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There was so much good stuff in the Mitt Romney videos, that people are still going through them and finding new things. Here Lawrence O'Donnell focuses on one of the $50,000/plate attendees who asked a really dumb but telling question! |
Check him out(& watch him coin the phrase "confederacy of dunces"): |
1. >>watch him coin the phrase "confederacy of dunces"<< |
No. Correction needed. |
A Confederacy of Dunces is the title of a book by John Kennedy Toolewhich was published posthumously in 1980. The author had committed suicide in 1969. It won the Pulitzer Prize for Fiction in 1981. |
Recommended reading. |
There were reports in May that yet another attempt to make a movie were under way. This time the star is to be Zach Galifianakis. Previous efforts have been somewhat star crossed. |
The film version of Dunces has failed to launch for almost 30 years. Harold Ramis originally planned to adapt the novel to film in 1982 before his intended star, John Belushi, passed away. The project has been bogged in difficulty since, with intended stars John Candy and Chris Farley passing away as well. Will Fer... |
2. I stand corrected. Thank you! i had never heard that phrase before and loved it! |
1. Anyone with more than a passing interest in A Confederacy of Dunces and the story of how it was nearly lost when the author was should watch the documentary film available here. |
3. Lawrence has a great delivery when it comes to expressing they key points of his argument. |
4. With all fairness, the things that Nixon and his guys were doing were small potatoes compared to what the Executive Branch has been doing over the last 12 years, and I include Obama's. |
As a voter, I'd like to see a very low bar set for what it takes to get booted from office. |
Inhale my kale |
Total time: Approximately 10 minutes |
Projected cost: $6 |
Drinking buddy: Sake or a light beer |
Ingredients (serves 2) |
1. 1 tbsp AVOCADO or vegetable oil |
2. 2 tbsp fish sauce |
3. 4 OZ rice noodles |
4. 1 bunch kale |
5. 1 small handful BASIL chopped coarsely |
6. 1 small handful sun-dried tomato chopped coarsely |
7. 1/2 lime |
8. 2 tbsp GINGER finely diced |
9. 2 Serrano chilies finely diced |
Step 1 |
Blast the high heat and saute the ginger, chilies, basil, sun-dried tomato with the oil. Wash the kale, cut the stems away, chop coarsely, and throw in the pan. Cook until the kale breaks down and goes greener than a Goldman Sach banker’s bonus (approx 3 min). |
Step 2 |
Rinse the rice noodles and toss them in boiling water until they soften (approx 90 sec). Pull noodles straight out of the water and add them to the pan. Squeeze in the fish sauce, lime juice, and add a 1/2 cup of water. Cook until the water dissolves (approx 2 min). |
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Open Access Research |
Vivek Anantharaman and L Aravind* |
Author Affiliations |
For all author emails, please log on. |
Genome Biology 2003, 4:R81 doi:10.1186/gb-2003-4-12-r81 |
Received:21 August 2003 |
Revisions received:13 October 2003 |
Accepted:10 October 2003 |
Published:26 November 2003 |
Several prokaryotic plasmids maintain themselves in their hosts by means of diverse post-segregational cell killing systems. Recent findings suggest that chromosomally encoded copies of toxins and antitoxins of post-segregational cell killing systems - such as the RelE system - might function as regulatory switches und... |
Using sequence profile analysis we were able unify the RelE- and ParE-type toxins with several families of small, uncharacterized proteins from diverse bacteria and archaea into a single superfamily. Gene neighborhood analysis showed that the majority of these proteins were encoded by genes in characteristic neighborho... |
The tightly maintained gene neighborhoods of post-segregational cell killing-related systems appear to have evolved by in situ displacement of genes for toxins or antitoxins by functionally equivalent but evolutionarily unrelated genes. We predict that the novel post-segregational cell killing-related systems containin... |
Post-segregational cell killing (PSK) is a widespread mechanism that aids several plasmids to maintain themselves in their bacterial hosts [1-4]. Operons containing genes for interacting toxin-antitoxin (T-A) pairs that are borne on these plasmids, are the basis for PSK. Typically, the first gene in these operons encod... |
A systematic survey of such T-A operons and their mechanisms was presented in the seminal work of Gerdes in 2000 [6]. Subsequently, there have also been some important studies that have elucidated the biochemical details regarding the action of several toxins. One of these toxins, ParE, was shown to act as an inhibitor... |
Although Gerdes proposed that all T-A operons could have a common origin [6], an objective evaluation of the evolutionary relationships of these proteins and the origin of these systems has not been conducted. The availability of a large number of prokaryotic genome sequences allows us to use a variety of computational... |
As a result of our analyses we were able to uncover several new T-A systems and establish an evolutionary relationship between them and the eukaryotic nonsense-mediated RNA degradation system. We also present evidence that the RelE and ParE families of toxins, despite their very distinct modes of action, have been ulti... |
Results and discussion |
Unification of the RelE and ParE families and identification of new related families of proteins |
