Medical Microbiology and Immunology

Research Output 1953 2019

2019
3 Citations (Scopus)

Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition

Litvak, Y., Mon, K. K. Z., Nguyen, H., Chanthavixay, G., Liou, M., Velazquez, E. M., Kutter, L., Alcantara, M. A., Byndloss, M. X., Tiffany, C. R., Walker, G. T., Faber, F., Zhu, Y., Bronner, D. N., Byndloss, A. J., Tsolis, R. M., Zhou, H. & Baumler, A. J., Jan 9 2019, In : Cell Host and Microbe. 25, 1, p. 128-139.e5

Research output: Contribution to journalArticle

Enterobacteriaceae
Salmonella
Oxygen
Escherichia coli
Spores
2 Citations (Scopus)

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

Velazquez, E. M., Nguyen, H., Heasley, K. T., Saechao, C. H., Gil, L. M., Rogers, A. W. L., Miller, B. M., Rolston, M. R., Lopez, C. A., Litvak, Y., Liou, M. J., Faber, F., Bronner, D. N., Tiffany, C. R., Byndloss, M. X., Byndloss, A. J. & Baumler, A. J., Jan 1 2019, In : Nature Microbiology.

Research output: Contribution to journalArticle

Salmonella Infections
Enterobacteriaceae
Microbiota
Probiotics
Salmonella

Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

Mordaunt, C. E., Kieffer, D. A., Shibata, N. M., Członkowska, A., Litwin, T., Weiss, K. H., Zhu, Y., Bowlus, C., Sarkar, S., Cooper, S., Wan, Y-J. Y., Ali, M. R., LaSalle, J. M. & Medici, V., Jan 1 2019, In : Epigenetics and Chromatin. 12, 1, 0255.

Research output: Contribution to journalArticle

Hepatolenticular Degeneration
Hematologic Diseases
Epigenomics
Liver
Genome

Examination of fluconazole-induced alopecia in an animal model and human cohort

Thompson, G. R., Krois, C. R., Affolter, V. K., Everett, A. D., Katarina Varjonen, E., Sharon, V. R., Singapuri, A., Dennis, M., Mchardy, I. H., Yoo, H. S., Fedor, D. M., Wiederhold, N. P., Aaron, P. A., Gelli, A. C., Napoli, J. L. & White, S. D., Feb 1 2019, In : Antimicrobial Agents and Chemotherapy. 63, 2, e01384-18.

Research output: Contribution to journalArticle

Fluconazole
Alopecia
Animal Models
Tretinoin
Hair

HIV-1 is rarely detected in blood and colon myeloid cells during viral-suppressive antiretroviral therapy

Cattin, A., Wiche Salinas, T. R., Gosselin, A., Planas, D., Shacklett, B., Cohen, E. A., Ghali, M. P., Routy, J. P. & Ancuta, P., Jul 1 2019, In : AIDS (London, England). 33, 8, p. 1293-1306 14 p.

Research output: Contribution to journalArticle

Myeloid Cells
HIV-1
Colon
HIV
Therapeutics

Isavuconazole in the treatment of coccidioidal meningitis

Heidari, A., Quinlan, M., Benjamin, D. J., Laurence, B., Mu, A., Ngai, T., Hoffman, W. J., Cohen, S. H., Mchardy, I. H., Johnson, R. & Thompson, G. R., Mar 1 2019, In : Antimicrobial Agents and Chemotherapy. e02232-18.

Research output: Contribution to journalArticle

Meningitis
Therapeutics
Salvage Therapy
isavuconazole

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Wilkins, L. G. E., Ettinger, C. L., Jospin, G. & Eisen, J. A., Dec 1 2019, In : Scientific Reports. 9, 1, 3059.

Research output: Contribution to journalArticle

Open Access
Metagenome
Russia
Hot Temperature
Genome
Hot Springs

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Bik, H. M., Alexiev, A., Aulakh, S. K., Bharadwaj, L., Flanagan, J., Haggerty, J. M., Hird, S. M., Jospin, G., Lang, J. M., Sauder, L. A., Neufeld, J. D., Shaver, A., Sethi, A., Eisen, J. A. & Coil, D. A., Feb 20 2019, In : mSphere. 4, 1

Research output: Contribution to journalArticle

Open Access
Food
Water
Oceans and Seas
Ecosystem
Nitrogen

Mucosal immunity in HIV/SIV infection: T Cells, B cells and beyond

Shacklett, B., Jan 1 2019, In : Current Immunology Reviews. 15, 1, p. 63-75 13 p.

