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3. Tracking radiation damage of Euclid VIS detectors after 1 year in space

Author

Skottfelt, Jesper, Wander, Matt, Cropper, Mark, Dryer, Ben, Hall, David J., Hayes, Richard, Kelman, Bradley, Kitching, Tom, Kohley, Ralf, Lagattuta, David, Lee-Payne, Zoe, Liebing, Patricia, Massey, Richard, McCracken, Henry Joy, Nakajima, Reiko, and Nightingale, James

Subjects
Physics - Instrumentation and Detectors
Abstract

Due to the space radiation environment at L2, ESA's Euclid mission will be subject to a large amount of highly energetic particles over its lifetime. These particles can cause damage to the detectors by creating defects in the silicon lattice. These defects degrade the returned image in several ways, one example being a degradation of the Charge Transfer Efficiency, which appears as readout trails in the image data. This can be problematic for the Euclid VIS instrument, which aims to measure the shapes of galaxies to a very high degree of accuracy. Using a special clocking technique called trap pumping, the single defects in the CCDs can be detected and characterised. Being the first instrument in space with this capability, it will provide novel insights into the creation and evolution of radiation-induced defects and give input to the radiation damage correction of the scientific data. We present the status of the radiation damage of the Euclid VIS CCDs and how it has evolved over the first year in space., Comment: Submitted to the Proceedings for the SPIE Space Telescopes and Instrumentation 2024: Optical, Infrared, and Millimeter Wave, paper no. 13092-24, 10 pages, 6 figures

Published
2024

5. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Author

Feng, Xuehuan, Zheng, Jinfang, Irisarri, Iker, Yu, Huihui, Zheng, Bo, Ali, Zahin, de Vries, Sophie, Keller, Jean, Fürst-Jansen, Janine MR, Dadras, Armin, Zegers, Jaccoline MS, Rieseberg, Tim P, Dhabalia Ashok, Amra, Darienko, Tatyana, Bierenbroodspot, Maaike J, Gramzow, Lydia, Petroll, Romy, Haas, Fabian B, Fernandez-Pozo, Noe, Nousias, Orestis, Li, Tang, Fitzek, Elisabeth, Grayburn, W Scott, Rittmeier, Nina, Permann, Charlotte, Rümpler, Florian, Archibald, John M, Theißen, Günter, Mower, Jeffrey P, Lorenz, Maike, Buschmann, Henrik, von Schwartzenberg, Klaus, Boston, Lori, Hayes, Richard D, Daum, Chris, Barry, Kerrie, Grigoriev, Igor V, Wang, Xiyin, Li, Fay-Wei, Rensing, Stefan A, Ben Ari, Julius, Keren, Noa, Mosquna, Assaf, Holzinger, Andreas, Delaux, Pierre-Marc, Zhang, Chi, Huang, Jinling, Mutwil, Marek, de Vries, Jan, and Yin, Yanbin

Subjects
Plant Biology, Biological Sciences, Genetics, Life on Land, Signal Transduction, Embryophyta, Evolution, Molecular, Phylogeny, Gene Regulatory Networks, Genome, Genome, Plant, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Published
2024

8. An Enhanced Cross-Sectional HIV Incidence Estimator that Incorporates Prior HIV Test Results

Author

Bannick, Marlena, Donnell, Deborah, Hayes, Richard, Laeyendecker, Oliver, and Gao, Fei

Subjects
Statistics - Methodology
Abstract

Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to perform longitudinal follow-up on a cohort of individuals. The utility of the approach is limited by its precision, driven by the (low) sensitivity of the RITA at identifying recent infection. By utilizing results of previous HIV tests that individuals may have taken, we consider an enhanced RITA with increased sensitivity (and specificity). We use it to propose an enhanced estimator for incidence estimation. We prove the theoretical properties of the enhanced estimator and illustrate its numerical performance in simulation studies. We apply the estimator to data from a cluster-randomized trial to study the effect of community-level HIV interventions on HIV incidence. We demonstrate that the enhanced estimator provides a more precise estimate of HIV incidence compared to the standard estimator.

