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2. Timing of Introduction to Solid Food, Growth, and Nutrition Risk in Later Childhood

Author

Cohn, Ronald, Lau, Eddy, Laupacis, Andreas, Parkin, Patricia C., Salter, Michael, Szatmari, Peter, Weir, Shannon, Anderson, Laura N., Borkhoff, Cornelia M., Kowal, Christine, Mason, Dalah, Abdurrahman, Murtala, Anderson, Kelly, Arbess, Gordon, Baker, Jillian, Barozzino, Tony, Bergeron, Sylvie, Bhagat, Dimple, Bloch, Gary, Bonifacio, Joey, Bowry, Ashna, Calpin, Caroline, Campbell, Douglas, Cheema, Sohail, Cheng, Elaine, Chisamore, Brian, Constantin, Evelyn, Danayan, Karoon, Das, Paul, Derocher, Mary Beth, Do, Anh, Doukas, Kathleen, Egger, Anne, Farber, Allison, Freedman, Amy, Freeman, Sloane, Gazeley, Sharon, Guiang, Charlie, Ha, Dan, Handford, Curtis, Hanson, Laura, Harrington, Leah, Jacobson, Sheila, Jagiello, Lukasz, Jansz, Gwen, Kadar, Paul, Kim, Florence, Kiran, Tara, Knowles, Holly, Kwok, Bruce, Lakhoo, Sheila, Lam-Antoniades, Margarita, Leduc, Denis, Leung, Fok-Han, Li, Alan, Li, Patricia, Malach, Jessica, Male, Roy, Mascoll, Vashti, Meret, Aleks, Mok, Elise, Moodie, Rosemary, Nader, Maya, Nash, Katherine, Naymark, Sharon, Owen, James, Peer, Michael, Pena, Kifi, Perlmutar, Marty, Persaud, Navindra, Pinto, Andrew, Porepa, Michelle, Qi, Vikky, Ramji, Nasreen, Ramji, Noor, Raza, Danyaal, Rosenthal, Alana, Rouleau, Katherine, Ruderman, Caroline, Saunderson, Janet, Schiralli, Vanna, Sgro, Michael, Shuja, Hafiz, Shepherd, Susan, Smiltnieks, Barbara, Srikanthan, Cinntha, Taylor, Carolyn, Treherne, Stephen, Turner, Suzanne, Uddin, Fatima, van den Heuvel, Meta, Vaughan, Joanne, Weisdorf, Thea, Wijayasinghe, Sheila, Wong, Peter, Yaremko, John, Ying, Ethel, Young, Elizabeth, Zajdman, Michael, Bazeghi, Farnaz, Bouchard, Vincent, Bustos, Marivic, Camacho, Charmaine, Dalwadi, Dharma, Koroshegyi, Christine, Malhi, Tarandeep, Thadani, Sharon, Thompson, Julia, Thompson, Laurie, Aglipay, Mary, Bayoumi, Imaan, Carsley, Sarah, Cost, Katherine, Eny, Karen, Kim, Theresa, Kinlin, Laura, Omand, Jessica, Vanderhout, Shelley, Vanderloo, Leigh, Allen, Christopher, Boodhoo, Bryan, Chan, Olivia, Dai, David W.H., Hall, Judith, Juni, Peter, Lebovic, Gerald, Pope, Karen, Thorpe, Kevin, Kandel, Rita, Rodrigues, Michelle, Vandenberghe, Hilde, D'Hollander, Curtis J., Keown-Stoneman, Charles D.G., Birken, Catherine S., O'Connor, Deborah L., and Maguire, Jonathon L.

Published
2021
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3. Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification.

Author

Zhong, Huan, Zhou, Xiaopu, Uhm, Hyebin, Jiang, Yuanbing, Cao, Han, Chen, Yu, Mak, Tiffany T. W., Lo, Ronnie Ming Nok, Wong, Bonnie Wing Yan, Cheng, Elaine Yee Ling, Mok, Kin Y., Chan, Andrew Lung Tat, Kwok, Timothy C. Y., Mok, Vincent C. T., Ip, Fanny C. F., Hardy, John, Fu, Amy K. Y., and Ip, Nancy Y.

Abstract

INTRODUCTION: Blood protein biomarkers demonstrate potential for Alzheimer's disease (AD) diagnosis. Limited studies examine the molecular changes in AD blood cells. METHODS: Bulk RNA‐sequencing of blood cells was performed on AD patients of Chinese descent (n = 214 and 26 in the discovery and validation cohorts, respectively) with normal controls (n = 208 and 38 in the discovery and validation cohorts, respectively). Weighted gene co‐expression network analysis (WGCNA) and deconvolution analysis identified AD‐associated gene modules and blood cell types. Regression and unsupervised clustering analysis identified AD‐associated genes, gene modules, cell types, and established AD classification models. RESULTS: WGCNA on differentially expressed genes revealed 15 gene modules, with 6 accurately classifying AD (areas under the receiver operating characteristics curve [auROCs] > 0.90). These modules stratified AD patients into subgroups with distinct disease states. Cell‐type deconvolution analysis identified specific blood cell types potentially associated with AD pathogenesis. DISCUSSION: This study highlights the potential of blood transcriptome for AD diagnosis, patient stratification, and mechanistic studies. Highlights: We comprehensively analyze the blood transcriptomes of a well‐characterized Alzheimer's disease cohort to identify genes, gene modules, pathways, and specific blood cells associated with the disease.Blood transcriptome analysis accurately classifies and stratifies patients with Alzheimer's disease, with some gene modules achieving classification accuracy comparable to that of the plasma ATN biomarkers.Immune‐associated pathways and immune cells, such as neutrophils, have potential roles in the pathogenesis and progression of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Published
2024
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4. A Positive Association Between Dietary Intake of Higher Cow's Milk-Fat Percentage and Non−High-Density Lipoprotein Cholesterol in Young Children

