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4. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.

Author

Vega, Fernando E, Brown, Stuart M, Chen, Hao, Shen, Eric, Nair, Mridul B, Ceja-Navarro, Javier A, Brodie, Eoin L, Infante, Francisco, Dowd, Patrick F, and Pain, Arnab

Subjects
Animals, Weevils, Coffea, Crops, Agricultural, Caffeine, Cytochrome P-450 Enzyme System, Enzymes, Carboxylesterase, ATP-Binding Cassette Transporters, Insect Proteins, RNA, Untranslated, Phylogeny, Gene Transfer, Horizontal, Multigene Family, Female, Genome, Insect, Inactivation, Metabolic, Infectious Diseases, Genetics, Crops, Agricultural, RNA, Untranslated, Gene Transfer, Horizontal, Genome, Insect, Inactivation, Metabolic, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

The coffee berry borer, Hypothenemus hampei, is the most economically important insect pest of coffee worldwide. We present an analysis of the draft genome of the coffee berry borer, the third genome for a Coleopteran species. The genome size is ca. 163 Mb with 19,222 predicted protein-coding genes. Analysis was focused on genes involved in primary digestion as well as gene families involved in detoxification of plant defense molecules and insecticides, such as carboxylesterases, cytochrome P450, gluthathione S-transferases, ATP-binding cassette transporters, and a gene that confers resistance to the insecticide dieldrin. A broad range of enzymes capable of degrading complex polysaccharides were identified. We also evaluated the pathogen defense system and found homologs to antimicrobial genes reported in the Drosophila genome. Ten cases of horizontal gene transfer were identified with evidence for expression, integration into the H. hampei genome, and phylogenetic evidence that the sequences are more closely related to bacterial rather than eukaryotic genes. The draft genome analysis broadly expands our knowledge on the biology of a devastating tropical insect pest and suggests new pest management strategies.

Published
2015

7. Plant defense multigene families: I. Divergence of Fusarium solani-induced expression in Pisum and Lathyrus

Author

Tewari, Sandhya, Brown, Stuart M., and Fristensky, Brian

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The defense response in plants challenged with pathogens is characterized by the activation of a diverse set of genes. Many of the same genes are induced in the defense responses of a wide range of plant species. How plant defense gene families evolve may therefore provide an important clue to our understanding of how disease resistance evolves. Because studies usually focus on a single host species, little data are available regarding changes in defense gene expression patterns as species diverge. The expression of defense-induced genes PR10, chitinase and chalcone synthase was assayed in four pea species (Pisum sativum, P. humile, P. elatius and P. fulvum) and two Lathyrus species (L. sativus and L. tingitanus) which exhibited a range of infection phenotypes with Fusarium solani . In P. sativum, resistance was accompanied by a strong induction of defense genes at 8 hr. post-inoculation. Weaker induction was seen in susceptible interactions in wild species. Divergence in the timing of PR10 expression was most striking between P. sativum and its closest realtive, P. humile. Two members of this multigene family, designated PR10.1 and PR10.2, are strongly-expressed in response to Fusarium, while the PR10.3 gene is more weakly expressed, among Pisum species. The rapidity with which PR10 expression evolves raises the question, is divergence of defense gene expression a part of the phenotypic diversity underlying plant/pathogen coevolution?, Comment: 13 pages, 6 figures arXiv reference added to first page; minor formatting changes

Published
2003

9. FUS pathology defines the majority of tau- and TDP-43-negative frontotemporal lobar degeneration.

Author

Urwin, Hazel, Josephs, Keith A, Rohrer, Jonathan D, Mackenzie, Ian R, Neumann, Manuela, Authier, Astrid, Seelaar, Harro, Van Swieten, John C, Brown, Jeremy M, Johannsen, Peter, Nielsen, Jorgen E, Holm, Ida E, FReJA Consortium, Dickson, Dennis W, Rademakers, Rosa, Graff-Radford, Neill R, Parisi, Joseph E, Petersen, Ronald C, Hatanpaa, Kimmo J, White, Charles L, Weiner, Myron F, Geser, Felix, Van Deerlin, Vivianna M, Trojanowski, John Q, Miller, Bruce L, Seeley, William W, van der Zee, Julie, Kumar-Singh, Samir, Engelborghs, Sebastiaan, De Deyn, Peter P, Van Broeckhoven, Christine, Bigio, Eileen H, Deng, Han-Xiang, Halliday, Glenda M, Kril, Jillian J, Munoz, David G, Mann, David M, Pickering-Brown, Stuart M, Doodeman, Valerie, Adamson, Gary, Ghazi-Noori, Shabnam, Fisher, Elizabeth MC, Holton, Janice L, Revesz, Tamas, Rossor, Martin N, Collinge, John, Mead, Simon, and Isaacs, Adrian M

