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  1. Article ; Online: Regulation of UV damage repair in quiescent yeast cells.

    Long, Lindsey J / Lee, Po-Hsuen / Small, Eric M / Hillyer, Cory / Guo, Yan / Osley, Mary Ann

    DNA repair

    2020  Volume 90, Page(s) 102861

    Abstract: Non-growing quiescent cells face special challenges when repairing lesions produced by exogenous DNA damaging agents. These challenges include the global repression of transcription and translation and a compacted chromatin structure. We investigated how ...

    Abstract Non-growing quiescent cells face special challenges when repairing lesions produced by exogenous DNA damaging agents. These challenges include the global repression of transcription and translation and a compacted chromatin structure. We investigated how quiescent yeast cells regulated the repair of DNA lesions produced by UV irradiation. We found that UV lesions were excised and repaired in quiescent cells before their re-entry into S phase, and that lesion repair was correlated with high levels of Rad7, a recognition factor in the global genome repair sub-pathway of nucleotide excision repair (GGR-NER). UV exposure led to an increased frequency of mutations that included C->T transitions and T > A transversions. Mutagenesis was dependent on the error-prone translesion synthesis (TLS) DNA polymerase, Pol zeta, which was the only DNA polymerase present in detectable levels in quiescent cells. Across the genome of quiescent cells, UV-induced mutations showed an association with exons that contained H3K36 or H3K79 trimethylation but not with those bound by RNA polymerase II. Together, the data suggest that the distinct physiological state and chromatin structure of quiescent cells contribute to its regulation of UV damage repair.
    MeSH term(s) Cell Cycle ; DNA Damage ; DNA Repair ; DNA, Fungal/metabolism ; DNA, Fungal/radiation effects ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Mutagenesis ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/radiation effects ; Saccharomyces cerevisiae Proteins/metabolism ; Ultraviolet Rays
    Chemical Substances DNA, Fungal ; DNA-Binding Proteins ; RAD7 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2020-04-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2020.102861
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Drosophila eugracilis - Akt.

    Morgan, Ashley / Kiser, Cole A / Bronson, Isabel / Lin, Hanjun / Guillette, Nicholas / McMahon, Robert / Kennell, Jennifer A / Long, Lindsey J / Reed, Laura K / Rele, Chinmay P

    microPublication biology

    2022  Volume 2022

    Abstract: Gene Model ... ...

    Abstract Gene Model for
    Language English
    Publishing date 2022-07-02
    Publishing country United States
    Document type Journal Article
    ISSN 2578-9430
    ISSN (online) 2578-9430
    DOI 10.17912/micropub.biology.000544
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Drosophila mojavensis

    Congleton, Hannah / Kiser, Cole A / Colom Diaz, Patricia A / Schlichting, Elizabeth / Walton, Dorothy A / Long, Lindsey J / Reed, Laura K / Martinez-Cruzado, Juan Carlos / Rele, Chinmay P

    microPublication biology

    2022  Volume 2022

    Language English
    Publishing date 2022-11-15
    Publishing country United States
    Document type Journal Article
    ISSN 2578-9430
    ISSN (online) 2578-9430
    DOI 10.17912/micropub.biology.000677
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Multidecade Mortality and a Homolog of Hepatitis C Virus in Bald Eagles (Haliaeetus leucocephalus), the National Bird of the USA.

    Goldberg, Tony L / Sibley, Samuel D / Pinkerton, Marie E / Dunn, Christopher D / Long, Lindsey J / White, LeAnn C / Strom, Sean M

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 14953

    Abstract: The bald eagle (Haliaeetus leucocephalus) once experienced near-extinction but has since rebounded. For decades, bald eagles near the Wisconsin River, USA, have experienced a lethal syndrome with characteristic clinical and pathological features but ... ...

    Abstract The bald eagle (Haliaeetus leucocephalus) once experienced near-extinction but has since rebounded. For decades, bald eagles near the Wisconsin River, USA, have experienced a lethal syndrome with characteristic clinical and pathological features but unknown etiology. Here, we describe a novel hepacivirus-like virus (Flaviviridae: Hepacivirus) identified during an investigation of Wisconsin River eagle syndrome (WRES). Bald eagle hepacivirus (BeHV) belongs to a divergent clade of avian viruses that share features with members of the genera Hepacivirus and Pegivirus. BeHV infected 31.9% of eagles spanning 4,254 km of the coterminous USA, with negative strand viral RNA demonstrating active replication in liver tissues. Eagles from Wisconsin were approximately 10-fold more likely to be infected than eagles from elsewhere. Eagle mitochondrial DNA sequences were homogeneous and geographically unstructured, likely reflecting a recent population bottleneck, whereas BeHV envelope gene sequences showed strong population genetic substructure and isolation by distance, suggesting localized transmission. Cophylogenetic analyses showed no congruity between eagles and their viruses, supporting horizontal rather than vertical transmission. These results expand our knowledge of the Flaviviridae, reveal a striking pattern of decoupled host/virus coevolution on a continental scale, and highlight knowledge gaps about health and conservation in even the most iconic of wildlife species.
    MeSH term(s) Animals ; Bird Diseases/virology ; Conservation of Natural Resources ; Eagles/virology ; Evolution, Molecular ; Flavivirus Infections/mortality ; Flavivirus Infections/veterinary ; Genetics, Population ; Genome, Viral ; Geography ; Hepacivirus ; High-Throughput Nucleotide Sequencing ; Likelihood Functions ; Phylogeny ; Population Dynamics ; RNA, Viral ; United States ; Wisconsin
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2019-10-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-50580-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparison of methods for depletion of albumin and IgG from equine serum.

