November 25, 2020

Micro & Immuno GOOD NEWS and Publications!

November 25, 2020

CONGRATULATIONS to Joel Swanson who was named a 2020 AAAS Fellow! VERY well deserved!

November 23, 2020

New Publications from M&I.  Congrats to all the authors!


Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron.

Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC.

Nat Microbiol. 2020 Sep;5(9):1170-1181. doi: 10.1038/s41564-020-0746-5. Epub 2020 Jun 29.

PMID: 32601452


The Early Evolution of Oral Poliovirus Vaccine Is Shaped by Strong Positive Selection and Tight Transmission Bottlenecks.

Valesano AL, Taniuchi M, Fitzsimmons WJ, Islam MO, Ahmed T, Zaman K, Haque R, Wong W, Famulare M, Lauring AS.

Cell Host Microbe. 2020 Nov 12:S1931-3128(20)30574-6. doi: 10.1016/j.chom.2020.10.011. Online ahead of print.

PMID: 33212020

Homologous Recombination in Clostridioides difficile Mediates Diversification of Cell Surface Features and Transport Systems.

Steinberg HD, Snitkin ES.

mSphere. 2020 Nov 18;5(6):e00799-20. doi: 10.1128/mSphere.00799-20.

PMID: 33208516

Hogwash: three methods for genome-wide association studies in bacteria.

Saund K, Snitkin ES.

Microb Genom. 2020 Nov 18. doi: 10.1099/mgen.0.000469. Online ahead of print.

PMID: 33206035


Gut Microbiota Predict Enterococcus Expansion but Not Vancomycin-Resistant Enterococcus Acquisition.

Chanderraj R, Brown CA, Hinkle K, Falkowski N, Ranjan P, Dickson RP, Woods RJ.

mSphere. 2020 Nov 18;5(6):e00537-20. doi: 10.1128/mSphere.00537-20.

PMID: 33208515


Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes.

Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL.

Proc Natl Acad Sci U S A. 2020 Sep 22;117(38):23835-23846. doi: 10.1073/pnas.2008615117. Epub 2020 Sep 8.



November 16, 2020

New Publications from M&I-Congrats to the authors!!!!


If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria.

Glowacki RWP, Martens EC.

J Bacteriol. 2020 Nov 9:JB.00481-20. doi: 10.1128/JB.00481-20. Online ahead of print.

PMID: 33168637 Review.


Humidity and Deposition Solution Play a Critical Role in Virus Inactivation by Heat Treatment of N95 Respirators.

Rockey N, Arts PJ, Li L, Harrison KR, Langenfeld K, Fitzsimmons WJ, Lauring AS, Love NG, Kaye KS, Raskin L, Roberts WW, Hegarty B, Wigginton KR.

mSphere. 2020 Oct 21;5(5):e00588-20. doi: 10.1128/mSphere.00588-20.

PMID: 33087516Free PMC article.

3. Treating exuberant, non-resolving inflammation in the lung; implications for acute respiratory distress syndrome and COVID-19.

Gilroy DW, De Maeyer RPH, Tepper M, O'Brien A, Uddin M, Chen J, Goldstein DR, Akbar AN.

Pharmacol Ther. 2020 Nov 11:107745. doi: 10.1016/j.pharmthera.2020.107745. Online ahead of print.

PMID: 33188794 Review.

4. The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe.

Barron MR, Cieza RJ, Hill DR, Huang S, Yadagiri VK, Spence JR, Young VB.

mSphere. 2020 Nov 11;5(6):e00777-20. doi: 10.1128/mSphere.00777-20.

PMID: 33177212

5. Myeloid interleukin-4 receptor α (IL4Rα) is essential in post-myocardial infarction healing by regulating inflammation and fibrotic remodeling.

Song J, Frieler RA, Whitesall SE, Chung Y, Vigil T, Muir LA, Ma J, Brombacher F, Goonewardena SN, Lumeng CN, Goldstein DR, Mortensen RM.

Am J Physiol Heart Circ Physiol. 2020 Nov 8. doi: 10.1152/ajpheart.00251.2020. Online ahead of print.

PMID: 33164548

6. Encapsulation of ovarian allograft precludes immune rejection and promotes restoration of endocrine function in immune-competent ovariectomized mice.

Day JR, David A, Barbosa MGM, Brunette MA, Cascalho M, Shikanov A.

Sci Rep. 2019 Nov 12;9(1):16614. doi: 10.1038/s41598-019-53075-8.

PMID: 31719632Free PMC article.

October 26, 2020

New publications from M&I—very exciting…look how many great papers came out this week!

HLA tapasin independence: broader peptide repertoire and HIV control.

Bashirova AA, Viard M, Naranbhai V, Grifoni A, Garcia-Beltran W, Akdag M, Yuki Y, Gao X, O'hUigin C, Raghavan M, Wolinsky S, Bream JH, Duggal P, Martinson J, Michael NL, Kirk GD, Buchbinder SP, Haas D, Goedert JJ, Deeks SG, Fellay J, Walker B, Goulder P, Cresswell P, Elliott T, Sette A, Carlson J, Carrington M.

Proc Natl Acad Sci U S A. 2020 Oct 23:202013554. doi: 10.1073/pnas.2013554117. Online ahead of print.

PMID: 33097667


Prolonged SARS-CoV-2 replication in an immunocompromised patient.

Baang JH, Smith C, Mirabelli C, Valesano AL, Manthei DM, Bachman M, Wobus CE, Adams M, Washer L, Martin ET, Lauring AS.

J Infect Dis. 2020 Oct 22:jiaa666. doi: 10.1093/infdis/jiaa666. Online ahead of print.

PMID: 33089317


The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice.

Tomkovich S, Stough JMA, Bishop L, Schloss PD.

mSphere. 2020 Oct 21;5(5):e00869-20. doi: 10.1128/mSphere.00869-20.

PMID: 33087520


Humidity and Deposition Solution Play a Critical Role in Virus Inactivation by Heat Treatment of N95 Respirators.

Rockey N, Arts PJ, Li L, Harrison KR, Langenfeld K, Fitzsimmons WJ, Lauring AS, Love NG, Kaye KS, Raskin L, Roberts WW, Hegarty B, Wigginton KR.

mSphere. 2020 Oct 21;5(5):e00588-20. doi: 10.1128/mSphere.00588-20.

PMID: 33087516


Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization.

Schnizlein MK, Vendrov KC, Edwards SJ, Martens EC, Young VB.

mSphere. 2020 Jan 8;5(1):e00708-19. doi: 10.1128/mSphere.00708-19.

PMID: 31915217Free PMC article.


The UDP-GalNAcA biosynthesis genes gna-gne2 are required to maintain cell envelope integrity and in vivo fitness in multi-drug resistant Acinetobacter baumannii.

Crépin S, Ottosen EN, Chandler CE, Sintsova A, Ernst RK, Mobley HLT.

Mol Microbiol. 2020 Jan;113(1):153-172. doi: 10.1111/mmi.14407. Epub 2019 Nov 19.

PMID: 31680352


Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'.

Tan JY, Wang S, Dick GJ, Young VB, Sherman DH, Burns MA, Lin XN.

