UFGI publication round-up 6/18 – 6/25

Sá ACC, Webb A, Gong Y, McDonough CW, Shahin MH, Datta S, Langaee TY, Turner ST, Beitelshees AL, Chapman AB, Boerwinkle E, Gums JG, Scherer SE, Cooper-DeHoff RM, Sadee W, Johnson JA.

BMC Med Genomics. 2018 Jun 20;11(1):55. doi: 10.1186/s12920-018-0370-x.

PMID: 29925376

Transgenic expression of EFR and Bs2 genes for field management of bacterial wilt and bacterial spot of tomato.

Kunwar S, Iriarte F, Fan Q, da Silva EE, Ritchie L, Nguyen NS, Freeman JH, Stall RE, Jones JB, Minsavage GV, Colee J, Scott J, Vallad GE, Zipfel C, Horvath D, Westwood J, Hutton S, Paret ML.

Phytopathology. 2018 Jun 20. doi: 10.1094/PHYTO-12-17-0424-R. [Epub ahead of print]

PMID: 29923802

Floxuridine Homomeric Oligonucleotides “Hitchhike” with Albumin In Situ for Cancer Chemotherapy.

Jin C, Zhang H, Zou J, Liu Y, Zhang L, Li F, Wang R, Xuan W, Ye M, Tan W.

Angew Chem Int Ed Engl. 2018 Jun 19. doi: 10.1002/anie.201804156. [Epub ahead of print]

PMID: 29923269

Tempo and timing of ecological trait divergence in bird speciation.

McEntee JP, Tobias JA, Sheard C, Burleigh JG.

Nat Ecol Evol. 2018 Jul;2(7):1120-1127. doi: 10.1038/s41559-018-0570-y. Epub 2018 Jun 18.

PMID: 29915344

Horizontally transferred genes in the ctenophore Mnemiopsis leidyi.

Hernandez AM, Ryan JF.

PeerJ. 2018 Jun 15;6:e5067. doi: 10.7717/peerj.5067. eCollection 2018.

PMID: 29922518

Piloting Consumer Health Information Services in Collaboration with a Community Research Engagement Program.

Ansell M, Tennant MR, Piazza V, Cottler LB.

Med Ref Serv Q. 2017 Oct-Dec;36(4):348-361. doi: 10.1080/02763869.2017.1369283.

PMID: 29043938

Anchored phylogenomics illuminates the skipper butterfly tree of life.

Toussaint EFA, Breinholt JW, Earl C, Warren AD, Brower AVZ, Yago M, Dexter KM, Espeland M, Pierce NE, Lohman DJ, Kawahara AY.

BMC Evol Biol. 2018 Jun 19;18(1):101. doi: 10.1186/s12862-018-1216-z.

PMID: 29921227

Impaired cardiac and skeletal muscle bioenergetics in children, adolescents, and young adults with Barth syndrome.

Bashir A, Bohnert KL, Reeds DN, Peterson LR, Bittel AJ, de Las Fuentes L, Pacak CA, Byrne BJ, Cade WT.

Physiol Rep. 2017 Feb;5(3). pii: e13130. doi: 10.14814/phy2.13130.

PMID: 28196853

Transcriptome analysis reveals novel insights into the response of low-dose benzo(a)pyrene exposure in male tilapia.

Colli-Dula RC, Fang X, Moraga-Amador D, Albornoz-Abud N, Zamora-Bustillos R, Conesa A, Zapata-Perez O, Moreno D, Hernandez-Nuñez E.

Aquat Toxicol. 2018 Jun 8;201:162-173. doi: 10.1016/j.aquatox.2018.06.005. [Epub ahead of print]

PMID: 29913432

Open-ended interview questions and saturation.

Weller SC, Vickers B, Bernard HR, Blackburn AM, Borgatti S, Gravlee CC, Johnson JC.

PLoS One. 2018 Jun 20;13(6):e0198606. doi: 10.1371/journal.pone.0198606. eCollection 2018.

PMID: 29924873

Creating an arsenal of Adeno-associated virus (AAV) gene delivery stealth vehicles.

Smith JK, Agbandje-McKenna M.