As Escherichia coli RelE and its close relatives are amongst the functionally best-characterized toxins of the PSK systems, with a wide phyletic pattern in bacteria and archaea [6], we chose them as the starting point of our investigation of the general cellular functions and natural history of these systems. In order ... |
A striking aspect of these searches was the establishment of the relationship between the ParE (typified by the plasmid RK2-encoded toxin, ParE) [22] and RelE families of toxins that were previously believed to be unrelated. These toxins have very different targets of action: ParE acts at the level of DNA replication a... |
A multiple sequence alignment of the entire RelE/ParE superfamily (Figure 1) was constructed by combining the alignments of the individual clusters using the Profile Consistency Multiple Sequence Alignment (PCMA) program and refining it based on PSI-BLAST pair-wise alignments and secondary structure predictions. The pr... |
thumbnailFigure 1. Multiple alignment of the RelE/ParE superfamily. Multiple sequence alignments of the different families of RelE/ParE were constructed using T-Coffee [20] and PCMA [50] after parsing high-scoring pairs from PSI-BLAST search results. The PHD-secondary structure [21] is shown above the alignment with E ... |
The multiple alignment of the RelE/ParE family shows that much of the conservation is associated with the residues forming the core of the conserved, predicted secondary structure elements (Figure 1). Two charged or polar residues, one associated with the first conserved helix and the second associated with the end of ... |
We then investigated the evolutionary history of the RelE/ParE superfamily by exploring its phyletic and phylogenetic diversity. The superfamily is widely distributed in the currently sequenced prokaryotes: at least a single member is encoded by the chromosome or one of the large genomic partitions in several bacterial... |
thumbnailFigure 2. Relative abundance of some major families of toxins, associated transcription factors (antitoxins) and the UMA2 superfamily in various genomes. The number of proteins containing PIN, RelE/ParE, Doc, Phd/YefM, AbrB, MazF/CcdB/KiD, Rv0623, AF0319 and AF0608 domains in different genomes is indicated for... |
We determined the major lineages of the RelE/ParE superfamily through single-linkage clustering of the proteins with the BLASTCLUST program and construction of neighbor-joining phylogenetic trees with a multiple alignment of all complete members of the superfamily. Several distinct families could be delineated within t... |
thumbnailFigure 3. Contextual information and an ordered graph of gene neighborhood and domain architectures of the PSK network. The top panel shows the gene neighborhoods (predicted operons) for some of the PSK systems and other relevant gene clusters. The arrows indicate the direction of transcription. For each gene ... |
Wider phyletic spread of the RelE family and its relatives, as compared to the ParE family, may suggest that the former group represents the more ancient member of the superfamily, with the ParE lineage being secondarily derived in bacteria. This would imply that the RNA-cleaving activity is likely to be the primitive ... |
Gene-neighborhood analysis of the RelE/ParE superfamily and identification of PSK-like systems encoding PilT-N terminal (PIN) domain proteins |
Given the tight coupling of the toxin-antitoxin gene pairs, we investigated contextual information derived from their gene neighborhoods [14-18]. We concentrated on the newly identified members of the RelE/ParE superfamily to glean previously unknown contextual connections to other genes. Upstream genes encoding transc... |
Genes for proteins belonging to the YoeB family of the RelE/ParE superfamily were consistently associated with upstream genes that coded small proteins (~75-90 residues) that were unrelated to the MetJ/Arc superfamily. We investigated this family of small proteins further by initiating iterative PSI-BLAST searches seed... |
thumbnailFigure 4. Multiple alignment of Phd/YefM. The labeling and coloring conventions are as followed in Figure 1. The species abbreviations are as shown in Figure 1, 2 and additionally: Bjap, Bradyrhizobium japonicum; Cjej, Campylobacter jejuni; Mdeg, Microbulbifer degradans; Spne, Streptococcus pneumoniae; Styp, S... |
Genes encoding members of the Rv3182, mlr1576, VCA0468 families of the RelE/ParE superfamily were consistently associated with conserved downstream genes that encoded small proteins (90-110 residues) unrelated to either the Phd/YefM or MetJ/Arc superfamilies (Figure 3). PSI-BLAST searches initiated with these proteins ... |
One possibility, which is supported by the specific relationship between these cHTH proteins and cro/cI repressors, is that these proteins act as repressors of the toxin gene. The degradation of the repressor under certain conditions could then allow the expression of the toxin component. The Z5902 family of the RelE/P... |
The above observations suggested that there is considerable unity in the organization of these toxin-antitoxin gene systems: typically these comprise of two small genes, in which one member of the pair encodes a toxin and the other encodes a DNA-binding protein that functions as an antitoxin and a transcription factor.... |
Importantly, the screening procedure recovered a novel widespread family of small proteins (~100 residues, typified by MJ1121) that was consistently found downstream of genes for MetJ/Arc transcription factors (Figure 3). In this respect they closely resembled the operons of the RelE/ParE and MazF superfamily PSK syste... |