Author

Birken, Catherine S., Maguire, Jonathon L., Cohn, Ronald, Lau, Eddy, Laupacis, Andreas, Parkin, Patricia C., Salter, Michael, Szatmari, Peter, Weir, Shannon, Anderson, Laura N., Borkhoff, Cornelia M., Keown-Stoneman, Charles, Kowal, Christine, Mason, Dalah, Abdurrahman, Murtala, Anderson, Kelly, Arbess, Gordon, Baker, Jillian, Barozzino, Tony, Bergeron, Sylvie, Bhagat, Dimple, Bloch, Gary, Bonifacio, Joey, Bowry, Ashna, Calpin, Caroline, Campbell, Douglas, Cheema, Sohail, Cheng, Elaine, Chisamore, Brian, Constantin, Evelyn, Danayan, Karoon, Das, Paul, Derocher, Mary Beth, Do, Anh, Doukas, Kathleen, Egger, Anne, Farber, Allison, Freedman, Amy, Freeman, Sloane, Gazeley, Sharon, Guiang, Charlie, Ha, Dan, Handford, Curtis, Hanson, Laura, Harrington, Leah, Jacobson, Sheila, Jagiello, Lukasz, Jansz, Gwen, Kadar, Paul, Kim, Florence, Kiran, Tara, Knowles, Holly, Kwok, Bruce, Lakhoo, Sheila, Lam-Antoniades, Margarita, Leduc, Denis, Leung, Fok-Han, Li, Alan, Li, Patricia, Malach, Jessica, Male, Roy, Mascoll, Vashti, Meret, Aleks, Mok, Elise, Moodie, Rosemary, Nader, Maya, Nash, Katherine, Naymark, Sharon, Owen, James, Peer, Michael, Pena, Kifi, Perlmutar, Marty, Persaud, Navindra, Pinto, Andrew, Porepa, Michelle, Qi, Vikky, Ramji, Nasreen, Ramji, Noor, Raza, Danyaal, Rosenthal, Alana, Rouleau, Katherine, Ruderman, Caroline, Saunderson, Janet, Schiralli, Vanna, Sgro, Michael, Shuja, Hafiz, Shepherd, Susan, Smiltnieks, Barbara, Srikanthan, Cinntha, Taylor, Carolyn, Treherne, Stephen, Turner, Suzanne, Uddin, Fatima, van den Heuvel, Meta, Vaughan, Joanne, Weisdorf, Thea, Wijayasinghe, Sheila, Wong, Peter, Yaremko, John, Ying, Ethel, Young, Elizabeth, Zajdman, Michael, Bazeghi, Farnaz, Bouchard, Vincent, Bustos, Marivic, Camacho, Charmaine, Dalwadi, Dharma, Koroshegyi, Christine, Malhi, Tarandeep, Thadani, Sharon, Thompson, Julia, Thompson, Laurie, Aglipay, Mary, Bayoumi, Imaan, Carsley, Sarah, Cost, Katherine, Eny, Karen, Kim, Theresa, Kinlin, Laura, Omand, Jessica, Vanderhout, Shelley, Vanderloo, Leigh, Allen, Christopher, Boodhoo, Bryan, Chan, Olivia, Dai, David W.H., Hall, Judith, Juni, Peter, Lebovic, Gerald, Pope, Karen, Thorpe, Kevin, Kandel, Rita, Rodrigues, Michelle, Vandenberghe, Hilde, Wong, Vincent C.H., Omand, Jessica A., and O'Connor, Deborah L.

Published
2019
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5. Higher Body Mass Index Is Associated with Iron Deficiency in Children 1 to 3 Years of Age

