UFGI Publication round-up week 12/17

Weyn-Vanhentenryck SM, Feng H, Ustianenko D, Duffié R, Yan Q, Jacko M, Martinez JC, Goodwin M, Zhang X, Hengst U, Lomvardas S, Swanson MS, Zhang C.

Nat Commun. 2018 Jun 6;9(1):2189. doi: 10.1038/s41467-018-04559-0.

PMID: 29875359

In healthy adults, resistant maltodextrin produces a greater change in fecal bifidobacteria counts and increases stool wet weight: a double-blind, randomized, controlled crossover study.

Burns AM, Solch RJ, Dennis-Wall JC, Ukhanova M, Nieves C Jr, Mai V, Christman MC, Gordon DT, Langkamp-Henken B.

Nutr Res. 2018 Dec;60:33-42. doi: 10.1016/j.nutres.2018.09.007. Epub 2018 Sep 21.

PMID: 30527258

The Good That Viruses Do.

Mietzsch M, Agbandje-McKenna M.

Annu Rev Virol. 2017 Sep 29;4(1):iii-v. doi: 10.1146/annurev-vi-04-071217-100011. Review. No abstract available.

PMID: 28961414

Relative Pancreas Volume Is Reduced in First-Degree Relatives of Patients With Type 1 Diabetes.

Campbell-Thompson ML, Filipp SL, Grajo JR, Nambam B, Beegle R, Middlebrooks EH, Gurka MJ, Atkinson MA, Schatz DA, Haller MJ.

Diabetes Care. 2018 Dec 14. pii: dc181512. doi: 10.2337/dc18-1512. [Epub ahead of print]

PMID: 30552130

Lignin-based polymers and nanomaterials.

Grossman A, Vermerris W.

Curr Opin Biotechnol. 2018 Nov 17;56:112-120. doi: 10.1016/j.copbio.2018.10.009. [Epub ahead of print] Review.

PMID: 30458357

Effect of losartan and fish oil on plasma IL-6 and mobility in older persons. The ENRGISE Pilot randomized clinical trial.

Pahor M, Anton SD, Beavers DP, Cauley JA, Fielding RA, Kritchevsky SB, Leeuwenburgh C, Lewis KH, Liu CK, Lovato LC, Lu J, Manini TM, McDermott MM, Miller ME, Newman AB, Radziszewska B, Stowe CL, Tracy RP, Walkup MP, Wu SS, Ambrosius WT; ENRGISE study investigators.

J Gerontol A Biol Sci Med Sci. 2018 Dec 12. doi: 10.1093/gerona/gly277. [Epub ahead of print]

PMID: 30541065

Simultaneous quantification of cannabinoids tetrahydrocannabinol, cannabidiol and CB1 receptor antagonist in rat plasma: An application to characterize pharmacokinetics after passive cannabis smoke inhalation and co-administration of rimonabant.

Ravula A, Chandasana H, Setlow B, Febo M, Bruijnzeel AW, Derendorf H.

J Pharm Biomed Anal. 2018 Oct 25;160:119-125. doi: 10.1016/j.jpba.2018.07.004. Epub 2018 Jul 19.

PMID: 30077950

Thermoregulatory response of Brangus heifers to naturally occurring heat exposure on pasture.

Hamblen H, Hansen PJ, Zolini AM, Oltenacu PA, Mateescu RG.

J Anim Sci. 2018 Jul 28;96(8):3131-3137. doi: 10.1093/jas/sky224.

PMID: 29860271

Global Regulation by CsrA and Its RNA Antagonists.

Romeo T, Babitzke P.

Microbiol Spectr. 2018 Mar;6(2). doi: 10.1128/microbiolspec.RWR-0009-2017. Review.

PMID: 29573256

Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy.

