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Article ; Online: Improving Biomedical Engineering Undergraduate Learning Through Use of Online Graduate Engineering Courses During the COVID-19 Pandemic.

Nesmith, Jessica E / Hickey, John W / Haase, Eileen

2021 Volume 1, Issue 2, Page(s) 317–324

Abstract: In order to provide undergraduate students with a full, rich online learning experience we adapted pre-existing online content including graduate courses from Johns Hopkins University Engineering for Professionals (JHU EP) program. These online courses ... ...

Abstract	In order to provide undergraduate students with a full, rich online learning experience we adapted pre-existing online content including graduate courses from Johns Hopkins University Engineering for Professionals (JHU EP) program. These online courses were designed using published methodologies and held to a high level of rigor of a Masters-level curriculum. Adapting pre-existing online course material enabled us to more rapidly adapt to the COVID-19 shutdown of in-person education. We adapted content to meet the majority of lab-based learning objectives rather than generating self-recorded lecture material and allowing us to focus faculty time on addressing student needs. Here we discuss benefits, challenges, and methods for replicating these courses, and lessons to be applied in future offerings from this experience.
Language	English
Publishing date	2021-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	3040682-1
ISSN	2730-5945 ; 2730-5937
ISSN (online)	2730-5945
ISSN	2730-5937
DOI	10.1007/s43683-020-00041-w
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Article ; Online: Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish.

Hostelley, Timothy L / Nesmith, Jessica E / Zaghloul, Norann A

Journal of visualized experiments : JoVE

2017 , Issue 128

Abstract: The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an excellent model for rapid assessment of whole transcriptome from whole animal or individual cell ... ...

Abstract	The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an excellent model for rapid assessment of whole transcriptome from whole animal or individual cell populations due to the ease of isolation of RNA from large numbers of animals. Here a protocol for global gene expression analysis in zebrafish embryos using RNA sequencing (RNASeq) is presented. We describe preparation of RNA from whole embryos or from cell populations obtained using cell sorting in transgenic animals. We also describe an approach for analysis of RNASeq data to identify enriched pathways and Gene Ontology (GO) terms in global gene expression data sets. Finally, we provide a protocol for validation of gene expression changes using quantitative reverse transcriptase PCR (qRT-PCR). These protocols can be used for comparative analysis of control and experimental sets of zebrafish to identify novel gene expression changes, and provide molecular insight into phenotypes of interest.
MeSH term(s)	Animals ; Gene Expression Profiling/methods ; RNA/chemistry ; RNA/genetics ; Sequence Analysis, RNA/methods ; Zebrafish
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2017-10-27
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/56187
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Article ; Online: Exocrine pancreas proteases regulate β-cell proliferation in zebrafish ciliopathy models and in murine systems.

Hostelley, Timothy L / Nesmith, Jessica E / Larkin, Emily / Jones, Amanda / Boyes, Daniel / Leitch, Carmen C / Fontaine, Magali / Zaghloul, Norann A

Biology open

2021 Volume 10, Issue 6

Abstract: Pancreatic β-cells are a critical cell type in the pathology of diabetes. Models of genetic syndromes featuring diabetes can provide novel mechanistic insights into regulation of β-cells in the context of disease. We previously examined β-cell mass in ... ...

