Publications

2021

1. Big Data Infrastructure at the Crossroads: Support Needs and Challenges for Universities Ruediger, Dylan, Atwood, Thea, Bharti, Neelam, Briones, Bryan, Campbell, Patrick, Carey, Paula, Castillo, Daniel, Ciccone, Karen, Cook, Cameron, Cooper, Danielle, Curry, Claire, De La Cruz, Justin, Dean, Will, Dragowsky, E.M., Durkin, Tom, Epps, Darnell, Erickson, Seth, Ferguson, Jen, Foster, Erin, Garcia, Moriana, Garrett, Zenobie, Glusker, Ann, Gorham, Ben, Green, Jen, Gunderman, Hannah, Huband, Jacalyn, Huck, Jennifer, Ivey, Susan, Jackson, Carolyn, Jordan, Kelsey, Keyder, Kate, Labou, Stephanie, Laufersweiler, Mark, Lewis, Tracie, Macalino, James, Magle, Tobin, Minor, David, Munip, Lana, Odom, Rosaline, Otsuji, Reid, Patiño, Jennifer, Pearson, Tyler, Phillips, Carissa, Pugachev, Sara, Quigley, Brian, Rachlin, David, Radik, Melanie, Rampin, Vicky, Rowland, Fred, Sare, Laura, Seifried, Rebecca, Shambaugh, Adam, Siddiqui, Sarah, Silfen, Kate, Sims, Iyanna, Sinclair, Bryan, Smith, Margaret, Sneff, Gretchen, Swygart-Hobaugh, Mandy, Tajallipour, Paria, Unis, Julia, Vickery, John, Vitale, Cynthia, Walker, Jeremy, Wang, Huajin, Watts, John, Wiley, Chris, Wissel, Katie, Wolf, Nicholas, Xin, Cindy Xuying, Yu, Jen-Chien, Zender, Roger, and Zickel, Lee 2021 [Abs] [HTML] [PDF]

   Ithaka S+R’s Research Support Services program explores current trends and support needs in academic research. Our most recent project in this program, “Supporting Big Data Research,” focused specifically on the rapidly emerging use of big data in research across disciplines and fields. As part of our study, we partnered with librarians from more than 20 colleges and universities, who then conducted over 200 interviews with faculty. These interviews provided insights into the research methodologies and support needs of researchers working across a wide range of disciplines. This report provides a detailed account of how big data research is pursued in academic contexts, focusing on identifying typical methodologies, workflows, outputs, and challenges big data researchers face. Full details and actionable recommendations for stakeholders are offered in the body of the report, which offers guidance to universities, funders, and others interested in improving institutional capacities and fostering intellectual climates to better support big data research.

2020

1. Conference Report: Artificial Intelligence for Data Discovery and Reuse (AIDR) and Open Science Symposium (OSS) 2020 Wang, Huajin 2020 [Abs] [HTML] [PDF]

   A report summarizing main themes and takeaways from two joint Symposia: Artificial Intelligence for Data Discovery and Reuse (AIDR) and Open Science Symposium (OSS), hosted by the Open Science & Data Collaborations program at Carnegie Mellon University Libraries in 2020.

2. Partitioning of MLX-Family Transcription Factors to Lipid Droplets Regulates Metabolic Mejhert, Niklas, Kuruvilla, Leena, Gabriel, Katlyn R., Elliott, Shane E., Guie, Marie-Aude, Wang, Huajin, Lai, Zon Weng, Lane, Elizabeth A., Christiano, Romain, Danial, Nika N, Farese Jr., Robert V., and Walther, Tobias C. Molecular Cell (in press) 2020 [Abs] [HTML] [PDF]

   Lipid droplets (LDs) store lipids for energy and are central to cellular lipid homeostasis. The mechanisms coordinating lipid storage in LDs with cellular metabolism are unclear but relevant to obesity-related diseases. Here we utilized genome-wide screening to identify genes that modulate lipid storage in macrophages, a cell type involved in metabolic diseases. Among ∼550 identified screen hits is MLX, a basic helix-loop-helix leucine-zipper transcription factor that regulates metabolic processes. We show that MLX and glucose-sensing family members MLXIP/MondoA and MLXIPL/ChREBP bind LDs via C-terminal amphipathic helices. When LDs accumulate in cells, these transcription factors bind to LDs, reducing their availability for transcriptional activity and attenuating the response to glucose. Conversely, the absence of LDs results in hyperactivation of MLX target genes. Our findings uncover a paradigm for a lipid storage response in which binding of MLX transcription factors to LD surfaces adjusts the expression of metabolic genes to lipid storage levels.

