Link to this post | posted 12 Jan, 2024 17:15

vcw0

Dear David, There is not a word big enough yet in languages I know to account for the impact you have had on the Science Education community and me. I thank you for all the inspiration and advice you provided that powered us forward with this work. I wish you all the peace and adventure you can handle. Just one question remains - what do I do with all the Hawaiian shirts I ordered over the holidays? Best regards, Vassie Vassie Ware Professor, Molecular Biology Lehigh University Bethlehem, PA vcw0@lehigh.edu

Link to this post | posted 28 May, 2020 22:13

vcw0

Members of the SMART 2020 team recently had a discussion about functional annotation of minor tail proteins in subcluster EA1 Microbacterium phages. Of particular interest is the functional assignment of the gene that is directly upstream of the endolysin gene (called lysin A in some older annotations, but should be called endolysin if only one lysin is annotated in a genome - see official functional assignment list for this update). This gene (Pham 17919 in Phamerator Actino_Draft 358; e.g., gp23 in TeddyBear and Pherferi or gp24 in Martin) should be called as a minor tail protein, along with the all the other proteins encoded by genes located between the tape measure and endolysin genes. BLAST data support the "minor tail" call. HHpred data, however, show a strong hit with several hydrolases, including glycoside hydrolases. "Glycoside hydrolase" is an official function on the list. (Please note that the reference example on the official function list for a phage with an annotated glycoside hydrolase will soon be updated by Debbie). But why is that particular function not called for that gene in the final annotation that should be submitted for a subcluster EA1 phage? Note that at least four "large" minor tail proteins are essential to construct a flexible phage tail. Based on BLAST and HHPred, some of the genes may be assigned as "hypothetical proteins"; yet, these genes can be assigned as minor tail proteins based on synteny even when a BLAST or HHpred hit may not be indicated. Difficulty with crystallization of some of the smaller proteins in this group is known to account for the lack of functional calls as minor tail components in HHpred. Many minor tail proteins are known to include enzymatic functions, and the presence of glycoside hydrolase activity is certainly consistent with an enzymatic activity that would assist in breaking down glycosidic bonds in complex sugars within bacterial cell walls. BUT, in the end, the minor tail function usurps the glycoside hydrolase function. So for now, call that gene (just upstream of the endolysin gene) a minor tail protein. At some point, a revision may come to the official function list that includes more functional specificity (e.g., minor tail protein/glycoside hydrolase domain).

Link to this post | posted 02 Mar, 2017 23:19
vcw0	Eric, This sounds like an astounding opportunity. How many slots are available in the program? Vassie

Link to this post | posted 10 Feb, 2017 15:37
vcw0	Dear all: Lee Hughes is visiting Lehigh from the University of North Texas and we are talking about phage, of course! We are wondering about findings from this project. Is there an anticipated date when we might learn about the results?

Link to this post | posted 25 May, 2016 21:01
vcw0	Dear all: David's obituary can be found at http://www.schislerfuneralhomes.com/obituary/david-dunbar-phd Condolences to his family can be sent to Mel and Linda Dunbar, 90 Kennetta Lane, Palmerton, PA 18071

Link to this post | posted 24 May, 2016 17:35

vcw0

The news of David's passing remains an enormous shock to us all. Many of you might not know that David was one of my Ph.D. students in the molecular biology program here at Lehigh. In the midst of this tragedy, I am reminded of the energy and enthusiasm he added to any discussion. What he shared with all of us in the SEA community has been his hallmark since the first day I met him years ago. We will miss this kind man, this fly-fisherman, this Polar plunger, this SEA-PHAGE enthusiast, and dear friend. My sincere condolences are extended to his family, the entire Cabrini community, and beyond. His reach was indeed far.