Abstract	Pancreatic β-cells are a critical cell type in the pathology of diabetes. Models of genetic syndromes featuring diabetes can provide novel mechanistic insights into regulation of β-cells in the context of disease. We previously examined β-cell mass in models of two ciliopathies, Alström Syndrome (AS) and Bardet-Biedl Syndrome (BBS), which are similar in the presence of metabolic phenotypes, including obesity, but exhibit strikingly different rates of diabetes. Zebrafish models of these disorders show deficient β-cells with diabetes in AS models and an increased β-cells absent diabetes in BBS models, indicating β-cell generation or maintenance that correlates with disease prevalence. Using transcriptome analyses, differential expression of several exocrine pancreas proteases with directionality that was consistent with β-cell numbers were identified. Based on these lines of evidence, we hypothesized that pancreatic proteases directly impact β-cells. In the present study, we examined this possibility and found that pancreatic protease genes contribute to proper maintenance of normal β-cell numbers, proliferation in larval zebrafish, and regulation of AS and BBS β-cell phenotypes. Our data suggest that these proteins can be taken up directly by cultured β-cells and ex vivo murine islets, inducing proliferation in both. Endogenous uptake of pancreatic proteases by β-cells was confirmed in vivo using transgenic zebrafish and in intact murine pancreata. Taken together, these findings support a novel proliferative signaling role for exocrine pancreas proteases through interaction with endocrine β-cells.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Cell Proliferation ; Chymotrypsin/genetics ; Chymotrypsin/metabolism ; Ciliopathies/etiology ; Ciliopathies/metabolism ; Ciliopathies/pathology ; Disease Susceptibility ; Gene Expression ; Insulin-Secreting Cells/metabolism ; Mice ; Mutation ; Pancreas, Exocrine/enzymology ; Peptide Hydrolases/genetics ; Peptide Hydrolases/metabolism ; Zebrafish
Chemical Substances	Peptide Hydrolases (EC 3.4.-) ; Chymotrypsin (EC 3.4.21.1)
Language	English
Publishing date	2021-06-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2632264-X
ISSN	2046-6390 ; 2046-6390
ISSN (online)	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.046839
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Article ; Online: Blood vessel anastomosis is spatially regulated by Flt1 during angiogenesis.

Nesmith, Jessica E / Chappell, John C / Cluceru, Julia G / Bautch, Victoria L

Development (Cambridge, England)

2017 Volume 144, Issue 5, Page(s) 889–896

Abstract: Blood vessel formation is essential for vertebrate development and is primarily achieved by angiogenesis - endothelial cell sprouting from pre-existing vessels. Vessel networks expand when sprouts form new connections, a process whose regulation is ... ...

Abstract	Blood vessel formation is essential for vertebrate development and is primarily achieved by angiogenesis - endothelial cell sprouting from pre-existing vessels. Vessel networks expand when sprouts form new connections, a process whose regulation is poorly understood. Here, we show that vessel anastomosis is spatially regulated by Flt1 (VEGFR1), a VEGFA receptor that acts as a decoy receptor.
MeSH term(s)	Animals ; Blood Vessels/physiology ; Endothelial Cells/metabolism ; Gene Expression Regulation, Developmental ; Human Umbilical Vein Endothelial Cells ; Humans ; Mice ; Microvessels ; Morphogenesis ; Neovascularization, Physiologic ; Protein Isoforms/metabolism ; Retina/embryology ; Signal Transduction ; Vascular Endothelial Growth Factor A/metabolism ; Vascular Endothelial Growth Factor Receptor-1/metabolism
Chemical Substances	Protein Isoforms ; Vascular Endothelial Growth Factor A ; FLT1 protein, human (EC 2.7.10.1) ; Flt1 protein, mouse (EC 2.7.10.1) ; Vascular Endothelial Growth Factor Receptor-1 (EC 2.7.10.1)
Language	English
Publishing date	2017-02-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.145672
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Article ; Online: Exocrine pancreas proteases regulate β-cell proliferation in zebrafish ciliopathy models and in murine systems

Timothy L. Hostelley / Jessica E. Nesmith / Emily Larkin / Amanda Jones / Daniel Boyes / Carmen C. Leitch / Magali Fontaine / Norann A. Zaghloul