Author

Aglipay, Mary, Anderson, Laura N., Dai, David W.H., Keown-Stoneman, Charles, Kowal, Christine, Mason, Dalah, Abdurrahman, Murtala, Anderson, Barbara, Anderson, Kelly, Arbess, Gordon, Baker, Jillian, Barozzino, Tony, Bayoumi, Imaan, Bergeron, Sylvie, Bhagat, Dimple, Blanchette, Nicholas, Bloch, Gary, Bonifacio, Joey, Bowry, Ashna, Brown, Anne, Bugera, Jennifer, Calpin, Caroline, Campbell, Douglas, Cheema, Sohail, Cheng, Elaine, Chisamore, Brian, Constantin, Evelyn, Culbert, Ellen, Danayan, Karoon, Das, Paul, Derocher, Mary Beth, Do, Anh, Dorey, Michael, Doukas, Kathleen, Egger, Anne, Farber, Allison, Freedman, Amy, Freeman, Sloane, Gazeley, Sharon, Guiang, Charlie, Ha, Dan, Handford, Curtis, Hanson, Laura, Harrington, Leah, Hatch, Hailey, Hughes, Teresa, Jacobson, Sheila, Jagiello, Lukasz, Jansz, Gwen, Jasuja, Mona, Kadar, Paul, Kiran, Tara, Knowles, Holly, Kwok, Bruce, Lakhoo, Sheila, Lam-Antoniades, Margarita, Lau, Eddy, Leduc, Denis, Leung, Fok-Han, Li, Alan, Li, Patricia, Loo, Jennifer, Louis, Joanne, Mahmoud, Sarah, Malach, Jessica, Male, Roy, Mascoll, Vashti, Meret, Aleks, Mok, Elise, Moodie, Rosemary, Morinis, Julia, Nader, Maya, Nash, Katherine, Naymark, Sharon, Owen, James, Parry, Jane, Peer, Michael, Pena, Kifi, Perlmutar, Marty, Persaud, Navindra, Pinto, Andrew, Porepa, Michelle, Qi, Vikky, Ramji, Nasreen, Ramji, Noor, Rana, Jesleen, Raza, Danyaal, Rosenthal, Alana, Rouleau, Katherine, Saunderson, Janet, Saxena, Rahul, Schiralli, Vanna, Sgro, Michael, Shuja, Hafiz, Shepherd, Susan, Smiltnieks, Barbara, Srikanthan, Cinntha, Taylor, Carolyn, Treherne, Stephen, Turner, Suzanne, Uddin, Fatima, van den Heuvel, Meta, Vaughan, Joanne, Weisdorf, Thea, Wijayasinghe, Sheila, Wong, Peter, Wormsbecker, Anne, Yaremko, John, Ying, Ethel, Young, Elizabeth, Zajdman, Michael, Bazeghi, Farnaz, Bouchard, Vincent, Bustos, Marivic, Camacho, Charmaine, Dalwadi, Dharma, Koroshegyi, Christine, Malhi, Tarandeep, Thadani, Sharon, Thompson, Julia, Thompson, Laurie, Sypes, Emma E., Parkin, Patricia C., Birken, Catherine S., Carsley, Sarah, MacArthur, Colin, Maguire, Jonathon L., and Borkhoff, Cornelia M.

Published
2019
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6. A blood‐based multi‐pathway biomarker assay for early detection and staging of Alzheimer's disease across ethnic groups.

Author

Jiang, Yuanbing, Uhm, Hyebin, Ip, Fanny C., Ouyang, Li, Lo, Ronnie M. N., Cheng, Elaine Y. L., Cao, Xiaoyun, Tan, Clara M. C., Law, Brian C. H., Ortiz‐Romero, Paula, Puig‐Pijoan, Albert, Fernández‐Lebrero, Aida, Contador, José, Mok, Kin Y., Hardy, John, Kwok, Timothy C. Y., Mok, Vincent C. T., Suárez‐Calvet, Marc, Zetterberg, Henrik, and Fu, Amy K. Y.

Abstract

INTRODUCTION: Existing blood‐based biomarkers for Alzheimer's disease (AD) mainly focus on its pathological features. However, studies on blood‐based biomarkers associated with other biological processes for a comprehensive evaluation of AD status are limited. METHODS: We developed a blood‐based, multiplex biomarker assay for AD that measures the levels of 21 proteins involved in multiple biological pathways. We evaluated the assay's performance for classifying AD and indicating AD‐related endophenotypes in three independent cohorts from Chinese or European‐descent populations. RESULTS: The 21‐protein assay accurately classified AD (area under the receiver operating characteristic curve [AUC] = 0.9407 to 0.9867) and mild cognitive impairment (MCI; AUC = 0.8434 to 0.8945) while also indicating brain amyloid pathology. Moreover, the assay simultaneously evaluated the changes of five biological processes in individuals and revealed the ethnic‐specific dysregulations of biological processes upon AD progression. DISCUSSION: This study demonstrated the utility of a blood‐based, multi‐pathway biomarker assay for early screening and staging of AD, providing insights for patient stratification and precision medicine. Highlights: The authors developed a blood‐based biomarker assay for Alzheimer's disease.The 21‐protein assay classifies AD/MCI and indicates brain amyloid pathology.The 21‐protein assay can simultaneously assess activities of five biological processes.Ethnic‐specific dysregulations of biological processes in AD were revealed. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The Association of Breastfeeding Duration and Early Childhood Cardiometabolic Risk