Subjects
FReJA Consortium, Hippocampus, Frontal Lobe, Humans, Dyskinesias, RNA-Binding Protein FUS, tau Proteins, DNA-Binding Proteins, Prevalence, Sequence Analysis, DNA, Mental Disorders, Age of Onset, Mutation, Adult, Middle Aged, Female, Male, Frontotemporal Lobar Degeneration, Sequence Analysis, DNA, Clinical Sciences, Neurosciences, Neurology & Neurosurgery
Abstract

Through an international consortium, we have collected 37 tau- and TAR DNA-binding protein 43 (TDP-43)-negative frontotemporal lobar degeneration (FTLD) cases, and present here the first comprehensive analysis of these cases in terms of neuropathology, genetics, demographics and clinical data. 92% (34/37) had fused in sarcoma (FUS) protein pathology, indicating that FTLD-FUS is an important FTLD subtype. This FTLD-FUS collection specifically focussed on aFTLD-U cases, one of three recently defined subtypes of FTLD-FUS. The aFTLD-U subtype of FTLD-FUS is characterised clinically by behavioural variant frontotemporal dementia (bvFTD) and has a particularly young age of onset with a mean of 41 years. Further, this subtype had a high prevalence of psychotic symptoms (36% of cases) and low prevalence of motor symptoms (3% of cases). We did not find FUS mutations in any aFTLD-U case. To date, the only subtype of cases reported to have ubiquitin-positive but tau-, TDP-43- and FUS-negative pathology, termed FTLD-UPS, is the result of charged multivesicular body protein 2B gene (CHMP2B) mutation. We identified three FTLD-UPS cases, which are negative for CHMP2B mutation, suggesting that the full complement of FTLD pathologies is yet to be elucidated.

Published
2010

10. Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions

Author

Van Deerlin, Vivianna M, Sleiman, Patrick MA, Martinez-Lage, Maria, Chen-Plotkin, Alice, Wang, Li-San, Graff-Radford, Neill R, Dickson, Dennis W, Rademakers, Rosa, Boeve, Bradley F, Grossman, Murray, Arnold, Steven E, Mann, David MA, Pickering-Brown, Stuart M, Seelaar, Harro, Heutink, Peter, van Swieten, John C, Murrell, Jill R, Ghetti, Bernardino, Spina, Salvatore, Grafman, Jordan, Hodges, John, Spillantini, Maria Grazia, Gilman, Sid, Lieberman, Andrew P, Kaye, Jeffrey A, Woltjer, Randall L, Bigio, Eileen H, Mesulam, Marsel, al-Sarraj, Safa, Troakes, Claire, Rosenberg, Roger N, White, Charles L, Ferrer, Isidro, Lladó, Albert, Neumann, Manuela, Kretzschmar, Hans A, Hulette, Christine Marie, Welsh-Bohmer, Kathleen A, Miller, Bruce L, Alzualde, Ainhoa, de Munain, Adolfo Lopez, McKee, Ann C, Gearing, Marla, Levey, Allan I, Lah, James J, Hardy, John, Rohrer, Jonathan D, Lashley, Tammaryn, Mackenzie, Ian RA, Feldman, Howard H, Hamilton, Ronald L, Dekosky, Steven T, van der Zee, Julie, Kumar-Singh, Samir, Van Broeckhoven, Christine, Mayeux, Richard, Vonsattel, Jean Paul G, Troncoso, Juan C, Kril, Jillian J, Kwok, John BJ, Halliday, Glenda M, Bird, Thomas D, Ince, Paul G, Shaw, Pamela J, Cairns, Nigel J, Morris, John C, McLean, Catriona Ann, DeCarli, Charles, Ellis, William G, Freeman, Stefanie H, Frosch, Matthew P, Growdon, John H, Perl, Daniel P, Sano, Mary, Bennett, David A, Schneider, Julie A, Beach, Thomas G, Reiman, Eric M, Woodruff, Bryan K, Cummings, Jeffrey, Vinters, Harry V, Miller, Carol A, Chui, Helena C, Alafuzoff, Irina, Hartikainen, Päivi, Seilhean, Danielle, Galasko, Douglas, Masliah, Eliezer, Cotman, Carl W, Tuñón, M Teresa, Martínez, M Cristina Caballero, Munoz, David G, Carroll, Steven L, Marson, Daniel, Riederer, Peter F, Bogdanovic, Nenad, Schellenberg, Gerard D, Hakonarson, Hakon, Trojanowski, John Q, and Lee, Virginia M-Y

