Where to listen. Go to next audio Go to next audio. Go to prev audio Go to prev audio. Episode Martha Kotite - Captain Ret. Captain Martha Kotite Ret. Service academies and colleges nationwide have active and powerful alumni associations, but those who enlist and substitute boot camp for higher education lack any similar organization they can leverage for their own social and professional network, or to give back to better the institution that positively impacted their lives.
With tens of thousands of potential members who have completed boot camp, the Coast Guard Recruit Training Alumni is looking to change this. Part II. Former Lieutenant Peter Eident talks surviving the capsizing and sinking of the USCGC Cuyahoga during a nighttime training cruise on the Chesapeake Bay and the legal and emotional aftermath stemming from the loss of eleven of her crew. Part I of II. He also talks what it takes to maintain boats and train crews to the levels needed for Coast Guard operations, and the responsibility of coxswains and surfmen not only to go out, but to bring their crews and those in peril back to shore.
LT Angel Hughes talks leading an aircrew on a challenging nighttime search for a distressed vessel and the aerial delivery of supplies to aid the rescue effort, Millsart - Blue Potential (CDr), flying in hurricane conditions, earning her wings on the HC Casa Ocean Sentry, and performing the many missions of the Coast Guard from these fixed wing aircraft.
Unique episodes released on both shows have the hosts talking enlisted leadership, advancement panels, and the differences and similarities between the greatest sea service the world has ever know Rear Admiral Cari Thomas Ret. He closes by sharing his own lessons learned on making the transition from active duty, from creating a financial safety net and finding a new career to paying for college and medical expenses.
Captain Millsart - Blue Potential (CDr) Craig Ret. Former Radioman Mark Holmes talks heading out and into a storm so severe it forced the Navy into port, responding to a foundering sailing vessel with a skeleton crew aboard CGC Courageous, procuring a replacement deck gun for a cutter from the front lawn of a VFW, surviving waterspouts and tornadoes, and how his experiences in the service caused him to begin writing. He also tells of responding to the aftermath of a typhoon in Guam and a few highlights from leading crews on search and rescue and law enforcement cases as a coxswain on 30 and 40 ft wooden hull boats and on the brand new 41 UTB at stations in Honolulu and Kauai.
For the most choice assignments in a single enlistment, Doug may have the record. Retired Quartermaster and Boatswain Kevin Gilheany talks a search and rescue case involving a commercial fishing vessel that was poised to play out like a Greek tragedy until he took action to establish a viable search area and direct assets to locate and save the survivor.
Episode Spooky Sea Yarns. To celebrate Halloween our hosts tell of their experiences with haunted Coast Guard cutters and stations. They also make an incredibly weak attempt to start a new legend about their favorite waterway. Retired Aviation Electronics Technician and Helicopter Flight Mechanic Ashlee Leppert talks earning the Air Medal for flying with her crew into the midst of Hurricane Harvey to rescue desperate survivors from rising flood waters, unknowingly hoisting a basket packed with babies up and into the safety of a helicopter, and how responders overcome the emotional trauma of disaster by leaning on their crews.
Thirty-nine years ago in the Pacific Ocean miles off the coast of Valdez, Alaska, a fire engulfed the engine room of the Prinsendam, a cruise ship carrying over passengers. As the fire raged, the captain gave the order to abandon ship. Recalled from liberty, the crew of US Coast Guard Cutter Boutwell turned into an approaching typhoon and responded to the scene.
Along with the efforts of other cutters, ships, and aircraft, the responders managed to save the lives of every passenger before the Prinsendam rolled and sank bow-first to the bottom. Retired Chief Maritime Enforcement Specialist Mike Vecchione talks risking his first coxswain letter with a search for survivors from a capsized vessel based on his own local knowledge rather than the algorithm used by a command center computer, deploying worldwide with the International Training Division, and losing a member of his team during a high risk training exercise.
Now the owner of a cigar shop and partner in a coffee company, he also tells how they are supporting veterans and their families. Retired Captain Ron LaBrec talks being on the bridge of a during a search for survivors from a wrecked vessel, leading law enforcement detachments on deployments worldwide to counter maritime smuggling, and his toughest duty while in command.
The complete list of matches and their Pfams is available as a downloadable text file Supplemental File 1. An example of how to use this file to generate a set of coordinates is provided in Supplemental Information. Because we are using alignments to a consensus sequence for each Pfam, matches of different lengths can have the same Pfam description.
Note that the total number of unique Pfams is not the sum of the number of unique Pfams broken down by length. Seven percent of the matches do not align to any Pfam, indicating that the match does not originate from a structurally conserved region of the protein or that it is beyond the bounds of the Pfam domain definition.
Forty percent of the matches align to a Pfam, but this Pfam alignment only occurs once. In the case of heterodimeric protein substrates i. Thus, C-terminal kinks are present in a wide variety of non-antibody proteins, and some other protein domain families use this feature for binding and selectivity in the same way as antibodies.
