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Multiple Causal Variants Underlie Genetic Associations in Humans [article]

Nathan S Abell, Marianne K DeGorter, Michael Gloudemans, Emily Greenwald, Kevin S Smith, Zihuai S He, Stephen B Montgomery
2021 bioRxiv   pre-print
To our knowledge, all previously described allelic interactions of this kind have been reported in S. cerevisiae (19, 20) .  ...  Marchini, S. McCarthy, G. A. McVean, G. R. Abecasis, A global reference for human genetic variation. Nature. 526, 68-74 (2015). 60. X. Wen, R. Pique-Regi, F.  ... 
doi:10.1101/2021.05.24.445471 fatcat:wldjlmqwqrdilfks7niljv772i

Histological Development and Integration of the Zebrafish Weberian Apparatus

Nathan C. Bird, Selena S. Richardson, Jeremy R. Abels
2020 Developmental Dynamics  
As such, the lagena (Figure 5A ; l) is now nearly three times taller than the saccule (Figure 5A ; s).  ...  The lagena (Figure 3A ; l) is approximately twice as tall as the saccule (Figure 3A ; s), and approximately twice the volume.  ...  A. and S. S. R.; Dr Robert and Brenda Good Research Fellowship to J. R. A. The authors would like to thank Dr Julie Kang for use of histological and imaging equipment.  ... 
doi:10.1002/dvdy.172 pmid:32243643 fatcat:opzbfz72ljf7nbxgzncgdq75fy

Post-Transcriptional Regulation of Antiviral Gene Expression by N6-Methyladenosine [article]

Michael J McFadden, Alexa B. R. McIntyre, Haralambos Mourelatos, Nathan S Abell, Nandan S Gokhale, Hélène Ipas, Blerta Xhemalçe, Christopher E Mason, Stacy M Horner
2020 bioRxiv   pre-print
s multiple comparisons test (C-E). ns = not significant.  ... 
doi:10.1101/2020.08.05.238337 fatcat:symkzeb7nrdmffsvrj2r73ugcy

MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes

Damon Polioudakis, Nathan S. Abell, Vishwanath R. Iyer, Alfons Navarro
2015 PLoS ONE  
Our results provide a comprehensive genome wide miR-191 target profile, and demonstrate miR-191's regulation of primary human fibroblast proliferation.  ... 
doi:10.1371/journal.pone.0126535 pmid:25992613 pmcid:PMC4439112 fatcat:fjc4tb3vkffgrfck4ynpjkyilq

BCDIN3D regulates tRNAHis 3' fragment processing

Calder W. Reinsborough, Hélène Ipas, Nathan S. Abell, Ryan M. Nottingham, Jun Yao, Sravan K. Devanathan, Samantha B. Shelton, Alan M. Lambowitz, Blerta Xhemalçe, Anita K. Hopper
2019 PLoS Genetics  
When we performed in vitro RNA methyltransferase assays with pre-miR-145-5'P using the radioactively labeled methyl group donor S-Adenosyl-Methionine [ 3 H]-S-SAM [5] , the small fraction of C[ 3 H] 3  ...  These findings suggest that tRNA His 3' fragments may have regulatory function(s) in cells.  ... 
doi:10.1371/journal.pgen.1008273 pmid:31329584 pmcid:PMC6675128 fatcat:l6qgtiadljbqhkl73i4lyfxusy

miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing

Damon Polioudakis, Nathan S Abell, Vishwanath R Iyer
2015 BMC Genomics  
The pathways regulating the transition of mammalian cells from quiescence to proliferation are mediated by multiple miRNAs. Despite significant improvements in our understanding of miRNA targeting, the majority of miRNA regulatory networks are still largely unknown and require experimental validation. Results: Here we identified miR-503, miR-103, and miR-494 as negative regulators of proliferation in primary human cells. We experimentally determined their genome wide target profiles using
more » ... duced silencing complex (RISC) immunoprecipitations and gene expression profiling. Analysis of the genome wide target profiles revealed evidence of extensive regulation of gene expression through non-canonical target pairing by miR-503. We identified the proto-oncogene DDHD2 as a target of miR-503 that requires pairing outside of the canonical 5′ seed region of miR-503, representing a novel mode of miRNA-target pairing. Further bioinformatics analysis implicated miR-503 and DDHD2 in breast cancer tumorigenesis. Conclusions: Our results provide an extensive genome wide set of targets for miR-503, miR-103, and miR-494, and suggest that miR-503 may act as a tumor suppressor in breast cancer by its direct non-canonical targeting of DDHD2.
doi:10.1186/s12864-015-1279-9 pmid:25653011 pmcid:PMC4326481 fatcat:ltani6tx4rbxverpgehn4rhtmi