Subjects
Biological Sciences, Genetics, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Frontotemporal Dementia (FTD), Dementia, Aging, Brain Disorders, Neurodegenerative, Acquired Cognitive Impairment, Alzheimer's Disease Related Dementias (ADRD), Neurosciences, 2.1 Biological and endogenous factors, Case-Control Studies, Chromosomes, Human, Pair 7, DNA-Binding Proteins, Frontotemporal Lobar Degeneration, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Inclusion Bodies, Intercellular Signaling Peptides and Proteins, Linkage Disequilibrium, Membrane Proteins, Polymorphism, Single Nucleotide, Progranulins, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Frontotemporal lobar degeneration (FTLD) is the second most common cause of presenile dementia. The predominant neuropathology is FTLD with TAR DNA-binding protein (TDP-43) inclusions (FTLD-TDP). FTLD-TDP is frequently familial, resulting from mutations in GRN (which encodes progranulin). We assembled an international collaboration to identify susceptibility loci for FTLD-TDP through a genome-wide association study of 515 individuals with FTLD-TDP. We found that FTLD-TDP associates with multiple SNPs mapping to a single linkage disequilibrium block on 7p21 that contains TMEM106B. Three SNPs retained genome-wide significance following Bonferroni correction (top SNP rs1990622, P = 1.08 x 10(-11); odds ratio, minor allele (C) 0.61, 95% CI 0.53-0.71). The association replicated in 89 FTLD-TDP cases (rs1990622; P = 2 x 10(-4)). TMEM106B variants may confer risk of FTLD-TDP by increasing TMEM106B expression. TMEM106B variants also contribute to genetic risk for FTLD-TDP in individuals with mutations in GRN. Our data implicate variants in TMEM106B as a strong risk factor for FTLD-TDP, suggesting an underlying pathogenic mechanism.

Published
2010

13. Genetic risk factors for the posterior cortical atrophy variant of Alzheimer's disease

Author

Schott, Jonathan M., Crutch, Sebastian J., Carrasquillo, Minerva M., Uphill, James, Shakespeare, Tim J., Ryan, Natalie S., Yong, Keir X., Lehmann, Manja, Ertekin-Taner, Nilufer, Graff-Radford, Neill R., Boeve, Bradley F., Murray, Melissa E., Khan, Qurat ul Ain, Petersen, Ronald C., Dickson, Dennis W., Knopman, David S., Rabinovici, Gil D., Miller, Bruce L., González, Aida Suárez, Gil-Néciga, Eulogio, Snowden, Julie S., Harris, Jenny, Pickering-Brown, Stuart M., Louwersheimer, Eva, van der Flier, Wiesje M., Scheltens, Philip, Pijnenburg, Yolande A., Galasko, Douglas, Sarazin, Marie, Dubois, Bruno, Magnin, Eloi, Galimberti, Daniela, Scarpini, Elio, Cappa, Stefano F., Hodges, John R., Halliday, Glenda M., Bartley, Lauren, Carrillo, Maria C., Bras, Jose T., Hardy, John, Rossor, Martin N., Collinge, John, Fox, Nick C., and Mead, Simon

Published
2016
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23. Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma

Author

Hao, Yuhan, primary, Karaoz, Ulas, additional, Yang, Liying, additional, Yachimski, Patrick S., additional, Tseng, Wenzhi, additional, Nossa, Carlos W., additional, Ye, Weimin, additional, Tseng, Mengkao, additional, Poles, Michael, additional, Francois, Fritz, additional, Traube, Morris, additional, Brown, Stuart M., additional, Chen, Yu, additional, Torralba, Manolito, additional, Peek, Richard M., additional, Brodie, Eoin L., additional, and Pei, Zhiheng, additional

Published
2022
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24. Nitrogen budgeting for water quality improvement in pineapple production systems of south eastern Queensland, Australia.

Author

Irvine-Brown, Stuart M., Abel, Rachel, Layden, Ian A., Irvine-Brown, Stuart M., Abel, Rachel, and Layden, Ian A.

