Bullet Blender Publications: Nucleotide Extraction

Cupples Connon, C. (Ed.). (2023). Forensic DNA Analysis: Methods and Protocols (1st ed. 2023). Springer US. https://doi.org/10.1007/978-1-0716-3295-6

Zheng, Y., Xie, J., Huang, X., Dong, J., Park, M. S., & Chan, W. K. (2016). Binding studies using Pichia pastoris expressed human aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator proteins. Protein Expression and Purification, 122, 72–81. https://doi.org/10.1016/j.pep.2016.02.011

Leach, M. D., Farrer, R. A., Tan, K., Miao, Z., Walker, L. A., Cuomo, C. A., Wheeler, R. T., Brown, A. J. P., Wong, K. H., & Cowen, L. E. (2016). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans. Nature Communications, 7, 11704. https://doi.org/10.1038/ncomms11704

Thangaraj, S. R., McCulloch, G. A., Subbarayalu, M., Subramaniam, C., & Walter, G. H. (2016). Development of microsatellite markers and a preliminary assessment of population structuring in the rice weevil, Sitophilus oryzae (L.). Journal of Stored Products Research, 66, 12–17. https://doi.org/10.1016/j.jspr.2015.12.005

Masterson, L., Winder, D. M., Ball, S. L. R., Vaughan, K., Lehmann, M., Scholtz, L.-U., Sterling, J. C., Sudhoff, H. H., & Goon, P. K. C. (2016). Molecular analyses of unselected head and neck cancer cases demonstrates that human papillomavirus transcriptional activity is positively associated with survival and prognosis. BMC Cancer, 16, 367. https://doi.org/10.1186/s12885-016-2398-7

Collas, M., Becking, T., Delpy, M., Pflieger, M., Bohn, P., Reynolds, J., & Grandjean, F. (2016). Monitoring of white-clawed crayfish ( Austropotamobius pallipes ) population during a crayfish plague outbreak followed by rescue. Knowledge and Management of Aquatic Ecosystems, (417), 1. https://doi.org/10.1051/kmae/2015037

Chick, L. (2015). Linking physiology and biogeography: Disentangling the constraints on the distributions of ant species [University of Tennessee-Knoxville]. http://trace.tennessee.edu/cgi/viewcontent.cgi?article=4928&context=utk_graddiss

de la Torre, A., Metivier, A., Chu, F., Laurens, L. M. L., Beck, D. A. C., Pienkos, P. T., Lidstrom, M. E., & Kalyuzhnaya, M. G. (2015). Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microbial Cell Factories, 14(1). https://doi.org/10.1186/s12934-015-0377-3

Evers, M. M., Schut, M. H., Pepers, B. A., Atalar, M., van Belzen, M. J., Faull, R. L., Roos, R. A., & van Roon-Mom, W. M. (2015). Making (anti-) sense out of huntingtin levels in Huntington disease. Molecular Neurodegeneration, 10(1). https://doi.org/10.1186/s13024-015-0018-7

Ranjan, R., Rani, A., Metwally, A., McGee, H. S., & Perkins, D. L. (2015). Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochemical and Biophysical Research Communications. https://doi.org/10.1016/j.bbrc.2015.12.083

Mon, K. K. Z., Saelao, P., Halstead, M. M., Chanthavixay, G., Chang, H.-C., Garas, L., Maga, E. A., & Zhou, H. (2015). Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks. Frontiers in Veterinary Science, 2. https://doi.org/10.3389/fvets.2015.00061

Becking, T., Mrugała, A., Delaunay, C., Svoboda, J., Raimond, M., Viljamaa-Dirks, S., Petrusek, A., Grandjean, F., & Braquart-Varnier, C. (2015). Effect of experimental exposure to differently virulent Aphanomyces astaci strains on the immune response of the noble crayfish Astacus astacus. Journal of Invertebrate Pathology, 132, 115–124. https://doi.org/10.1016/j.jip.2015.08.007