Published
2023

9. Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Author

Oliver, Tiffany, Varghese, Neha, Roux, Simon, Schulz, Frederik, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Riley, Robert, LaButti, Kurt, Egan, Robert, Hajek, Patrick, Mukherjee, Supratim, Ovchinnikova, Galina, Reddy, T. B. K., Calhoun, Sara, Hayes, Richard D., Rohwer, Robin R., Zhou, Zhichao, Daum, Chris, Copeland, Alex, Chen, I-Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Mouncey, Nigel J., del Rio, Tijana Glavina, Grigoriev, Igor V., Hofmeyr, Steven, Oliker, Leonid, Yelick, Katherine, Anantharaman, Karthik, McMahon, Katherine D., Woyke, Tanja, and Eloe-Fadrosh, Emiley A.

Published
2024
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10. Prevalence and risk of burnout among HIV service providers in South Africa and Zambia: findings from the HPTN 071 (PopART) trial

Author

Steinhaus, Mara C., Nicholson, Tamaryn J., Pliakas, Triantafyllos, Harper, Abigail, Lilleston, Pamela, Mainga, Tila, Milimo, Deborah, Jennings, Karen, Grobbelaar, Nelis, Louis, Francoise, Liebenberg, Handri, Hayes, Richard J., Fidler, Sarah, Ayles, Helen, Bock, Peter, Hoddinott, Graeme, Hargreaves, James R., Bond, Virginia, and Stangl, Anne L.

Published
2024
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12. Associations between HIV stigma and health-related quality-of-life among people living with HIV: cross-sectional analysis of data from HPTN 071 (PopART)

Author

Hall, Emily, Davis, Katherine, Ohrnberger, Julius, Pickles, Michael, Gregson, Simon, Thomas, Ranjeeta, Hargreaves, James R., Pliakas, Triantafyllos, Bwalya, Justin, Dunbar, Rory, Mainga, Tila, Shanaube, Kwame, Hoddinott, Graeme, Bond, Virginia, Bock, Peter, Ayles, Helen, Stangl, Anne L., Donnell, Deborah, Hayes, Richard, Fidler, Sarah, and Hauck, Katharina

Published
2024
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13. The impact of an innovative community-based peer-led intervention on uptake and coverage of sexual and reproductive health services among adolescents and young people 15–24 years old: results from the Yathu Yathu cluster randomised trial

Author

Phiri, Mwelwa Muleba, Schaap, Albertus, Hensen, Bernadette, Sigande, Lucheka, Simuyaba, Melvin, Mwenge, Lawrence, Zulu-Phiri, Rosemary, Mwape, Louis, Floyd, Sian, Fidler, Sarah, Hayes, Richard, Simwinga, Musonda, and Ayles, Helen

Published
2024
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14. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Published
2024
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17. Abell 1201: Detection of an Ultramassive Black Hole in a Strong Gravitational Lens

Author

Nightingale, James. W., Smith, Russell J., He, Qiuhan, O'Riordan, Conor M., Kegerreis, Jacob A., Amvrosiadis, Aristeidis, Edge, Alastair C., Etherington, Amy, Hayes, Richard G., Kelly, Ash, Lucey, John R., and Massey, Richard J. Massey Richard J.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, General Relativity and Quantum Cosmology
Abstract

Supermassive black holes (SMBHs) are a key catalyst of galaxy formation and evolution, leading to an observed correlation between SMBH mass $M_{\rm BH}$ and host galaxy velocity dispersion $\sigma_{\rm e}$. Outside the local Universe, measurements of $M_{\rm BH}$ are usually only possible for SMBHs in an active state: limiting sample size and introducing selection biases. Gravitational lensing makes it possible to measure the mass of non-active SMBHs. We present models of the $z=0.169$ galaxy-scale strong lens Abell~1201. A cD galaxy in a galaxy cluster, it has sufficient `external shear' that a magnified image of a $z = 0.451$ background galaxy is projected just $\sim 1$ kpc from the galaxy centre. Using multi-band Hubble Space Telescope imaging and the lens modeling software $\texttt{PyAutoLens}$ we reconstruct the distribution of mass along this line of sight. Bayesian model comparison favours a point mass with $M_{\rm BH} = 3.27 \pm 2.12\times10^{10}\,$M$_{\rm \odot}$ (3$\sigma$ confidence limit); an ultramassive black hole. One model gives a comparable Bayesian evidence without a SMBH, however we argue this model is nonphysical given its base assumptions. This model still provides an upper limit of $M_{\rm BH} \leq 5.3 \times 10^{10}\,$M$_{\rm \odot}$, because a SMBH above this mass deforms the lensed image $\sim 1$ kpc from Abell 1201's centre. This builds on previous work using central images to place upper limits on $M_{\rm BH}$, but is the first to also place a lower limit and without a central image being observed. The success of this method suggests that surveys during the next decade could measure thousands more SMBH masses, and any redshift evolution of the $M_{\rm BH}$--$\sigma_{\rm e}$ relation. Results are available at https://github.com/Jammy2211/autolens_abell_1201., Comment: Accepted in MNRAS, 27 pages, 22 figures

Published
2023
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20. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex.