Biology Open, Vol 10, Iss

2021 Volume 6

Abstract	Pancreatic β-cells are a critical cell type in the pathology of diabetes. Models of genetic syndromes featuring diabetes can provide novel mechanistic insights into regulation of β-cells in the context of disease. We previously examined β-cell mass in models of two ciliopathies, Alström Syndrome (AS) and Bardet-Biedl Syndrome (BBS), which are similar in the presence of metabolic phenotypes, including obesity, but exhibit strikingly different rates of diabetes. Zebrafish models of these disorders show deficient β-cells with diabetes in AS models and an increased β-cells absent diabetes in BBS models, indicating β-cell generation or maintenance that correlates with disease prevalence. Using transcriptome analyses, differential expression of several exocrine pancreas proteases with directionality that was consistent with β-cell numbers were identified. Based on these lines of evidence, we hypothesized that pancreatic proteases directly impact β-cells. In the present study, we examined this possibility and found that pancreatic protease genes contribute to proper maintenance of normal β-cell numbers, proliferation in larval zebrafish, and regulation of AS and BBS β-cell phenotypes. Our data suggest that these proteins can be taken up directly by cultured β-cells and ex vivo murine islets, inducing proliferation in both. Endogenous uptake of pancreatic proteases by β-cells was confirmed in vivo using transgenic zebrafish and in intact murine pancreata. Taken together, these findings support a novel proliferative signaling role for exocrine pancreas proteases through interaction with endocrine β-cells.
Keywords	β-cells ; ciliopathies ; diabetes ; zebrafish ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	The Company of Biologists
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An RNAi-based suppressor screen identifies interactors of the Myt1 ortholog of Caenorhabditis elegans.

Allen, Anna K / Nesmith, Jessica E / Golden, Andy

G3 (Bethesda, Md.)

2014 Volume 4, Issue 12, Page(s) 2329–2343

Abstract: Oocyte maturation in all species is controlled by a protein complex termed the maturation promoting factor (MPF). MPF comprises a cyclin-dependent kinase (CDK) and its partner cyclin, and it is regulated by dueling regulatory phosphorylation events on ... ...

Abstract	Oocyte maturation in all species is controlled by a protein complex termed the maturation promoting factor (MPF). MPF comprises a cyclin-dependent kinase (CDK) and its partner cyclin, and it is regulated by dueling regulatory phosphorylation events on the CDK. In Caenorhabditis elegans, the Wee1/Myt1 ortholog WEE-1.3 provides the inhibitory phosphorylations on CDK-1 that keep MPF inactive and halt meiosis. Prior work has shown that depletion of WEE-1.3 in C. elegans results in precocious oocyte maturation in vivo and a highly penetrant infertility phenotype. This study sought to further define the precocious maturation phenotype and to identify novel interactors with WEE-1.3. We found that WEE-1.3 is expressed throughout the germline and in developing embryos in a perinuclear pattern, and demonstrated that oocytes in WEE-1.3-depleted germlines have begun to transcribe embryonic genes and exhibit inappropriate expression of proteins normally restricted to fertilized eggs. In addition, we performed an RNAi suppressor screen of the infertile phenotype to identify novel factors that, when co-depleted with WEE-1.3, restore fertility to these animals. We screened ∼1900 essential genes by RNAi feeding and identified 44 (∼2% of the tested genes) that are suppressors of the WEE-1.3 depletion phenotype. The suppressors include many previously unidentified players in the meiotic cell cycle and represent a pool of potential WEE-1.3 interacting proteins that function during C. elegans oocyte maturation and zygotic development.
MeSH term(s)	Animals ; CDC2 Protein Kinase/genetics ; CDC2 Protein Kinase/metabolism ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/growth & development ; Caenorhabditis elegans Proteins/antagonists & inhibitors ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Embryo, Nonmammalian/metabolism ; Microscopy, Fluorescence ; Oocytes/metabolism ; Phenotype ; Protein-Serine-Threonine Kinases/deficiency ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Protein-Tyrosine Kinases/deficiency ; Protein-Tyrosine Kinases/genetics ; Protein-Tyrosine Kinases/metabolism ; RNA Interference
Chemical Substances	Caenorhabditis elegans Proteins ; wee-1.3 protein, C elegans (EC 2.7.1.-) ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; CDC2 Protein Kinase (EC 2.7.11.22)
Language	English
Publishing date	2014-10-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.114.013649
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Article: Sample preparation and analysis of rnaseq-based gene expression data from zebrafish