Integr Biol (Camb). 2020 Oct 22:zyaa021. doi: 10.1093/intbio/zyaa021. Online ahead of print.

PMID: 33089329


Electronic DNA Analysis of CSF Cell-free Tumor DNA to Quantify Multi-gene Molecular Response in Pediatric High-grade Glioma.

Bruzek AK, Ravi K, Muruganand A, Wadden J, Babila CM, Cantor E, Tunkle L, Wierzbicki K, Stallard S, Dickson RP, Wolfe I, Mody R, Schwartz J, Franson A, Robertson PL, Muraszko KM, Maher CO, Garton HJL, Qin T, Koschmann C.

Clin Cancer Res. 2020 Oct 21. doi: 10.1158/1078-0432.CCR-20-2066. Online ahead of print.

PMID: 33087334


Making the case for causality: what role do lung microbiota play in idiopathic pulmonary fibrosis?

Dickson RP, Harari S, Kolb M.

Eur Respir J. 2020 Apr 3;55(4):2000318. doi: 10.1183/13993003.00318-2020. Print 2020 Apr.

PMID: 32245776 No abstract available.


Molecular Determinants of Substrate Selectivity of a Pneumococcal Rgg-Regulated Peptidase-Containing ABC Transporter.

Wang CY, Medlin JS, Nguyen DR, Disbennett WM, Dawid S.

mBio. 2020 Feb 11;11(1):e02502-19. doi: 10.1128/mBio.02502-19.

PMID: 32047125 Free PMC article.


October 12, 2020

New publications from M&I  Congrats all!Variations in MHC class I antigen presentation and immunopeptidome selection pathways.

Zaitoua AJ, Kaur A, Raghavan M.F1000Res. 2020 Sep 28;9:F1000 Faculty Rev-1177. doi: 10.12688/f1000research.26935.1. eCollection 2020.PMID: 33014341 Free PMC article. Review.


SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease.

Menon R, Otto EA, Sealfon R, Nair V, Wong AK, Theesfeld CL, Chen X, Wang Y, Boppana AS, Luo J, Yang Y, Kasson PM, Schaub JA, Berthier CC, Eddy S, Lienczewski CC, Godfrey B, Dagenais SL, Sohaney R, Hartman J, Fermin D, Subramanian L, Looker HC, Harder JL, Mariani LH, Hodgin JB, Sexton JZ, Wobus CE, Naik AS, Nelson RG, Troyanskaya OG, Kretzler M.Kidney Int. 2020 Oct 7:S0085-2538(20)31113-3. doi: 10.1016/j.kint.2020.09.015. Online ahead of print.PMID: 33038424


Functional characterization of the HMP-P synthase of Legionella pneumophila (Lpg1565).

Paxhia MD, Swanson MS, Downs DM.Mol Microbiol. 2020 Oct 8. doi: 10.1111/mmi.14622. Online ahead of print.PMID: 33034117


Dendritic cell-derived TGF-β mediates the induction of mucosal regulatory T-cell response to Helicobacter infection essential for maintenance of immune tolerance in mice.

Owyang SY, Zhang M, El-Zaatari M, Eaton KA, Bishu S, Hou G, Grasberger H, Kao JY.Helicobacter. 2020 Oct 6:e12763. doi: 10.1111/hel.12763. Online ahead of print.PMID: 33025641


Cellular Senescence: Friend or Foe to Respiratory Viral Infections?


October 6, 2020

New Publications for M&I:

Fusobacterium nucleatum infection correlates with two types of microsatellite alterations in colorectal cancer and triggers DNA damage.

Okita Y, Koi M, Takeda K, Ross R, Mukherjee B, Koeppe E, Stoffel EM, Galanko JA, McCoy AN, Keku TO, Okugawa Y, Kitajima T, Toiyama Y, Martens E, Carethers JM.

Gut Pathog. 2020 Sep 29;12:46. doi: 10.1186/s13099-020-00384-3. eCollection 2020.

PMID: 33005238Free PMC article.


Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production.

Cardoso RS, Tavares LA, Jesus BLS, Criado MF, de Carvalho AN, Souza JP, Bedi S, de Souza MM, Silva ML, Lanfredi GP, Vitti BC, Scudero OB, Faça VM, Ono A, Ventura AM, daSilva LLP, Arruda E.

mBio. 2020 Sep 29;11(5):e01869-20. doi: 10.1128/mBio.01869-20.

PMID: 32994321


Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis.

Skiba MA, Tran CL, Dan Q, Sikkema AP, Klaver Z, Gerwick WH, Sherman DH, Smith JL.

Structure. 2020 Jan 7;28(1):63-74.e4. doi: 10.1016/j.str.2019.11.004. Epub 2019 Nov 27.

PMID: 31785925

September 28, 2020

Congrats to the New OMIS leadership!  This is the M&I student leadership group and they have a lot of cool new ideas!  Stay tuned to watch them take over our social media!

President - Jaime Fuentes

Masters Student Liaison - Melissa Bush

Social Chairs - Sadie Gugel & Kyle Gontjes

PIBs Recruiting Chairs - Madison Fitzgerald & Lavinia Unverdorben

Student Invited Speaker Coordinator - Amanda Photenhauer

BGSG Representatives - Yolanda Rivera-Cuevas & Megan Procario 

Press Coordinator - Jen Baker

DEI Liaison - Austin Campbell

New papers from M&I!

Calreticulin enhances the secretory trafficking of a misfolded alpha-1-antitrypsin.

Mohan HM, Yang B, Dean NA, Raghavan M.

J Biol Chem. 2020 Sep 25:jbc.RA120.014372. doi: 10.1074/jbc.RA120.014372. Online ahead of print.

PMID: 32978262


Polysaccharide Capsules Equip the Human Symbiont Bacteroides thetaiotaomicron to Modulate Immune Responses to a Dominant Antigen in the Intestine.

Hsieh S, Porter NT, Donermeyer DL, Horvath S, Strout G, Saunders BT, Zhang N, Zinselmeyer B, Martens EC, Stappenbeck TS, Allen PM.

J Immunol. 2020 Feb 15;204(4):1035-1046. doi: 10.4049/jimmunol.1901206. Epub 2020 Jan 3.

PMID: 31900343


Structural analysis of the Legionella pneumophila Dot/Icm type IV secretion system core complex. Elife  2020 Sep 2;9:e59530. 
Clarissa L Durie, Michael J Sheedlo, Jeong Min Chung, Brenda G Byrne, Min Su, Thomas Knight, Michele Swanson, D Borden Lacy, Melanie D Ohi


September 22, 2020

New Publications:

Reengineering biocatalysts: Computational redesign of chondroitinase ABC improves efficacy and stability.

Hettiaratchi MH, O'Meara MJ, O'Meara TR, Pickering AJ, Letko-Khait N, Shoichet MS.

Sci Adv. 2020 Aug 19;6(34):eabc6378. doi: 10.1126/sciadv.abc6378. Print 2020 Aug.

PMID: 32937356


Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal.

Ding P, Kharytonchyk S, Waller A, Mbaekwe U, Basappa S, Kuo N, Frank HM, Quasney C, Kidane A, Swanson C, Van V, Sarkar M, Cannistraci E, Chaudhary R, Flores H, Telesnitsky A, Summers MF.

Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17737-17746. doi: 10.1073/pnas.2008519117. Epub 2020 Jul 9.

PMID: 32647061Free PMC article.


Blocking elevated p38 MAPK restores efferocytosis and inflammatory resolution in the elderly.

De Maeyer RPH, van de Merwe RC, Louie R, Bracken OV, Devine OP, Goldstein DR, Uddin M, Akbar AN, Gilroy DW.

Nat Immunol. 2020 Jun;21(6):615-625. doi: 10.1038/s41590-020-0646-0. Epub 2020 Apr 6.

PMID: 32251403


Studying Adipose Tissue in the Breast Tumor Microenvironment In Vitro: Progress and Opportunities.

Mertz D, Sentosa J, Luker G, Takayama S.

Tissue Eng Regen Med. 2020 Sep 16. doi: 10.1007/s13770-020-00299-9. Online ahead of print.

PMID: 32939672 Review.


Changes in the Association between Diagnostic Testing Method, PCR Ribotype, and Clinical Outcomes from Clostridioides difficile Infection: One Institution's Experience.

Menon A, Perry DA, Motyka J, Weiner S, Standke A, Penkevich A, Keidan M, Young VB, Rao K.

Clin Infect Dis. 2020 Sep 15:ciaa1395. doi: 10.1093/cid/ciaa1395. Online ahead of print.

PMID: 32930705


Parametric Response Mapping of FLAIR MRI Provides an Early Indication of Progression Risk in Glioblastoma.

Hoff BA, Lemasson B, Chenevert TL, Luker GD, Tsien CI, Amouzandeh G, Johnson TD, Ross BD.

Acad Radiol. 2020 Sep 11:S1076-6332(20)30496-7. doi: 10.1016/j.acra.2020.08.015. Online ahead of print.

PMID: 32928633


Fungal-derived brevianamide assembly by a stereoselective semipinacolase.

Ye Y, Du L, Zhang X, Newmister SA, McCauley M, Alegre-Requena JV, Zhang W, Mu S, Minami A, Fraley AE, Adrover-Castellano ML, Carney NA, Shende VV, Qi F, Oikawa H, Kato H, Tsukamoto S, Paton RS, Williams RM, Sherman DH, Li S.

Nat Catal. 2020 Jun;3(6):497-506. doi: 10.1038/s41929-020-0454-9. Epub 2020 May 18.

PMID: 32923978


DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.

Li T, Tripathi A, Yu F, Sherman DH, Rao A.

Bioinformatics. 2020 Feb 1;36(3):942-944. doi: 10.1093/bioinformatics/btz677.

PMID: 31504190


DEI read of the day:  Learn the difference between empathy, sympathy and pity in this short article:


Also, please find attached a list of wellness resources put together by a student in Pharmacology and the Black in Microbiology flyers for the programs that start next week!

September 14, 2020

New Publications from M&I  CONGRATS TO THE AUTHORS!!!!


Phosphorylation of Toxoplasma gondii Secreted Proteins during Acute and Chronic Stages of Infection.

Young JC, Broncel M, Teague H, Russell MRG, McGovern OL, Renshaw M, Frith D, Snijders AP, Collinson L, Carruthers VB, Ewald SE, Treeck M.

mSphere. 2020 Sep 9;5(5):e00792-20. doi: 10.1128/mSphere.00792-20.

PMID: 32907954


Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes.

Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL.

Proc Natl Acad Sci U S A. 2020 Sep 8:202008615. doi: 10.1073/pnas.2008615117. Online ahead of print.

PMID: 32900948


Accessing the academic influence of vascular surgeons within the National Institutes of Health iCite database.

Davis FM, Obi AT, Gallagher KA, Henke PK.

J Vasc Surg. 2020 May;71(5):1741-1748.e2. doi: 10.1016/j.jvs.2019.09.036. Epub 2019 Dec 9.

PMID: 31831311



DEI read of the day:  This this interesting perspective from a light-skinned Black woman and the types of things people have said to her not realizing she was Black:

September 9, 2020

New publications from M&I

The evolving role of the lung microbiome in pulmonary fibrosis.

Lipinski JH, Moore BB, O'Dwyer DN.

Am J Physiol Lung Cell Mol Physiol. 2020 Sep 2. doi: 10.1152/ajplung.00258.2020. Online ahead of print.

PMID: 32877221

Co-Clinical Imaging Resource Program (CIRP): Bridging the Translational Divide to Advance Precision Medicine.

Shoghi KI, Badea CT, Blocker SJ, Chenevert TL, Laforest R, Lewis MT, Luker GD, Manning HC, Marcus DS, Mowery YM, Pickup S, Richmond A, Ross BD, Vilgelm AE, Yankeelov TE, Zhou R.

Tomography. 2020 Sep;6(3):273-287. doi: 10.18383/j.tom.2020.00023.

PMID: 32879897Free PMC article.

Epigenetic regulation of the PGE2 pathway modulates macrophage phenotype in normal and pathologic wound repair.

Davis FM, Tsoi LC, Wasikowski R, denDekker A, Joshi A, Wilke C, Deng H, Wolf S, Obi A, Huang S, Billi AC, Robinson S, Lipinski J, Melvin WJ, Audu CO, Weidinger S, Kunkel SL, Smith A, Gudjonsson JE, Moore BB, Gallagher KA.

JCI Insight. 2020 Sep 3;5(17):138443. doi: 10.1172/jci.insight.138443.

PMID: 32879137

The importance of airway and lung microbiome in the critically ill.

Martin-Loeches I, Dickson R, Torres A, Hanberger H, Lipman J, Antonelli M, de Pascale G, Bozza F, Vincent JL, Murthy S, Bauer M, Marshall J, Cilloniz C, Bos LD.

Crit Care. 2020 Aug 31;24(1):537. doi: 10.1186/s13054-020-03219-4.

PMID: 32867808Free PMC article. Review.

Adipostatins E-J, New Potent Antimicrobials Identified as Inhibitors of Coenzyme-A Biosynthesis.

Gómez-Rodríguez L, Schultz PJ, Tamayo-Castillo G, Dotson GD, Sherman DH, Tripathi A.

Tetrahedron Lett. 2020 Jan 30;61(5):151469. doi: 10.1016/j.tetlet.2019.151469. Epub 2019 Dec 2.

PMID: 32863451

Response to COVID-19 phenotyping correspondence.

Bos LDJ, Sinha P, Dickson RP.

Eur Respir J. 2020 Aug 27;56(2):2002756. doi: 10.1183/13993003.02756-2020. Print 2020 Aug.

PMID: 32747393Free PMC article.


DEI Resource of the Day:  Time magazine and Zoom have teamed up to provide a series of episodes about race in the workplace.  Episode 3 has been specifically recommended for thinking about strategies for recruiting and hiring professionals of color, but all of the content is worth checking out and 6 more episodes are coming.  See here:

August 31, 2020

M&I Publications

A deliberate path toward diversity, equity, and inclusion within the ASCI.

Ware LB, Collins KL, Hawley JB, Ahima RS.

J Clin Invest. 2020 Aug 24:142423. doi: 10.1172/JCI142423. Online ahead of print.

PMID: 32831295 No abstract available.

Ten simple rules to increase computational skills among biologists with Code Clubs.

Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough JMA, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD.

PLoS Comput Biol. 2020 Aug 27;16(8):e1008119. doi: 10.1371/journal.pcbi.1008119. eCollection 2020 Aug.

PMID: 32853198 No abstract available.

Rethinking Gain-of-Function Experiments in the Context of the COVID-19 Pandemic.

Imperiale MJ, Casadevall A.

mBio. 2020 Aug 7;11(4):e01868-20. doi: 10.1128/mBio.01868-20.

PMID: 32769091Free PMC article.

Norovirus infection causes acute self-resolving diarrhea in wild-type neonatal mice.

Roth AN, Helm EW, Mirabelli C, Kirsche E, Smith JC, Eurell LB, Ghosh S, Altan-Bonnet N, Wobus CE, Karst SM.

Nat Commun. 2020 Jun 11;11(1):2968. doi: 10.1038/s41467-020-16798-1.

PMID: 32528015Free PMC article.

August 26, 2020

New papers from M&I now in print:

Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts.

 Valesano AL, Fitzsimmons WJ, McCrone JT, Petrie JG, Monto AS, Martin ET, Lauring AS.

J Virol. 2020 Feb 14;94(5):e01710-19. doi: 10.1128/JVI.01710-19. Print 2020 Feb 14.

PMID: 31801858Free PMC article.

Turning the Lungs Inside Out: The Intersecting Microbiomes of the Lungs and the Built Environment.

Combs MP, Dickson RP.

Am J Respir Crit Care Med. 2020 Aug 21. doi: 10.1164/rccm.202007-2973ED. Online ahead of print.

PMID: 32822203 No abstract available.

PGE2 accounts for bidirectional changes in alveolar macrophage self-renewal with aging and smoking.

Penke LR, Speth JM, Draijer C, Zaslona Z, Chen J, Mancuso P, Freeman CM, Curtis JL, Goldstein DR, Peters-Golden M.

Life Sci Alliance. 2020 Aug 20;3(11):e202000800. doi: 10.26508/lsa.202000800. Print 2020 Nov.

PMID: 32820026

Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice.

Ashley SL, Sjoding MW, Popova AP, Cui TX, Hoostal MJ, Schmidt TM, Branton WR, Dieterle MG, Falkowski NR, Baker JM, Hinkle KJ, Konopka KE, Erb-Downward JR, Huffnagle GB, Dickson RP.

Sci Transl Med. 2020 Aug 12;12(556):eaau9959. doi: 10.1126/scitranslmed.aau9959.

PMID: 32801143


DEI Read of the Day: The book “Caste: The Origins of Our Discontents” by Isabel Wilkerson has been highly recommended by several people…one calling it “mandatory reading for every human on the planet” and suggesting we never turn away from the past as we reach for the future.  A review can be found here:

Save the date:The virtual DEI Summit Community Assembly and Discussion will take place on Monday, October 26, 2020, 10-11:30 a.m. A Save the Date reminder, and a formal invitation will follow in the weeks ahead.

The DEI Summit Community Assembly and Discussion will feature a TEDx format, with presenters sharing how they use the arts as a vehicle for social change, interspersed with selections from crowdsourced creative works or performances. This will be followed by a roundtable discussion and Q&A featuring social media and chat activity

August 21, 2020

NEW GRANTS:  Congrats to Vince Young who is co-PI on a new NSF grant entitled: MTM 2: Combining structural informatics and crosslinking mass spectrometry to predict the key protein-protein interactions shaping symbiotic microbial communities.  Great to see NSF funding coming in..congrats!  Also great news for Eric Martens who is part of a new PO1 grant related to Graft vs. Host Disease that was just awarded!

DEI read of the day:

Working from Home While Black
by Laura Morgan Roberts and
Courtney L. McCluney
Roberts and McCluney (both U-M alums) share the unique challenges Black workers face in navigating remote work environments, as well as three recommendations for inclusive practices as we continue to work from home.

August 17, 2020


Good-bye to Robert Glowacki:  Please be sure to say good-bye to Dr. Robert Glowacki if you see him before end of August when he will leave us after his time in the Martens lab to take a post-doctoral fellowship with Dr. Phillip Ahern at Cleveland Clinic.  Good luck Robert!  Note that he just got a nice article published in time to leave (see second paper below).

Congrats to Irina Grigorova and collaborator Duxin Sun for their new RO1 “Virus-Like Nanoparticles for Non-Capsid Antigen Delivery with Virus Structure/Functional Mimicry to Activate B Cell Immunity”

Cheong-Hee Chang also recently received an RO1 titled: “Regulation of Metabolic Pathways in NKT Cells”.  Both of these awards were mentioned in the Rogel Cancer Center news recently!

Publications from M&I:

The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model.

Frick-Cheng AE, Sintsova A, Smith SN, Krauthammer M, Eaton KA, Mobley HLT.

mBio. 2020 Aug 11;11(4):e01412-20. doi: 10.1128/mBio.01412-20.

PMID: 32788379

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown.

Crouch LI, Liberato MV, Urbanowicz PA, Baslé A, Lamb CA, Stewart CJ, Cooke K, Doona M, Needham S, Brady RR, Berrington JE, Madunic K, Wuhrer M, Chater P, Pearson JP, Glowacki R, Martens EC, Zhang F, Linhardt RJ, Spencer DIR, Bolam DN.

Nat Commun. 2020 Aug 11;11(1):4017. doi: 10.1038/s41467-020-17847-5.

PMID: 32782292

MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation.

Jiang W, Ubhayasekera W, Breed MC, Norsworthy AN, Serr N, Mobley HLT, Pearson MM, Knight SD.

PLoS Pathog. 2020 Aug 11;16(8):e1008707. doi: 10.1371/journal.ppat.1008707. Online ahead of print.

PMID: 32780778

Rethinking Gain-of-Function Experiments in the Context of the COVID-19 Pandemic.

Imperiale MJ, Casadevall A.

mBio. 2020 Aug 7;11(4):e01868-20. doi: 10.1128/mBio.01868-20.

PMID: 32769091

IL-10 Impairs Local Immune Response in Lung Granulomas and Lymph Nodes during Early Mycobacterium tuberculosis Infection.

Wong EA, Evans S, Kraus CR, Engelman KD, Maiello P, Flores WJ, Cadena AM, Klein E, Thomas K, White AG, Causgrove C, Stein B, Tomko J, Mattila JT, Gideon H, Lin PL, Reimann KA, Kirschner DE, Flynn JL.

J Immunol. 2020 Feb 1;204(3):644-659. doi: 10.4049/jimmunol.1901211. Epub 2019 Dec 20.

PMID: 31862711

Self-Antigens Displayed on Liposomal Nanoparticles above a Threshold of Epitope Density Elicit Class-Switched Autoreactive Antibodies Independent of T Cell Help.

Chen Z, Wholey WY, Hassani Najafabadi A, Moon JJ, Grigorova I, Chackerian B, Cheng W.

J Immunol. 2020 Jan 15;204(2):335-347. doi: 10.4049/jimmunol.1801677. Epub 2019 Dec 13.

PMID: 31836655

Age-associated arterial calcification: the current pursuit of aggravating and mitigating factors.