PLoS Pathog. 2018 May 3;14(5):e1006929. doi: 10.1371/journal.ppat.1006929. eCollection 2018 May.

PMID: 29723270

Viral FGARAT ORF75A promotes early events in lytic infection and gammaherpesvirus pathogenesis in mice.

Van Skike ND, Minkah NK, Hogan CH, Wu G, Benziger PT, Oldenburg DG, Kara M, Kim-Holzapfel DM, White DW, Tibbetts SA, French JB, Krug LT.

PLoS Pathog. 2018 Feb 1;14(2):e1006843. doi: 10.1371/journal.ppat.1006843. eCollection 2018 Feb.

PMID: 29390024

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands.

Barboza ADM, Pylro VS, Jacques RJS, Gubiani PI, de Quadros FLF, da Trindade JK, Triplett EW, Roesch L.

PeerJ. 2018 Jun 13;6:e4991. doi: 10.7717/peerj.4991. eCollection 2018.

PMID: 29915701

Brain-gut communications via distinct neuroendocrine signals bidirectionally regulate longevity in C. elegans.

Zhang B, Gong J, Zhang W, Xiao R, Liu J, Xu XZS.

Genes Dev. 2018 Feb 1;32(3-4):258-270. doi: 10.1101/gad.309625.117.

PMID: 29491136

Development and characterization of a high quality plum tomato essence.

Zhu Y, Klee HJ, Sarnoski PJ.

Food Chem. 2018 Nov 30;267:337-343. doi: 10.1016/j.foodchem.2017.07.160. Epub 2017 Aug 4.

PMID: 29934176

Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes.

Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, Vereide DT.

Dev Biol. 2018 Jul 1;439(1):30-41. doi: 10.1016/j.ydbio.2018.04.007. Epub 2018 Apr 17.

PMID: 29678445

Six Years and Counting: Restoration of Photopic Retinal Function and Visual Behavior Following Gene Augmentation Therapy in a Sheep Model of CNGA3 Achromatopsia.

Ofri R, Averbukh E, Ezra-Elia R, Ross M, Honig H, Obolensky A, Rosov A, Hauswirth WW, Gootwine E, Banin E.

Hum Gene Ther. 2018 Jun 21. doi: 10.1089/hum.2018.076. [Epub ahead of print]

PMID: 29926749

Integrated epigenetic and genetic analysis identifies markers of prognostic significance in pediatric acute myeloid leukemia.

Lamba JK, Cao X, Raimondi SC, Rafiee R, Downing JR, Lei S, Gruber T, Ribeiro RC, Rubnitz JE, Pounds SB.

Oncotarget. 2018 Jun 1;9(42):26711-26723. doi: 10.18632/oncotarget.25475. eCollection 2018 Jun 1.

PMID: 29928480

genes in Haloferax volcanii.

Martin JH, Rawls KS, Chan JC, Hwang S, Martinez-Pastor M, McMillan LJ, Prunetti L, Schmid AK, Maupin-Furlow JA.

J Bacteriol. 2018 Jun 18. pii: JB.00244-18. doi: 10.1128/JB.00244-18. [Epub ahead of print]

PMID: 29914986

A porcine model of neurofibromatosis type 1 that mimics the human disease.

White KA, Swier VJ, Cain JT, Kohlmeyer JL, Meyerholz DK, Tanas MR, Uthoff J, Hammond E, Li H, Rohret FA, Goeken A, Chan CH, Leidinger MR, Umesalma S, Wallace MR, Dodd RD, Panzer K, Tang AH, Darbro BW, Moutal A, Cai S, Li W, Bellampalli SS, Khanna R, Rogers CS, Sieren JC, Quelle DE, Weimer JM.

JCI Insight. 2018 Jun 21;3(12). pii: 120402. doi: 10.1172/jci.insight.120402. [Epub ahead of print]

PMID: 29925695

Metabolomics of Early Stage Plant Cell-Microbe Interaction Using Stable Isotope Labeling.

Pang Q, Zhang T, Wang Y, Kong W, Guan Q, Yan X, Chen S.

Front Plant Sci. 2018 Jun 5;9:760. doi: 10.3389/fpls.2018.00760. eCollection 2018.