Author

Lau, Eddy, Laupacis, Andreas, Salter, Michael, Szatmari, Peter, Weir, Shannon, Camacho, Charmaine, Chandraraj, Arthana, Dalwadi, Dharma, Islam, Ayesha, Jegathesan, Thivia, Malhi, Tarandeep, Smith, Megan, Thompson, Laurie, Allen, Christopher, Boodhoo, Bryan, Hall, Judith, Juni, Peter, Lebovic, Gerald, Pope, Karen, Shim, Jodi, Thorpe, Kevin, Azad, Azar, Abdullah, Kawsari, Ali, Yamna, Bayoumi, Imaan, Borkhoff, Cornelia M., Carsley, Sarah, Chen, Shiyi, Chen, Yang, Darmawikarta, Denise, Dennis, Cindy-Lee, Eny, Karen, Erdle, Stephanie, Furlong, Kayla, Kavikondala, Kanthi, Koroshegyi, Christine, Kowal, Christine, Lee, Grace Jieun, Mason, Dalah, Omand, Jessica, Persaud, Navindra, Plumptre, Lesley, van den Heuvel, Meta, Vanderhout, Shelley, Zabih, Weeda, Abdurrahman, Murtala, Anderson, Barbara, Anderson, Kelly, Arbess, Gordon, Baker, Jillian, Barozzino, Tony, Bergeron, Sylvie, Bhagat, Dimple, Blanchette, Nicholas, Bloch, Gary, Bonifacio, Joey, Bowry, Ashna, Brown, Anne, Bugera, Jennifer, Campbell, Douglas, Cheema, Sohail, Cheng, Elaine, Chisamore, Brian, Culbert, Ellen, Danayan, Karoon, Das, Paul, Derocher, Mary Beth, Do, Anh, Dorey, Michael, Doukas, Kathleen, Egger, Anne, Farber, Allison, Freedman, Amy, Freeman, Sloane, Fung, Keewai, Gazeley, Sharon, Guiang, Charlie, Ha, Dan, Handford, Curtis, Hanson, Laura, Hatch, Hailey, Hughes, Teresa, Jacobson, Sheila, Jagiello, Lukasz, Jansz, Gwen, Kadar, Paul, Kiran, Tara, Kitney, Lauren, Knowles, Holly, Kwok, Bruce, Lakhoo, Sheila, Lam-Antoniades, Margarita, Leung, Fok-Han, Li, Alan, Loo, Jennifer, Louis, Joanne, Mahmoud, Sarah, Male, Roy, Mascoll, Vashti, Moodie, Rosemary, Morinis, Julia, Nader, Maya, Naymark, Sharon, Neelands, Patricia, Owen, James, Parry, Jane, Peer, Michael, Pena, Kifi, Perlmutar, Marty, Pinto, Andrew, Pitt, Tracy, Porepa, Michelle, Qi, Vikky, Ramji, Nasreen, Ramji, Noor, Rana, Jesleen, Rosenthal, Alana, Rouleau, Katherine, Saunderson, Janet, Saxena, Rahul, Schiralli, Vanna, Sgro, Michael, Shuja, Hafiz, Shepherd, Susan, Smiltnieks, Barbara, Srikanthan, Cinntha, Taylor, Carolyn, Turner, Suzanne, Uddin, Fatima, Vaughan, Joanne, Weisdorf, Thea, Wijayasinghe, Sheila, Wormsbecker, Anne, Ying, Ethel, Young, Elizabeth, Zajdman, Michael, Zenlea, Ian, Wong, Peter D., Anderson, Laura N., Dai, David D.W., Parkin, Patricia C., Maguire, Jonathan L., and Birken, Catherine S.

Published
2018
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14. The Photophysiology of Benthic Diatoms in the Intertidal Flats of Pulau Pinang (Malaysia).

Author

Salleh, Sazlina, Ee Ling Cheng, Elaine, Hossain, Md. Solaiman, Samad, Shakila, Mubin, Nur Ain Amani Abdul, Darif, Nur Aqilah Muhamad, Jonik, Michelle Glory G., and Mohammad, Mahadi

Subjects
ALGAL communities, NAVICULA, BIOMASS estimation, CHLOROPHYLL spectra, DIATOMS, ELECTRON transport, TWO-way analysis of variance, SPECIES diversity
Abstract

The in-situ photosynthetic activity in tropical intertidal benthic diatom in response to environmental variation was assessed in this study by measuring chlorophyll fluorescence. The investigation was carried out during the lowest tide in January (non-rainy day) and February 2013 (post-rainy day) at two sampling sites (A and B) from each selected location (Pantai Jerejak, Teluk Bahang and Tanjung Bungah, Pulau Pinang, Malaysia). Samples of surface sediment (top 0.5 cm) were collected, and chlorophyll a extracted as biomass estimation. Assessments of the photosynthetic activity of benthic diatoms were made using a pulse-amplitude modulated (PAM) fluorometer. Fifty-three species were identified, representing 27 genera from the three studied locations. Both locations showed similarities in species diversity and abundance. Two-way ANOVA showed no significant differences (p = 0.430) in species richness (Margalef Index) among sampling locations, with an average value of 6.33±0.247. Both intertidal flats were dominated by Cocconeis, Navicula, Actinoptychus, and Diploneis. The community has low maximum quantum yields, Fv/Fm (ranging from 0.170 to 0.340) and is often light-limited (Photoacclimation Index, Ek, ranging from 67.96 to 236.71 µmol photons m-2 s-1). The relative electron transport rate (rETRmax) was low, with values ranging from 3.45 to 35.51 across three sampling locations. Fluctuation in salinity has caused a decrease in photosynthetic activity. This study suggests that the low values indicated a poorly adapted benthic microalgal community that is constantly light-limited. However, time-series data is needed to determine the ability of these communities to adapt to the changing environment. [ABSTRACT FROM AUTHOR]

Published
2023
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16. The Association of Breastfeeding Duration and Early Childhood Cardiometabolic Risk