    Olver, Christine S / Webb, Teckla L / Long, Lindsey J / Scherman, Hataichanok / Prenni, Jessica E

    Veterinary clinical pathology

    2010  Volume 39, Issue 3, Page(s) 337–345

    Abstract: Background: Disease-specific biomarkers hold diagnostic promise in both human and veterinary medicine, but serum biomarkers in low concentrations may be masked by the presence of abundant proteins, mostly albumin and IgG. Methods to deplete albumin and ... ...

    Abstract Background: Disease-specific biomarkers hold diagnostic promise in both human and veterinary medicine, but serum biomarkers in low concentrations may be masked by the presence of abundant proteins, mostly albumin and IgG. Methods to deplete albumin and IgG exist, but efficacy of these methods for depleting equine serum of these proteins has not been established.
    Objective: The aim of this study was to determine if albumin and IgG could be depleted from equine serum using several commercially available kits and procedures.
    Methods: One-dimensional gel electrophoresis followed by densitometry was used to determine percent of albumin, IgG, and both in pooled serum from 3 horses before and after application of 7 depletion methods. Repeatability was determined by applying the 2 best methods to serum samples from 6 grade horses.
    Results: For pooled serum, depletion rates varied from 35-90% for albumin and 0-94% for IgG. In the repeatability study, the ProteoExtract method combined with protein G Sepharose beads to remove additional IgG provided the best overall performance with 66% albumin depletion and 100% IgG depletion. A protocol using protein G Sepharose beads to remove IgG followed by ethanol precipitation of nonalbumin proteins with albumin remaining in the supernatant was the second most effective, with 85% albumin depletion and 55% IgG depletion. Although a multiprotein immunodepletion column effectively removed 90% of the albumin, the method was ineffective at removing IgG.
    Conclusion: Albumin and IgG removal kits optimized for human use have variable efficacy for equine serum. Combined use of the ProteoExtract kit and manual incubation with protein G Sepharose beads provided the most effective depletion.
    MeSH term(s) Animals ; Biomarkers/blood ; Blood Proteins/analysis ; Blood Proteins/isolation & purification ; Densitometry/methods ; Densitometry/veterinary ; Electrophoresis, Agar Gel/methods ; Electrophoresis, Agar Gel/veterinary ; Female ; Horses/blood ; Immunoglobulin G/blood ; Immunoglobulin G/isolation & purification ; Male ; Reproducibility of Results ; Sensitivity and Specificity ; Serum Albumin/analysis ; Serum Albumin/isolation & purification
    Chemical Substances Biomarkers ; Blood Proteins ; Immunoglobulin G ; Serum Albumin
    Language English
    Publishing date 2010-09
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 2114702-4
    ISSN 1939-165X ; 0275-6382
    ISSN (online) 1939-165X
    ISSN 0275-6382
    DOI 10.1111/j.1939-165X.2010.00241.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Student Attitudes Contribute to the Effectiveness of a Genomics CURE.

