulnificus. Appl Environ Microbiol 78: 3407-15.

• Mailloux, B. J., A. Dochenetz, M. Bishop, H. Dong, L. A. Ziolkowski, K. E. Wommack, E. G. Sakowski, T. C. Onstott and G. F. Slater. 2012. A carbon free filter for collection of large volume samples of cellular biomass from oligotrophic waters. J Microbiol Methods.

• Mamuya, F. A. and M. K. Duncan. 2012. aV integrins and TGF-beta-induced EMT: a circle of regulation. J Cell Mol Med 16: 445-55.

• McCoy, S. Y., K. A. Falgowski, P. P. Srinivasan, W. R. Thompson, E. M. Selva and C. B. Kirn-Safran. 2012. Serum xylosyltransferase 1 level increases during early posttraumatic osteoarthritis in mice with high bone forming potential. Bone.

• Miles, F. L., N. S. Tung, A. A. Aguiar, S. Kurtoglu and R. A. Sikes. 2012. Increased TGF-beta1-mediated suppression of growth and motility in castrate-resistant prostate cancer cells is consistent with Smad2/3 signaling. Prostate.

• Song, J. L., M. Stoeckius, J. Maaskola, M. Friedlander, N. Stepicheva, C. Juliano, S. Lebedeva, W. Thompson, N. Rajewsky and G. M. Wessel. 2012. Select microRNAs are essential for early development in the sea urchin. Dev Biol 362: 104-13.

• Srinivasan, P. P., S. Y. McCoy, A. K. Jha, W. Yang, X. Jia, M. C. Farach-Carson and C. B. Kirn-Safran. 2012. Injectable perlecan domain 1-hyaluronan microgels potentiate the cartilage repair effect of BMP2 in a murine model of early osteoarthritis. Biomed Mater 7: 024109.

• Vuppalanchi, D., T. T. Merianda, C. Donnelly, G. Williams, S. Yoo, R. R. Ratan, D. E. Willis and J. L. Twiss. 2012. Lysophosphatidic acid differentially regulates axonal mRNA translation through 5'UTR elements. Mol Cell Neurosci.

• Xu, X., A. K. Jha, D. A. Harrington, M. C. Farach-Carson and X. Q. Jia. 2012. Hyaluronic acid-based hydrogels: from a natural polysaccharide to complex networks. Soft Matter 8: 3280-3294.

• Alapure, B. V., J. K. Stull, Z. Firtina and M. K. Duncan. The unfolded protein response is activated in connexin 50 mutant mouse lenses. Exp Eye Res 102C: 28-37.