Hostelley, Timothy L / Nesmith, Jessica E / Zaghloul, Norann A

Journal of visualized experiments. 2017 Oct. 27, , no. 128

2017

Abstract	The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an excellent model for rapid assessment of whole transcriptome from whole animal or individual cell populations due to the ease of isolation of RNA from large numbers of animals. Here a protocol for global gene expression analysis in zebrafish embryos using RNA sequencing (RNASeq) is presented. We describe preparation of RNA from whole embryos or from cell populations obtained using cell sorting in transgenic animals. We also describe an approach for analysis of RNASeq data to identify enriched pathways and Gene Ontology (GO) terms in global gene expression data sets. Finally, we provide a protocol for validation of gene expression changes using quantitative reverse transcriptase PCR (qRT-PCR). These protocols can be used for comparative analysis of control and experimental sets of zebrafish to identify novel gene expression changes, and provide molecular insight into phenotypes of interest.
Keywords	Danio rerio ; RNA ; data collection ; embryo (animal) ; gene expression ; gene ontology ; models ; phenotype ; quantitative polymerase chain reaction ; rapid methods ; reverse transcriptase polymerase chain reaction ; transcriptome ; transgenic animals
Language	English
Dates of publication	2017-1027
Size	p. e56187.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/56187
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Article ; Online: Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes.

Nesmith, Jessica E / Hostelley, Timothy L / Leitch, Carmen C / Matern, Maggie S / Sethna, Saumil / McFarland, Rebecca / Lodh, Sukanya / Westlake, Christopher J / Hertzano, Ronna / Ahmed, Zubair M / Zaghloul, Norann A

Human molecular genetics

2019 Volume 28, Issue 13, Page(s) 2212–2223

Abstract: Alström syndrome (OMIM #203800) is an autosomal recessive obesity ciliopathy caused by loss-of-function mutations in the ALMS1 gene. In addition to multi-organ dysfunction, such as cardiomyopathy, retinal degeneration and renal dysfunction, the disorder ... ...

Abstract	Alström syndrome (OMIM #203800) is an autosomal recessive obesity ciliopathy caused by loss-of-function mutations in the ALMS1 gene. In addition to multi-organ dysfunction, such as cardiomyopathy, retinal degeneration and renal dysfunction, the disorder is characterized by high rates of obesity, insulin resistance and early-onset type 2 diabetes mellitus (T2DM). To investigate the underlying mechanisms of T2DM phenotypes, we generated a loss-of-function deletion of alms1 in the zebrafish. We demonstrate conservation of hallmark clinical characteristics alongside metabolic syndrome phenotypes, including a propensity for obesity and fatty livers, hyperinsulinemia and glucose response defects. Gene expression changes in β-cells isolated from alms1-/- mutants revealed changes consistent with insulin hypersecretion and glucose sensing failure, which were corroborated in cultured murine β-cells lacking Alms1. We also found evidence of defects in peripheral glucose uptake and concomitant hyperinsulinemia in the alms1-/- animals. We propose a model in which hyperinsulinemia is the primary and causative defect underlying generation of T2DM associated with alms1 deficiency. These observations support the alms1 loss-of-function zebrafish mutant as a monogenic model for mechanistic interrogation of T2DM phenotypes.
MeSH term(s)	Alstrom Syndrome/genetics ; Alstrom Syndrome/physiopathology ; Animals ; Animals, Genetically Modified ; Cell Line ; Diabetes Mellitus, Type 2/genetics ; Disease Models, Animal ; Glucose Intolerance ; Hyperinsulinism/genetics ; Insulin Resistance/genetics ; Insulin-Secreting Cells/metabolism ; Mice ; Models, Biological ; Obesity/genetics ; Phenotype ; Renal Insufficiency/genetics ; Retinal Degeneration/genetics ; Zebrafish/embryology ; Zebrafish/genetics
Language	English
Publishing date	2019-06-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddz053
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Article ; Online: Functional redundancy of paralogs of an anaphase promoting complex/cyclosome subunit in Caenorhabditis elegans meiosis.

Stein, Kathryn K / Nesmith, Jessica E / Ross, Benjamin D / Golden, Andy

Genetics

2010 Volume 186, Issue 4, Page(s) 1285–1293

Abstract: The anaphase promoting complex/cyclosome (APC/C) mediates the metaphase-to-anaphase transition by instructing the ubiquitination and turnover of key proteins at this stage of the cell cycle. We have recovered a gain-of-function allele in an APC5 subunit ... ...