Author

Yu, Houlin, Yang, He, Haridas, Sajeet, Hayes, Richard D, Lynch, Hunter, Andersen, Sawyer, Newman, Madison, Li, Gengtan, Martínez-Soto, Domingo, Milo-Cochavi, Shira, Hazal Ayhan, Dilay, Zhang, Yong, Grigoriev, Igor V, and Ma, Li-Jun

Subjects
Fusarium oxysporum species complex, TFome, accessory chromosome, conservation, expansion, transcription factors, Infectious Diseases, Genetics, Human Genome, Infection
Abstract

The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.

Published
2023

21. IMA genome-F18

Author

Visagie, Cobus M, Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A, Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E, Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C, Hakalova, Eliska, Hayes, Richard D, Houbraken, Jos, Grigoriev, Igor V, LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J, Zhang, Yu, and Wingfield, Brenda D

Subjects
Microbiology, Plant Biology, Biological Sciences, Plant biology
Published
2023

22. Scanning For Dark Matter Subhalos in Hubble Space Telescope Imaging of 54 Strong Lenses

Author

Nightingale, James W., He, Qiuhan, Cao, Xiaoyue, Amvrosiadis, Aristeidis, Etherington, Amy, Frenk, Carlos S., Hayes, Richard G., Robertson, Andrew, Cole, Shaun, Lange, Samuel, Li, Ran, and Massey, Richard

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

The cold dark matter (DM) model predicts that every galaxy contains thousands of DM subhalos; almost all other DM models include a physical process that smooths away the subhalos. The subhalos are invisible, but could be detected via strong gravitational lensing, if they lie on the line of sight to a multiply-imaged background source, and perturb its apparent shape. We present a predominantly automated strong lens analysis framework, and scan for DM subhalos in Hubble Space Telescope imaging of 54 strong lenses. We identify five DM subhalo candidates, including two especially compelling candidates (one previously known in SLACS0946+1006) where a subhalo is favoured after all of our tests for systematics. We find that the detectability of subhalos depends upon the assumed parametric form for the lens galaxy's mass distribution, especially its degree of azimuthal freedom. Using separate components for dark matter and stellar mass reveals two DM subhalo candidates and removes four false-positives compared to the single power-law mass model that is common in the literature. We identify 45 lenses without substructures, the number of which is key to statistical tests able to rule out models of e.g. warm or self-interacting DM. Our full analysis results are available at https://github.com/Jammy2211/autolens_subhalo., Comment: 25 Pages, 15 Figures

Published
2022

27. IMA genome-F18: The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicilliumbiforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

Author

Visagie, Cobus M., Magistà, Donato, Ferrara, Massimo, Balocchi, Felipe, Duong, Tuan A., Eichmeier, Ales, Gramaje, David, Aylward, Janneke, Baker, Scott E., Barnes, Irene, Calhoun, Sara, De Angelis, Maria, Frisvad, Jens C., Hakalova, Eliska, Hayes, Richard D., Houbraken, Jos, Grigoriev, Igor V., LaButti, Kurt, Leal, Catarina, Lipzen, Anna, Ng, Vivian, Pangilinan, Jasmyn, Pecenka, Jakub, Perrone, Giancarlo, Piso, Anja, Savage, Emily, Spetik, Milan, Wingfield, Michael J., Zhang, Yu, and Wingfield, Brenda D.

Published
2023
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28. Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations

Author

Thomas, Minta, Su, Yu-Ru, Rosenthal, Elisabeth A., Sakoda, Lori C., Schmit, Stephanie L., Timofeeva, Maria N., Chen, Zhishan, Fernandez-Rozadilla, Ceres, Law, Philip J., Murphy, Neil, Carreras-Torres, Robert, Diez-Obrero, Virginia, van Duijnhoven, Franzel J. B., Jiang, Shangqing, Shin, Aesun, Wolk, Alicja, Phipps, Amanda I., Burnett-Hartman, Andrea, Gsur, Andrea, Chan, Andrew T., Zauber, Ann G., Wu, Anna H., Lindblom, Annika, Um, Caroline Y., Tangen, Catherine M., Gignoux, Chris, Newton, Christina, Haiman, Christopher A., Qu, Conghui, Bishop, D. Timothy, Buchanan, Daniel D., Crosslin, David R., Conti, David V., Kim, Dong-Hyun, Hauser, Elizabeth, White, Emily, Siegel, Erin, Schumacher, Fredrick R., Rennert, Gad, Giles, Graham G., Hampel, Heather, Brenner, Hermann, Oze, Isao, Oh, Jae Hwan, Lee, Jeffrey K., Schneider, Jennifer L., Chang-Claude, Jenny, Kim, Jeongseon, Huyghe, Jeroen R., Zheng, Jiayin, Hampe, Jochen, Greenson, Joel, Hopper, John L., Palmer, Julie R., Visvanathan, Kala, Matsuo, Keitaro, Matsuda, Koichi, Jung, Keum Ji, Li, Li, Le Marchand, Loic, Vodickova, Ludmila, Bujanda, Luis, Gunter, Marc J., Matejcic, Marco, Jenkins, Mark A., Slattery, Martha L., D’Amato, Mauro, Wang, Meilin, Hoffmeister, Michael, Woods, Michael O., Kim, Michelle, Song, Mingyang, Iwasaki, Motoki, Du, Mulong, Udaltsova, Natalia, Sawada, Norie, Vodicka, Pavel, Campbell, Peter T., Newcomb, Polly A., Cai, Qiuyin, Pearlman, Rachel, Pai, Rish K., Schoen, Robert E., Steinfelder, Robert S., Haile, Robert W., Vandenputtelaar, Rosita, Prentice, Ross L., Küry, Sébastien, Castellví-Bel, Sergi, Tsugane, Shoichiro, Berndt, Sonja I., Lee, Soo Chin, Brezina, Stefanie, Weinstein, Stephanie J., Chanock, Stephen J., Jee, Sun Ha, Kweon, Sun-Seog, Vadaparampil, Susan, Harrison, Tabitha A., Yamaji, Taiki, Keku, Temitope O., Vymetalkova, Veronika, Arndt, Volker, Jia, Wei-Hua, Shu, Xiao-Ou, Lin, Yi, Ahn, Yoon-Ok, Stadler, Zsofia K., Van Guelpen, Bethany, Ulrich, Cornelia M., Platz, Elizabeth A., Potter, John D., Li, Christopher I., Meester, Reinier, Moreno, Victor, Figueiredo, Jane C., Casey, Graham, Lansdorp Vogelaar, Iris, Dunlop, Malcolm G., Gruber, Stephen B., Hayes, Richard B., Pharoah, Paul D. P., Houlston, Richard S., Jarvik, Gail P., Tomlinson, Ian P., Zheng, Wei, Corley, Douglas A., Peters, Ulrike, and Hsu, Li

Published
2023
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33. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Author

Franco, Mario EE, Wisecaver, Jennifer H, Arnold, A Elizabeth, Ju, Yu‐Ming, Slot, Jason C, Ahrendt, Steven, Moore, Lillian P, Eastman, Katharine E, Scott, Kelsey, Konkel, Zachary, Mondo, Stephen J, Kuo, Alan, Hayes, Richard D, Haridas, Sajeet, Andreopoulos, Bill, Riley, Robert, LaButti, Kurt, Pangilinan, Jasmyn, Lipzen, Anna, Amirebrahimi, Mojgan, Yan, Juying, Adam, Catherine, Keymanesh, Keykhosrow, Ng, Vivian, Louie, Katherine, Northen, Trent, Drula, Elodie, Henrissat, Bernard, Hsieh, Huei‐Mei, Youens‐Clark, Ken, Lutzoni, François, Miadlikowska, Jolanta, Eastwood, Daniel C, Hamelin, Richard C, Grigoriev, Igor V, and U’Ren, Jana M

Subjects
Microbiology, Environmental Sciences, Biological Sciences, Ecology, Genetics, 2.1 Biological and endogenous factors, Endophytes, Fungi, Lichens, Multigene Family, Symbiosis, Xylariales, Ascomycota, endophyte, plant-fungal interactions, saprotroph, specialised metabolism, symbiosis, trophic mode, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