Burns DT, Donkervoort S, Müller JS, Knierim E, Bharucha-Goebel D, Faqeih EA, Bell SK, AlFaifi AY, Monies D, Millan F, Retterer K, Dyack S, MacKay S, Morales-Gonzalez S, Giunta M, Munro B, Hudson G, Scavina M, Baker L, Massini TC, Lek M, Hu Y, Ezzo D, AlKuraya FS, Kang PB, Griffin H, Foley AR, Schuelke M, Horvath R, Bönnemann CG.

Am J Hum Genet. 2018 May 3;102(5):858-873. doi: 10.1016/j.ajhg.2018.03.011.

PMID: 29727687

Linking in vitro estrogenicity to adverse effects in the inland silverside (Menidia beryllina).

Mehinto AC, Kroll KJ, Jayasinghe BS, Lavelle CM, VanDervort D, Adeyemo OK, Bay SM, Maruya KA, Denslow ND.

Environ Toxicol Chem. 2018 Mar;37(3):884-892. doi: 10.1002/etc.4024. Epub 2018 Jan 16.

PMID: 29091346

Alpha 1 Antitrypsin Gene Therapy Extends the Lifespan of Lupus-Prone Mice.

Elshikha AS, Yuan Y, Lu Y, Chen MJ, Abboud G, Akbar MA, Plate H, Wolney H, Hoffmann T, Tagari E, Zeumer L, Morel L, Song S.

Mol Ther Methods Clin Dev. 2018 Oct 18;11:131-142. doi: 10.1016/j.omtm.2018.10.007. eCollection 2018 Dec 14.

PMID: 30547047

Low molecular weight glutenin subunit gene composition at Glu-D3 loci of Aegilops tauschii and common wheat and a further view of wheat evolution.

Shen L, Luo G, Song Y, Song S, Li Y, Yang W, Li X, Sun J, Liu D, Zhang A.

Theor Appl Genet. 2018 Dec;131(12):2745-2763. doi: 10.1007/s00122-018-3188-1. Epub 2018 Sep 17.

PMID: 30225644

The ferredoxin-like protein, FerR, regulates PrbP activity in Liberibacter asiaticus.

Pan L, da Silva D, Pagliai FA, Harrison NA, Gonzalez CF, Lorca GL.

Appl Environ Microbiol. 2018 Dec 14. pii: AEM.02605-18. doi: 10.1128/AEM.02605-18. [Epub ahead of print]

PMID: 30552192

Complete Sequence and Annotation of the Mycoplasma phocidae Strain 105T Genome.

Frasca S Jr, Kutish GF, Michaels DL, Brown DR.

Microbiol Resour Announc. 2018 Oct 11;7(14). pii: e01237-18. doi: 10.1128/MRA.01237-18. eCollection 2018 Oct.

PMID: 30533705

Genome-wide identification of direct RTA targets reveals key host factors for KSHV lytic reactivation.

Papp B, Motlagh N, Smindak RJ, Jang SJ, Sharma A, Alonso JD, Toth Z.

J Virol. 2018 Dec 12. pii: JVI.01978-18. doi: 10.1128/JVI.01978-18.

PMID: 30541837

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering.

Johnson MG, Pokorny L, Dodsworth S, Botigué LR, Cowan RS, Devault A, Eiserhardt WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis DE, Soltis PS, Ka-Shu Wong G, Baker WJ, Wickett NJ.

Syst Biol. 2018 Dec 10. doi: 10.1093/sysbio/syy086.

PMID: 30535394

Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella.

Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS.

Curr Opin Plant Biol. 2018 Apr;42:81-89. doi: 10.1016/j.pbi.2018.04.003. Epub 2018 Apr 27. Review.

PMID: 29694936

Elimination or more accurate estimation? Investigation of trends in malaria diagnoses in the Ouest Department of Haiti from 2008 to 2017.

Weppelmann TA, Stephenson CJ, Musih E, Dame JB, Remy MY, Nicolas R, von Fricken ME.

PLoS One. 2018 Jun 7;13(6):e0198070. doi: 10.1371/journal.pone.0198070. eCollection 2018.

PMID: 29879170

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa.

Eimanifar A, Kimball RT, Braun EL, Ellis JD.