Abstract	The anaphase promoting complex/cyclosome (APC/C) mediates the metaphase-to-anaphase transition by instructing the ubiquitination and turnover of key proteins at this stage of the cell cycle. We have recovered a gain-of-function allele in an APC5 subunit of the anaphase promoting complex/cyclosome. This finding led us to investigate further the role of APC5 in Caenorhabditis elegans, which contains two APC5 paralogs. We have shown that these two paralogs, such-1 and gfi-3, are coexpressed in the germline but have nonoverlapping expression patterns in other tissues. Depletion of such-1 or gfi-3 alone does not have a notable effect on the meiotic divisions; however, codepletion of these two factors results in meiotic arrest. In sum, the two C. elegans APC5 paralogs have a redundant function during the meiotic divisions.
MeSH term(s)	Alleles ; Anaphase-Promoting Complex-Cyclosome ; Animals ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans Proteins/physiology ; Gene Expression Regulation ; Meiosis ; Protein Subunits/physiology ; Tissue Distribution ; Ubiquitin-Protein Ligase Complexes/physiology
Chemical Substances	Caenorhabditis elegans Proteins ; Protein Subunits ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; Anaphase-Promoting Complex-Cyclosome (EC 2.3.2.27)
Language	English
Publishing date	2010-10-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.110.123463
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Article ; Online: The ACT NOW Clinical Practice Survey: Gaps in the Care of Infants With Neonatal Opioid Withdrawal Syndrome.

Snowden, Jessica N / Akshatha, A / Annett, Robert D / Crawford, Margaret M / Das, Abhik / Devlin, Lori A / Higgins, Rosemary D / Hu, Zhuopei / Lindsay, Elizabeth / Merhar, Stephanie / Campbell Nesmith, Clare / Pratt-Chavez, Heather / Ross, Judith / Simon, Alan E / Smith, M Cody / Turley, Christine B / Walden, Anita / Young, Leslie / Whalen, Bonny

Hospital pediatrics

2019 Volume 9, Issue 8, Page(s) 585–592

Abstract: Objectives: The incidence of neonatal opioid withdrawal syndrome (NOWS) has increased fivefold over the last 10 years. Standardized NOWS care protocols have revealed many improved patient outcomes. Our objective for this study is to describe results of ... ...

Abstract	Objectives: The incidence of neonatal opioid withdrawal syndrome (NOWS) has increased fivefold over the last 10 years. Standardized NOWS care protocols have revealed many improved patient outcomes. Our objective for this study is to describe results of a clinical practice survey of NOWS management practices designed to inform future clinical studies in the diagnosis and management of NOWS. Methods: A cross-sectional survey was administered to medical unit directors at 32 Institutional Development Award States Pediatric Clinical Trial Network and 22 Neonatal Research Network sites in the fall of 2017. Results are presented as both the number and percentage of positive responses. Ninety-five percent Wilson confidence intervals (CIs) were generated around estimates, and χ Results: Sixty-two responses representing 54 medical centers were received. Most participating NICU and non-ICU sites reported protocols for NOWS management, including NOWS scoring (98% NICU; 86% non-ICU), pharmacologic treatment (92% NICU; 64% non-ICU), and nonpharmacologic care (79% NICU; 79% non-ICU). Standardized protocols for pharmacologic care and weaning were reported more frequently in the NICU (92% [95% CI: 80%-97%] and 94% [95% CI: 83%-98%], respectively) compared with non-ICU settings (64% [95% CI: 39%-84%] for both) ( Conclusions: Observed variations in care between NICUs and non-ICUs revealed opportunities for targeted interventions in training and standardized care plans in non-ICU sites.
MeSH term(s)	Analgesics, Opioid/therapeutic use ; Clinical Protocols ; Cross-Sectional Studies ; Health Care Surveys/methods ; Health Care Surveys/statistics & numerical data ; Humans ; Infant, Newborn ; Neonatal Abstinence Syndrome/drug therapy ; Neonatal Abstinence Syndrome/therapy
Chemical Substances	Analgesics, Opioid
Language	English
Publishing date	2019-07-19
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural
ISSN	2154-1671
ISSN (online)	2154-1671
DOI	10.1542/hpeds.2019-0089
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