Falendysz, E. A., Lopera, J. G., Lorenzsonn, F., Salzer, J. S., Hutson, C. L., Doty, J., Gallardo-Romero, N., Carroll, D. S., Osorio, J. E., & Rocke, T. E. (2015). Further Assessment of Monkeypox Virus Infection in Gambian Pouched Rats (Cricetomys gambianus) Using In Vivo Bioluminescent Imaging. PLOS Neglected Tropical Diseases, 9(10), e0004130. https://doi.org/10.1371/journal.pntd.0004130

Barr-Beare, E., Saxena, V., Hilt, E. E., Thomas-White, K., Schober, M., Li, B., Becknell, B., Hains, D. S., Wolfe, A. J., & Schwaderer, A. L. (2015). The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits. PLOS ONE, 10(10), e0139575. https://doi.org/10.1371/journal.pone.0139575

Janocko, L., Althouse, A. D., Brand, R. M., Cranston, R. D., & McGowan, I. (2015). The Molecular Characterization of Intestinal Explant HIV Infection Using Polymerase Chain Reaction-Based Techniques. AIDS Research and Human Retroviruses, 31(10), 981–991. https://doi.org/10.1089/aid.2015.0165

Tian, X., Liu, M., Su, X., Jiang, Z., Ma, Q., Liao, X., Li, X., Zhou, Z., Li, C., & Zhou, R. (2015). Mapping the epitope of neutralizing monoclonal antibodies against human adenovirus type 3. Virus Research, 208, 66–72. https://doi.org/10.1016/j.virusres.2015.06.002

Agga, G. E., Arthur, T. M., Durso, L. M., Harhay, D. M., & Schmidt, J. W. (2015). Antimicrobial-Resistant Bacterial Populations and Antimicrobial Resistance Genes Obtained from Environments Impacted by Livestock and Municipal Waste. PLOS ONE, 10(7), e0132586. https://doi.org/10.1371/journal.pone.0132586

Andersson, S., Sikora, P., Karlberg, M. L., Winiecka-Krusnell, J., Alm, E., Beser, J., & Arrighi, R. B. G. (2015). It’s a dirty job — A robust method for the purification and de novo genome assembly of Cryptosporidium from clinical material. Journal of Microbiological Methods, 113, 10–12. https://doi.org/10.1016/j.mimet.2015.03.018

Nasrollahzadeh, D., Malekzadeh, R., Ploner, A., Shakeri, R., Sotoudeh, M., Fahimi, S., Nasseri-Moghaddam, S., Kamangar, F., Abnet, C. C., Winckler, B., Islami, F., Boffetta, P., Brennan, P., Dawsey, S. M., & Ye, W. (2015). Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia. Scientific Reports, 5, 8820. https://doi.org/10.1038/srep08820

Kraaijeveld, K., de Weger, L. A., Ventayol García, M., Buermans, H., Frank, J., Hiemstra, P. S., & den Dunnen, J. T. (2015). Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing. Molecular Ecology Resources, 15(1), 8–16. https://doi.org/10.1111/1755-0998.12288

Sanchez, S., & Sellers, H. (2015). Biological Specimen Collection and Processing for Molecular Analysis. In M. V. Cunha & J. Inácio (Eds.), Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies (Vol. 1247, pp. 61–75). Springer New York. http://link.springer.com/10.1007/978-1-4939-2004-4_5

Quach, K., Grover, S. A., Kenigsberg, S., & Librach, C. L. (2014). A combination of single nucleotide polymorphisms in the 3′untranslated region of HLA-G is associated with preeclampsia. Human Immunology, 75(12), 1163–1170. https://doi.org/10.1016/j.humimm.2014.10.009

Krull, A. C., Shearer, J. K., Gorden, P. J., Cooper, V. L., Phillips, G. J., & Plummer, P. J. (2014). Deep Sequencing Analysis Reveals Temporal Microbiota Changes Associated with Development of Bovine Digital Dermatitis. Infection and Immunity, 82(8), 3359–3373. https://doi.org/10.1128/IAI.02077-14

Lakritz, J. R., Poutahidis, T., Levkovich, T., Varian, B. J., Ibrahim, Y. M., Chatzigiagkos, A., Mirabal, S., Alm, E. J., & Erdman, S. E. (2014). Beneficial bacteria stimulate host immune cells to counteract dietary and genetic predisposition to mammary cancer in mice: Probiotic bacteria protect against mammary cancer. International Journal of Cancer, 135(3), 529–540. https://doi.org/10.1002/ijc.28702