Research output: Contribution to journalReview article

Mucosal Immunity
HIV Infections
B-Lymphocytes
T-Lymphocytes
HIV-1

Neutralization mechanism of human monoclonal antibodies against Rift Valley fever virus

Wang, Q., Ma, T., Wu, Y., Chen, Z., Zeng, H., Tong, Z., Gao, F., Qi, J., Zhao, Z., Chai, Y., Yang, H., Wong, G., Bi, Y., Wu, L., Shi, R., Yang, M., Song, J., Jiang, H., An, Z., Wang, J. & 7 othersYilma, T., Shi, Y., Liu, W. J., Liang, M., Qin, C., Gao, G. F. & Yan, J., Jan 1 2019, In : Nature Microbiology.

Research output: Contribution to journalArticle

Rift Valley fever virus
Monoclonal Antibodies
Vaccines
Viral Envelope Proteins
Livestock

Omu, a metabolomics count data analysis tool for intuitive figures and convenient metadata collection

Tiffany, C. R. & Baumler, A. J., Jan 1 2019, In : Microbiology Resource Announcements. 8, 15, e00129-19.

Research output: Contribution to journalArticle

Open Access
Molecular Sequence Annotation
Metabolomics
Workflow
Microbiota
Enzymes
1 Citation (Scopus)

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms

Sanctuary, M. R., Kain, J. N., Chen, S. Y., Kalanetra, K., Lemay, D. G., Rose, D. R., Yang, H. T., Tancredi, D. J., Bruce German, J., Slupsky, C. M., Ashwood, P., Mills, D. A., Smilowitz, J. T. & Angkustsiri, K., Jan 1 2019, In : PLoS One. 14, 1, e0210064.

Research output: Contribution to journalArticle

cow colostrum
Prebiotics
Colostrum
Bifidobacterium longum subsp. infantis
Probiotics

Species-specific inhibition of antiviral protein kinase R by capripoxviruses and vaccinia virus

Park, C., Peng, C., Brennan, G. & Rothenburg, S., Jan 1 2019, (Accepted/In press) In : Annals of the New York Academy of Sciences.

Research output: Contribution to journalArticle

Capripoxvirus
Vaccinia virus
Viruses
Protein Kinases
Antiviral Agents

T-cell derived acetylcholine aids host defenses during enteric bacterial infection with Citrobacter rodentium

Ramirez, V. T., Godinez, D. R., Brust-Mascher, I., Nonnecke, E. B., Castillo, P. A., Gardner, M. B., Tu, D., Sladek, J. A., Miller, E. N., Lebrilla, C. B., Bevins, C. L., Gareau, M. & Reardon, C., Apr 1 2019, In : PLoS pathogens. 15, 4, p. e1007719

Research output: Contribution to journalArticle

Open Access
Citrobacter rodentium
Bacterial Infections
Acetylcholine
T-Lymphocytes
Infection
Open Access
Microbiota

Tissue issues: mucosal T-cell responses in HIV-1 infection

Shacklett, B., Ferre, A. L. & Kiniry, B. E., Mar 1 2019, In : Current Opinion in HIV and AIDS. 14, 2, p. 100-107 8 p.

Research output: Contribution to journalArticle

HIV Infections
HIV-1
Mucous Membrane
T-Lymphocytes
Gastrointestinal Tract
1 Citation (Scopus)

UBE3A: An E3 ubiquitin ligase with genome-wide impact in neurodevelopmental disease

Lopez, S. J., Segal, D. & LaSalle, J. M., Jan 4 2019, In : Frontiers in Molecular Neuroscience. 11, 476.

Research output: Contribution to journalShort survey

Open Access
Ubiquitin-Protein Ligases
Genome
Ubiquitin
Brain
Angelman Syndrome

What Proportion of Female Sex Workers Practise anal Intercourse and How Frequently? A Systematic Review and Meta-analysis

Owen, B. N., Baggaley, R. F., Elmes, J., Harvey, A., Shubber, Z., Butler, A. R., Silhol, R., Anton, P., Shacklett, B., van der Straten, A. & Boily, M. C., Jan 1 2019, In : AIDS and Behavior.

Research output: Contribution to journalReview article

Open Access
Sex Workers
Meta-Analysis
Condoms
HIV
Interviews

Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights

Laufer, B. I., Hwang, H., Vogel Ciernia, A., Mordaunt, C. E. & LaSalle, J. M., Jan 1 2019, In : Epigenetics.