Chakrabarti A, Goldstein DR, Sutton NR.

Curr Opin Lipidol. 2020 Aug 6. doi: 10.1097/MOL.0000000000000703. Online ahead of print.

PMID: 32773466

August 11, 2020

Congrats to Arwen Frick-Cheng on her new publication in the Mobley lab…which provides transcriptomic profiling of E. coli in both the mouse model and humans and as Harry says…validates a 30 year old animal model of UTI!  Congrats Arwen.  Read it here:  Frick-Cheng AE, Sintsova A, Smith SN, Krauthammer M, Eaton KA, Mobley HLT. 2020. The gene expression profile of uropathogenic Escherichia coli in women with uncomplicated urinary tract infections is recapitulated in the mouse model. mBio 11:e01412-20.

New papers from M&I:

The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis.

Kitamoto S, Nagao-Kitamoto H, Jiao Y, Gillilland MG 3rd, Hayashi A, Imai J, Sugihara K, Miyoshi M, Brazil JC, Kuffa P, Hill BD, Rizvi SM, Wen F, Bishu S, Inohara N, Eaton KA, Nusrat A, Lei YL, Giannobile WV, Kamada N.

Cell. 2020 Jul 23;182(2):447-462.e14. doi: 10.1016/j.cell.2020.05.048. Epub 2020 Jun 16.

PMID: 32758418


Rendezvous at Plasma Membrane: Cellular Lipids and tRNA Set up Sites of HIV-1 Particle Assembly and Incorporation of Host Transmembrane Proteins.

Thornhill D, Murakami T, Ono A.

Viruses. 2020 Jul 31;12(8):E842. doi: 10.3390/v12080842.

PMID: 32752131 Review.


Response to "COVID-19 conundrum: Clinical phenotyping based on pathophysiology as a promising approach to guide therapy in a novel illness" and "Strengthening the foundation of the house of CARDS by phenotyping on the fly" and "COVID-19 phenotypes: leading or misleading?".

Bos LDJ, Sinha P, Dickson RP.

Eur Respir J. 2020 Aug 3:2002756. doi: 10.1183/13993003.02756-2020. Online ahead of print.

PMID: 32747393Free PMC article.


The perils of premature phenotyping in COVID-19: a call for caution.

Bos LDJ, Sinha P, Dickson RP.

Eur Respir J. 2020 Jul 23;56(1):2001768. doi: 10.1183/13993003.01768-2020. Print 2020 Jul.

PMID: 32482788Free PMC article.


DEI read for the day:  Here is a “passing the torch” message regarding carrying on  the legacy of John Lewis.

If you missed President Obama’s eulogy you can find that here:

August 4, 2020

Congratulations to Sukhmani Kaur Bedi on being named the Mac Neal Dissertation award winner for 2020!

Congratulations to Eli Olson (Raghavan lab) and Emily Yarosz (Chang lab) for being named Miller Fund awardees for the Graduate Program in Immunology for 2020!

New publications for M&I:

Vpr Is a VIP: HIV Vpr and Infected Macrophages Promote Viral Pathogenesis.

Lubow J, Collins KL.

Viruses. 2020 Jul 27;12(8):E809. doi: 10.3390/v12080809.

PMID: 32726944 Review.


Methods in Lung Microbiome Research.

Carney SM, Clemente JC, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan TD, Molyneaux PL, Moore BB, O'Dwyer DN, Segal LN, Garantziotis S.

Am J Respir Cell Mol Biol. 2020 Mar;62(3):283-299. doi: 10.1165/rcmb.2019-0273TR.

PMID: 31661299 Review.


A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination.

Wessler T, Joslyn LR, Borish HJ, Gideon HP, Flynn JL, Kirschner DE, Linderman JJ.

PLoS Comput Biol. 2020 May 20;16(5):e1007280. doi: 10.1371/journal.pcbi.1007280. eCollection 2020 May.

PMID: 32433646Free PMC article.

July 28, 2020

New publications from M&I:


Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota.

Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG 3rd, Kuffa P, Goto Y, Jenq RR, Ishii C, Hirayama A, Seekatz AM, Martens EC, Eaton KA, Kao JY, Fukuda S, Higgins PDR, Karlsson NG, Young VB, Kamada N.

Nat Med. 2020 Apr;26(4):608-617. doi: 10.1038/s41591-020-0764-0. Epub 2020 Feb 17.

PMID: 32066975


B and Th cell response to Ag in vivo: Implications for vaccine development and diseases.

Kennedy RB, Grigorova I.

Immunol Rev. 2020 Jul;296(1):5-8. doi: 10.1111/imr.12899.

PMID: 32683786 No abstract available.


Virion-incorporated PSGL-1 and CD43 inhibit both cell-free infection and transinfection of HIV-1 by preventing virus-cell binding.

Murakami T, Carmona N, Ono A.

Proc Natl Acad Sci U S A. 2020 Apr 7;117(14):8055-8063. doi: 10.1073/pnas.1916055117. Epub 2020 Mar 19.

PMID: 32193343


Mcubed Program Winds Down


After funding nearly 800 interdisciplinary projects across U-M's three campuses, the Mcubed program is closing. The website, including the Mcubed Communities platform, went offline on July 19.


Mcube's closing does not affect current project end dates, and teams may continue to spend down project funds as planned. Program operations have been transferred to OVPR, which will see active projects through to close-out.


For questions, no-cost time extension requests, or other support, please contact



DEI read for the day:  With rotations starting again soon and new students arriving, here is an opinion piece from Science that is a good reminder for us all.  Beware the imbalance of power in lab hierarchies and choose your language carefully:

July 20, 2020

New Publications from M&I

B and Th cell response to Ag in vivo: Implications for vaccine development and diseases.

Kennedy RB, Grigorova I.

Immunol Rev. 2020 Jul;296(1):5-8. doi: 10.1111/imr.12899. No abstract available.

PMID: 32683786 [PubMed - as supplied by publisher]

Predicting the second wave of COVID-19 in Washtenaw County, MI.

Renardy M, Kirschner DE.

medRxiv. 2020 Jul 7. pii: 2020.07.06.20147223. doi: 10.1101/2020.07.06.20147223.

PMID: 32676613 [PubMed] Free PMC Article

Predicting the second wave of COVID-19 in Washtenaw County, MI.

Renardy M, Kirschner DE.

medRxiv. 2020 Jul 7. pii: 2020.07.06.20147223. doi: 10.1101/2020.07.06.20147223.

PMID: 32676613 [PubMed] Free PMC Article

The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon.

Grau KR, Zhu S, Peterson ST, Helm EW, Philip D, Phillips M, Hernandez A, Turula H, Frasse P, Graziano VR, Wilen CB, Wobus CE, Baldridge MT, Karst SM.

Nat Microbiol. 2020 Jan;5(1):84-92. doi: 10.1038/s41564-019-0602-7. Epub 2019 Nov 25.

Dietary L-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut.

Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, Sugihara K, Himpsl SD, Bazzi M, Miyoshi M, Nishioka T, Hayashi A, Morhardt TL, Kuffa P, Grasberger H, El-Zaatari M, Bishu S, Ishii C, Hirayama A, Eaton KA, Dogan B, Simpson KW, Inohara N, Mobley HLT, Kao JY, Fukuda S, Barnich N, Kamada N.