2019

1. Automated chat transcript analysis using topic modeling for library reference services Chen, Xiaoju, and Wang, Huajin In Proceedings of the Association for Information Science and Technology 2019 [Abs] [HTML] [PDF]

   Chat reference service has been used in academic libraries to more efficiently serve patrons in the digital age. Identifying question topics on chat can help librarians understand patrons’ needs and improve reference services. Researchers have used qualitative methods to understand question types in chat records; however, these methods are inefficient to analyze large chat datasets. Here, we conducted a novel research using Latent Dirichlet Allocation (LDA) topic modeling to automatically extract topics from chat transcripts generated in 5 years from a large university library. With little human intervention, the model identified major topics based on statistical distributions of terms- document relationships in chat transcripts. We also applied VOSviewer to analyze the same dataset and found consistent results. From these results, we found that the most prominent chat topics were about accessing various library resources. This finding can help libraries allocate resources, design educational materials, and provide trainings for future librarians.

2. The Evolution of Information Literacy Learning Outcomes in Interdisciplinary Undergraduate Science Courses Gainey, Melanie A., Bharti, Neelam, Marsteller, Matthew R., Wang, Huajin, Young, Sarah, and Melville, Michael Issues in Science and Techonolgoy Librarianship 2019 [Abs] [HTML] [PDF]

   The ACRL Framework for Information Literacy presents opportunities for moving beyond ‘one- shot’ information literacy sessions and creating a more scaffolded and embedded approach for instruction. We collaborated with faculty at Carnegie Mellon University to create Framework- inspired information literacy learning objectives for first-year and third-year science undergraduates and are continuously refining the objectives as the curriculum evolves. This article describes our learning objective design and refinement process, challenges encountered, and ideas on how to create opportunities for embedding information literacy into a curriculum. We also share our full activity lesson plans and assessment tool.

3. Editorial: Artificial Intelligence for Data Discovery and Reuse Demands Healthy Data Ecosystem and Community Efforts Wang, Huajin, and Webster, Keith In AIDR ’19: Proceedings of the Conference on Artificial Intelligence for Data Discovery and Reuse 2019 [Abs] [HTML] [PDF]

   There is great value embedded in reusing scientific data for secondary discoveries. However, it is challenging to find and reuse the large amount of existing scientific data distributed across the web and data repositories. Some of the challenges reside in the volume and complexity of scientific data, others pertain to the current practices and workflow of research data management. AIDR 2019 (Artificial Intelligence for Data Discovery and Reuse) is a new conference that brings together researchers across a broad range of disciplines, computer scientists, tool developers, data providers, and data curators, to share innovative solutions that apply artificial intelligence to scientific data discovery and reuse, and discuss how various stakeholders work together to create a health data ecosystem. This editorial summarizes the main themes and takeaways from the inaugural AIDR conference.

4. AIDR ’19: Proceedings of the Conference on Artificial Intelligence for Data Discovery and Reuse 2019 [HTML]
5. Confocal Microscopy Data : A Primer for Curators Executive summary Curation workflow decision tree Ivey, Susan, Koshoffer, Amy, Sneff, Gretchen, and Wang, Huajin 2019 [Abs] [HTML] [PDF]

2018

1. Functional Contribution of the Spastic Paraplegia-Related Triglyceride Hydrolase DDHD2 to the Formation and Content of Lipid Droplets Inloes, Jordon M., Kiosses, William B., Wang, Huajin, Walther, Tobias C., Farese, Robert V., and Cravatt, Benjamin F. Biochemistry 2018 [Abs] [HTML] [PDF]

