Verschoor CP, Dorrington MG, Novakowski KE, Kaiser J, Radford K, Nair P, Anipindi V, Kaushic C, Surette MG, Bowdish DME. MicroRNA-155 Is Required for Clearance of Streptococcus pneumoniae from the Nasopharynx. Infect Immun. 2014 Nov;82(11):4824-33. doi: 10.1128/IAI.02251-14.

Verschoor CP, Dorrington MG, Novakowski KE, Kaiser J, Radford K, Nair P, Anipindi V, Kaushic C, Surette MG, Bowdish DME. MicroRNA-155 Is Required for Clearance of Streptococcus pneumoniae from the Nasopharynx. Infect Immun. 2014 Nov;82(11):4824-33. doi: 10.1128/IAI.02251-14.

This paper outlines how microRNA- (miR-)155 regulates the immune response to S. pneumoniae colonization in the nasal passages of mice by stimulating the differentiation of Th17 cells. 

Kaiser JC, Verschoor CP, Surette MG, Bowdish DME. Host cytokine responses distinguish invasive from airway isolates of the Streptococcus milleri/anginosis group. BMC Infect Dis. 2014 Sep 11;14:498. doi: 10.1186/1471-2334-14-498.

Kaiser JC, Verschoor CP, Surette MG, Bowdish DME. Host cytokine responses distinguish invasive from airway isolates of the Streptococcus milleri/anginosis group. BMC Infect Dis. 2014 Sep 11;14:498. doi: 10.1186/1471-2334-14-498.

This paper demonstrates that there are host- and strain- specific responses to isolates of the Streptococcus milleri/anginosis group and that isolates from invasive disease appear to be more immunostimulatory than those from commensal relationships.

“Comprehensive & simultaneous coverage of lipid and polar metabolites for endogenous cellular metabolomics using HILIC-TOF-MS” 2014. Fei et al. Anal Bioanal Chem.

 

Bowdish-McCarry PhD candidate, Fan Fei, publishes a protocol she created to study the endometabolome of macrophages and microbes in Analytical & Bioanalytical Chemistry. Click the image for the .pdf.
Fei 2014 covershot ABC

Whelan et al. The Loss of Topography in the Microbial Communities of the Upper Respiratory Tract in the Elderly. Ann Am Thorac Soc. 2014 Mar 6.

Whelan FJ, Verschoor CP, Stearns JC, Rossi L, Luinstra K, Loeb M, Smieja M, Johnstone J, Surette MG, Bowdish DM. The Loss of Topography in the Microbial Communities of the Upper Respiratory Tract in the Elderly. Ann Am Thorac Soc. 2014 Mar 6.

This paper describes how the microbial communities of the anterior nares and nasopharynx change between adults and the elderly. 

PradhuDas et al. Standardizing Scavenger Receptor Nomenclature. J Immunol. 2014 Mar 1;192(5):1997-2006.

PrabhuDas M, Bowdish D, Drickamer K, Febbraio M, Herz J, Kobzik L, Krieger M, Loike J, Means TK, Moestrup SK, Post S, Sawamura T, Silverstein S, Wang XY, El Khoury J. Standardizing scavenger receptor nomenclature. J Immunol. 2014 Mar 1;192(5):1997-2006. doi: 10.4049/jimmunol.1490003.

PradhuDas et al screen shot

Puchta et al. Characterization of inflammatory responses during intranasal colonization with Streptococcus pneumoniae. Vis Exp. 2014 Jan 17;(83):e50490. doi: 10.3791/50490.

Puchta A, Verschoor CP, Thurn T, Bowdish DMCharacterization of inflammatory responses during intranasal colonization with Streptococcus pneumoniae. J Vis Exp. 2014 Jan 17;(83):e50490. doi: 10.3791/50490.

A guide to Bioinformatics for Immunologists

Congratulations to Fiona Whelan (MSc, Bowdish lab; PhD student, Surette lab) for publishing the review article “A guide to bioinformatics for immunologists” in Frontiers Immunology. The idea of this article spawned from the research that Fiona conducted in the Bowdish lab on the elucidation of the evolutionary history and relationships between the members of the class A scavenger receptors, proteins required for host defense and homeostasis. During this time, Fiona used multiple bioinformatic techniques and tools to form hypotheses as to the function of one under-annotated member of this family, SCARA3.  Even though most of these tools are easy-to-use and require little computational knowledge, Fiona and Dawn discovered through their interactions with other immunologists that these tools were being under utilized.  Thus, they decided to write a review of how bioinformatic techniques can help the average immunologist in their quest for knowledge about the structure of their protein of interest, how to find SNPs that may correlate with disease phenotype, and how to conduct sequence alignments in order to find areas that are conserved across various genes.

This review article is written as a case study that follows Fiona’s research into SCARA3 that begins with obtaining the NCBI Reference FASTA sequence of the protein, predicting post-translational modifications, identifying conserved motifs, hypothesizing as to the structure of the protein, examining SCARA3’s transcriptomic profile in different immunological cell types, and analyzing any potential SNPs within the DNA sequence of SCARA3 that may correlate with disease. The article is written with the immunologist in mind and includes the use of only “point and click” tools that require no computational background whatsoever.

Is Fiona’s paper is Open Access? Of course it is! Enjoy reading it here and reading the description on the Surette lab website here.

The laboratories of both Dr. Bowdish and Dr. Surette are always interested in undergraduate and graduate students interested in exploring the impact bioinformatics can have on immunological and microbiological research.

“Myeloid-Derived Suppressor Cells, Age & Cancer” 2013. Oncoimmunology.

Dr. Bowdish discusses the implication of our Verschoor et al publication “Blood CD33(+)HLA-DR(-) myeloid-derived suppressor cells are increased with age and a history of cancer.” in studies of aging and cancer in the below commentary.

Click image for .pdf.

MDSC commentary

 

This is an open access publication so please feel free to use the following image in presentations/publications providing that it is properly referenced.

MDSC commen figure

“Immunosenescence & novel vaccination strategies for the elderly” 2013. Dorrington et al. Frontiers in Immunology

What is the best way to reduce infectious disease in the elderly? Vaccination! Unfortunately the aging immune system presents a number of challenges for vaccine development. Bowdish lab PhD candidate Mike Dorrington discusses them in this review and presents a case for developing novel vaccines that work within the constraints of the aging immune system.

Media coverage: This paper was picked up by MDLinx. See their coverage here.

Click image for .pdf.

Dorrington Fronteirs review