Nat Microbiol. 2020 Jan;5(1):116-125. doi: 10.1038/s41564-019-0591-6. Epub 2019 Nov 4.

PMID: 31686025 [PubMed - indexed for MEDLINE] Free PMC Article

Targeting disseminated estrogen-receptor-positive breast cancer cells in bone marrow.

Buschhaus JM, Humphries BA, Eckley SS, Robison TH, Cutter AC, Rajendran S, Haley HR, Bevoor AS, Luker KE, Luker GD.

Oncogene. 2020 Jul 16. doi: 10.1038/s41388-020-01391-z. [Epub ahead of print]

PMID: 32678295 [PubMed - as supplied by publisher]

Palmitate-TLR4 signaling regulates the histone demethylase, JMJD3, in macrophages and impairs diabetic wound healing.

Davis FM, denDekker A, Joshi AD, Wolf SJ, Audu C, Melvin WJ, Mangum K, Riordan MO, Kunkel SL, Gallagher KA.

Eur J Immunol. 2020 Jul 14. doi: 10.1002/eji.202048651. [Epub ahead of print]

PMID: 32662520 [PubMed - as supplied by publisher]

Role of Aging and the Immune Response to Respiratory Viral Infections: Potential Implications for COVID-19.

Chen J, Kelley WJ, Goldstein DR.

J Immunol. 2020 Jul 15;205(2):313-320. doi: 10.4049/jimmunol.2000380. Epub 2020 Jun 3. Review.

PMID: 32493812 [PubMed - indexed for MEDLINE]

The emergence of microbiome centres.

Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL.

Nat Microbiol. 2020 Jan;5(1):2-3. doi: 10.1038/s41564-019-0644-x. No abstract available.

PMID: 31857734 [PubMed - indexed for MEDLINE] Free Article

July 17, 2020

Our own Kathy Collins who is the new MSTP director was approved by the Regents as the new Associate Dean for Physician Scientist Education and Training.  Kathy now holds 3 major leadership roles…Editor in Chief of JCI Insight, MSTP Director and now an Associate Dean role….impressive indeed!  Congrats Kathy!  You are a terrific choice and we are excited to call you one of us!

July 13, 2020

Congrats to Cheong-Hee Chang’s lab on a new R01 that started this month!

Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.

Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL.

Cell Host Microbe. 2020 Jul 8. pii: S1931-3128(20)30352-8. doi: 10.1016/j.chom.2020.06.011. [Epub ahead of print]

Tocilizumab for treatment of mechanically ventilated patients with COVID-19.

Somers EC, Eschenauer GA, Troost JP, Golob JL, Gandhi TN, Wang L, Zhou N, Petty LA, Baang JH, Dillman NO, Frame D, Gregg KS, Kaul DR, Nagel J, Patel TS, Zhou S, Lauring AS, Hanauer DA, Martin E, Sharma P, Fung CM, Pogue JM.

Clin Infect Dis. 2020 Jul 11. pii: ciaa954. doi: 10.1093/cid/ciaa954. [Epub ahead of print]

Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal.

Ding P, Kharytonchyk S, Waller A, Mbaekwe U, Basappa S, Kuo N, Frank HM, Quasney C, Kidane A, Swanson C, Van V, Sarkar M, Cannistraci E, Chaudhary R, Flores H, Telesnitsky A, Summers MF.

Proc Natl Acad Sci U S A. 2020 Jul 9. pii: 202008519. doi: 10.1073/pnas.2008519117. [Epub ahead of print]

Alveolar macrophage-derived extracellular vesicles inhibit endosomal fusion of influenza virus.

Schneider DJ, Smith KA, Latuszek CE, Wilke CA, Lyons DM, Penke LR, Speth JM, Marthi M, Swanson JA, Moore BB, Lauring AS, Peters-Golden M.

EMBO J. 2020 Jul 9:e105057. doi: 10.15252/embj.2020105057. [Epub ahead of print]

Recurring Themes.

Imperiale MJ.

mSphere. 2020 Jul 8;5(4). pii: e00633-20. doi: 10.1128/mSphere.00633-20. No abstract available.

Cohorting KPC+ <i>Klebsiella pneumoniae</i> (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH).

Hawken SE, Hayden MK, Lolans K, Yelin RD, Weinstein RA, Lin MY, Snitkin ES.

Infect Control Hosp Epidemiol. 2020 Jun 23:1-7. doi: 10.1017/ice.2020.261. [Epub ahead of print]

In sickness and health: Effects of gut microbial metabolites on human physiology.

Glowacki RWP, Martens EC.

PLoS Pathog. 2020 Apr 9;16(4):e1008370. doi: 10.1371/journal.ppat.1008370. eCollection 2020 Apr. No abstract available.

CD300lf is the primary physiologic receptor of murine norovirus but not human norovirus.

Graziano VR, Walker FC, Kennedy EA, Wei J, Ettayebi K, Strine MS, Filler RB, Hassan E, Hsieh LL, Kim AS, Kolawole AO, Wobus CE, Lindesmith LC, Baric RS, Estes MK, Orchard RC, Baldridge MT, Wilen CB.

PLoS Pathog. 2020 Apr 6;16(4):e1008242. doi: 10.1371/journal.ppat.1008242. eCollection 2020 Apr.

Clinical xenotransplantation of the heart: At the watershed.

Platt JL, Piedrahita JA, Cascalho M.

J Heart Lung Transplant. 2020 Jun 20. pii: S1053-2498(20)31603-X. doi: 10.1016/j.healun.2020.06.002. [Epub ahead of print] No abstract available.

Inhibition of human adenovirus replication by the importin α/β1 nuclear import inhibitor ivermectin.

King CR, Tessier TM, Dodge MJ, Weinberg JB, Mymryk JS.

J Virol. 2020 Jul 8. pii: JVI.00710-20. doi: 10.1128/JVI.00710-20. [Epub ahead of print]

July 9, 2020

Congratulations to Evan Snitkin!  Evan just heard from NIH that his R01 application was selected for funding!  Way to go Evan!

Alumni update:  Clement Ndongmo, who got his PhD for work in Alice Telesnitsky’s lab (as a visiting student from the University of Oslo) is now  CDC Cameroon Associate Director for Program and Science and handling the COVID response in Cameroon!

New publications involving M&I out in Pubmed this week:

Polymorphisms of HLA-B: influences on assembly and immunity.

Olson E, Geng J, Raghavan M.

Curr Opin Immunol. 2020 Jun 30;64:137-145. doi: 10.1016/j.coi.2020.05.008. [Epub ahead of print] Review.


Hospital Associated Respiratory Virus Infection in Children and Adults: It Does Not Just Occur During Cold and Flu Season.

Petrie JG, Lauring AS, Martin ET, Kaye KS.

Open Forum Infect Dis. 2020 May 26;7(6):ofaa200. doi: 10.1093/ofid/ofaa200. eCollection 2020 Jun.


Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron.

Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC.

Nat Microbiol. 2020 Jun 29. doi: 10.1038/s41564-020-0746-5. [Epub ahead of print]


Influenza Vaccine Effectiveness in the Inpatient Setting: Evaluation of Potential Bias in the Test-Negative Design by Use of Alternate Control Groups.