   Deleterious mutations in the serine lipase DDHD2 are a causative basis of complex hereditary spastic paraplegia (HSP, subtype SPG54) in humans. We recently found that DDHD2 is a principal triglyceride hydrolase in the central nervous system (CNS) and that genetic deletion of this enzyme in mice leads to ectopic lipid droplet (LD) accumulation in neurons throughout the brain. Nonetheless, how HSP-related mutations in DDHD2 relate to triglyceride metabolism and LD formation remains poorly understood. Here, we have characterized a set of HSP-related mutations in DDHD2 and found that they disrupt triglyceride hydrolase activity in vitro and impair the capacity of DDHD2 to protect cells from LD accumulation following exposure to free fatty acid, an outcome that was also observed with a DDHD2-selective inhibitor. We furthermore isolated and characterized LDs from brain tissue of DDHD2–/– mice, revealing that they contain both established LD-associated proteins identified previously in other organs and CNS-enric...

2016

1. Seipin is required for converting nascent to mature lipid droplets Wang, Huajin, Becuwe, Michel, Housden, Benjamin E, Chitraju, Chandramohan, Porras, Ashley J, Graham, Morven M, Liu, Xinran N, Thiam, Abdou Rachid, Savage, David B, Agarwal, Anil K, Garg, Abhimanyu, Olarte, Maria-Jesus, Lin, Qingqing, Fröhlich, Florian, Hannibal-Bach, Hans Kristian, Upadhyayula, Srigokul, Perrimon, Norbert, Kirchhausen, Tomas, Ejsing, Christer S, Walther, Tobias C, and Farese, Robert V eLife 2016 [Abs] [HTML] [PDF]

   How proteins control the biogenesis of cellular lipid droplets (LDs) is poorly understood. Using Drosophila and human cells, we show here that seipin, an ER protein implicated in LD biology, mediates a discrete step in LD formation-the conversion of small, nascent LDs to larger, mature LDs. Seipin forms discrete and dynamic foci in the ER that interact with nascent LDs to enable their growth. In the absence of seipin, numerous small, nascent LDs accumulate near the ER and most often fail to grow. Those that do grow prematurely acquire lipid synthesis enzymes and undergo expansion, eventually leading to the giant LDs characteristic of seipin deficiency. Our studies identify a discrete step of LD formation, namely the conversion of nascent LDs to mature LDs, and define a molecular role for seipin in this process, most likely by acting at ER-LD contact sites to enable lipid transfer to nascent LDs.

2013

1. Triacylglycerol synthesis enzymes mediate lipid droplet growth by relocalizing from the ER to lipid droplets Wilfling, Florian, Wang, Huajin, Haas, Joel T., Krahmer, Natalie, Gould, Travis J., Uchida, Aki, Cheng, Ji Xin, Graham, Morven, Christiano, Romain, Fr??hlich, Florian, Liu, Xinran, Buhman, Kimberly K., Coleman, Rosalind A., Bewersdorf, Joerg, Farese, Robert V., and Walther, Tobias C. Developmental Cell 2013 [Abs] [HTML] [PDF]

   Lipid droplets (LDs) store metabolic energy and membrane lipid precursors. With excess metabolic energy, cells synthesize triacylglycerol (TG) and form LDs that grow dramatically. It is unclear how TG synthesis relates to LD formation and growth. Here, we identify two LD subpopulations: smaller LDs of relatively constant size, and LDs that grow larger. The latter population contains isoenzymes for each step of TG synthesis. Glycerol-3-phosphate acyltransferase 4 (GPAT4), which catalyzes the first and rate-limiting step, relocalizes from the endoplasmic reticulum (ER) to a subset of forming LDs, where it becomes stably associated. ER-to-LD targeting of GPAT4 and other LD-localized TG synthesis isozymes is required for LD growth. Key features of GPAT4 ER-to-LD targeting and function in LD growth are conserved between Drosophila and mammalian cells. Our results explain how TG synthesis is coupled with LD growth and identify two distinct LD subpopulations based on their capacity for localized TG synthesis. ?? 2013 Elsevier Inc.