Author

Wong, Peter D., Anderson, Laura N., Dai, David D.W., Parkin, Patricia C., Maguire, Jonathan L., Birken, Catherine S., Lau, Eddy, Laupacis, Andreas, Salter, Michael, Szatmari, Peter, Weir, Shannon, Camacho, Charmaine, Chandraraj, Arthana, Dalwadi, Dharma, Islam, Ayesha, Jegathesan, Thivia, Malhi, Tarandeep, Smith, Megan, Thompson, Laurie, Allen, Christopher, Boodhoo, Bryan, Hall, Judith, Juni, Peter, Lebovic, Gerald, Pope, Karen, Shim, Jodi, Thorpe, Kevin, Azad, Azar, Abdullah, Kawsari, Ali, Yamna, Bayoumi, Imaan, Borkhoff, Cornelia M., Carsley, Sarah, Chen, Shiyi, Chen, Yang, Darmawikarta, Denise, Dennis, Cindy-Lee, Eny, Karen, Erdle, Stephanie, Furlong, Kayla, Kavikondala, Kanthi, Koroshegyi, Christine, Kowal, Christine, Lee, Grace Jieun, Mason, Dalah, Omand, Jessica, Persaud, Navindra, Plumptre, Lesley, van den Heuvel, Meta, Vanderhout, Shelley, Zabih, Weeda, Abdurrahman, Murtala, Anderson, Barbara, Anderson, Kelly, Arbess, Gordon, Baker, Jillian, Barozzino, Tony, Bergeron, Sylvie, Bhagat, Dimple, Blanchette, Nicholas, Bloch, Gary, Bonifacio, Joey, Bowry, Ashna, Brown, Anne, Bugera, Jennifer, Campbell, Douglas, Cheema, Sohail, Cheng, Elaine, Chisamore, Brian, Culbert, Ellen, Danayan, Karoon, Das, Paul, Derocher, Mary Beth, Do, Anh, Dorey, Michael, Doukas, Kathleen, Egger, Anne, Farber, Allison, Freedman, Amy, Freeman, Sloane, Fung, Keewai, Gazeley, Sharon, Guiang, Charlie, Ha, Dan, Handford, Curtis, Hanson, Laura, Hatch, Hailey, Hughes, Teresa, Jacobson, Sheila, Jagiello, Lukasz, Jansz, Gwen, Kadar, Paul, Kiran, Tara, Kitney, Lauren, Knowles, Holly, Kwok, Bruce, Lakhoo, Sheila, Lam-Antoniades, Margarita, Leung, Fok-Han, Li, Alan, Loo, Jennifer, Louis, Joanne, Mahmoud, Sarah, Male, Roy, Mascoll, Vashti, Moodie, Rosemary, Morinis, Julia, Nader, Maya, Naymark, Sharon, Neelands, Patricia, Owen, James, Parry, Jane, Peer, Michael, Pena, Kifi, Perlmutar, Marty, Pinto, Andrew, Pitt, Tracy, Porepa, Michelle, Qi, Vikky, Ramji, Nasreen, Ramji, Noor, Rana, Jesleen, Rosenthal, Alana, Rouleau, Katherine, Saunderson, Janet, Saxena, Rahul, Schiralli, Vanna, Sgro, Michael, Shuja, Hafiz, Shepherd, Susan, Smiltnieks, Barbara, Srikanthan, Cinntha, Taylor, Carolyn, Turner, Suzanne, Uddin, Fatima, Vaughan, Joanne, Weisdorf, Thea, Wijayasinghe, Sheila, Wormsbecker, Anne, Ying, Ethel, Young, Elizabeth, Zajdman, Michael, and Zenlea, Ian

Published
2018
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20. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

Author

Krauthammer, Michael, Kong, Yong, Ha, Byung Hak, Evans, Perry, Bacchiocchi, Antonella, McCusker, Jamie P, Cheng, Elaine, Davis, Matthew J, Goh, Gerald, Choi, Murim, Ariyan, Stephan, Narayan, Deepak, Dutton-Regester, Ken, Capatana, Ana, Holman, Edna C, Bosenberg, Marcus, Sznol, Mario, Kluger, Harriet M, Brash, Douglas E, Stern, David F, Materin, Miguel A, Lo, Roger S, Mane, Shrikant, Ma, Shuangge, Kidd, Kenneth K, Hayward, Nicholas K, Lifton, Richard P, Schlessinger, Joseph, Boggon, Titus J, and Halaban, Ruth

Published
2012
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29. Characterization of vineyard-associated wine yeasts and flavonoid profiles of Pinot Noir grapes in the Okanagan Valley of British Columbia, Canada