PMID: 29922325

The Ubx Polycomb response element bypasses an unpaired Fab-8 insulator via cis transvection in Drosophila.

Lu D, Li Z, Li L, Yang L, Chen G, Yang D, Zhang Y, Singh V, Smith S, Xiao Y, Wang E, Ye Y, Zhang W, Zhou L, Rong Y, Zhou J.

PLoS One. 2018 Jun 21;13(6):e0199353. doi: 10.1371/journal.pone.0199353. eCollection 2018.

PMID: 29928011

Evolutionary history of the angiosperm flora of China.

Lu LM, Mao LF, Yang T, Ye JF, Liu B, Li HL, Sun M, Miller JT, Mathews S, Hu HH, Niu YT, Peng DX, Chen YH, Smith SA, Chen M, Xiang KL, Le CT, Dang VC, Lu AM, Soltis PS, Soltis DE, Li JH, Chen ZD.

Nature. 2018 Feb 8;554(7691):234-238. doi: 10.1038/nature25485. Epub 2018 Jan 31.

PMID: 29420476

Variable selection in omics data: A practical evaluation of small sample sizes.

Kirpich A, Ainsworth EA, Wedow JM, Newman JRB, Michailidis G, McIntyre LM.

PLoS One. 2018 Jun 21;13(6):e0197910. doi: 10.1371/journal.pone.0197910. eCollection 2018.

PMID: 29927942

Genome-Wide Surveillance of Genital Herpes Simplex Virus Type 1 From Multiple Anatomic Sites Over Time.

Shipley MM, Renner DW, Ott M, Bloom DC, Koelle DM, Johnston C, Szpara ML.

J Infect Dis. 2018 Jun 18. doi: 10.1093/infdis/jiy216. [Epub ahead of print]

PMID: 29920588

Genome-Wide Exon-Capture Approach Identifies Genetic Variants of Norway Spruce Genes Associated With Susceptibility to Heterobasidion parviporum Infection.

Mukrimin M, Kovalchuk A, Neves LG, Jaber EHA, Haapanen M, Kirst M, Asiegbu FO.

Front Plant Sci. 2018 Jun 12;9:793. doi: 10.3389/fpls.2018.00793. eCollection 2018.

PMID: 29946332

Transcriptomic and Network Analyses Reveal Mechanistic-Based Biomarkers of Endocrine Disruption in the Marine Mussel, Mytilus edulis.

Blalock BJ, Robinson WE, Loguinov A, Vulpe CD, Krick KS, Poynton HC.

Environ Sci Technol. 2018 Jun 28. doi: 10.1021/acs.est.8b01604. [Epub ahead of print]

PMID: 29953215

Quantitative trait loci analysis identifies a prominent gene involved in the production of fatty-acid-derived flavor volatiles in tomato.

Garbowicz K, Liu Z, Alseekh S, Tieman D, Taylor M, Kuhalskaya A, Ofner I, Zamir D, Klee HJ, Fernie AR, Brotman Y.

Mol Plant. 2018 Jun 27. pii: S1674-2052(18)30190-4. doi: 10.1016/j.molp.2018.06.003. [Epub ahead of print]

PMID: 29960108

The effects of beta blockade and clonidine on persistent injury-associated anemia.

Loftus TJ, Rosenthal MD, Croft CA, Smith RS, Moore FA, Brakenridge SC, Efron PA, Mohr AM.

J Surg Res. 2018 Jun 28. pii: S0022-4804(18)30387-1. doi: 10.1016/j.jss.2018.06.001. [Epub ahead of print]

PMID: 29960715

Anemia and blood transfusion in elderly trauma patients.

Loftus TJ, Brakenridge SC, Murphy TW, Nguyen LL, Moore FA, Efron PA, Mohr AM.

J Surg Res. 2018 Sep;229:288-293. doi: 10.1016/j.jss.2018.04.021.

PMID: 29937004

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome.

Liu X, Mei W, Soltis PS, Soltis DE, Barbazuk WB.

Mol Ecol Resour. 2017 Nov;17(6):1243-1256. doi: 10.1111/1755-0998.12670. Epub 2017 Jun 5.