Research output: Contribution to journalArticle

Down Syndrome
Genome
DNA
Brain
DNA Methylation
2018

Acknowledgment of Ad Hoc Reviewers

Baumler, A. J., Dec 1 2018, In : Infection and Immunity. 86, 12

Research output: Contribution to journalEditorial

9 Citations (Scopus)

Ambient particulate matter activates the aryl hydrocarbon receptor in dendritic cells and enhances Th17 polarization

Castañeda, A. R., Pinkerton, K. E., Bein, K. J., Magaña-Méndez, A., Yang, H. T., Ashwood, P. & Vogel, C. F. A., Aug 1 2018, In : Toxicology Letters. 292, p. 85-96 12 p.

Research output: Contribution to journalArticle

Aryl Hydrocarbon Receptors
Particulate Matter
Dendritic Cells
Polarization
T-cells
3 Citations (Scopus)

Anti-Candida albicans IgG antibodies in children with autism spectrum disorders

Hughes, H. K. & Ashwood, P., Jan 1 2018, In : Frontiers in Psychiatry. 9, 627.

Research output: Contribution to journalArticle

Open Access
Candida albicans
Immunoglobulin G
Antibodies
Microbiota
Dysbiosis
4 Citations (Scopus)
Environmental Exposure
Autistic Disorder
Biomarkers
Learning
Prospective Studies

A summary of the third annual HIV microbiome workshop

Williams, B., Boucher, C., Bushman, F., Carrington-Lawrence, S., Collman, R., Dandekar, S., Dang, Q., Malaspina, A., Paredes, R., Wilson, C., Nowak, P., Klatt, N., Lagenaur, L. & Landay, A., Oct 1 2018, In : AIDS Research and Human Retroviruses. 34, 10, p. 828-834 7 p.

Research output: Contribution to journalArticle

Microbiota
HIV
Education
Virology
Health
5 Citations (Scopus)

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment

Dahlhausen, K. E., Doroud, L., Firl, A. J., Polkinghorne, A. & Eisen, J. A., Jan 1 2018, In : PeerJ. 2018, 3, 4452.

Research output: Contribution to journalArticle

Phascolarctidae
Phascolarctos cinereus
microbial communities
antibiotics
Anti-Bacterial Agents
1 Citation (Scopus)

Coccidioidomycosis complement fixation titer trends in the age of antifungals

Mchardy, I. H., Dinh, B. T. N., Waldman, S., Stewart, E., Bays, D., Pappagianis, D. & Thompson, G. R., Dec 1 2018, In : Journal of Clinical Microbiology. 56, 12, e01318-18.

Research output: Contribution to journalArticle

Coccidioidomycosis
Lung
Meningitis
Confidence Intervals
Infection
2 Citations (Scopus)

Cognitive deficits in the Snord116 deletion mouse model for Prader-Willi syndrome

Adhikari, A., Copping, N. A., Onaga, B., Pride, M. C., Coulson, R. L., Yang, M., Yasui, D. H., LaSalle, J. M. & Silverman, J. L., Jan 1 2018, (Accepted/In press) In : Neurobiology of Learning and Memory.

Research output: Contribution to journalArticle

Prader-Willi Syndrome
Aptitude
Phenotype
Small Nucleolar RNA
Learning
6 Citations (Scopus)

Colonocyte metabolism shapes the gut microbiota

Litvak, Y., Byndloss, M. X. & Baumler, A. J., Nov 30 2018, In : Science. 362, 6418, eaat9076.

Research output: Contribution to journalArticle

Anaerobic Bacteria
Microbiota
Homeostasis
Dysbiosis
Oxidative Phosphorylation
3 Citations (Scopus)

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

Fletcher, K., Klosterman, S. J., Derevnina, L., Martin, F., Bertier, L. D., Koike, S., Reyes-Chin-Wo, S., Mou, B. & Michelmore, R. W., Nov 29 2018, In : BMC Genomics. 19, 1, 5214.

Research output: Contribution to journalArticle

Peronospora
Phytophthora
Genomics
Spinacia oleracea
Genes

Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation

Dou, J., Schmidt, R. J., Benke, K. S., Newschaffer, C., Hertz-Picciotto, I., Croen, L. A., Iosif, A-M., LaSalle, J. M., Fallin, M. D. & Bakulski, K. M., Feb 1 2018, (Accepted/In press) In : Epigenetics. p. 1-9 9 p.