Sci Rep. 2018 Jan 22;8(1):1333. doi: 10.1038/s41598-018-19759-3.

PMID: 29358597

Genome-wide association study identifies pharmacogenomic loci linked with specific antihypertensive drug treatment and new-onset diabetes.

Chang SW, McDonough CW, Gong Y, Johnson TA, Tsunoda T, Gamazon ER, Perera MA, Takahashi A, Tanaka T, Kubo M, Pepine CJ, Johnson JA, Cooper-DeHoff RM.

Pharmacogenomics J. 2018 Jan;18(1):106-112. doi: 10.1038/tpj.2016.67. Epub 2016 Sep 27.

PMID: 27670767

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.

Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM.

G3 (Bethesda). 2018 Aug 30;8(9):2923-2940. doi: 10.1534/g3.118.200373.

PMID: 30021829

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

Increasing phenological asynchrony between spring green-up and arrival of migratory birds.

Mayor SJ, Guralnick RP, Tingley MW, Otegui J, Withey JC, Elmendorf SC, Andrew ME, Leyk S, Pearse IS, Schneider DC.

Sci Rep. 2017 May 15;7(1):1902. doi: 10.1038/s41598-017-02045-z.

PMID: 28507323

Low molecular weight glutenin subunit gene composition at Glu-D3 loci of Aegilops tauschii and common wheat and a further view of wheat evolution.

Shen L, Luo G, Song Y, Song S, Li Y, Yang W, Li X, Sun J, Liu D, Zhang A.

Theor Appl Genet. 2018 Dec;131(12):2745-2763. doi: 10.1007/s00122-018-3188-1. Epub 2018 Sep 17.

PMID: 30225644

Mutant torsinA in the heterozygous DYT1 state compromises HSV propagation in infected neurons and fibroblasts.

György B, Cruz L, Yellen D, Aufiero M, Alland I, Zhang X, Ericsson M, Fraefel C, Li YC, Takeda S, Hyman BT, Breakefield XO.

Sci Rep. 2018 Feb 2;8(1):2324. doi: 10.1038/s41598-018-19865-2.

PMID: 29396398

In situ targeted MRI detection of Helicobacter pylori with stable magnetic graphitic nanocapsules.

Li Y, Hu X, Ding D, Zou Y, Xu Y, Wang X, Zhang Y, Chen L, Chen Z, Tan W.

Nat Commun. 2017 Jun 15;8:15653. doi: 10.1038/ncomms15653. Erratum in: Nat Commun. 2017 Aug 30;8:16154.

PMID: 28643777

Mouse Gamma Herpesvirus MHV-68 Induces Severe Gastrointestinal (GI) Dilatation in Interferon Gamma Receptor-Deficient Mice (IFNγR-/-) That Is Blocked by Interleukin-10.

Chen H, Bartee MY, Yaron JR, Liu L, Zhang L, Zheng D, Hogue IB, Bullard WL, Tibbetts S, Lucas AR.

Viruses. 2018 Sep 23;10(10). pii: E518. doi: 10.3390/v10100518.

PMID: 30249047

Single-cell RNAseq for the study of isoforms-how is that possible?

Arzalluz-Luque Á, Conesa A.

Genome Biol. 2018 Aug 10;19(1):110. doi: 10.1186/s13059-018-1496-z. Review.

PMID: 30097058

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.

Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM.

G3 (Bethesda). 2018 Aug 30;8(9):2923-2940. doi: 10.1534/g3.118.200373.

PMID: 30021829

All in the Family: Repeats and ALS/FTD.

Pattamatta A, Cleary JD, Ranum LPW.

Trends Neurosci. 2018 May;41(5):247-250. doi: 10.1016/j.tins.2018.03.010. Review.

PMID: 29703376

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering.

Syst Biol. 2018 Dec 10. doi: 10.1093/sysbio/syy086. [Epub ahead of print]

PMID: 30535394

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data.

Liu L, Wang Y, He P, Li P, Lee J, Soltis DE, Fu C.