Published
2022

35. PyAutoLens: Open-Source Strong Gravitational Lensing

Author

Nightingale, James. W., Hayes, Richard G., Kelly, Ashley, Amvrosiadis, Aristeidis, Etherington, Amy, He, Qiuhan, Li, Nan, Cao, XiaoYue, Frawley, Jonathan, Cole, Shaun, Enia, Andrea, Frenk, Carlos S., Harvey, David R., Li, Ran, Massey, Richard J., Negrello, Mattia, and Robertson, Andrew

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

Strong gravitational lensing, which can make a background source galaxy appears multiple times due to its light rays being deflected by the mass of one or more foreground lens galaxies, provides astronomers with a powerful tool to study dark matter, cosmology and the most distant Universe. PyAutoLens is an open-source Python 3.6+ package for strong gravitational lensing, with core features including fully automated strong lens modeling of galaxies and galaxy clusters, support for direct imaging and interferometer datasets and comprehensive tools for simulating samples of strong lenses. The API allows users to perform ray-tracing by using analytic light and mass profiles to build strong lens systems. Accompanying PyAutoLens is the autolens workspace (see https://github.com/Jammy2211/autolens_workspace), which includes example scripts, lens datasets and the HowToLens lectures in Jupyter notebook format which introduce non experts to strong lensing using PyAutoLens. Readers can try PyAutoLens right now by going to the introduction Jupyter notebook on Binder (see https://mybinder.org/v2/gh/Jammy2211/autolens_workspace/master) or checkout the readthedocs (see https://pyautolens.readthedocs.io/en/latest/) for a complete overview of PyAutoLens's features., Comment: 2 pages, 1 figure

Published
2021
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37. Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study

Author

Agyei, Yaw, Beyers, Nulda, Bock, Peter, Bond, Virginia, Bwalya, Justin, Cori, Anne, Deventer, Anneen, Dunbar, Rory, El-Sadr, Wafaa, Emel, Lynda, Floyd, Sian, Griffith, Sam, Hargreaves, James, Hauck, Katharina, Headen, Tanette, Hoddinott, Graeme, James, Anelet, Jennings, Karen, Kanema, Sarah, Kosloff, Barry, Kruger, James, Kumar, Ramya, Macleod, David, Makola, Nozizwe, Mandla, Nomtha, Miller, Eric, Moore, Ayana, Mwenge, Lawrence, Noble, Heather, Phiri, Mwelwa, Pickles, Michael, Sabapathy, Kalpana, Sakala, Ephraim, Sauter, Rafael, Shanaube, Kwame, Silumesi, Andrew, Sista, Nirupama, Skalland, Tim, Smith, Peter, Thomas, Ranjeeta, Vermund, Sten, White, Rhonda, Wilson, Ethan, Yang, Blia, Yuhas, Krista, Bowden, Rory, Calvez, Vincent, Essex, Max, Grabowski, Kate, Gupta, Ravindra, Herbeck, Joshua, Kagaayi, Joseph, Kaleebu, Pontiano, Lingappa, Jairam, Moyo, Sikhulile, Novitsky, Vladimir, Ndung’u, Thumbi, Pillay, Deenan, Quinn, Thomas, Rambaut, Andrew, Seeley, Janet, Ssemwanga, Deogratius, Tanser, Frank, Wawer, Maria, Hall, Matthew, Golubchik, Tanya, Bonsall, David, Abeler-Dörner, Lucie, Limbada, Mohammed, Schaap, Ab, de Cesare, Mariateresa, MacIntyre-Cockett, George, Otecko, Newton, Probert, William, Ratmann, Oliver, Bulas Cruz, Ana, Piwowar-Manning, Estelle, Burns, David N, Cohen, Myron S, Donnell, Deborah J, Eshleman, Susan H, Simwinga, Musonda, Fidler, Sarah, Hayes, Richard, Ayles, Helen, and Fraser, Christophe

Published
2024
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38. PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting

Author

Nightingale, James. W., Hayes, Richard G., and Griffiths, Matthew

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Programming Languages, Physics - Data Analysis, Statistics and Probability, Physics - Physics Education
Abstract