PMID: 28316149

Methionine Sulfoxide Reductase A (MsrA) and Its Function in Ubiquitin-Like Protein Modification in Archaea.

Fu X, Adams Z, Liu R, Hepowit NL, Wu Y, Bowmann CF, Moskovitz J, Maupin-Furlow JA.

MBio. 2017 Sep 5;8(5). pii: e01169-17. doi: 10.1128/mBio.01169-17.

PMID: 28874471

New functions of an old kinase MPK4 in guard cells.

Lin C, Chen S.

Plant Signal Behav. 2018 Jun 26:1-4. doi: 10.1080/15592324.2018.1477908. [Epub ahead of print]

PMID: 29944443

Evolution of Floral Traits and Impact of Reproductive Mode on Diversification in the Phlox Family (Polemoniaceae).

Landis JB, Bell CD, Hernandez M, Zenil-Ferguson R, McCarthy EW, Soltis DE, Soltis PS.

Mol Phylogenet Evol. 2018 Jun 26. pii: S1055-7903(18)30151-9. doi: 10.1016/j.ympev.2018.06.035. [Epub ahead of print]

PMID: 29958983

Phylogeny and staminal evolution of Salvia (Lamiaceae, Nepetoideae) in East Asia.

Hu GX, Takano A, Drew BT, Liu ED, Soltis DE, Soltis PS, Peng H, Xiang CL.

Ann Bot. 2018 Jun 25. doi: 10.1093/aob/mcy104. [Epub ahead of print]

PMID: 29945172

Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon.

Nieto-Lugilde M, Werner O, McDaniel SF, Koutecký P, Kučera J, Rizk SM, Ros RM.

Am J Bot. 2018 Jun 29. doi: 10.1002/ajb2.1107. [Epub ahead of print]

PMID: 29957852

Mechanisms of RsaL mediated tolerance to ciprofloxacin and carbenicillin in Pseudomonas aeruginosa.

Fan Z, Xu C, Pan X, Dong Y, Ren H, Jin Y, Bai F, Cheng Z, Jin S, Wu W.

Curr Genet. 2018 Jun 27. doi: 10.1007/s00294-018-0863-3. [Epub ahead of print]

PMID: 29951698

Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling.

Igolkina AA, Armoskus C, Newman JRB, Evgrafov OV, McIntyre LM, Nuzhdin SV, Samsonova MG.

Front Mol Neurosci. 2018 Jun 11;11:192. doi: 10.3389/fnmol.2018.00192. eCollection 2018.

PMID: 29942251

Whole Genome Sequencing in Severe Chronic Obstructive Pulmonary Disease.

Prokopenko D, Sakornsakolpat P, Loehlein Fier H, Qiao D, Parker MM, McDonald MN, Manichaikul A, Rich SS, Barr RG, Williams CJ, Brantly ML, Lange C, Beaty TH, Crapo JD, Silverman EK, Cho MH; COPDGene Investigators, NHLBI TOPMed Investigators.

Am J Respir Cell Mol Biol. 2018 Jun 27. doi: 10.1165/rcmb.2018-0088OC. [Epub ahead of print]

PMID: 29949718

A Secreted ‘Candidatus Liberibacter asiaticus’ Peroxiredoxin Simultaneously Suppresses Both Localized and Systemic Innate Immune Responses in Planta.

Jain M, Munoz-Bodnar A, Zhang S, Gabriel DW.

Mol Plant Microbe Interact. 2018 Jun 28. doi: 10.1094/MPMI-03-18-0068-R. [Epub ahead of print]

PMID: 29953333

Rapid morphological change of a top predator with the invasion of a novel prey.

Cattau CE, Fletcher RJ Jr, Kimball RT, Miller CW, Kitchens WM.

Nat Ecol Evol. 2018 Jan;2(1):108-115. doi: 10.1038/s41559-017-0378-1. Epub 2017 Nov 27.

PMID: 29180705

An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins.

Braun EL.

Bioinformatics. 2018 Jul 1;34(13):i350-i356. doi: 10.1093/bioinformatics/bty261.

PMID: 29950007

MBNL splicing activity depends on RNA binding site structural context.