Abstract

The Glass House Mountains area was identified as a source of elevated nitrogen (N) which flows into the Pumicestone Passage and Moreton Bay. Elevated N causes decline in water quality and ecological function of these internationally important Ramsar wetlands, fisheries habitat, and recreational tourism natural amenities. Investigations into the origin of elevated aquatic N levels identified intensive horticultural activities were likely key contributors. A review of horticulture in the catchment was undertaken. The review determined that pineapple production systems in this area presented the largest opportunity for addressing aquatic N levels. Using a systems agronomy approach a partial N budget and review of nutrient management practices investigated nitrogen use efficiency (NUE). Findings identified N loading in waterways was impact by rainfall volume and frequency. Agronomic timing of N application to meet plant demand was imbalanced. Deep drainage is the predominant N loss pathway in major soil types of the catchment.

Published
2022

25. Mineral nutrition for avocado fruit quality – a brief review and recommendations

Author

Joyce, Daryl C., Perkins, Melinda L., Newett, Simon, Coates, Lindel May, Irvine-Brown, Stuart M., Joyce, Daryl C., Perkins, Melinda L., Newett, Simon, Coates, Lindel May, and Irvine-Brown, Stuart M.

Abstract

Irregular avocado fruit quality to consumers is generally problematic in the avocado industry. Better understanding the role of mineral nutrition in determining fruit quality, including robustness at harvest to tolerate subsequent supply chain rigours, offers opportunity for improvements. Based on a review of the scientific and technical literature as commissioned for the industry in Australia, plant nutrition recommendations that might be integrated towards fruit quality improvement were identified. They include providing adequate Ca to trees during flowering, fruit set and early development; conducting fruit tissue analysis as a reliable indicator of fruit Ca concentrations; ensuring leaf nutrient concentrations for N and K do not exceed the optimum range; delaying K application until late stages of fruit development and application only if needed; achieving a good balance between vegetative growth and crop load; and selecting appropriate rootstocks for new plantings. The rationale for these recommendations is briefly discussed along with priorities for future research to underpin avocado fruit robustness at harvest and in-market quality to consumers. © 2022 International Society for Horticultural Science. All rights reserved.

Published
2022

36. TDP-43 pathological changes in early onset familial and sporadic Alzheimer’s disease, late onset Alzheimer’s disease and Down’s Syndrome: association with age, hippocampal sclerosis and clinical phenotype

Author

Davidson, Yvonne S., Raby, Samantha, Foulds, Penelope G., Robinson, Andrew, Thompson, Jennifer C., Sikkink, Stephen, Yusuf, Imran, Amin, Hanan, DuPlessis, Daniel, Troakes, Claire, Al-Sarraj, Safa, Sloan, Carolyn, Esiri, Margaret M., Prasher, Vee P., Allsop, David, Neary, David, Pickering-Brown, Stuart M., Snowden, Julie S., and Mann, David M. A.

Published
2011
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42. Effectiveness of Denitrifying Bioreactors on Water Pollutant Reduction from Agricultural Areas

Author

Christianson, Laura E., Cooke, Richard A., Hay, Christopher H., Helmers, Matthew J., Feyereisen, Gary W., Ranaivoson, Andry Z., McMaine, John T., McDaniel, Rachel, Rosen, Timothy R., Pluer, William T., Schipper, Louis A., Dougherty, Hannah, Robinson, Rhianna J., Layden, Ian A., Irvine-Brown, Stuart M., Manca, Fabio, Dhaese, Kris, Nelissen, Victoria, von Ahnen, Mathis, Christianson, Laura E., Cooke, Richard A., Hay, Christopher H., Helmers, Matthew J., Feyereisen, Gary W., Ranaivoson, Andry Z., McMaine, John T., McDaniel, Rachel, Rosen, Timothy R., Pluer, William T., Schipper, Louis A., Dougherty, Hannah, Robinson, Rhianna J., Layden, Ian A., Irvine-Brown, Stuart M., Manca, Fabio, Dhaese, Kris, Nelissen, Victoria, and von Ahnen, Mathis