Bartnikowski, M., Klein, T. J., Melchels, F. P. W., & Woodruff, M. A. (2014). Effects of scaffold architecture on mechanical characteristics and osteoblast response to static and perfusion bioreactor cultures: Scaffold Architecture Static Perfusion Bioreactor. Biotechnology and Bioengineering, 111(7), 1440–1451. https://doi.org/10.1002/bit.25200

Ramos, P., Karnezis, A. N., Craig, D. W., Sekulic, A., Russell, M. L., Hendricks, W. P. D., Corneveaux, J. J., Barrett, M. T., Shumansky, K., Yang, Y., Shah, S. P., Prentice, L. M., Marra, M. A., Kiefer, J., Zismann, V. L., McEachron, T. A., Salhia, B., Prat, J., D’Angelo, E., … Trent, J. M. (2014). Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nature Genetics, 46(5), 427–429. https://doi.org/10.1038/ng.2928

Melero, M., García-Párraga, D., Corpa, J., Ortega, J., Rubio-Guerri, C., Crespo, J., Rivera-Arroyo, B., & Sánchez-Vizcaíno, J. (2014). First molecular detection and characterization of herpesvirus and poxvirus in a Pacific walrus (Odobenus rosmarus divergens). BMC Veterinary Research, 10(1), 968. https://doi.org/10.1186/s12917-014-0308-2

Volk, H., Piskernik, S., Kurinčič, M., Klančnik, A., Toplak, N., & Jeršek, B. (2014). Evaluation of different methods for DNA extraction from milk. Jounal of Food and Nutrition Research, 53(2), 97–104.

Liang, W. S., Aldrich, J., Tembe, W., Kurdoglu, A., Cherni, I., Phillips, L., Reiman, R., Baker, A., Weiss, G. J., Carpten, J. D., & Craig, D. W. (2014). Long insert whole genome sequencing for copy number variant and translocation detection. Nucleic Acids Research, 42(2), e8–e8. https://doi.org/10.1093/nar/gkt865

Shanmugam, V., Ramanathan, R. K., Lavender, N. A., Sinari, S., Chadha, M., Liang, W. S., Kurdoglu, A., Izatt, T., Christoforides, A., Benson, H., Phillips, L., Baker, A., Murray, C., Hostetter, G., Von Hoff, D. D., Craig, D. W., & Carpten, J. D. (2014). Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer. BMC Medical Genomics, 7(1), 36. https://doi.org/10.1186/1755-8794-7-36

Tong, K., Zhang, Y., Liu, G., Ye, Z., & Chu, P. K. (2013). Treatment of heavy oil wastewater by a conventional activated sludge process coupled with an immobilized biological filter. International Biodeterioration & Biodegradation, 84, 65–71. https://doi.org/10.1016/j.ibiod.2013.06.002

Silver, A. C., Dunne, D. W., Zeiss, C. J., Bockenstedt, L. K., Radolf, J. D., Salazar, J. C., & Fikrig, E. (2013). MyD88 Deficiency Markedly Worsens Tissue Inflammation and Bacterial Clearance in Mice Infected with Treponema pallidum, the Agent of Syphilis. PLoS ONE, 8(8), e71388. https://doi.org/10.1371/journal.pone.0071388

Kurtzman, C. P., & Robnett, C. J. (2013). Alloascoidea hylecoeti gen. nov., comb. nov., Alloascoidea africana comb. nov., Ascoidea tarda sp. nov., and Nadsonia starkeyi-henricii comb. nov., new members of the Saccharomycotina ( Ascomycota ). FEMS Yeast Research, 13(5), 423–432. https://doi.org/10.1111/1567-1364.12044

Filipová, L., Petrusek, A., Matasová, K., Delaunay, C., & Grandjean, F. (2013). Prevalence of the Crayfish Plague Pathogen Aphanomyces astaci in Populations of the Signal Crayfish Pacifastacus leniusculus in France: Evaluating the Threat to Native Crayfish. PLoS ONE, 8(7), e70157. https://doi.org/10.1371/journal.pone.0070157