A major trend in academia and data science is the rapid adoption of Bayesian statistics for data analysis and modeling, leading to the development of probabilistic programming languages (PPL). A PPL provides a framework that allows users to easily specify a probabilistic model and perform inference automatically. PyAutoFit is a Python-based PPL which interfaces with all aspects of the modeling (e.g., the model, data, fitting procedure, visualization, results) and therefore provides complete management of every aspect of modeling. This includes composing high-dimensionality models from individual model components, customizing the fitting procedure and performing data augmentation before a model-fit. Advanced features include database tools for analysing large suites of modeling results and exploiting domain-specific knowledge of a problem via non-linear search chaining. Accompanying PyAutoFit is the autofit workspace (see https://github.com/Jammy2211/autofit_workspace), which includes example scripts and the HowToFit lecture series which introduces non-experts to model-fitting and provides a guide on how to begin a project using PyAutoFit. Readers can try PyAutoFit right now by going to the introduction Jupyter notebook on Binder (see https://mybinder.org/v2/gh/Jammy2211/autofit_workspace/HEAD) or checkout our readthedocs(see https://pyautofit.readthedocs.io/en/latest/) for a complete overview of PyAutoFit's features., Comment: Published in the Journal of Open Source Software

Published
2021
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39. Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

Author

Hagestad, Ole Christian, Hou, Lingwei, Andersen, Jeanette H, Hansen, Espen H, Altermark, Bjørn, Li, Chun, Kuhnert, Eric, Cox, Russell J, Crous, Pedro W, Spatafora, Joseph W, Lail, Kathleen, Amirebrahimi, Mojgan, Lipzen, Anna, Pangilinan, Jasmyn, Andreopoulos, William, Hayes, Richard D, Ng, Vivian, Grigoriev, Igor V, Jackson, Stephen A, Sutton, Thomas DS, Dobson, Alan DW, and Rämä, Teppo

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Microbiology, Biotechnology, Human Genome, Life Below Water, Bioprospecting, Genome mining, Illumina, Lignocellulolytic enzymes, Physiology, Taxonomy, new taxon, Plant biology
Abstract

Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

Published
2021

42. Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes.

Author

Rueda-Mejia, Maria Paula, Nägeli, Lukas, Lutz, Stefanie, Hayes, Richard D, Varadarajan, Adithi R, Grigoriev, Igor V, Ahrens, Christian H, and Freimoser, Florian M

Subjects
Aureobasidium, Fusarium, antagonism, biocontrol, genome, proteome, secretome, transcriptome, yeast, Genetics, 1.1 Normal biological development and functioning
Abstract

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

Published
2021

43. Active Connections: Means for Faculty to Create an Environment in Which Students WANT to Engage!

Author

Forrer, Don, Bechtel, Stephanie, Brown, Kendra, Mabesa, Jose, Gunn, Linda, Hayes, Richard L., Fall, Lisa, and Wilmore, Todd

Abstract

This interactive, cross-disciplinary research explores face-to-face and online strategies for faculty to deploy in the classroom that encourage connections beyond forced engagement methodologies commonly used. Concentration is on methods of connecting that are "out of the mainstream" and benefit both students and faculty. Findings indicate that the more students feel as a valued participant of the learning community, the more they engage in the class activities.

Published
2019

44. Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study

Author

Hayes, Richard, Fidler, Sarah, Beyers, Nulda, Ayles, Helen, Bock, Peter, El-Sadr, Wafaa, Cohen, Myron, Eshleman, Susan, Agyei, Yaw, Piwowar-Manning, Estelle, Bond, Virginia, Hoddinott, Graeme, Donnell, Deborah, Floyd, Sian, Wilson, Ethan, Emel, Lynda, Noble, Heather, Macleod, David, Burns, David, Fraser, Christophe, Cori, Anne, Sista, Nirupama, Griffith, Sam, Moore, Ayana, Headen, Tanette, White, Rhonda, Miller, Eric, Hargreaves, James, Hauck, Katharina, Thomas, Ranjeeta, Limbada, Mohammed, Bwalya, Justin, Pickles, Michael, Sabapathy, Kalpana, Schaap, Ab, Dunbar, Rory, Shanaube, Kwame, Yang, Blia, Simwinga, Musonda, Smith, Peter, Vermund, Sten, Mandla, Nomtha, Makola, Nozizwe, van Deventer, Anneen, James, Anelet, Jennings, Karen, Kruger, James, Phiri, Mwelwa, Kosloff, Barry, Mwenge, Lawrence, Kanema, Sarah, Sauter, Rafael, Probert, William, Kumar, Ramya, Sakala, Ephraim, Silumesi, Andrew, Skalland, Tim, Yuhas, Krista, Probert, William J M, Bell-Mandla, Nomtha F, Abeler-Dörner, Lucie, Donnell, Deborah J, Skalland, Timothy, and Hayes, Richard J

Published
2022
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45. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
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