@article{hidalgo-cantabrana_crawley_sanchez_barrangou_2017, title={Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.01851}, abstractNote={Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Hidalgo-Cantabrana, Claudio and Crawley, Alexandra B. and Sanchez, Borja and Barrangou, Rodolphe}, year={2017}, month={Sep} }
 @article{gomaa_klumpe_luo_selle_barrangou_beisel_2014, title={Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems}, volume={5}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00928-13}, abstractNote={ABSTRACT}, number={1}, journal={MBIO}, publisher={American Society for Microbiology}, author={Gomaa, Ahmed A. and Klumpe, Heidi E. and Luo, Michelle L. and Selle, Kurt and Barrangou, Rodolphe and Beisel, Chase L.}, year={2014} }
 @article{barrangou_drake_daubert_foegeding_2006, title={Sensory texture related to large-strain rheological properties of agar/glycerol gels as a model food}, volume={37}, ISSN={["1745-4603"]}, DOI={10.1111/j.1745-4603.2006.00050.x}, abstractNote={ABSTRACT}, number={3}, journal={JOURNAL OF TEXTURE STUDIES}, author={Barrangou, Lisa M. and Drake, Mary Anne and Daubert, Christopher R. and Foegeding, E. Allen}, year={2006}, month={Jun}, pages={241–262} }
 @article{barrangou_daubert_foegeding_2006, title={Textural properties of agarose gels. I. Rheological and fracture properties}, volume={20}, ISSN={["0268-005X"]}, DOI={10.1016/j.foodhyd.2005.02.019}, abstractNote={Small- and large-strain rheological methods were used to develop rheological profiles of agarose gels, including linear, non-linear, and fracture properties. Gel properties were examined under conditions of varying agarose concentration (0.5–2.5% w/w), glycerol concentration (0–60% w/w), and strain rate (0.0017–0.17 s−1). Small-strain behaviors were primarily elastic with only slight frequency dependence. Large-strain behaviors and fracture properties were dependent upon strain rate, agarose and glycerol concentration. Increasing concentrations of agarose produced an increasingly stronger, more brittle network, while increasing concentrations of glycerol produced an increasingly stronger, more deformable network. All fracture properties and non-linear behaviors increased with increasing strain rate in a similar manner, suggesting a general mechanism responsible for strain rate effects that is similar for non-linear and fracture behavior. Increasing concentrations of agarose and glycerol, respectively, increased and decreased the strain rate dependence of non-linear behavior. Phenomenological models were evaluated for describing non-linear behavior. A second-order polynomial equation was determined to describe the data more accurately than the commonly used BST equation [Blatz, P. J., Sharda, S. C., & Tschoegl, N. W. (1974). Strain energy function for rubberlike materials based on a generalized measure of strain. Transactions of the Society of Rheology, 18 (1) 145–161.], providing an estimated parameter that allowed relative non-linear behavior to be reliably quantified.}, number={2-3}, journal={FOOD HYDROCOLLOIDS}, author={Barrangou, LM and Daubert, CR and Foegeding, EA}, year={2006}, pages={184–195} }
 @article{barrangou_drake_daubert_foegeding_2006, title={Textural properties of agarose gels. II. Relationships between rheological properties and sensory texture}, volume={20}, ISSN={["1873-7137"]}, DOI={10.1016/j.foodhyd.2005.03.013}, abstractNote={Descriptive analysis was used to quantify the perceived hand texture characteristics of agarose gels, and results were compared with previously developed fundamental rheological profiles to determine if relationships could be established. Four texture attributes were used to describe the gels, including ‘hand small-strain force’, ‘hand springiness’, ‘hand fracture force’, and ‘hand fracture deformation’. Gels were differentiated similarly by sensory analysis and fracture properties (p≤0.05). Hand small-strain force and ‘hand-fracture force’ terms were capable of differentiating the gels equally as well, indicating that relative gel strength was perceived similarly with non-destructive and fracture causing deformations. Surprisingly, the hand force terms correlated more highly with fracture modulus (fractures stress/fracture strain) values (r≥0.98, p≤0.001) than fracture stress values (r=0.76–0.82, p≤0.05), suggesting sensory perception of force includes a coupling of stress and strain. The definition of the term hand fracture deformation was very similar to the commonly used sensory term ‘cohesiveness’, and was highly correlated with fracture strain values (r=0.98, p≤0.001). Linear viscoelastic properties could not distinguish gels as sensitively as fracture properties. These findings clearly demonstrate fracture properties are capable of predicting sensory texture properties.}, number={2-3}, journal={FOOD HYDROCOLLOIDS}, author={Barrangou, LM and Drake, M and Daubert, CR and Foegeding, EA}, year={2006}, pages={196–203} }
 @article{mcfeeters_barrangou_barish_morrison_2004, title={Rapid softening of acidified peppers: Effect of oxygen and sulfite}, volume={52}, DOI={10.1021/jf003459533}, number={14}, journal={Journal of Agricultural and Food Chemistry}, author={McFeeters, R. F. and Barrangou, L. M. and Barish, A. O. and Morrison, S. S.}, year={2004}, pages={4554–4557} }