update latest

integratedbio.bib

@@ -54,6 +54,22 @@ @article{cassaniPbodylikeCondensatesGermline2024
   keywords = {Animals,Gene Expression Regulation,Germ cells,Germ Cells,Germ granules,Germline,Mammals,Nanos,P-body,Processing Bodies,RNA,RNA-Binding Proteins,{RNA, Messenger}}
 }
 
+@article{chenAlternativePolyadenylationMethods2017,
+  title = {Alternative {{Polyadenylation}}: {{Methods}}, {{Findings}}, and {{Impacts}}},
+  shorttitle = {Alternative {{Polyadenylation}}},
+  author = {Chen, Wei and Jia, Qi and Song, Yifan and Fu, Haihui and Wei, Gang and Ni, Ting},
+  year = {2017},
+  month = oct,
+  journal = {Genomics, Proteomics \& Bioinformatics},
+  series = {{{RNA Epigenetics}} ({{II}})},
+  volume = {15},
+  number = {5},
+  issn = {1672-0229},
+  doi = {10.1016/j.gpb.2017.06.001},
+  urldate = {2024-02-06},
+  keywords = {3{$\prime$}UTR,Alternative polyadenylation,Alternative splicing,Gene regulation,Next-generation sequencing}
+}
+
 @article{cooperDistributionIntensityConstraint2005,
   title = {Distribution and Intensity of Constraint in Mammalian Genomic Sequence},
   author = {Cooper, Gregory M. and Stone, Eric A. and Asimenos, George and Green, Eric D. and Batzoglou, Serafim and Sidow, Arend},
@@ -119,6 +135,24 @@ @article{dijkstraDirectMalemaleCompetition2005
   keywords = {Cichlids,Lake Victoria,Male-male competition,Sexual selection,Speciation}
 }
 
+@article{elkonAlternativeCleavagePolyadenylation2013,
+  title = {Alternative Cleavage and Polyadenylation: Extent, Regulation and Function},
+  shorttitle = {Alternative Cleavage and Polyadenylation},
+  author = {Elkon, Ran and Ugalde, Alejandro P. and Agami, Reuven},
+  year = {2013},
+  month = jul,
+  journal = {Nature Reviews Genetics},
+  volume = {14},
+  number = {7},
+  publisher = {{Nature Publishing Group}},
+  issn = {1471-0064},
+  doi = {10.1038/nrg3482},
+  urldate = {2024-02-06},
+  copyright = {2013 Springer Nature Limited},
+  langid = {english},
+  keywords = {Gene expression,Genomics,RNA}
+}
+
 @article{filippovaExceptionallyConservedTranscriptional1996,
   title = {An {{Exceptionally Conserved Transcriptional Repressor}}, {{CTCF}}, {{Employs Different Combinations}} of {{Zinc Fingers To Bind Diverged Promoter Sequences}} of {{Avian}} and {{Mammalian}} c-Myc {{Oncogenes}}},
   author = {Filippova, Galina N. and Fagerlie, Sara and Klenova, Elena M. and Myers, Cena and Dehner, Yvonne and Goodwin, Graham and Neiman, Paul E. and Collins, Steve J. and Lobanenkov, Victor V.},
@@ -388,6 +422,20 @@ @article{roeder50YearsEukaryotic2019
   langid = {english}
 }
 
+@article{shahBenchmarkingSequencingMethods2021,
+  title = {Benchmarking Sequencing Methods and Tools That Facilitate the Study of Alternative Polyadenylation},
+  author = {Shah, Ankeeta and Mittleman, Briana E. and Gilad, Yoav and Li, Yang I.},
+  year = {2021},
+  month = oct,
+  journal = {Genome Biology},
+  volume = {22},
+  number = {1},
+  issn = {1474-760X},
+  doi = {10.1186/s13059-021-02502-z},
+  urldate = {2024-02-06},
+  keywords = {3{$\prime$}-Seq,Alternative polyadenylation,Benchmarking,Isoform analysis,Long-read sequencing,PacBio Iso-Seq,QTL,RNA processing,RNA-seq}
+}
+
 @article{silvaCREBMemory1998,
   title = {{{CREB}} and Memory},
   author = {Silva, A. J. and Kogan, J. H. and Frankland, P. W. and Kida, S.},

qmrc-morelli.qmd

@@ -106,26 +106,41 @@ Types appeared to separate into their phylogenetic history.
 
 ### Q
 
-
+Are the sequences in the domains of interest conserved across species in details?
 
 ### M
 
+Examine the consensus sequences among the two domains of interest for NSP1 by host-species.
+
 ### R
 
+NSP1 sequences used in this study are indicated.
+The sequences appear to be highly conserved across the species in the OSU group (porcine) and to some extent the human one.
+
 ### C
 
+All full-length RVA NSP1 proteins are thought to utilize an N-terminal RING domain to interact with a cellular E2 ubiquitin-conjugating enzyme and a C-terminal sequence element to provide binding specificity for a host innate immune target
+
 ## Panel D
 
 ![](2024-02-04-16-01-10.png)
 
 ### Q
 
+Are the PDL sequences conserved within the human sequences?
+
 ### M
 
+Review the sequences.
+
 ### R
 
+Alignment of viral PDL motifs and phosphodegrons from known targets of $beta$-TrCP shown with high degree of conservation except maybe VAC.
+
 ### C
 
+Yes, it appears that there is some alignment.
+
 
 
 # Figure 2
@@ -150,6 +165,8 @@ A truncation mutant was made.
 
 ### C
 
+This figure just shows that the delta C truncation mutant was made.
+
 
 
 ## Panel B
@@ -158,15 +175,20 @@ A truncation mutant was made.
 
 ### Q
 
+With the truncation of the C-termininus domain, will we see the immunoregulatory features?
+
+
 ### M
 
 HEK cells were transfected with NSP1 anf NFkB with a luciferase reporter.
 The NSP1 mutant was transfected.
 Activated with TNF-alpha.
+Thus if NfkB is expressed, we will see it with the luciferase reporter with higher level indicating that the expected antiviral response is taking place.
 
 ### R
 
-OSU NSP1 blocked activation while truncation mutant did not.
+OSU NSP1 blocked activation (wt) while truncation mutant did not in the presence of TNF alpha.
+This mutant was also seen in both the OSU-C42A (point mutant predicted to disrupt the N-terminal RING domain) and SA11-4F (which mediates the degradation of IRFs but not -TrCP)
 
 
 ### C
@@ -181,14 +203,19 @@ What is the role of the PDL motif in NSP1 mediation of beta TrCP?
 
 ### M
 
-HEK cells transfected with NSP1 and FLAG-beta Trcp assayed by immunoblotting. 
+HEK cells transfected with NSP1 and FLAG-beta Trcp assayed by quantitative immunoblotting.
+The level of -TrCP is expressed as a percentage of -TrCP in OSU-C13-transfected cells.
 
 ### R
 
-50% lower in cells with the mutant vs the wild type.
+50% lower in cells with the wild type vs the mutants.
 
 ### C
 
+This shows again that the intact C-terminus appears to be important.
+
+
+
 # Figure 3
 
 >Human and porcine RVA NSP1 proteins conserve NF-B antagonist activity. (A) Alignment of the C termini from OSU, related RVA, and SA11-4F NSP1 proteins. The last four residues of SA11-4F NSP1 (DDNE) are not shown. Sites of variability in the consensus sequence (excluding SA11-4F) are shaded in gray, dots indicate positions of identity, and asterisks indicate the PDL motif. Hu, human; Po, porcine; Si, simian. (B) HEK293T cells were cotransfected with NSP1 and NF-B firefly and HSV-tk Renilla luciferase reporters. At 24 h p.t., cells were stimulated for 4 h with 25 ng/ml TNF-. Relative luciferase activity was calculated by normalizing firefly to Renilla luciferase activity. Data (mean  SD from one of three experiments performed in triplicate) were analyzed by two-way ANOVA (pairwise wt/C NSP1) using Sidak’s multiple comparisons test. (C) HEK293T cells cotransfected with NSP1 and FLAG--TrCP were assayed 24 h p.t. by quantitative immunoblotting (IB) (normalized to PCNA). For each NSP1, the level of -TrCP is expressed as a percentage of -TrCP in cells cotransfected with the corresponding C mutant. Data (mean  SD) are from three independent transfections. ***, P  0.001. See also Fig. S5 and S6 in the supplemental material
@@ -201,6 +228,8 @@ HEK cells transfected with NSP1 and FLAG-beta Trcp assayed by immunoblotting.
 
 ### M
 
+Alignment of the C termini from OSU, related RVA, and SA11-4F NSP1 protein
+
 ### R
 
 ### C
@@ -421,4 +450,4 @@ HEK cells transfected with NSP1 and FLAG-beta Trcp assayed by immunoblotting.
 
 ### R
 
-### C
+### C