Author

Cheng, Elaine

Subjects
fungi, food and beverages
Abstract

Wine is a product of grape juice fermentation by yeast. Terroir is a term that encompasses all environmental factors and interactions at a specific geographical site, resulting in the development of regional-specific microbial strains and differences in grape phenotypes. The objectives of this study were to determine the distribution of vineyard-associated wine yeast strains, identify potential regional-specific wine yeast strains and characterize the flavonoid profile of Pinot Noir grapes among three different sub-regions in the Okanagan Valley (OV), a major wine region in British Columbia, Canada, in the 2017 vintage. Grape samples were collected from thirteen vineyards among three sub-regions of the OV, namely Kelowna (KE), Naramata-Penticton (NP) and Oliver-Osoyoos (OO), within a week prior to the winery harvesting date, which occurred between September 2017 and October 2017. Vineyard-associated S. cerevisiae and S. uvarum on the grape samples were enriched and isolated from spontaneous fermentations conducted in the lab. The isolates were genotyped by microsatellite analysis. Regional-specific wine yeast strains were differentiated from commercial wine yeast strains using Bruvo’s genetic distance. The anthocyanin and flavonol profiles of Pinot Noir grapes were analyzed by HPLC/UV-vis/MS and the tannin profile was analyzed by a spectrophotometric method. In total, 10 commercial S. cerevisiae strains, 22 potentially indigenous S. cerevisiae strains, 2 previously isolated S. uvarum strains from OV, 1 previously isolated S. uvarum strain from Hornby Island and 2 newly discovered S. uvarum strains were isolated in this study. S. cerevisiae strains is genetically more closely related within each sub-region as compared to between sub-regions. The population structure of the S. cerevisiae strains was significant at the regional level. The anthocyanin content were significantly lower in Pinot Noir grapes isolated from OO as compared to KE. Furthermore, the relative abundance of methoxylated anthocyanin and flavonol compounds were higher in Pinot Noir grapes collected in OO as compared to KE. Therefore, the flavonoid profile of Pinot Noir grapes was significantly affected by sub-regional terroirs. Further research is required to determine how regional-specific wine yeast strains and the flavonoid profile of Pinot Noir grapes affect the quality of wine production in the OV.

Published
2019
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32. Outcomes of primary and secondary tracheoesophageal puncture: a 16-year retrospective analysis

Author

Cheng, Elaine, Ho, Margie, Ganz, Cindy, Shaha, Ashok, Boyle, Jay O., Singh, Bhuvanesh, Wong, Richard J., Patel, Snehal, Shah, Jatin, Branski, Ryan C., and Kraus, Dennis H.

Subjects
Laryngectomy -- Research, Laryngectomy -- Case studies, Laryngectomy -- Analysis, Pulmonary manifestations of general diseases -- Case studies, Pulmonary manifestations of general diseases -- Research
Abstract

Abstract The current study retrospectively reviewed the cases of 68 patients who had undergone total laryngectomy and tracheoesophageal puncture (TEP) over a 16-year period. Fifty-one patients underwent primary TEP and [...]

Published
2006

36. Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

Author

Xu Fang, Cheng Elaine, Hoyt Kathleen, Bacchiocchi Antonella, Narayan Deepak, Ariyan Stephan, Parisi Fabio, Li Peining, Halaban Ruth, and Kluger Yuval

Subjects
copy number, SNP arrays, Next generation sequencing, melanoma, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Genomic aberrations can be used to determine cancer diagnosis and prognosis. Clinically relevant novel aberrations can be discovered using high-throughput assays such as Single Nucleotide Polymorphism (SNP) arrays and next-generation sequencing, which typically provide aggregate signals of many cells at once. However, heterogeneity of tumor subclones dramatically complicates the task of detecting aberrations. Results The aggregate signal of a population of subclones can be described as a linear system of equations. We employed a measure of allelic imbalance and total amount of DNA to characterize each locus by the copy number status (gain, loss or neither) of the strongest subclonal component. We designed simulated data to compare our measure to existing approaches and we analyzed SNP-arrays from 30 melanoma samples and transcriptome sequencing (RNA-Seq) from one melanoma sample. We showed that any system describing aggregate subclonal signals is underdetermined, leading to non-unique solutions for the exact copy number profile of subclones. For this reason, our illustrative measure was more robust than existing Hidden Markov Model (HMM) based tools in inferring the aberration status, as indicated by tests on simulated data. This higher robustness contributed in identifying numerous aberrations in several loci of melanoma samples. We validated the heterogeneity and aberration status within single biopsies by fluorescent in situ hybridization of four affected and transcriptionally up-regulated genes E2F8, ETV4, EZH2 and FAM84B in 11 melanoma cell lines. Heterogeneity was further demonstrated in the analysis of allelic imbalance changes along single exons from melanoma RNA-Seq. Conclusions These studies demonstrate how subclonal heterogeneity, prevalent in tumor samples, is reflected in aggregate signals measured by high-throughput techniques. Our proposed approach yields high robustness in detecting copy number alterations using high-throughput technologies and has the potential to identify specific subclonal markers from next-generation sequencing data.

Published
2011
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37. Incidence of the V600K mutation among melanoma patients with BRAF mutations, and potential therapeutic response to the specific BRAF inhibitor PLX4032

Author

Bacchiocchi Antonella, Cheng Elaine, Ariyan Stephan, Pavlick Anna C, Sznol Mario, Rubinstein Jill C, Kluger Harriet M, Narayan Deepak, and Halaban Ruth

Subjects
Medicine
Abstract

Abstract Activating mutations in BRAF kinase are common in melanomas. Clinical trials with PLX4032, the mutant-BRAF inhibitor, show promising preliminary results in patients selected for the presence of V600E mutation. However, activating V600K mutation is the other most common mutation, yet patients with this variant are currently excluded from the PLX4032 trials. Here we present evidence that a patient bearing the BRAF V600K mutation responded remarkably to PLX4032, suggesting that clinical trials should include all patients with activating BRAF V600E/K mutations.

Published
2010
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39. The Role of Humoral Alloreactivity in Liver Transplantation: Lessons Learned and New Perspectives

Author

Cheng, Elaine Y.