BMC Genomics. 2018 Apr 4;19(1):235. doi: 10.1186/s12864-018-4633-x.

PMID: 29618324

Factors promoting polyploid persistence and diversification and limiting diploid speciation during the K-Pg interlude.

Levin DA, Soltis DE.

Curr Opin Plant Biol. 2018 Apr;42:1-7. doi: 10.1016/j.pbi.2017.09.010. Epub 2017 Oct 27. Review.

PMID: 29107221

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA.

Plant J. 2018 Feb;93(3):515-533. doi: 10.1111/tpj.13801.

PMID: 29237241

Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa.

You J, Sun L, Yang X, Pan X, Huang Z, Zhang X, Gong M, Fan Z, Li L, Cui X, Jing Z, Jin S, Rao Z, Wu W, Yang H.

Nat Commun. 2018 May 10;9(1):1846. doi: 10.1038/s41467-018-04232-6.

PMID: 29748556

Human iPSC Models to Study Orphan Diseases: Muscular Dystrophies.

Xia G, Terada N, Ashizawa T.

Curr Stem Cell Rep. 2018;4(4):299-309. doi: 10.1007/s40778-018-0145-5. Epub 2018 Oct 4. Review.

PMID: 30524939

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.

Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM.

G3 (Bethesda). 2018 Aug 30;8(9):2923-2940. doi: 10.1534/g3.118.200373.

PMID: 30021829

Wrist accelerometer shape feature derivation methods for assessing activities of daily living.

Kheirkhahan M, Chakraborty A, Wanigatunga AA, Corbett DB, Manini TM, Ranka S.

BMC Med Inform Decis Mak. 2018 Dec 12;18(Suppl 4):124. doi: 10.1186/s12911-018-0671-1.

PMID: 30537957

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments.

Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R.

BMC Bioinformatics. 2018 Oct 16;19(1):380. doi: 10.1186/s12859-018-2405-x.

PMID: 30326833

DNA-Based Dynamic Reaction Networks.

Fu T, Lyu Y, Liu H, Peng R, Zhang X, Ye M, Tan W.

Trends Biochem Sci. 2018 Jul;43(7):547-560. doi: 10.1016/j.tibs.2018.04.010. Epub 2018 May 21. Review.

PMID: 29793809

A Smart, Photocontrollable Drug Release Nanosystem for Multifunctional Synergistic Cancer Therapy.

Yi Y, Wang H, Wang X, Liu Q, Ye M, Tan W.

ACS Appl Mater Interfaces. 2017 Feb 22;9(7):5847-5854. doi: 10.1021/acsami.6b15414. Epub 2017 Feb 9.

PMID: 28124556

The CPLANE protein Intu protects kidneys from ischemia-reperfusion injury by targeting STAT1 for degradation.

Wang S, Liu A, Wu G, Ding HF, Huang S, Nahman S, Dong Z.

Nat Commun. 2018 Mar 26;9(1):1234. doi: 10.1038/s41467-018-03628-8.

PMID: 29581513

Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.).

Feng G, Xu L, Wang J, Nie G, Bushman BS, Xie W, Yan H, Yang Z, Guan H, Huang L, Zhang X.

BMC Genomics. 2018 Oct 3;19(1):727. doi: 10.1186/s12864-018-5104-0.

PMID: 30285619

Isotope niche dimension and trophic overlap between bigheaded carps and native filter-feeding fish in the lower Missouri River, USA.

Wang J, Chapman D, Xu J, Wang Y, Gu B.

PLoS One. 2018 May 21;13(5):e0197584. doi: 10.1371/journal.pone.0197584. eCollection 2018. Erratum in: PLoS One. 2018 Jun 22;13(6):e0199805.

PMID: 29782547

Multi-drug resistant Pseudomonas aeruginosa nosocomial strains: Molecular epidemiology and evolution.

Angeletti S, Cella E, Prosperi M, Spoto S, Fogolari M, De Florio L, Antonelli F, Dedej E, De Flora C, Ferraro E, Incalzi RA, Coppola R, Dicuonzo G, Francescato F, Pascarella S, Ciccozzi M.