Segaloff HE, Cheng B, Miller AV, Petrie JG, Malosh RE, Cheng C, Lauring AS, Lamerato LE, Ferdinands JM, Monto AS, Martin ET.

Am J Epidemiol. 2020 Mar 2;189(3):250-260. doi: 10.1093/aje/kwz248.

July 2, 2020

New Publications for M&I

Congrats to Eli, Jie and Malini for their article in Current Opinion in Immunology on Polymorphisms of HLA-B and influences on assembly and immunity!  See the article here:


CD300LF polymorphisms of inbred mouse strains confer resistance to murine norovirus infection in a cell type-dependent manner.

Furlong K, Biering SB, Choi J, Wilen CB, Orchard RC, Wobus CE, Nelson CA, Fremont DH, Baldridge MT, Randall G, Hwang S.

J Virol. 2020 Jun 24. pii: JVI.00837-20. doi: 10.1128/JVI.00837-20. [Epub ahead of print]


Cancer Cell Invasion of Mammary Organoids with Basal-In Phenotype.

Parigoris E, Lee S, Mertz D, Turner M, Liu AY, Sentosa J, Djomehri S, Chang HC, Luker K, Luker G, Kleer CG, Takayama S.

Adv Healthc Mater. 2020 Jun 25:e2000810. doi: 10.1002/adhm.202000810. [Epub ahead of print]

June 26, 2020

Suzy Dawid elected to Advisory Committee on Appointments, Promotions and Tenure (ACAPT). Congratulations Suzy!

June 23, 2020

UM Post-Doctoral Association (UMPDA) Election Results:  We are very excited to announce that M&I continues the strong history of service to the UMPDA.  Arianna Miles-Jay from the Snitkin lab was just elected as the new DEI chair of the UMPDA Board.  Our close colleague, Caity Holmes (Bachman Lab) was elected as the new Co-President of the UMPDA.  Congratulations to Arianna and Caity.  I share Arianna’s personal statement for the role below.  This carries on the long tradition of M&I involvement including Lisa Abernathy-Close (Networking Co-chair from 2018-2020), Will Close (Postdoctoral Affairs chair 2018-2019), and Jay Vornhagen (Co-President 2017-2018, Treasurer, 2019). Thank you to our active and engaged post-docs!



Arianna UMPDA DEI candidate statement

New Publications from M&I:

Orally Bioavailable Endochin-like Quinolone Carbonate Ester Prodrug Reduces <i>Toxoplasma gondii</i> Brain Cysts.

Doggett JS, Schultz T, Miller AJ, Bruzual I, Pou S, Winter R, Dodean R, Zakharov LN, Nilsen A, Riscoe MK, Carruthers VB.

Antimicrob Agents Chemother. 2020 Jun 15. pii: AAC.00535-20. doi: 10.1128/AAC.00535-20. [Epub ahead of print]


HIV-1 spliced RNAs display transcription start site bias.

Esquiaqui JM, Kharytonchyk S, Drucker D, Telesnitsky A.

RNA. 2020 Jun;26(6):708-714. doi: 10.1261/rna.073650.119. Epub 2020 Mar 23.


Effects of tumor necrosis factor on viral replication and pulmonary inflammation during acute mouse adenovirus type 1 respiratory infection.

Pant K, Chandrasekaran A, Chang CJ, Vageesh A, Popkov AJ, Weinberg JB.

Virology. 2020 Aug;547:12-19. doi: 10.1016/j.virol.2020.05.004. Epub 2020 May 23.


Exploring the molecular basis for selective C-H functionalization in plant P450s.

Espinoza RV, Sherman DH.

Synth Syst Biotechnol. 2020 Jun 9;5(2):97-98. doi: 10.1016/j.synbio.2020.05.001. eCollection 2020 Jun. No abstract available.

June 18, 2020

Congratulations to Denise Kirschner!  The department was notified today of an award from the Gates Foundation to Denise’ lab to use her modeling approach to optimize tuberculosis drugs.  This is great news!  Important work on another important problem in our world! 

New M&I Publications!

A Framework for Network-Based Epidemiological Modeling of Tuberculosis Dynamics Using Synthetic Datasets.

Renardy M, Kirschner DE.

Norovirus infection causes acute self-resolving diarrhea in wild-type neonatal mice.

Roth AN, Helm EW, Mirabelli C, Kirsche E, Smith JC, Eurell LB, Ghosh S, Altan-Bonnet N, Wobus CE, Karst SM.

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.

Topçuoğlu BD, Lesniak NA, Ruffin MT 4th, Wiens J, Schloss PD.

Within-Host Viral Diversity: A Window into Viral Evolution.

Lauring AS.

Host glycan utilization within the Bacteroidetes Sus-like paradigm.

Brown HA, Koropatkin NM.

Infectious Norovirus Is Chronically Shed by Immunocompromised Pediatric Hosts.

Davis A, Cortez V, Grodzki M, Dallas R, Ferrolino J, Freiden P, Maron G, Hakim H, Hayden RT, Tang L, Huys A, Kolawole AO, Wobus CE, Jones MK, Karst SM, Schultz-Cherry S.

Viruses. 2020 Jun 5;12(6). pii: E619. doi: 10.3390/v12060619.

June 12, 2020

Congrats to Phil King who just learned that his A0 competitive renewal for his lymphatic R01 scored in the 7th percentile.  That is well below the NHBLI 16th percentile payline!  CONGRATS PHIL! 

June 10, 2020


Good bye and good luck to Dr. Shawn Hawken from Evan Snitkin’s lab.  Shawn is leaving June 20th for North Carolina where she will be in a 2 year Clinical and Public Health Microbiology fellowship at UNC hospitals.  Best of luck to you Shawn and good luck getting your final paper from here submitted asap!

June 8, 2020

Happy 60th Birthday to Brenda Franklin!  Our hero!


Congrats to Elissa Hult in Beth Moore’s lab who won the People’s Choice poster award in the Molecular and Integrative Physiology virtual meeting!

New publications from M&I faculty labs available in Pub Med this week:

A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo.

Covés-Datson EM, King SR, Legendre M, Gupta A, Chan SM, Gitlin E, Kulkarni VV, Pantaleón García J, Smee DF, Lipka E, Evans SE, Tarbet EB, Ono A, Markovitz DM.

Proc Natl Acad Sci U S A. 2020 Jan 28;117(4):2122-2132. doi: 10.1073/pnas.1915152117. Epub 2020 Jan 13.

The oxidative fumarase FumC is a key contributor for E. coli fitness under iron-limitation and during UTI.

Himpsl SD, Shea AE, Zora J, Stocki JA, Foreman D, Alteri CJ, Mobley HLT.

PLoS Pathog. 2020 Feb 27;16(2):e1008382. doi: 10.1371/journal.ppat.1008382. eCollection 2020 Feb.

Gut microbiota features on nursing home admission are associated with subsequent acquisition of antibiotic resistant organism colonization.

Wang J, Cassone M, Gibson K, Lansing B, Mody L, Snitkin ES, Rao K.

Clin Infect Dis. 2020 Jun 1. pii: ciaa662. doi: 10.1093/cid/ciaa662. [Epub ahead of print]

Systems biology of host-Candida interactions: understanding how we shape each other.