2. Analysis of lipid droplets in hepatocytes Wang, Huajin, Quiroga, Ariel D., and Lehner, Richard Methods in Cell Biology 2013 [Abs] [HTML] [PDF]

   The liver plays an important role in triacylglycerol (TG) metabolism. It can store large amounts of TG in cytosolic lipid droplets (CLDs), or it can package TG into very-low density lipoproteins (VLDL) that are secreted from the cell. TG packaged into VLDL is derived from TG stored within the endoplasmic reticulum in lumenal lipid droplets (LLDs). Therefore, the liver contains at least three kinds of LDs that differ in their protein composition, subcellular localization, and function. Hepatic LDs undergo tremendous changes in their size and protein composition depending on the energetic (fasting/feeding) and pathological (viral infection, nonalcoholic fatty liver disease, etc.) states. It is crucial to develop methodologies that allow the isolation and analyses of the various hepatic LDs in order to gain insight into the differential metabolism of these important lipid storage/transport particles in health and disease. Here, we present detailed protocols for the isolation and analysis of CLDs and LLDs and for monitoring CLD dynamics. ?? 2013 Elsevier Inc.

2011

1. Lipin-1gamma isoform is a novel lipid droplet-associated protein highly expressed in the brain Wang, Huajin, Zhang, Jing, Qiu, Wei, Han, Gil Soo, Carman, George M., and Adeli, Khosrow FEBS Letters 2011 [Abs] [HTML] [PDF]

   Lipin-1 proteins are phosphatidic acid phosphatases (PAPs) catalyzing the conversion from phosphatidic acid (PA) to diacylglycerol (DG). Two alternative splicing isoforms, lipin-1?? and -1??, are localized at different subcellular compartments. A third splicing isoform, lipin-1?? was recently cloned and its subcellular localization is unknown. Here, we demonstrate that lipin-1?? is localized to lipid droplets (LDs), an association mediated by a hydrophobic, lipin-1??-specific domain. Additional expression of lipin-1?? altered LD morphology without affecting the triacylglycerol (TG) level. In human tissues, lipin-1?? is the main lipin-1 isoform expressed in normal human brain, suggesting a specialized role in regulating brain lipid metabolism. ?? 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

2. Hepatic autophagy mediates endoplasmic reticulum stress-induced degradation of misfolded apolipoprotein B. Qiu, Wei, Zhang, Jing, Dekker, Mark J., Wang, Huajin, Huang, Ju, Brumell, John H., and Adeli, Khosrow Hepatology (Baltimore, Md.) 2011 [Abs] [HTML] [PDF]

   UNLABELLED Induction of endoplasmic reticulum (ER) stress was previously shown to impair hepatic apolipoprotein B100 (apoB) production by enhancing cotranslational and posttranslational degradation of newly synthesized apoB. Here, we report the involvement of autophagy in ER stress-induced degradation of apoB and provide evidence for a significant role of autophagy in regulating apoB biogenesis in primary hepatocyte systems. Induction of ER stress following short-term glucosamine treatment of McA-RH7777 cells resulted in significantly increased colocalization of apoB with green fluorescent protein-microtubule-associated protein 1 light chain 3 (GFP-LC3), referred to as apoB-GFP-LC3 puncta, in a dose-dependent manner. Colocalization with this autophagic marker correlated positively with the reduction in newly synthesized apoB100. Treatment of McA-RH7777 cells with 4-phenyl butyric acid, a chemical ER stress inhibitor, prevented glucosamine- and tunicamycin-induced increases in GRP78 and phosphorylated eIF2α, rescued newly synthesized [(35) S]-labeled apoB100, and substantially blocked the colocalization of apoB with GFP-LC3. Autophagic apoB degradation was also observed in primary rat and hamster hepatocytes at basal conditions as well as upon the induction of ER stress. In contrast, this pathway was inactive in HepG2 cells under ER stress conditions, unless proteasomal degradation was blocked with N-acetyl-leucinyl-leucinyl-norleucinal and the medium was supplemented with oleate. Transient transfection of McA-RH7777 cells with a wild-type protein kinase R-like ER kinase (PERK) complementary DNA resulted in dramatic induction of apoB autophagy. In contrast, transfection with a kinase inactive mutant PERK gave rise to reduced apoB autophagy, suggesting that apoB autophagy may occur via a PERK signaling-dependent mechanism. CONCLUSION Taken together, these data suggest that induction of ER stress leads to markedly enhanced apoB autophagy in a PERK-dependent pathway, which can be blocked with the chemical chaperone 4-phenyl butyric acid. ApoB autophagy rather than proteasomal degradation may be a more pertinent physiological mechanism regulating hepatic lipoprotein production in primary hepatocytes.