Glucose-induced increase in circulating progenitor cells is blunted in polycystic amenorrhoeic subjects

Soumi Bairagi, Jayashree Gopal, Abel A. Nathan, Subash S. Babu, N. Pavan Kumar, Madhulika Dixit
2012 Human Reproduction  
We have recently shown that oral glucose challenge increases circulating levels of CD34 + and CD133 + CD34 + cells in young Asian Indian males, which is attenuated in insulin resistant individuals (Nathan  ... 
doi:10.1093/humrep/der457 pmid:22252083 fatcat:bn4x7glq35dz7leculv5de6z6i

Evaluation of In Vitro Activity of Essential Oils againstTrypanosoma brucei bruceiandTrypanosoma evansi

Nathan Habila, Abel S. Agbaji, Zakari Ladan, Isaac A. Bello, Emmanuel Haruna, Monday A. Dakare, Taofiq O. Atolagbe
2010 Journal of Parasitology Research  
The Compounds were identified by GC retention time (RT) and by comparism with those present in the National Institute for Standard Technology computer data bank (NIST; 05 s. LIB).  ... 
doi:10.1155/2010/534601 pmid:20700425 pmcid:PMC2911591 fatcat:svdcdcrglnestm4wpxdg7e4kma

Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression [article]

Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath
2018 bioRxiv   pre-print
Full eQTL and sQTL summary statistics have been made deposited into Box: https://stanford.box.com/s/asrxy0o66xxe1j7mfj56p3z3d405gijj and are available at http://montgomerylab.stanford.edu/resources.html  ... 
doi:10.1101/446799 fatcat:fxca5nu3qjer3dlykpzg7kxpbq

Behavioral and neural responses to gustatory stimuli delivered non-contingently through intra-oral cannulas

Ernesto S. Soares, Jennifer R. Stapleton, Abel Rodriguez, Nathan Fitzsimmons, Laura Oliveira, Miguel A.L. Nicolelis, Sidney A. Simon
2007 Physiology and Behavior  
While in the 4TW and L-S protocols the former population displayed more changes than the latter, in the App L-S protocol variability was homogeneously distributed between the two populations.  ...  In the third one, the App L-S protocol, only hedonically positive tastants were used.  ...  /POST ≫ τ L-S, PRE/POST and τ AppL-S,PRE/POST ≫ τ 4TW, PRE/POST , respectively).  ... 
doi:10.1016/j.physbeh.2007.05.038 pmid:17588623 pmcid:PMC2148501 fatcat:2hyme2yjwnddzaru27noucdrmi

Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export

Emily K. Tsang, Nathan S. Abell, Xin Li, Vanessa Anaya, Konrad J. Karczewski, David A. Knowles, Raymond G. Sierra, Kevin S. Smith, Stephen B. Montgomery
2016 G3: Genes, Genomes, Genetics  
doi:10.1534/g3.116.036137 pmid:27799337 pmcid:PMC5217120 fatcat:ykiu2giuena7vavwjlob7rpxka