Rubio-Guerri, C., Melero, M., Esperón, F., Bellière, E., Arbelo, M., Crespo, J., Sierra, E., García-Párraga, D., & Sánchez-Vizcaíno, J. (2013). Unusual striped dolphin mass mortality episode related to cetacean morbillivirus in the Spanish Mediterranean sea. BMC Veterinary Research, 9(1), 106. https://doi.org/10.1186/1746-6148-9-106

Hawkins, M. G., Winder, D. M., Ball, S. L. R., Vaughan, K., Sonnex, C., Stanley, M. A., Sterling, J. C., & Goon, P. K. C. (2013). Detection of specific HPV subtypes responsible for the pathogenesis of condylomata acuminata. Virology Journal, 10(1), 137. https://doi.org/10.1186/1743-422X-10-137

Araújo-Pérez, F., McCoy, A. N., Okechukwu, C., Carroll, I. M., Smith, K. M., Jeremiah, K., Sandler, R. S., Asher, G. N., & Keku, T. O. (2012). Differences in microbial signatures between rectal mucosal biopsies and rectal swabs. Gut Microbes, 3(6), 530–535. https://doi.org/10.4161/gmic.22157

Liang, W. S., Craig, D. W., Carpten, J., Borad, M. J., Demeure, M. J., Weiss, G. J., Izatt, T., Sinari, S., Christoforides, A., Aldrich, J., Kurdoglu, A., Barrett, M., Phillips, L., Benson, H., Tembe, W., Braggio, E., Kiefer, J. A., Legendre, C., Posner, R., … Von Hoff, D. (2012). Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing. PLoS ONE, 7(10), e43192. https://doi.org/10.1371/journal.pone.0043192

Yin, Y., Liu, Y., Jin, H., Wang, S., Zhao, S., Geng, X., Li, M., & Xu, F. (2012). Polyethylene glycol-mediated transformation of fused egfp-hph gene under the control of gpd promoter in Pleurotus eryngii. Biotechnology Letters, 34(10), 1895–1900. https://doi.org/10.1007/s10529-012-0985-5

Suzuki, Y., Murray, S. L., Wong, K. H., Davis, M. A., & Hynes, M. J. (2012). Reprogramming of carbon metabolism by the transcriptional activators AcuK and AcuM in Aspergillus nidulans: Transcription factors controlling carbon metabolism. Molecular Microbiology, 84(5), 942–964. https://doi.org/10.1111/j.1365-2958.2012.08067.x

Weiss, G. J., Liang, W. S., Izatt, T., Arora, S., Cherni, I., Raju, R. N., Hostetter, G., Kurdoglu, A., Christoforides, A., Sinari, S., Baker, A. S., Metpally, R., Tembe, W. D., Phillips, L., Von Hoff, D. D., Craig, D. W., & Carpten, J. D. (2012). Paired Tumor and Normal Whole Genome Sequencing of Metastatic Olfactory Neuroblastoma. PLoS ONE, 7(5), e37029. https://doi.org/10.1371/journal.pone.0037029

Wang, Y., Zhang, Y., Yang, J., Ni, X., Liu, S., Li, Z., E. Hodges, S., E. Fisher, W., C. Brunicardi, F., A. Gibbs, R., Gingras, M.-C., & Li, M. (2012). Genomic Sequencing of Key Genes in Mouse Pancreatic Cancer Cells. Current Molecular Medicine, 12(3), 331–341. https://doi.org/10.2174/156652412799218868

Smith, K. M., Anthony, S. J., Switzer, W. M., Epstein, J. H., Seimon, T., Jia, H., Sanchez, M. D., Huynh, T. T., Galland, G. G., Shapiro, S. E., Sleeman, J. M., McAloose, D., Stuchin, M., Amato, G., Kolokotronis, S.-O., Lipkin, W. I., Karesh, W. B., Daszak, P., & Marano, N. (2012). Zoonotic Viruses Associated with Illegally Imported Wildlife Products. PLoS ONE, 7(1), e29505. https://doi.org/10.1371/journal.pone.0029505

Buck, J. C., Truong, L., & Blaustein, A. R. (2011). Predation by zooplankton on Batrachochytrium dendrobatidis: biological control of the deadly amphibian chytrid fungus? Biodiversity and Conservation, 20(14), 3549–3553. https://doi.org/10.1007/s10531-011-0147-4

Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., Guennel, T., Shin, Y., Johnson, M. B., Krsnik, Ž., Mayer, S., Fertuzinhos, S., Umlauf, S., Lisgo, S. N., Vortmeyer, A., … Šestan, N. (2011). Spatio-temporal transcriptome of the human brain. Nature, 478(7370), 483–489. https://doi.org/10.1038/nature10523

Augustine, R. C., Pattavina, K. A., Tuzel, E., Vidali, L., & Bezanilla, M. (2011). Actin Interacting Protein1 and Actin Depolymerizing Factor Drive Rapid Actin Dynamics in Physcomitrella patens. The Plant Cell, 23(10), 3696–3710. https://doi.org/10.1105/tpc.111.090753

Foott, J. S., & Fogarty, R. (2011). Juvenile Stanislaus River Chinook salmon pathogen and physiology assessment: January – May 2011. U.S. Fish & Wildlife Service California  – Nevada Fish Health Center,  Anderson, CA. http://www.fws.gov/lodi/afrp/documents/STAN11%20REPORT%207-14%20final.pdf

NIMH Transcriptional Atlas of Human Brain Development. (2010). Transcriptome profiling by RNA sequencing.

Repnik, K., & Potočnik, U. (2010). CTLA4 CT60 Single-Nucleotide Polymorphism Is Associated with Slovenian Inflammatory Bowel Disease Patients and Regulates Expression of CTLA4 Isoforms. DNA and Cell Biology, 29(10), 603–610. https://doi.org/10.1089/dna.2010.1021

Bourgeois, L., Sheppard, W. S., Sylvester, H. A., & Rinderer, T. E. (2010). Genetic Stock Identification of Russian Honey Bees. Journal of Economic Entomology, 103(3), 917–924. https://doi.org/10.1603/EC09335

Bourgeois, A. L., & Rinderer, T. E. (2009). Genetic Characterization of Russian Honey Bee Stock Selected for Improved Resistance to Varroa destructor. Journal of Economic Entomology, 102(3), 1233–1238. https://doi.org/10.1603/029.102.0349

Kurtzman, C. P., & Robnett, C. J. (2014). Three new anascosporic genera of the Saccharomycotina: Danielozyma gen. nov., Deakozyma gen. nov. and Middelhovenomyces gen. nov. Antonie van Leeuwenhoek, 105(5), 933–942. https://doi.org/10.1007/s10482-014-0149-9

Sivam, S., Sciurba, F. C., Lucht, L. A., Zhang, Y., Duncan, S. R., Norris, K. A., & Morris, A. (2011). Distribution of Pneumocystis jirovecii in lungs from colonized COPD patients. Diagnostic Microbiology and Infectious Disease, 71(1), 24–28. https://doi.org/10.1016/j.diagmicrobio.2011.05.008

Repnik, K., & Potočnik, U. (2011). Haplotype in the IBD5 region is associated with refractory Crohn’s disease in Slovenian patients and modulates expression of the SLC22A5 gene. Journal of Gastroenterology, 46(9), 1081–1091. https://doi.org/10.1007/s00535-011-0426-6

Bourgeois, A. L., Rinderer, T. E., Beaman, L. D., & Danka, R. G. (2010). Genetic detection and quantification of Nosema apis and N. ceranae in the honey bee. Journal of Invertebrate Pathology, 103(1), 53–58. https://doi.org/10.1016/j.jip.2009.10.009

Bourgeois, A. L., Rinderer, T. E., Sylvester, H. A., Holloway, B., & Oldroyd, B. P. (2012). Patterns of Apis mellifera infestation by Nosema ceranae support the parasite hypothesis for the evolution of extreme polyandry in eusocial insects. Apidologie, 43(5), 539–548. https://doi.org/10.1007/s13592-012-0121-5

Liu, G., Ye, Z., Tong, K., & Zhang, Y. (2013). Biotreatment of heavy oil wastewater by combined upflow anaerobic sludge blanket and immobilized biological aerated filter in a pilot-scale test. Biochemical Engineering Journal, 72, 48–53. https://doi.org/10.1016/j.bej.2012.12.017