Subjects
surgical procedures, operative, Article Subject
Abstract

More than ten years after the initial description of the humoral theory of transplantation by Dr. Paul I. Terasaki, the significance of humoral alloimmunity in liver transplantation has yet to be clearly defined. The liver allograft has an inherent tolerogenic capacity which confers its resistance to cell-mediated as well as antibody-mediated rejection. Nevertheless, the protection against alloimmunity is not complete, and antibody-mediated tissue injury can occur in the liver graft under specific circumstances. In this article the evidence on the clinicopathologic effects of donor-specific alloantibodies in liver transplantation will be examined and interpreted in parallel with lessons learned from renal transplantation. The unique anatomic and immunologic features of the liver will be reviewed to gain new insights into the complex interactions between humoral immune system and the liver allograft.

Published
2017
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40. An Evaluation of the Prevalence of Hypokalemia and Hypomagnesemia in the VGH and BC Wide PeritonealDialysis Population and Frequency and Cost of Prescription of Potassium and Magnesium Supplements

Author

Cheng, Elaine

Abstract

Background: Potassium and magnesium are minerals essential in the functioning of the human body, and low levels of either may adversely affect normal neuromuscular, cardiovascular, and metabolic processes. Peritoneal dialysis (PD) patients are at increased risk for hypokalemia and hypomagnesemia due to continuous loss of these minerals via dialysate dwells. There is no current funding for potassium or magnesium supplements through the BC Provincial Renal Agency (BC PRA); thus, expanding BC PRA formulary coverage to include these supplements may increase accessibility and affordability, and improve PD patient outcomes.Objectives:To determine the one-year prevalence rate of hypokalemia and hypomagnesemia, and to assess the one-year frequency and cost of prescription of potassium and magnesium supplements in the Vancouver General Hospital (VGH) and BC wide PD patient population. Methods:This was a multi-center, retrospective review utilizing the Patient Records and Outcome Management Information System (PROMIS) database. All BC patients on PD at any point between May 1, 2017 to April 30, 2018 were included. Hypokalemia was defined as K < 3.5 mmol/L and hypomagnesemia was defined as Mg < 0.7 mmol/L. Yearly cost estimates of potassium and magnesium supplementation were based on unit costs and dispensing fees provided by MacDonaldu2019s Renal Pharmacy and Laurel Prescriptions.Results:For all PD patients in BC (n=1217), 97.5% of patients had serum potassium levels checked at least every 3 months; however, the frequency of serum magnesium level monitoring was much lower at 58.3% of patients. The prevalence of hypokalemia was 45.6% with 25.5% of patients on potassium supplements, and the prevalence of hypomagnesemia was 27.5% with 4.1% of patients on magnesium supplements. The one-year cost estimates for potassium and magnesium supplementation for all BC PD patients were $15,110 and $2,209, respectively. The prevalence of hypokalemia and hypomagnesemia were higher than the actual prescription of potassium and magnesium supplements, respectively. Cost may present as a barrier, even in patients with private health insurance. Compared to other nutritional supplements and hyperkalemia exchange resins listed on the BC PRA formulary, potassium and magnesium supplements have similar or lower costs. Conclusion:We would propose that potassium and magnesium supplements be added to the BC Provincial Renal Agency dialysis formulary for improved PD patient outcomes.

Published
2017

42. Characterization of Sub-Regional Variation in Saccharomyces Populations and Grape Phenolic Composition in Pinot Noir Vineyards of a Canadian Wine Region.

Author

Cheng, Elaine, Martiniuk, Jonathan T., Hamilton, Jonah, McCarthy, Garrett, Castellarin, Simone Diego, and Measday, Vivien

Subjects
PINOT noir, WINE districts, GRAPE products, SACCHAROMYCES, GRAPES, HARVESTING time
Abstract

Wine is a product of grape juice fermentation by yeast. Terroir is a term that encompasses all environmental factors and interactions at a specific geographical site, resulting in the development of regional-specific microbial strains and grape metabolites. In this study we determine the distribution of vineyard-associated wine yeast strains and characterize the flavonoid profile of Pinot Noir grapes among 3 sub-regions in the Okanagan Valley (OV), a major wine region in British Columbia, Canada. Pinot Noir grape samples were collected from 13 vineyards among 3 sub-regions of the OV, namely Kelowna (KE), Naramata-Penticton (NP) and Oliver-Osoyoos (OO), within a week prior to the winery harvesting date in 2016 and 2017. A total of 156 spontaneous Pinot Noir fermentations were conducted and vineyard-associated Saccharomyces strains were isolated from fermentations that reached two-thirds sugar depletion. Using microsatellite genotyping, we identified 103 Saccharomyces cerevisiae strains and 9 Saccharomyces uvarum strains. We also identified Saccharomyces paradoxus in one vineyard using ITS sequencing. We developed a microsatellite database of 160 commercial S. cerevisiae strains to determine the identity of the isolated strains and we include the database herein. Commercial strains were widely distributed across the three sub-regions. Forty-two of our 103 S. cerevisiae strains were equivalent or highly similar to commercial strains whereas the remaining 61 were considered as 'unknown' strains. Two S. uvarum strains were previously isolated in other OV studies and none matched the S. uvarum commercial strain BMV58. S. cerevisiae population structure was driven by sub-region, although S. cerevisiae populations did not differ significantly across vintages. S. uvarum and S. paradoxus were only identified in the 2017 vintage, demonstrating dynamic wine yeast populations between vintages. We found that the flavonoid profile of Pinot Noir grapes from the same 13 vineyards was also affected by sub-regional terroir. The anthocyanin content was lower and the proportion of methoxylated anthocyanins and flavonols was higher in Pinot Noir grapes from OO, the warmer sub-region as compared to KE, the cooler sub-region. Our study demonstrates that both yeast populations and metabolites associated with the Pinot Noir variety have sub-regional variation within a viticultural area. [ABSTRACT FROM AUTHOR]

Published
2020
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45. Clinical characteristics and outcomes of PTLD following intestinal transplantation.