A Myc–microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes

Damon Polioudakis, Akshay A. Bhinge, Patrick J. Killion, Bum-Kyu Lee, Nathan S. Abell, Vishwanath R. Iyer
2013 Nucleic Acids Research  
The transition of mammalian cells from quiescence to proliferation is accompanied by the differential expression of several microRNAs (miRNAs) and transcription factors. However, the interplay between transcription factors and miRNAs in modulating gene regulatory networks involved in human cell proliferation is largely unknown. Here we show that the miRNA miR-22 promotes proliferation in primary human cells, and through a combination of Argonaute-2 immunoprecipitation and reporter assays, we
more » ... ntified multiple novel targets of miR-22, including several cell-cycle arrest genes that mediate the effects of the tumor-suppressor p53. In addition, we found that miR-22 suppresses interferon gene expression by directly targeting high mobility group box-1 and interferon regulatory factor (IRF)-5, preventing activation of IRF3 and NF-iB, which are activators of interferon genes. The expression of interferon genes is elevated in quiescent cells and their expression is inhibitory for cell proliferation. In addition, we find that miR-22 is activated by the transcription factor Myc when quiescent cells enter proliferation and that miR-22 inhibits the Myc transcriptional repressor MXD4, mediating a feed-forward loop to elevate Myc expression levels. Our results implicate miR-22 in downregulating the anti-proliferative p53 and interferon pathways and reveal a new transcription factor-miRNA network that regulates the transition of primary human cells from quiescence to proliferation.
doi:10.1093/nar/gks1452 pmid:23303785 pmcid:PMC3575845 fatcat:nrgok7ao7ngrpkh4anaiupotfe

Variation of Fatty Acids and Vitamin E Composition in Seed Oils of Some Plant Species

Nathan Habila, Mairo H Inuwa, Idowu A Aimola, Abel S Agbaji, Zakari Ladan, Rose Sangodare, Solomon I Williams, Benedict O Odjobo, Edward Ogabiela
2012 Journal of Plant Studies  
The composition of fatty acids (FA) and vitamin E in seed oils of Albezia lebbeck (AL), Citrus sinensis (CS), Terminalia catapa (TC), Tamarindus indica (TI) and Citrullus vulgaris (CV) was investigated. The oil yields were obtained by solvent extraction and analysed for fatty acids by Gas Chromatography Mass Spectroscopy (GC-MS). The oil yields of the seeds were found to be 8.22 ± 0.55, 20.00 ± 1.50, 35.60 ± 1.60, 24.00 ± 1.20% and 9.42 ± 1.30 percent AL, CS, TC, CV, and TI respectively. Both
more » ... turated and unsaturated FA were identified in all the seed oils with the latter being the predominant with 77.70% in CV, 60.76% in CS, 56.98% in AL, 54.58% in TC and 34.52% in TI. Vitamin E was highest in CV 27.51 ± 2.42 mg/ml and lowest in TI 10.60 ± 1.50 mg/ml. There was significant decrease in percentage saturated FA, increase in percentage unsaturated FA with increase in vitamins E concentration in all the seed oils. The oils have many FA such as oleic acid, eicosadienoic acid and α-linoleic acid which could be of biological and industrial significance to humans.
doi:10.5539/jps.v1n2p55 fatcat:6gsvfnascvfkvitctn4woydmca

Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms

Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath
2019 Communications Biology  
The amplification conditions were: 94°C 2 min followed by 38 cycles of 94°C 30 s, 60°C 30 s, 72°C 15 s.  ...  The amplification conditions were: 94°C 2 min followed by 50 cycles of 94°C 30 s, 60°C 30 s, 72°C 15 s. AmpliTaq (ThermoFisher) and 2.5 mM MgCl 2 were used for all reactions.  ...  Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s)  ... 
doi:10.1038/s42003-019-0430-6 pmid:31123710 pmcid:PMC6527609 fatcat:udmzzlrntzc6lcxvvj4vlb3vh4

Genetic dysregulation of gene expression and splicing during a ten-year period of human aging [article]

Brunilda Balliu, Matthew Durrant, Olivia de Goede, Nathan Abell, Xin Li, Boxiang Liu, Michael J. Gloudemans, Naomi L. Cook, Kevin S. Smith, Mauro Pala, Francesco Cucca, David Schlessinger (+5 others)
2019 bioRxiv   pre-print
We test for a statistically significant increase in global AI with age (H 0 : µ ≤ 1 vs H 1 : µ > 1, where µ median of the φ i * * 's) using the one-sample Wilcoxon signed rank test.  ... 
doi:10.1101/519520 fatcat:3mh5ewhfyzhapowdit36h6qghu
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