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Full-Text Articles in Life Sciences
Physical Mapping Of The Anopheles (Nyssorhynchus) Darlingi Genomic Scaffolds, Míriam Silva Rafael, Leticia Cegatti Bridi, Igor V. Sharakhov, Osvaldo Marinotti, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Giselle Moura Guimarães-Marques, Valéria Silva Santos, Carlos Gustavo Nunes Da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei
Physical Mapping Of The Anopheles (Nyssorhynchus) Darlingi Genomic Scaffolds, Míriam Silva Rafael, Leticia Cegatti Bridi, Igor V. Sharakhov, Osvaldo Marinotti, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Giselle Moura Guimarães-Marques, Valéria Silva Santos, Carlos Gustavo Nunes Da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei
Biology Faculty Publications
The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping …
Deep Multilayer Brain Proteomics Identifies Molecular Networks In Alzheimer's Disease Progression, Bing Bai, Xusheng Wang, Yuxin Li, Ping-Chung Chen, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutz, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn A. Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu, Junmin Peng
Deep Multilayer Brain Proteomics Identifies Molecular Networks In Alzheimer's Disease Progression, Bing Bai, Xusheng Wang, Yuxin Li, Ping-Chung Chen, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutz, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn A. Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu, Junmin Peng
Biology Faculty Publications
Alzheimer's disease (AD) displays a long asymptomatic stage before dementia. We characterize AD stage-associated molecular networks by profiling 14,513 proteins and 34,173 phosphosites in the human brain with mass spectrometry, highlighting 173 protein changes in 17 pathways. The altered proteins are validated in two independent cohorts, showing partial RNA dependency. Comparisons of brain tissue and cerebrospinal fluid proteomes reveal biomarker candidates. Combining with 5xFAD mouse analysis, we determine 15 Aβ-correlated proteins (e.g., MDK, NTN1, SMOC1, SLIT2, and HTRA1). 5xFAD shows a proteomic signature similar to symptomatic AD but exhibits activation of autophagy and interferon response and lacks human-specific deleterious events, …
Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie
Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie
Biology Faculty Publications
We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater …
Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, Welkin H. Pope, Kirk R. Anders, Madison Baird, Charles A. Bowman, Michelle M. Boyle, Gregory W. Broussard, Tiffany Chow, Kari L. Clase, Shannon Cooper, Kathleen A. Cornely, Randall J. Dejong, Veronique A. Delesalle, Lisa Deng, David Dunbar, Nicholas P. Edgington, Christina M. Ferreira, Kathleen Weston Hafer, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Khristina Ipapo, Gregory P. Krukonis, Christopher G. Meier, Denise L. Monti, Matthew R. Olm, Shallee T. Page, Craig L. Peebles, Claire A. Rinehart, Michael R. Rubin, Daniel A. Russell, Erin R. Sanders, Morgan Schoer, Christopher D. Shaffer, James Wherley, Edwin Vazquez, Han Yuan, Daiyuan Zhang, Steven G. Cresawn, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull
Cluster M Mycobacteriophages Bongo, Pegleg, And Rey With Unusually Large Repertoires Of Trna Isotopes, Welkin H. Pope, Kirk R. Anders, Madison Baird, Charles A. Bowman, Michelle M. Boyle, Gregory W. Broussard, Tiffany Chow, Kari L. Clase, Shannon Cooper, Kathleen A. Cornely, Randall J. Dejong, Veronique A. Delesalle, Lisa Deng, David Dunbar, Nicholas P. Edgington, Christina M. Ferreira, Kathleen Weston Hafer, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Khristina Ipapo, Gregory P. Krukonis, Christopher G. Meier, Denise L. Monti, Matthew R. Olm, Shallee T. Page, Craig L. Peebles, Claire A. Rinehart, Michael R. Rubin, Daniel A. Russell, Erin R. Sanders, Morgan Schoer, Christopher D. Shaffer, James Wherley, Edwin Vazquez, Han Yuan, Daiyuan Zhang, Steven G. Cresawn, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull
Biology Faculty Publications
Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average …
Between Two Fern Genomes, E. B. Sessa, J. A. Banks, M. S. Barker, J. P. Der, A. M. Duffy, S. W. Graham, M. Hasebe, J. Langdale, F. W. Li, D. B. Marchant, K. M. Pryer, C. J. Rothfels, S. J. Roux, M. L. Salmi, E. M. Sigel, D. E. Soltis, P. S. Soltis, D. W. Stevenson, Paul G. Wolf
Between Two Fern Genomes, E. B. Sessa, J. A. Banks, M. S. Barker, J. P. Der, A. M. Duffy, S. W. Graham, M. Hasebe, J. Langdale, F. W. Li, D. B. Marchant, K. M. Pryer, C. J. Rothfels, S. J. Roux, M. L. Salmi, E. M. Sigel, D. E. Soltis, P. S. Soltis, D. W. Stevenson, Paul G. Wolf
Biology Faculty Publications
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the …
Genotyping-By-Sequencing For Populus Population Genomics: An Assessment Of Genome Sampling Patterns And Filtering Approaches, M. Schilling, Paul G. Wolf, A. M. Duffy, H. S. Rai, C. A. Rowe, B. A. Richardson, K. E. Mock
Genotyping-By-Sequencing For Populus Population Genomics: An Assessment Of Genome Sampling Patterns And Filtering Approaches, M. Schilling, Paul G. Wolf, A. M. Duffy, H. S. Rai, C. A. Rowe, B. A. Richardson, K. E. Mock
Biology Faculty Publications
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging …
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May
Biology Faculty Publications
Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …
Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, David K. Kump, Stephen R. Voss
Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, David K. Kump, Stephen R. Voss
Biology Faculty Publications
Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and …
Differences In The Transcriptome Signatures Of Two Genetically Related Entamoeba Histolytica Cell Lines Derived From The Same Isolate With Different Pathogenic Properties, Laura Biller, Paul H. Davis, Manuela Tillack, Jenny Matthiesen, Hannelore Lotter, Samuel L. Stanley, Egbert Tannich, Iris Bruchhaus
Differences In The Transcriptome Signatures Of Two Genetically Related Entamoeba Histolytica Cell Lines Derived From The Same Isolate With Different Pathogenic Properties, Laura Biller, Paul H. Davis, Manuela Tillack, Jenny Matthiesen, Hannelore Lotter, Samuel L. Stanley, Egbert Tannich, Iris Bruchhaus
Biology Faculty Publications
Results: The availability of two genetically very similar cell lines (A and B) derived from the laboratory isolate Entamoeba histolytica HM-1:IMSS, which differ in their virulence properties, provides a powerful tool for identifying pathogenicity factors of the causative agent of human amoebiasis. Cell line A is incapable inducing liver abscesses in gerbils, whereas interaction with cell line B leads to considerable abscess formation. Phenotypic characterization of both cell lines revealed that trophozoites from the pathogenic cell line B have a larger cell size, an increased growth rate in vitro, an increased cysteine peptidase activity and higher resistance to nitric …