Author

Wozniak, Laura J., Mauer, Tian L., Venick, Robert S., Said, Jonathan W., Kao, Roy L., Kempert, Pamela, Marcus, Elizabeth A., Hwang, Vilayphone, Cheng, Elaine Y., Busuttil, Ronald W., McDiarmid, Sue V., and Farmer, Douglas G.

Subjects
LYMPHOPROLIFERATIVE disorders, INTESTINAL biopsy, DISEASE incidence, MEDICAL databases, RETROSPECTIVE studies, THERAPEUTICS
Abstract

Abstract: Post‐transplant lymphoproliferative disease (PTLD) has the highest incidence following intestinal transplantation (ITx). Our center has seen a recent increase in PTLD. Our aim was to review a single‐center PTLD experience with a focus on clinical characteristics and outcomes. We completed a retrospective review of biopsy‐proven PTLD cases using a prospectively maintained database of 115 ITx recipients transplanted between 1991 and 2014. Nineteen (17%) ITx recipients developed 25 PTLD cases during a median follow‐up time of 6.4 (1.6‐14.6) years. The incidence of early PTLD was 6% (n = 7). There was a trend toward increased risk of PTLD in children compared with adults (P = .11) and a significantly increased risk of PTLD in re‐ITx compared with primary ITx recipients (P = .03). Most PTLD cases were diagnosed between 2010 and 2014 (n = 14). All early PTLD cases were EBV+ on in situ hybridization. Overall graft and patient survival are 68% and 74%, respectively. Second episodes of PTLD were diagnosed in 43% of surviving pediatric patients. Our program has a low incidence of early PTLD with overall excellent graft and patient survival following diagnosis. However, we have also seen a rising incidence of late PTLD. The cause of the increase is unknown as no major changes in immunosuppression protocols have occurred since 1999. [ABSTRACT FROM AUTHOR]

Published
2018
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46. Obliterative portal venopathy: A histopathologic finding associated with chronic antibody‐mediated rejection in pediatric liver allografts.

Author

Guerra, Marjorie‐Anne R., Vargas, Jorge H., Wozniak, Laura J., Venick, Robert S., McDiarmid, Sue V., Naini, Bita V., Scapa, Jason V., Reed, Elaine F., Busuttil, Ronald W., Cheng, Elaine Y., and Farmer, Douglas G.

Subjects
ANTIBODY formation, PORTAL vein, BIOPSY, CHILDREN'S health
Abstract

Abstract: The significance of post‐transplant HLA DSA and chronic AMR in LT is an emerging field of study. Although OPV has previously been described as a histopathologic finding in DSA‐positive adult LT recipients, it was not included in the recent Banff criteria for chronic AMR. Our aim was to describe the association between OPV and chronic AMR in pediatric LT recipients. A retrospective review of 67 liver biopsies performed between November 2014 and April 2016 in 45 pediatric LT recipients identified four patients with OPV. Clinical status, liver biochemistry, the presence of DSA, and available non‐HLA antibody testing, as well as histopathologic features of chronic AMR, were assessed. All four patients with OPV had class II DSA and histopathologic features of chronic AMR based on the Banff criteria. Two patients were noted to have non‐HLA antibodies. Three patients are undergoing treatment with IVIG but have persistent DSA. Two patients have graft failure and are awaiting retransplantation. In conclusion, OPV is a histopathologic finding associated with chronic AMR in pediatric LT recipients. Further studies are needed to elucidate whether OPV is reversible and/or amenable to medical therapy. [ABSTRACT FROM AUTHOR]

Published
2018
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48. Promoting education, awareness, participation and effectiveness in composting on campus

Author

Allason, Christa, Ramsey, Byron, Cheng, Elaine, Lau, Michelle, Tole, Nicola, and Zou, Brite

Subjects
fungi, complex mixtures
Abstract

Acadia and University Apartments of the University of British Columbia (UBC) are home to some 800 families. Each month there is a heavy influx and efflux of families due to the temporary nature of the housing. As a result, it’s difficult to ensure composting awareness and practice remains steady among residents. To increase awareness of composting at UBC, and specifically in the Acadia Family Residences and University Apartments, we designed an informational article about composting, a survey for the residents of Acadia to evaluate their composting awareness and habits, and a children’s activity page. The adult information page, the survey, and the children’s activity page were added to the April edition of Acadia’s monthly newsletter and distributed April 1st, 2007. Upon return of our surveys (April 8th, 2007), it was determined that the majority of the residents were interested in improving composting practices in their residence. We collaborated with Carol Young, the Residence Life Manager at Acadia Family Housing, to provide practical solutions to increase the awareness and incidence of composting at this housing unit. We would recommend that upcoming students continue to strengthen this relationship and work together with Ms. Young to further facilitate composting at Acadia and University Apartments. We believe this is a relatively untapped population that can aid in increasing composting and decreasing waste at the University of British Columbia. Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”

Published
2007
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