Hodgins-Davis A, O'Meara TR.

Curr Opin Microbiol. 2020 May 30;58:1-7. doi: 10.1016/j.mib.2020.04.001. [Epub ahead of print] Review.

MRSA transmission in ICUs: Genomic analysis of patients, their environments and healthcare workers.

Popovich KJ, Green SJ, Okamoto K, Rhee Y, Hayden MK, Schoeny M, Snitkin ES, Weinstein RA.

Clin Infect Dis. 2020 Jun 6. pii: ciaa731. doi: 10.1093/cid/ciaa731. [Epub ahead of print]

A synthesis of bacterial and archaeal phenotypic trait data.

Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA, Westoby M.

Sci Data. 2020 Jun 5;7(1):170. doi: 10.1038/s41597-020-0497-4.

Enhanced mitochondrial fission suppresses signaling and metastasis in triple-negative breast cancer.

Humphries BA, Cutter AC, Buschhaus JM, Chen YC, Qyli T, Palagama DSW, Eckley S, Robison TH, Bevoor A, Chiang B, Haley HR, Sahoo S, Spinosa PC, Neale DB, Boppisetti J, Sahoo D, Ghosh P, Lahann J, Ross BD, Yoon E, Luker KE, Luker GD.

Breast Cancer Res. 2020 Jun 5;22(1):60. doi: 10.1186/s13058-020-01301-x.

The perils of premature phenotyping in COVID: a call for caution.

Bos LDJ, Sinha P, Dickson RP.

Eur Respir J. 2020 Jun 1. pii: 2001768. doi: 10.1183/13993003.01768-2020. [Epub ahead of print] No abstract available.

June 5, 2020

Good-bye and good luck to Geetha Kannan who just finished a 5 year post-doc with Vern Carruthers.  Dr. Kannan will be joining Lycera, a local biotech company here in Ann Arbor, as a Senior Research Scientist.  That company develops therapeutics for autoimmunity and cancer.  We wish her the best of luck!


Congrats to Adam Lauring.  He was named a recipient of the Internal Medicine Chair’s Award for Impact along with 2 other colleagues from ID. 

From the Division of Infectious Diseases

Adam Lauring –for initiating infectious disease care in the RICU

Powel Kazanjian – Division Chief – for mobilizing infectious disease COVID care at Michigan Medicine

Laraine Washer –Hospital Infection Co

Role of Aging and the Immune Response to Respiratory Viral Infections: Potential Implications for COVID-19

Judy Chen,*,†,1 William J. Kelley,*,1 and Daniel R. Goldstein


Also, congrats to Teresa O’Meara and Andrea Hogins-Davis on the acceptance of the first review article from their lab!  I’ll share the link as soon as it is available.

ntrol and Prevention – for being on top and communicating a myriad of questions, policy changes, and issues with COVID-19


June 3, 2020

Congratulations to our own Bob Dickson!

The Jerome W. Conn Award for Excellence in Research is given for outstanding research investigation by a physician-scientist at the assistant professor level. It honors Jerome Conn, M.D., former division chief of endocrinology at the University of Michigan who was the first to describe primary hyperaldosteronism, later known as Conn’s syndrome.



This year's award goes to Dr. Robert (Bob) Dickson from the Division of Pulmonary and Critical Care.  Dr. Dickson received his Medical Degree from Duke University and completed Internal Medicine Residency Training at the University of Washington where he also served as chief resident. Dr. Dickson was a Pulmonary and Critical Care Fellow at the University of Michigan and was promoted to Assistant Professor in our department in 2015. In 2019, he was also appointed as Assistant Professor in the Department of Microbiology and Immunology. Dr. Dickson’s research focuses on pulmonary pathogens and adult respiratory distress syndrome.  In particular, his work has studied the role of gut and lung microbiome on the pathogenesis of pulmonary disease. In more recent research, Dr. Dickson has identified methods to rapidly diagnose pulmonary infections. His research is supported by NIH K23, R01 and R21 awards as well as a University of Michigan Health System - Peking University Health Science Center Joint Institute Award.  Dr. Dickson has received numerous honors including a Young Physician Scientist Award from the American Society of Clinical Investigation, the Bruce C. Richardson MD Department of Internal Medicine Early Career Endowment Award and the Science and Innovation Center Rising Star Award from the American Thoracic Society. Please congratulate Dr. Robert Dickson on receiving this prestigious award from the Department of Internal Medicine for 2020.

June 2, 2020

Congrats to Vince Young who was elected by his peers for the role of Community Leader for ASM’s Host Microbe Biology (HMB) Community beginning July 1stIt is great to see our microbiome expertise recognized in this way.  Well done Vince!

New Publications from M&I:  Congrats to the authors!

Signals 1, 2 and B cell fate or: Where, when and for how long?

Turner JS, Benet ZL, Grigorova IL.

Immunol Rev. 2020 May 29. doi: 10.1111/imr.12865. [Epub ahead of print] Review.


Transposon Insertion Site Sequencing of Providencia stuartii: Essential Genes, Fitness Factors for Catheter-Associated Urinary Tract Infection, and the Impact of Polymicrobial Infection on Fitness Requirements.

Johnson AO, Forsyth V, Smith SN, Learman BS, Brauer AL, White AN, Zhao L, Wu W, Mobley HLT, Armbruster CE.

mSphere. 2020 May 27;5(3). pii: e00412-20. doi: 10.1128/mSphere.00412-20.


Increasing Relative Abundance of Pseudomonads Predicts Chronic Rejection after Lung Transplant.

Combs MP, Wheeler DS, Luth J, Falkowski NR, Chanderraj R, Walker NM, Dickson RP, Lama VN.

J Heart Lung Transplant. 2020 Apr;39(4S):S65. doi: 10.1016/j.healun.2020.01.1266. Epub 2020 Mar 30.


The Bacterial Connection between the Oral Cavity and the Gut Diseases.

Kitamoto S, Nagao-Kitamoto H, Hein R, Schmidt TM, Kamada N.

J Dent Res. 2020 May 28:22034520924633. doi: 10.1177/0022034520924633. [Epub ahead of print]

May 27, 2020

It’s official!  Congrats on your Research Track Faculty Promotions!

•       Basel Abuaita to Assistant Research Scientist

•       Jie Geng to Assistant Research Scientist


Congrats to Séb Crepin on getting the notice of award for his first R21! (First of many I am sure!) 

New publications from M&I:

Analysis of viruses present in urine from patients with interstitial cystitis.

Robles MTS, Cantalupo PG, Duray AM, Freeland M, Murkowski M, van Bokhoven A, Stephens-Shields AJ, Pipas JM, Imperiale MJ.

Virus Genes. 2020 May 23. doi: 10.1007/s11262-020-01767-z. [Epub ahead of print]


Multi-scale Models of Lung Fibrosis.

Leonard-Duke J, Evans S, Hannan RT, Barker TH, Bates JHT, Bonham CA, Moore BB, Kirschner DE, Peirce SM.

Matrix Biol. 2020 May 10. pii: S0945-053X(20)30042-1. doi: 10.1016/j.matbio.2020.04.003. [Epub ahead of print]


A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit