Research articles, presentations, and other scholarship

Recent Submissions

  • Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression 

    Qi, Yumin; Wu, Yang; Saunders, Randy; Chen, Xiao-Guang; Mao, Chunhong; Biedler, James Kite; Tu, Zhijian Jake (2019-03-19)
    We previously showed that Guy1, a primary signal expressed from the Y chromosome, is a strong candidate for a male-determining factor that confers female-specific lethality in Anopheles stephensi (Criscione et al., 2016). ...
  • Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes 

    Prasad, T. S. Keshava; Mohanty, Ajeet Kumar; Kumar, Manish; Sreenivasamurthy, Sreelakshmi K.; Dey, Gourav; Nirujogi, Raja Sekhar; Pinto, Sneha M.; Madugundu, Anil K.; Pati, Arun H.; Advani, Jayshree; Manda, Srikanth S.; Gupta, Manoj Kumar; Dwivedi, Sutopa B.; Kelkar, Dhanashree S.; Hall, Brantley; Jiang, Xiaofang; Peery, Ashley; Rajagopalan, Pavithra; Yelamanchi, Soujanya D.; Solanki, Hitendra S.; Raja, Remya; Sathe, Gajanan J.; Chavan, Sandip; Verma, Renu; Patel, Krishna M.; Jain, Ankit P.; Syed, Nazia; Datta, Keshava K.; Khan, Aafaque Ahmed; Dammalli, Manjunath; Jayaram, Savita; Radhakrishnan, Aneesha; Mitchell, Christopher J.; Na, Chan-Hyun; Kumar, Nirbhay; Sinnis, Photini; Sharakhov, Igor V.; Wang, Charles; Gowda, Harsha; Tu, Zhijian; Kumar, Ashwani; Pandey, Akhilesh (2017-01)
    Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for ...
  • Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533(T), a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia 

    Susanti, Dwi; Johnson, Eric F.; Lapidus, Alla; Han, James; Reddy, T. B. K.; Mukherjee, Supratim; Pillay, Manoj; Perevalova, Anna A.; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Mukhopadhyay, Biswarup (2017-04)
    Desulfurococcus amylolyticus Z-533(T), a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO2, and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose ...
  • Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine 

    Efendi, Yusuf Sofyan; Susanti, Dwi; Tritama, Erman; Pasier, Michelle Lueders; Putri, Gilang Nadia Niwan; Raharso, Sugeng; Iskandar; Aditiawati, Pingkan; Giri-Rachman, Ernawati Arifin; Mukhopadhyay, Biswarup; Purwantini, Endang (2017-04)
    PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer, manufactures a whole-cell whooping cough vaccine (wP) that, as part of a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus ...
  • EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity 

    Sun, Zhixiong; Xu, Xiguang; He, Jianlin; Murray, Alexander; Sun, Ming-an; Wei, Xiaoran; Wang, Xia; McCoig, Emmarose; Xie, Evan; Jiang, Xi; Li, Liwu; Zhu, Jinsong; Chen, Jianjun; Morozov, Alexei; Pickrell, Alicia M.; Theus, Michelle H.; Xie, Hehuang (2019-08-29)
    Life experience can leave lasting marks, such as epigenetic changes, in the brain. How life experience is translated into storable epigenetic information remains largely unknown. With unbiased data-driven approaches, we ...
  • De novo formation of an aggregation pheromone precursor by an isoprenyl diphosphate synthase-related terpene synthase in the harlequin bug 

    Lancaster, Jason; Khrimian, Ashot; Young, Sharon; Lehner, Bryan; Luck, Katrin; Wallingford, Anna; Ghosh, Saikat Kumar B.; Zerbe, Philipp; Muchlinski, Andrew; Marek, Paul E.; Sparks, Michael E.; Tokuhisa, James G.; Tittiger, Claus; Koellner, Tobias G.; Weber, Donald C.; Gundersen-Rindal, Dawn E.; Kuhar, Thomas P.; Tholl, Dorothea (2018-09-11)
    Insects use a diverse array of specialized terpene metabolites as pheromones in intraspecific interactions. In contrast to plants and microbes, which employ enzymes called terpene synthases (TPSs) to synthesize terpene ...
  • Improved reference genome of Aedes aegypti informs arbovirus vector control 

    Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E.; Glassford, William J.; Herre, Margaret; Redmond, Seth N.; Rose, Noah H.; Weedall, Gareth D.; Wu, Yang; Batra, Sanjit S.; Brito-Sierra, Carlos A.; Buckingham, Steven D.; Campbell, Corey L.; Chan, Saki; Cox, Eric; Evans, Benjamin R.; Fansiri, Thanyalak; Filipovic, Igor; Fontaine, Albin; Gloria-Soria, Andrea; Hall, Richard; Joardar, Vinita S.; Jones, Andrew K.; Kay, Raissa G. G.; Kodali, Vamsi K.; Lee, Joyce; Lycett, Gareth J.; Mitchell, Sara N.; Muehling, Jill; Murphy, Michael R.; Omer, Arina D.; Partridge, Frederick A.; Peluso, Paul; Aiden, Aviva Presser; Ramasamy, Vidya; Rasic, Gordana; Roy, Sourav; Saavedra-Rodriguez, Karla; Sharan, Shruti; Sharma, Atashi; Smith, Melissa Laird; Turner, Joe; Weakley, Allison M.; Zhao, Zhilei; Akbari, Omar S.; Black, William C.; Cao, Han; Darby, Alistair C.; Hill, Catherine A.; Johnston, J. Spencer; Murphy, Terence D.; Raikhel, Alexander S.; Sattelle, David B.; Sharakhov, Igor V.; White, Bradley J.; Zhao, Li; Aiden, Erez Lieberman; Mann, Richard S.; Lambrechts, Louis; Powell, Jeffrey R.; Sharakhova, Maria V.; Tu, Zhijian; Robertson, Hugh M.; McBride, Carolyn S.; Hastic, Alex R.; Korlach, Jonas; Neafsey, Daniel E.; Phillippy, Adam M.; Vosshall, Leslie B. (2018-11-22)
    Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and ...
  • Sequential and differential interaction of assembly factors during nitrogenase MoFe protein maturation 

    Jimenez-Vicente, Emilio; Yang, Zhi-Yong; Keith Ray, W.; Echavarri-Erasun, Carlos; Cash, Valerie L.; Rubio, Luis M.; Seefeldt, Lance C.; Dean, Dennis R. (2018-06-22)
    Nitrogenases reduce atmospheric nitrogen, yielding the basic inorganic molecule ammonia. The nitrogenase MoFe protein contains two cofactors, a [7Fe-9S-Mo-C-homocitrate] active-site species, designated FeMo-cofactor, and ...
  • Structuring and Supporting Excellence in Undergraduate Biochemistry and Molecular Biology Education: The ASBMB Degree Accreditation Program 

    Moore, Victoria Del Gaizo; Loertscher, Jennifer; Dean, Diane M.; Bailey, Cheryl P.; Kennelly, Peter J.; Wolfson, Adele J. (2018-12-01)
  • The NifZ accessory protein has an equivalent function in maturation of both nitrogenase MoFe protein P-clusters 

    Jimenez-Vicente, Emilio; Yang, Zhi-Yong; del Campo, Julia S. Martin; Cash, Valerie L.; Seefeldt, Lance C.; Dean, Dennis R. (2019-04-19)
    The Mo-dependent nitrogenase comprises two interacting components called the Fe protein and the MoFe protein. The MoFe protein is an (22) heterotetramer that harbors two types of complex metalloclusters, both of which are ...
  • The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase 

    Jutras, Brandon L.; Savage, Christina R.; Arnold, William K.; Lethbridge, Kathryn G.; Carroll, Dustin W.; Tilly, Kit; Bestor, Aaron; Zhu, Haining; Seshu, Janakiram; Zuckert, Wolfram R.; Stewart, Philip E.; Rosa, Patricia A.; Brissette, Catherine A.; Stevenson, Brian (2019-07)
    When the Lyme disease spirochete, Borrelia burgdorferi, transfers from a feeding tick into a human or other vertebrate host, the bacterium produces vertebrate-specific proteins and represses factors needed for arthropod ...
  • Two of the three Transformer-2 genes are required for ovarian development in Aedes albopictus 