2010

1. Altered Lipid Droplet Dynamics in Hepatocytes Lacking Triacylglycerol Hydrolase Expression Wang, Huajin, Wei, Enhui, Quiroga, Ariel D., Sun, Xuejin, Touret, Nicolas, and Lehner, Richard Molecular biology of the cell 2010 [Abs] [HTML] [PDF]

   Lipid droplets (LDs) form from the endoplasmic reticulum (ER) and grow in size by obtaining triacylglycerols (TG). Triacylglycerol hydrolase (TGH), a lipase residing in the ER, is involved in the mobilization of TG stored in LDs for the secretion of very-low-density lipoproteins. In this study, we investigated TGH-mediated changes in cytosolic LD dynamics. We have found that TGH deficiency resulted in decreased size and increased number of LDs in hepatocytes. Using fluorescent fatty acid analogues to trace LD formation, we observed that TGH deficiency did not affect the formation of nascent LDs on the ER. However, the rate of lipid transfer into preformed LDs was significantly slower in the absence of TGH. Absence of TGH expression resulted in increased levels of membrane diacylglycerol and augmented phospholipid synthesis, which may be responsible for the delayed lipid transfer. Therefore, altered maturation (growth) rather than nascent formation (de novo synthesis) may be responsible for the observed morphological changes of LDs in TGH-deficient hepatocytes.

2. Loss of TGH/Ces3 in Mice Decreases Blood Lipids, Improves Glucose Tolerance, and Increases Energy Expenditure Wei, Enhui, Ben Ali, Yassine, Lyon, James, Wang, Huajin, Nelson, Randy, Dolinsky, Vernon W., Dyck, Jason R B, Mitchell, Grant, Korbutt, Gregory S., and Lehner, Richard Cell Metabolism 2010 [Abs] [HTML] [PDF]

   Excessive accumulation of triacylglycerol in peripheral tissues is tightly associated with obesity and has been identified as an independent risk factor for insulin resistance, type 2 diabetes, and cardiovascular complications. Here we show that ablation of carboxylesterase 3 (Ces3)/triacylglycerol hydrolase (TGH) expression in mice (Tgh-/-) results in decreased plasma triacylglycerol, apolipoprotein B, and fatty acid levels in both fasted and fed states. Despite the attenuation of very low-density lipoprotein secretion, TGH deficiency does not increase hepatic triacylglycerol levels. Tgh-/- mice exhibit increased food intake, respiratory quotient, and energy expenditure without change in body weight. These metabolic changes are accompanied by improved insulin sensitivity and glucose tolerance. Tgh-/- mice have smaller sized pancreatic islets but maintain normal glucose-stimulated insulin secretion. These studies demonstrate the potential of TGH as a therapeutic target for lowering blood lipid levels. ?? 2010 Elsevier Inc. All rights reserved.

2007

1. Proteomic and lipid characterization of apolipoprotein B-free luminal lipid droplets from mouse liver microsomes: Implications for very low density lipoprotein assembly Wang, Huajin, Gilham, Dean, and Lehner, Richard Journal of Biological Chemistry 2007 [Abs] [HTML] [PDF]

   The assembly of very low density lipoproteins involves the formation of a primordial, poorly lipidated apoB-containing particle in the endoplasmic reticulum, followed by the addition of neutral lipid from luminal lipid droplets (LLD). However, the lipid and protein compositions of LLD have not been determined. We have isolated LLD from mouse liver microsomes and analyzed their lipid and protein compositions. LLD are variably sized particles relatively poor in triacylglycerol (TG) content when compared with the lipid composition of cytosolic lipid droplets (CLD). They are devoid of apoB, adipophilin, and albumin but contain numerous proteins different from those found on CLD, including TG hydrolase (TGH), carboxylesterase 1 (Ces1), microsomal triglyceride transfer protein (MTP), and apoE. Ectopic expression of TGH in McArdle RH7777 hepatoma cells resulted in decreased cellular TG levels, demonstrating a role for TGH in the mobilization of hepatic neutral lipid stores. The isolation and characterization of LLD provide new supporting evidence for the two-step assembly of very low density lipoproteins.