Research output: Contribution to journalArticle

Blood Buffy Coat
DNA Methylation
Fetal Blood
Methylation
Glycocalyx
Simian immunodeficiency virus
virology
Simian Immunodeficiency Virus
Virology
Human immunodeficiency virus
Metagenome
HTML
Archaea
Biotechnology
Bacteria
2 Citations (Scopus)

Cross-genetic determination of maternal and neonatal immune mediators during pregnancy

Traglia, M., Croen, L. A., Jones, K. L., Heuer, L. S., Yolken, R., Kharrazi, M., DeLorenze, G. N., Ashwood, P., Van de Water, J. A. & Weiss, L. A., Aug 22 2018, In : Genome Medicine. 10, 1, 67.

Research output: Contribution to journalArticle

Genetic Crosses
Mothers
Pregnancy
Immune System
Chemokines

Cryopreservation of human mucosal tissues

Hughes, S. M., Ferre, A. L., Yandura, S. E., Shetler, C., Baker, C. A. R., Calienes, F., Levy, C. N., Astronomo, R. D., Shu, Z., Lentz, G. M., Fialkow, M., Kirby, A. C., Juliana McElrath, M., Sinclair, E., Rohan, L. C., Anderson, P. L., Shacklett, B., Dezzutti, C. S., Gao, D. & Hladik, F., Jul 1 2018, In : PLoS One. 13, 7, e0200653.

Research output: Contribution to journalArticle

Cryopreservation
cryopreservation
Mucous Membrane
Tissue
Vitrification
1 Citation (Scopus)
Bipolar Disorder
Schizophrenia
Cytokines
Brain
Interferons
10 Citations (Scopus)

Detection of HIV-1-specific gastrointestinal tissue resident CD8 + T-cells in chronic infection

Kiniry, B. E., Li, S., Ganesh, A., Hunt, P. W., Somsouk, M., Skinner, P. J., Deeks, S. G. & Shacklett, B., May 1 2018, In : Mucosal Immunology. 11, 3, p. 909-920 12 p.

Research output: Contribution to journalArticle

HIV-1
T-Lymphocytes
Infection
Phenotype
Mucous Membrane
3 Citations (Scopus)

Differential expression of CD8+ T cell cytotoxic effector molecules in blood and gastrointestinal mucosa in HIV-1 infection

Kiniry, B. E., Hunt, P. W., Hecht, F. M., Somsouk, M., Deeks, S. G. & Shacklett, B., Mar 1 2018, In : Journal of Immunology. 200, 5, p. 1876-1888 13 p.

Research output: Contribution to journalArticle

Perforin
HIV Infections
HIV-1
Mucous Membrane
T-Lymphocytes
14 Citations (Scopus)

Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms

Rose, D. R., Yang, H., Serena, G., Sturgeon, C., Ma, B., Careaga, M., Hughes, H. K., Angkustsiri, K., Rose, M., Hertz-Picciotto, I., Van de Water, J. A., Hansen, R. L., Ravel, J., Fasano, A. & Ashwood, P., Jan 1 2018, (Accepted/In press) In : Brain, Behavior, and Immunity.

Research output: Contribution to journalArticle

Microbiota
Cytokines
Permeability
Autism Spectrum Disorder
Metagenome
Open Access
Tumor Necrosis Factor Receptors
Autistic Disorder
T-Lymphocytes
Tumor Necrosis Factor-alpha
Autism Spectrum Disorder

Does per-act HIV-1 transmission risk through anal sex vary by gender? An updated systematic review and meta-analysis

Baggaley, R. F., Owen, B. N., Silhol, R., Elmes, J., Anton, P., McGowan, I., van der Straten, A., Shacklett, B., Dang, Q., Swann, E. M., Bolton, D. L. & Boily, M. C., Nov 1 2018, In : American Journal of Reproductive Immunology. 80, 5, e13039.

Research output: Contribution to journalReview article

Sexual Behavior
Meta-Analysis
HIV-1
Heterosexuality
Therapeutics
2 Citations (Scopus)

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

Horng, K. R., Ganz, H. H., Eisen, J. A. & Marks, S. L., Jan 1 2018, In : PeerJ. 2018, 5, e4827.