Abstract

HighlightsDenitrifying woodchip bioreactors treat nitrate-N in a variety of applications and geographies.This review focuses on subsurface drainage bioreactors and bed-style designs (including in-ditch).Monitoring and reporting recommendations are provided to advance bioreactor science and engineering. Denitrifying bioreactors enhance the natural process of denitrification in a practical way to treat nitrate-nitrogen (N) in a variety of N-laden water matrices. The design and construction of bioreactors for treatment of subsurface drainage in the U.S. is guided by USDA-NRCS Conservation Practice Standard 605. This review consolidates the state of the science for denitrifying bioreactors using case studies from across the globe with an emphasis on full-size bioreactor nitrate-N removal and cost-effectiveness. The focus is on bed-style bioreactors (including in-ditch modifications), although there is mention of denitrifying walls, which broaden the applicability of bioreactor technology in some areas. Subsurface drainage denitrifying bioreactors have been assessed as removing 20% to 40% of annual nitrate-N loss in the Midwest, and an evaluation across the peer-reviewed literature published over the past three years showed that bioreactors around the world have been generally consistent with that (N load reduction median: 46%; mean ±SD: 40% ±26%; n = 15). Reported N removal rates were on the order of 5.1 g N m-3 d-1 (median; mean ±SD: 7.2 ±9.6 g N m-3 d-1; n = 27). Subsurface drainage bioreactor installation costs have ranged from less than $5,000 to $27,000, with estimated cost efficiencies ranging from less than $2.50 kg-1 N year-1 to roughly $20 kg-1 N year-1 (although they can be as high as $48 kg-1 N year-1). A suggested monitoring setup is described primarily for the context of conservation practitioners and watershed groups for assessing annual nitrate-N load removal performance of subsurface drainage denitrifying bioreactors. Recommended minimum reporting me

Published
2021

43. An immunohistochemical study of cases of sporadic and inherited frontotemporal lobar degeneration using 3R- and 4R-specific tau monoclonal antibodies

Author

de Silva, Rohan, Lashley, Tammaryn, Strand, Catherine, Shiarli, Anna-Maria, Shi, Jing, Tian, Jinzhou, Bailey, Kathryn L., Davies, Peter, Bigio, Eileen H., Arima, Kunimasa, Iseki, Eizo, Murayama, Shigeo, Kretzschmar, Hans, Neumann, Manuela, Lippa, Carol, Halliday, Glenda, MacKenzie, James, Ravid, Rivka, Dickson, Dennis, Wszolek, Zbigniew, Iwatsubo, Takeshi, Pickering-Brown, Stuart M., Holton, Janice, Lees, Andrew, Revesz, Tamas, and Mann, David M. A.

Published
2006
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44. Phenotypic variability associated with progranulin haploinsufficiency in patients with the common 1477C→T (Arg493X) mutation: an international initiative

Author

Rademakers, Rosa, Baker, Matt, Gass, Jennifer, Adamson, Jennifer, Huey, Edward D, Momeni, Parastoo, Spina, Salvatore, Coppola, Giovanni, Karydas, Anna M, Stewart, Heather, Johnson, Nancy, Hsiung, Ging-Yuek, Kelley, Brendan, Kuntz, Karen, Steinbart, Ellen, Wood, Elisabeth McCarty, Yu, Chang-En, Josephs, Keith, Sorenson, Eric, Womack, Kyle B, Weintraub, Sandra, Pickering-Brown, Stuart M, Schofield, Peter R, Brooks, William S, Van Deerlin, Vivianna M, Snowden, Julie, Clark, Christopher M, Kertesz, Andrew, Boylan, Kevin, Ghetti, Bernardino, Neary, David, Schellenberg, Gerard D, Beach, Thomas G, Mesulam, Marsel, Mann, David, Grafman, Jordan, Mackenzie, Ian R, Feldman, Howard, Bird, Thomas, Petersen, Ron, Knopman, David, Boeve, Bradley, Geschwind, Dan H, Miller, Bruce, Wszolek, Zbigniew, Lippa, Carol, Bigio, Eileen H, Dickson, Dennis, Graff-Radford, Neill, and Hutton, Mike

Published
2007
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48. Atopic dermatitis: a new treatment paradigm using pimecrolimus

Author

Weinberg, Jeffrey M, Bowerman, James G, Brown, Stuart M, Gerstein, David, Kane, Kay S, Selevan, James, and Virdee, Sat

Subjects
Skin diseases -- Drug therapy, Topical medication -- Dosage and administration, Topical medication -- Evaluation, Nonsteroidal anti-inflammatory drugs -- Dosage and administration, Nonsteroidal anti-inflammatory drugs -- Evaluation, Atopic dermatitis -- Care and treatment, Atopic dermatitis -- Drug therapy, Health, Pharmaceuticals and cosmetics industries
Abstract

Abstract Atopic dermatitis (AD), often called eczema, is a disease characterized by intense pruritus, erythema, dry skin, and inflammation. Pimecrolimus is a novel steroid-free treatment for An. Consistently positive results [...]

Published
2003

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