PDZ domains interacting with substrates through a kinked loop. The matching region is colored in rainbow with blue at the N-terminus and red at the C-terminus of the loop. The structural diversity of the identified loop is on display. In this view, the substrate is blue with the C-terminal residues shown in spheres and the PDZ containing chain is pale green.
The matching loop is shown in orange and all contacts between the substrate and the loop are shown in magenta. Other contacts within 5. Using our description of the kink, we tested the predictive power of the identity of the base residues at positions 94 andwhich are frequently Arg and Asp respectively in antibodies. Table S1 shows the percentage of kinked CDR H3 loops with all combinations of the presence or absence of the supposed stabilizing base residues.
In agreement with North et al. S3 and S4we find that the majority of CDR H3 loops are kinked even when none of these residues are present. We also applied the rules developed in a study by Kuroda et al.
Kuroda et al. The accuracy of these rules is However, when one classification dominates a population, balanced accuracy BACC is a more meaningful measurement of Millsart - Blue Potential (CDr) performance of a model Wei and Dunbrack, While We investigated the CDR H3-like non-antibody loops for the presence of these stabilizing residues and observed neither the Arg Asp combination nor the tryptophan at the equivalent of position As shown in Fig.
Thus, we hypothesized that glycine in a central position may be indicative of an extended conformation. Within CDR H3 loops, glycine residues are preferred on the N-terminal side of the loop in kinked structures. For structures with an extended or unclear base geometry, they are preferred in more central positions.
The PDB LAT matches prefer glycine in more central positions for kinked structures, which is likely a consequence of averaging the result of disparate evolutionary pathways. This result supports our hypothesis, but the dearth of extended CDR H3 structures at various lengths precludes using this result predictively.
CDR H3 is the most diverse region in antibodies due to its position relative to the V D J recombination sites, junctional diversification at these sites, and somatic hypermutation. Accordingly, the CDR H3 loop often plays a central role in antigen recognition and is a major contributor to binding strength. The success of several therapeutic antibodies and the advent of next-generation sequencing techniques have led to an increased interest in computational antibody structure prediction and design.
While there has been progress in these efforts, accurate modeling of CDR H3 has remained challenging, leading us to question whether 1 the diversification of CDR H3 can lead to extremely rare conformations; or 2 there are environmental factors encoded into the F V. Our results indicate that CDR H3-like conformations, while not common, occur with some regularity, occurring in 7.
Environmental factors are most likely responsible for kink stabilization. We identified 1, protein segments of at least 9 residues from distinct Pfam alignments that match the same 3D transformation as the anchors of the H3 loop and include the C-terminal kink motif that is common in antibodies. Without the inclusion of the kink in our search criteria, most of the matches are extended strand-turn-strand conformations, suggesting that adopting CDR H3-like conformations is unusual.
This is helpful for understanding why de novo loop structure prediction of CDR H3 tends to produce models with extended base geometry and indicates that using constraints for this purpose is likely a wise course of action. In fact, when prediction algorithms use fragment or template-based approaches, the libraries are predominantly composed of structures that do not adopt the kinked base geometry, making it challenging to identify appropriate conformations. The data presented here can be used to enrich fragment or template libraries effectively.
For example, RosettaAntibody accounts for the kink either by using a curated set of fragments or by filtering H3 loops with poor kink geometry Sivasubramanian et al. Here we have established a more detailed geometric description of the kink and identified a significantly larger set of structures from which fragments can be selected.
Both results can be used as a starting point for improving de novo CDR H3 loop structure prediction. In most Pfams, kinked loops appear to arise only in some family members, while in others they are highly conserved structural features. One such protein family, PDZ domains, has evolved a motif for protein recognition and binding that is strikingly similar in structure and function to CDR H3.
The appearance of the kink irrespective of the presence of the stabilizing residues indicates that environmental factors are crucial to kink formation. Furthermore, we have produced a set of H3-like structures of a wide variety of lengths from non-antibody proteins. Across all loop lengths, and especially for long loop lengths, there are more potential template loops from non-antibody structures than from antibody structures.
If the quality and homology constraints that were used to cull the PDB were relaxed, it is likely we would identify even more, albeit lower quality, H3-like regions in non-antibody proteins. This set of structures could be incorporated into a database that could be used to assist CDR H3 structure prediction by threading the sequence of interest onto many possible H3-like backbones, analogous to successful database-based methods for loop structure prediction Choi and Deane, ; Holtby et al.
The green curve in Fig. Another possible use for this set of structures is in the field of computational antibody design. The extremely large sequence and conformational spaces of long loops often make incorporating backbone motions into design methods infeasible. Effective sampling is further complicated if docking simulations are desired, as may be the case in designing a binding region such as CDR H3.