Research output: Contribution to journalArticle

Canis lupus
Microbiota
Canidae
Dogs
dogs
2 Citations (Scopus)

Epigenetic changes of the thioredoxin system in the tx-j mouse model and in patients with Wilson disease

Mordaunt, C. E., Shibata, N. M., Kieffer, D. A., Czlonkowska, A., Litwin, T., Weiss, K. H., Gotthardt, D. N., Olson, K. A., Wei, D., Cooper, S., Wan, Y-J. Y., Ali, M. R., LaSalle, J. M. & Medici, V., Nov 15 2018, In : Human Molecular Genetics. 27, 22, p. 3854-3869 16 p.

Research output: Contribution to journalArticle

Hepatolenticular Degeneration
Thioredoxins
Epigenomics
Choline
Liver

Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

Vogel Ciernia, A., Laufer, B. I., Dunaway, K. W., Mordaunt, C. E., Coulson, R. L., Totah, T. S., Stolzenberg, D. S., Frahm, J. C., Singh-Taylor, A., Baram, T. Z., LaSalle, J. M. & Yasui, D. H., May 1 2018, (Accepted/In press) In : Epigenetics. p. 1-13 13 p.

Research output: Contribution to journalArticle

Neuronal Plasticity
Epigenomics
Hypothalamus
Mothers
DNA Methylation

Ex vivo cytokine release, determined by a multiplex cytokine assay, in response to coccidioidal antigen stimulation of whole blood among subjects with recently diagnosed primary pulmonary coccidioidomycosis

Ampel, N. M., Robey, I., Nguyen, C. T., Roller, B., August, J., Knox, K. S. & Pappagianis, D., May 1 2018, In : mSphere. 3, 3, e00065-18.

Research output: Contribution to journalArticle

Coccidioidomycosis
Interleukin-13
Cytokines
Antigens
Lung
3 Citations (Scopus)

Family history of immune conditions and autism spectrum and developmental disorders: Findings from the study to explore early development

Croen, L. A., Qian, Y., Ashwood, P., Daniels, J. L., Fallin, D., Schendel, D., Schieve, L. A., Singer, A. B. & Zerbo, O., Jan 1 2018, (Accepted/In press) In : Autism Research.

Research output: Contribution to journalArticle

Autistic Disorder
Mothers
Eczema
Psoriasis
Hypersensitivity

From short reads to chromosome-scale genome assemblies

Fletcher, K. & Michelmore, R. W., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 151-197 47 p. (Methods in Molecular Biology; vol. 1848).

Research output: Chapter in Book/Report/Conference proceedingChapter

Oomycetes
Workflow
Software
Chromosomes
Genome
7 Citations (Scopus)

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease

Bronner, D. N., Faber, F., Olsan, E. E., Byndloss, M. X., Sayed, N. A., Xu, G., Yoo, W., Kim, D., Ryu, S., Lebrilla, C. B. & Baumler, A. J., Feb 14 2018, In : Cell Host and Microbe. 23, 2, p. 266-273.e4

Research output: Contribution to journalArticle

Butyrates
Gastrointestinal Diseases
Salmonella
Microbiota
Inflammation
1 Citation (Scopus)

Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity

Wróblewski, T., Spiridon, L., Martin, E. C., Petrescu, A. J., Cavanaugh, K., Truco, M. J., Xu, H., Gozdowski, D., Pawłowski, K., Michelmore, R. W. & Takken, F. L. W., Dec 1 2018, In : PLoS Biology. 16, 12, e2005821.

Research output: Contribution to journalArticle

Oligomerization
Pathogens
Leucine
leucine
Immunity
5 Citations (Scopus)

Healthy hosts rule within: ecological forces shaping the gut microbiota

Byndloss, M. X., Pernitzsch, S. R. & Baumler, A. J., May 9 2018, (Accepted/In press) In : Mucosal Immunology. p. 1-7 7 p.

Research output: Contribution to journalArticle

Dysbiosis
Paneth Cells
Anaerobiosis
Sugar Acids
Large Intestine
4 Citations (Scopus)

High-resolution analysis of the efficiency, heritability, and editing outcomes of CRISPR/Cas9-induced modifications of NCED4 in lettuce (Lactuca sativa)

Bertier, L. D., Ron, M., Huo, H., Bradford, K. J., Britt, A. B. & Michelmore, R. W., May 1 2018, In : G3: Genes, Genomes, Genetics. 8, 5, p. 1513-1521 9 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Lettuce
Guide RNA
Seeds
Germ-Line Mutation