thumbnailFigure 5. Multiple alignment of novel transcription factors associated with the PSK operons. (a) AF0608 family, (b) Rv0623 family and (c) AF0319 family. The labeling and coloring conventions are as followed in the legend to Figure 1. The species abbreviations are as shown in Figure 1 and additionally: Pab, Pyr... |
Based on this web of contextual connections offered by gene neighborhoods (Figure 3) we predict that the above-detected group of solo PIN domain proteins defines a toxin-like component of novel PSK-related regulatory systems. These predicted PSK-related systems with the PIN domain are as widespread as the systems with ... |
Functional and evolutionary connections of the PIN and Doc domains and eukaryotic nonsense-mediated mRNA decay |
In contrast to the RelE proteins that are restricted to prokaryotes, the PIN domain is found in all three superkingdoms of life. This suggested that the PSK-related regulatory systems with PIN domain proteins might throw light on the more general roles of such systems. Given the RNA-binding role for the PIN domain [34-... |
The above observations suggest that the crucial PIN domain protein of the NMD system is perhaps a remnant of an ancient PSK-type regulatory system. The emergence of the nucleus in eukaryotes, and the uncoupling of translation and transcription could have caused the PIN domain protein to be released from the tight regul... |
We examined other superfamilies of toxins to determine if they included widely distributed members with a general functional significance similar to the solo PIN domain proteins. Several PSK-systems have a very limited phyletic distribution [6] and are not further detailed here because they are unlikely to throw light ... |
The Doc toxin of the Phd-Doc PSK system has been hitherto detected only in P1-like phages and related mobile DNA elements from γ-proteobacteria [6]. Our sequence profile searches with the PSI-BLAST program recovered several homologs of Doc from several proteobacterial lineages, low GC Gram positive bacteria, actinobact... |
A multiple alignment of the Doc domain superfamily (Figure 6) shows that these proteins share several nearly absolutely-conserved charged or polar residues, and the proteins are predicted to assume an α-helical fold. The amino-terminal half contains a highly-conserved histidine and a basic residue (almost always argini... |
thumbnailFigure 6. Multiple alignment of the Doc domain. The three major families of the Doc domain superfamily have been delineated by small blank spacers. The labeling and coloring conventions are as followed in the legend to Figure 1. The species abbreviations are as shown in Figure 1, Figure 2 and additionally: Cje... |
A phylogenetic analysis of the Doc superfamily reveals that it contains three distinct families (Figure 6). The first family contains the Doc protein from phage P1 and its homologs from several bacterial genomes. Typically, upstream genes for an antitoxin transcription factor accompany genes encoding members of this fa... |
The above analysis suggests that there is considerable diversity amongst the T-A systems. Most widespread prokaryotic PSK or related systems appear to have been derived by mixing and matching a few major classes of toxins and antitoxins (Figure 2) that appear to have independent evolutionary origins. The major classes ... |
Finally, the abundant presence of PSK-related systems in prokaryotic chromosomes supports the original proposal of Gerdes and recent experimental studies that these systems could function as more generic regulatory systems [5,6,8,19]. In particular, they appear to have proliferated on the chromosomes of some prokaryote... |
Furthermore, in some cases, domains such as Doc, PIN, RelE/ParE and YefM proteins appear to have been incorporated in systems that function outside the context of classic PSK-related systems. |
Using sequence profile analysis and contextual data derived from comparative genomics, we investigated the evolutionary relationships of prokaryotic T-A systems. As a result we were able to unify the functionally unrelated toxin families defined by the ParE and RelE proteins and detect several new families of this prot... |
Materials and methods |
The non-redundant (NR) database of protein sequences (National Center for Biotechnology Information, NIH, Bethesda) was searched using the BLASTP program [11]. Profile searches were conducted using the PSI-BLAST program with either a single sequence or an alignment used as the query, with a default profile inclusion ex... |
Structural manipulations were carried out using the Swiss-PDB viewer program [52] and the ribbon diagrams were constructed with MOLSCRIPT [53]. Searches of the PDB database with query structures was conducted using the DALI program [54]. Protein secondary structure was predicted using a multiple alignment as the input ... |
Additional data files |
A complete list of all the novel proteins belonging to the various superfamilies discussed in this paper will be made available for download via [61]. A multiple alignment of selected PIN domains (Additional data file 1), including the predicted toxins of PSK-like systems is provided with the online version of this art... |
Additional data file 1. A multiple alignment of selected PIN domains |
Format: DOC Size: 40KB Download file |
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