Taylor K, Sznajder LJ, Cywoniuk P, Thomas JD, Swanson MS, Sobczak K.

Nucleic Acids Res. 2018 Jun 28. doi: 10.1093/nar/gky565. [Epub ahead of print]

PMID: 29955876

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies.

Ren Y, Sarkar A, Kahveci T.

BMC Bioinformatics. 2018 Jun 26;19(1):242. doi: 10.1186/s12859-018-2236-9.

PMID: 29940838

Conditional mouse models support the role of SLC39A14 (ZIP14) in Hyperostosis Cranialis Interna and in bone homeostasis.

Hendrickx G, Borra VM, Steenackers E, Yorgan TA, Hermans C, Boudin E, Waterval JJ, Jansen IDC, Aydemir TB, Kamerling N, Behets GJ, Plumeyer C, D’Haese PC, Busse B, Everts V, Lammens M, Mortier G, Cousins RJ, Schinke T, Stokroos RJ, Manni JJ, Van Hul W.

PLoS Genet. 2018 Apr 5;14(4):e1007321. doi: 10.1371/journal.pgen.1007321. eCollection 2018 Apr.

PMID: 29621230

Introduction of Large Sequence Inserts by CRISPR-Cas9 To Create Pathogenicity Mutants in the Multinucleate Filamentous Pathogen Sclerotinia sclerotiorum.

Li J, Zhang Y, Zhang Y, Yu PL, Pan H, Rollins JA.

MBio. 2018 Jun 26;9(3). pii: e00567-18. doi: 10.1128/mBio.00567-18.

PMID: 29946044

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.

Rife Magalis B, Kosakovsky Pond SL, Summers MF, Salemi M.

Virus Evol. 2018 Jun 21;4(1):vey018. doi: 10.1093/ve/vey018. eCollection 2018 Jan.

PMID: 29951250

C-terminal proline deletions in KCNC3 cause delayed channel inactivation and an adult-onset progressive SCA13 with spasticity.

Khare S, Galeano K, Zhang Y, Nick JA, Nick HS, Subramony SH, Sampson J, Kaczmarek LK, Waters MF.

Cerebellum. 2018 Jun 13. doi: 10.1007/s12311-018-0950-5. [Epub ahead of print]

PMID: 29949095

Pancreatic Histopathology of Human Monogenic Diabetes Due to Causal Variants in KCNJ11, HNF1A, GATA6, and LMNA.

Sanyoura M, Jacobsen L, Carmody D, Del Gaudio D, Alkorta-Aranburu G, Arndt K, Hu Y, Kobiernicki F, Kusmartseva I, Atkinson MA, Philipson LH, Schatz D, Campbell-Thompson M, Greeley SAW.

J Clin Endocrinol Metab. 2018 Jan 1;103(1):35-45. doi: 10.1210/jc.2017-01159.

PMID: 28938416

Pharmacokinetics and Comprehensive Analysis of the Tissue Distribution of Eravacycline in Rabbits.

Petraitis V, Petraitiene R, Maung BBW, Khan F, Alisauskaite I, Olesky M, Newman J, Mutlib A, Niu X, Satlin M, Singh RS, Derendorf H, Walsh TJ.

Antimicrob Agents Chemother. 2018 Jun 25. pii: AAC.00275-18. doi: 10.1128/AAC.00275-18. [Epub ahead of print]

PMID: 29941646

High-throughput assessment of oxidative respiration in fish embryos: Advancing adverse outcome pathways for mitochondrial dysfunction.

Souders CL 2nd, Liang X, Wang X, Ector N, Zhao YH, Martyniuk CJ.

Aquat Toxicol. 2018 Jun;199:162-173. doi: 10.1016/j.aquatox.2018.03.031. Epub 2018 Mar 27. Review.

PMID: 29631217

Dieldrin-induced neurotoxicity involves impaired mitochondrial bioenergetics and an endoplasmic reticulum stress response in rat dopaminergic cells.

Schmidt JT, Rushin A, Boyda J, Souders CL 2nd, Martyniuk CJ.

Neurotoxicology. 2017 Dec;63:1-12. doi: 10.1016/j.neuro.2017.08.007. Epub 2017 Aug 24.

PMID: 28844784