Microb Pathog. 2018 Oct;123:233-241. doi: 10.1016/j.micpath.2018.07.020. Epub 2018 Jul 19.

PMID: 30031889

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

Projected clinical benefit of surveillance imaging for early detection and treatment of breast cancer metastases.

O’Dell W, Takita C, Casey-Sawicki K, Daily K, Heldermon CD, Okunieff P.

Breast J. 2018 Dec 12. doi: 10.1111/tbj.13153. [Epub ahead of print]

PMID: 30548515

Relative Pancreas Volume Is Reduced in First-Degree Relatives of Patients With Type 1 Diabetes.

Campbell-Thompson ML, Filipp SL, Grajo JR, Nambam B, Beegle R, Middlebrooks EH, Gurka MJ, Atkinson MA, Schatz DA, Haller MJ.

Diabetes Care. 2018 Dec 14. pii: dc181512. doi: 10.2337/dc18-1512. [Epub ahead of print]

PMID: 30552130

Transgenerational hypocortisolism and behavioral disruption are induced by the antidepressant fluoxetine in male zebrafish Danio rerio.

Vera-Chang MN, St-Jacques AD, Gagné R, Martyniuk CJ, Yauk CL, Moon TW, Trudeau VL.

Proc Natl Acad Sci U S A. 2018 Dec 10. pii: 201811695. doi: 10.1073/pnas.1811695115. [Epub ahead of print]

PMID: 30530669

Developmental neurotoxicity of maneb: Notochord defects, mitochondrial dysfunction and hypoactivity in zebrafish (Danio rerio) embryos and larvae.

Cao F, Souders CL 2nd, Li P, Pang S, Liang X, Qiu L, Martyniuk CJ.

Ecotoxicol Environ Saf. 2018 Dec 6;170:227-237. doi: 10.1016/j.ecoenv.2018.11.110. [Epub ahead of print]

PMID: 30529917

Environmentally relevant concentrations of carbamazepine induce liver histopathological changes and a gender-specific response in hepatic proteome of Chinese rare minnows (Gobiocypris rarus).

Yan S, Wang M, Liang X, Martyniuk CJ, Zha J, Wang Z.

Environ Pollut. 2018 Dec;243(Pt A):480-491. doi: 10.1016/j.envpol.2018.09.009. Epub 2018 Sep 5.

PMID: 30216880

The challenge of modulating β-cell autoimmunity in type 1 diabetes.

Atkinson MA, Roep BO, Posgai A, Wheeler DCS, Peakman M.

Lancet Diabetes Endocrinol. 2018 Oct 24. pii: S2213-8587(18)30112-8. doi: 10.1016/S2213-8587(18)30112-8. [Epub ahead of print] Review.

PMID: 30528099

Epidemiology of childhood-onset type 1 diabetes in Azerbaijan: Incidence, clinical features, biochemistry, and HLA-DRB1 status.

Ahmadov GA, Govender D, Atkinson MA, Sultanova RA, Eubova AA, Wasserfall CH, Mack SJ, Lane JA, Noble JA, Ogle GD.

Diabetes Res Clin Pract. 2018 Oct;144:252-259. doi: 10.1016/j.diabres.2018.09.009. Epub 2018 Sep 13.

PMID: 30218742

Mixing rates in weakly differentiated stocks of greater amberjack (Seriola dumerili) in the Gulf of Mexico.

Hargrove JS, Murie DJ, Parkyn DC, Saarinen EV, Austin JD.

Genetica. 2018 Oct;146(4-5):393-402. doi: 10.1007/s10709-018-0031-1. Epub 2018 Jul 25.

PMID: 30046930

Time to revisit warfarin pharmacogenetics.

Cavallari LH.

Future Cardiol. 2017 Nov;13(6):511-513. doi: 10.2217/fca-2017-0061. Epub 2017 Oct 2. Review. No abstract available.

PMID: 28967279