    Lopatto, David / Rosenwald, Anne G / Burgess, Rebecca C / Silver Key, Catherine / Van Stry, Melanie / Wawersik, Matthew / DiAngelo, Justin R / Hark, Amy T / Skerritt, Matthew / Allen, Anna K / Alvarez, Consuelo / Anderson, Sara / Arrigo, Cindy / Arsham, Andrew / Barnard, Daron / Bedard, James E J / Bose, Indrani / Braverman, John M / Burg, Martin G /
    Croonquist, Paula / Du, Chunguang / Dubowsky, Sondra / Eisler, Heather / Escobar, Matthew A / Foulk, Michael / Giarla, Thomas / Glaser, Rivka L / Goodman, Anya L / Gosser, Yuying / Haberman, Adam / Hauser, Charles / Hays, Shan / Howell, Carina E / Jemc, Jennifer / Jones, Christopher J / Kadlec, Lisa / Kagey, Jacob D / Keller, Kimberly L / Kennell, Jennifer / Kleinschmit, Adam J / Kleinschmit, Melissa / Kokan, Nighat P / Kopp, Olga Ruiz / Laakso, Meg M / Leatherman, Judith / Long, Lindsey J / Manier, Mollie / Martinez-Cruzado, Juan C / Matos, Luis F / McClellan, Amie Jo / McNeil, Gerard / Merkhofer, Evan / Mingo, Vida / Mistry, Hemlata / Mitchell, Elizabeth / Mortimer, Nathan T / Myka, Jennifer Leigh / Nagengast, Alexis / Overvoorde, Paul / Paetkau, Don / Paliulis, Leocadia / Parrish, Susan / Toering Peters, Stephanie / Preuss, Mary Lai / Price, James V / Pullen, Nicholas A / Reinke, Catherine / Revie, Dennis / Robic, Srebrenka / Roecklein-Canfield, Jennifer A / Rubin, Michael R / Sadikot, Takrima / Sanford, Jamie Siders / Santisteban, Maria / Saville, Kenneth / Schroeder, Stephanie / Shaffer, Christopher D / Sharif, Karim A / Sklensky, Diane E / Small, Chiyedza / Smith, Sheryl / Spokony, Rebecca / Sreenivasan, Aparna / Stamm, Joyce / Sterne-Marr, Rachel / Teeter, Katherine C / Thackeray, Justin / Thompson, Jeffrey S / Velazquez-Ulloa, Norma / Wolfe, Cindy / Youngblom, James / Yowler, Brian / Zhou, Leming / Brennan, Janie / Buhler, Jeremy / Leung, Wilson / Elgin, Sarah C R / Reed, Laura K

    Journal of microbiology & biology education

    2022  Volume 23, Issue 2

    Abstract: The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously ... ...

    Abstract The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.
    Language English
    Publishing date 2022-05-16
    Publishing country United States
    Document type Journal Article
    ISSN 1935-7877
    ISSN 1935-7877
    DOI 10.1128/jmbe.00208-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience.

    Lopatto, David / Rosenwald, Anne G / DiAngelo, Justin R / Hark, Amy T / Skerritt, Matthew / Wawersik, Matthew / Allen, Anna K / Alvarez, Consuelo / Anderson, Sara / Arrigo, Cindy / Arsham, Andrew / Barnard, Daron / Bazinet, Christopher / Bedard, James E J / Bose, Indrani / Braverman, John M / Burg, Martin G / Burgess, Rebecca C / Croonquist, Paula /
    Du, Chunguang / Dubowsky, Sondra / Eisler, Heather / Escobar, Matthew A / Foulk, Michael / Furbee, Emily / Giarla, Thomas / Glaser, Rivka L / Goodman, Anya L / Gosser, Yuying / Haberman, Adam / Hauser, Charles / Hays, Shan / Howell, Carina E / Jemc, Jennifer / Johnson, M Logan / Jones, Christopher J / Kadlec, Lisa / Kagey, Jacob D / Keller, Kimberly L / Kennell, Jennifer / Key, S Catherine Silver / Kleinschmit, Adam J / Kleinschmit, Melissa / Kokan, Nighat P / Kopp, Olga Ruiz / Laakso, Meg M / Leatherman, Judith / Long, Lindsey J / Manier, Mollie / Martinez-Cruzado, Juan C / Matos, Luis F / McClellan, Amie Jo / McNeil, Gerard / Merkhofer, Evan / Mingo, Vida / Mistry, Hemlata / Mitchell, Elizabeth / Mortimer, Nathan T / Mukhopadhyay, Debaditya / Myka, Jennifer Leigh / Nagengast, Alexis / Overvoorde, Paul / Paetkau, Don / Paliulis, Leocadia / Parrish, Susan / Preuss, Mary Lai / Price, James V / Pullen, Nicholas A / Reinke, Catherine / Revie, Dennis / Robic, Srebrenka / Roecklein-Canfield, Jennifer A / Rubin, Michael R / Sadikot, Takrima / Sanford, Jamie Siders / Santisteban, Maria / Saville, Kenneth / Schroeder, Stephanie / Shaffer, Christopher D / Sharif, Karim A / Sklensky, Diane E / Small, Chiyedza / Smith, Mary / Smith, Sheryl / Spokony, Rebecca / Sreenivasan, Aparna / Stamm, Joyce / Sterne-Marr, Rachel / Teeter, Katherine C / Thackeray, Justin / Thompson, Jeffrey S / Peters, Stephanie Toering / Van Stry, Melanie / Velazquez-Ulloa, Norma / Wolfe, Cindy / Youngblom, James / Yowler, Brian / Zhou, Leming / Brennan, Janie / Buhler, Jeremy / Leung, Wilson / Reed, Laura K / Elgin, Sarah C R

    Journal of microbiology & biology education

    2020  Volume 21, Issue 1

    Abstract: A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. ... ...

    Abstract A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.
    Language English
    Publishing date 2020-02-28
    Publishing country United States
    Document type Journal Article
    ISSN 1935-7877
    ISSN 1935-7877
    DOI 10.1128/jmbe.v21i1.2005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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