    Li, Xiaocong; Jin, Binbin; Dong, Yunqiao; Chen, Xiaoguang; Tu, Zhijian; Gu, Jinbao (2019-06)
    In Drosophila melanogaster, transformer-2 (tra2) plays an essential role in the sex-specific splicing of doublesex (dsx) and fruitless (fru), two key transcription factor genes that program sexual differentiation and ...
  • Comparison of Common Analytical Methods for the Quantification of Total Polyphenols and Flavanols in Fruit Juices and Ciders 

    Ma, Sihui; Kim, Cathlean; Neilson, Andrew P.; Griffin, Laura E.; Peck, Gregory M.; O'Keefe, Sean F.; Stewart, Amanda C. (2019-07-17)
    Multiple analytical methods are used for quantification of total polyphenols and total flavanols in fruit juices and beverages. Four methods were evaluated in this study: Folin-Ciocalteu (F-C), Lowenthal permanganate (L-P), ...
  • Internalization of Erythrocyte Acylpeptide Hydrolase Is Required for Asexual Replication of Plasmodium falciparum 

    Elahi, Rubayet; Dapper, Christie; Klemba, Michael (American Society for Microbiology, 2019-05-08)
    The human malaria parasite Plasmodium falciparum causes disease as it replicates within the host's erythrocytes. We have found that an erythrocyte serine hydrolase, acylpeptide hydrolase (APEH), accumulates within developing ...
  • Expression analysis and knockdown of two antennal odorant-binding protein genes in Aedes aegypti 

    Sengul, Meryem S.; Tu, Zhijian (Entomological Society of America, 2010-10-05)
    The presence and expression of odorant-binding proteins (OBPs) in the olfactory organs suggest that they play an important role in mosquito olfaction. However, no direct evidence has been found for their involvement in the ...
  • Odorant receptor c-terminal motifs in divergent insect species 

    Miller, Raymond; Tu, Zhijian (Entomological Society of America, 2008-09-22)
    Insect odorant receptors are a large family of seven transmembrane proteins believed to be G-protein coupled receptors. The peptide sequences of two odorant receptors within a given species may share as little as 17% ...
  • Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids 

    Vavricka, Christopher J.; Yoshida, Takanobu; Kuriya, Yuki; Takahashi, Shunsuke; Ogawa, Teppei; Ono, Fumie; Agari, Kazuko; Kiyota, Hiromasa; Li, Jianyong; Ishii, Jun; Tsuge, Kenji; Minami, Hiromichi; Araki, Michihiro; Hasunuma, Tomohisa; Kondo, Akihiko (Springer Nature, 2019-05-01)
    Previous studies have utilized monoamine oxidase (MAO) and L-3,4-dihydroxyphenylalanine decarboxylase (DDC) for microbe-based production of tetrahydropapaveroline (THP), a benzylisoquinoline alkaloid (BIA) precursor to ...
  • Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286 

    Umaña, Ariana; Lemkul, Justin A.; Slade, Daniel J. (American Society for Microbiology, 2019-02-21)
    Fusobacterium necrophorum is a pathogenic Gram-negative, anaerobic bacterium. In this study, we present the first complete genome sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286. These data provide a ...
  • Borrelia burgdorferi peptidoglycan is a persistent antigen in patients with Lyme arthritis 

    Jutras, Brandon L.; Lochhead, Robert B.; Kloos, Zachary A.; Biboy, Jacob; Strle, Klemen; Booth, Carmen J.; Govers, Sander K.; Gray, Joe; Schumann, Peter; Vollmer, Waldemar; Bockenstedt, Linda K.; Steere, Allen C.; Jacobs-Wagner, Christine (National Academy of Sciences, 2019-06-17)
    Lyme disease is a multisystem disorder caused by the spirochete Borrelia burgdorferi. A common late-stage complication of this disease is oligoarticular arthritis, often involving the knee. In ∼10% of cases, arthritis ...
  • Identification of aaNAT5b as a spermine N-acetyltransferase in the mosquito, Aedes aegypti 

    Guan, Huai; Wang, Maoying; Liao, Chenghong; Liang, Jing; Mehere, Prajwalini; Tian, Meiling; Liu, Hairong; Robinson, Howard; Li, Jianyong; Han, Qian (PLOS, 2018-03-19)
    Mosquitoes transmit a number of diseases in animals and humans, including Dengue, Chikungunya and Zika viruses that affect millions of people each year. Controlling the disease-transmitting mosquitoes has proven to be a ...

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