The large number of PDB matches at long loop lengths for which there are few or no H3 loops provides an opportunity to present multiple H3-like scaffolds for fixed and flexible backbone design routines. Thus, it is expected that the identified structures will improve antibody design. While the kink has been discussed in the past Kuroda et al. For example, we observed that the previous kink geometrical description can be satisfied in multiple ways Weitzner et al.
Our work shows that the residues that had been previously indicated in kink formation are not present in kinked structures from non-antibody proteins Fig. In fact, no local interactions among the loop residues fully explain the presence of the kink. Instead, we are led to the conclusion that the Ig heavy chain fold stabilizes the kink, and thus it is the extended H3 structures that are the exceptions and not the kinked loops.
All of our results lead to our hypothesis of why the kinked base geometry is preferred: it is an agent of loop diversification. In other words, if it were not for the kink, most sequences would form extended strand-turn-strand conformations, giving little structural diversity, but with a kink, many structures of similar free energy can form instead.
Such a feature is advantageous to an antibody undergoing somatic hypermutation to improve affinity and specificity to a newly introduced antigen.
For this reason, we believe the heavy chain fold has been selected to form the kink, and it is only in rare circumstances that the extended geometry is energetically favorable compared to the kinked conformation.
A set of IgG heavy chain V domains, constructed and filtered as described by North et al. For this reason, we developed a description of the CDR H3 loop environment based on structure independent of sequence.
The definitions used by North et al. North et al. The six degrees of freedom of the 3D transformation of the C-terminal coordinate frame onto the N-terminal coordinate frame together compose what we term the loop anchor transform LAT. The covariance for each pair of degrees of freedom revealed that each degree of freedom could be treated independently see Supplemental Methods.
LATs were calculated using the feature analysis framework Leaver-Fay et al. Analysis scripts were developed to display distributions of the results using the ggplot2 Wickham, library in R R Development Core Team, Sequence and secondary structure comparisons were performed using a local copy of WebLogo Crooks et al.
When comparing secondary structures, the DSSP code Kabsch and Sander, is used in place of the one-letter amino acid abbreviation. Figure S1, related to Figure 1 : Density Millsart - Blue Potential (CDr) for each of the six degrees of freedom of the loop anchor transform for each residue segment from 1 the culled PDB set gray ; and 2 the known CDR H3 loops black show the relative structural diversity between the two sets.
The tightness of the H3 distributions indicates the defined CDR H3 anchor points at structurally conserved positions, while the diffuse distributions from the PDB Millsart - Blue Potential (CDr) the structural diversity of residue segments in the other proteins.
Because the six degrees of freedom are not covariant, each Millsart - Blue Potential (CDr) be considered independent and modeled with a Gaussian distribution. These six Gaussian distributions are used to extract a set of non-antibody regions that match the span and orientation of the CDR H3 loop anchors. Shaffer, Andrew P. Hein and Robert Schleif for providing critical feedback on the manuscript. Conflict of interest statement.
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National Center for Biotechnology InformationU. Author manuscript; available in PMC Feb 3. Brian D. Weitzner1 Roland L. Dunbrack, Jr. Roland L. Jeffrey J. Author information Copyright and License information Disclaimer. Copyright notice. The publisher's final edited version of this article is available at Structure.
See other articles in PMC that cite the published article. Associated Data Supplementary Materials supplement: Figure S1, related to Figure 1 : Density estimates for each of the six degrees of freedom of the loop anchor transform for each residue segment from 1 the culled PDB set gray ; and 2 the known CDR H3 loops black show the relative structural diversity between the two sets.
Introduction Structural diversity of antibodies is achieved through a highly coordinated, intricate process of genetic recombination and hypermutation through which a relatively small number of genes are able to produce antibodies against an immense array of pathogens. Open in a separate window. Figure 1. Geometric parameters defining the C-terminal kink We sought a quantitative description of the previously observed C-terminal kink Kuroda et al.
Figure 2. Figure 3. CDR H3-like regions in non-antibody proteins We constructed conformation logos — seqLogos made using the DSSP secondary structure assignments Kabsch and Sander, — to compare the conformational diversity of sets of structures.
Figure 4. Figure 5. Figure 6. Summary of loop anchor transform matches To assess the degeneracy of the non-antibody LAT matches, we examined the proteins and protein families from which they originate.
Figure 7. Discussion CDR H3 is the most diverse region in antibodies due to its position relative to the V D J recombination sites, junctional diversification at these sites, and somatic hypermutation. Supplementary Material supplement Figure S1, related to Figure 1 : Density estimates for each of the six degrees of freedom of the loop anchor transform for each residue segment from 1 the culled PDB set gray ; and 2 the known CDR H3 loops black show the relative structural diversity between the two sets.
Click here to view. Footnotes Author contribution statement BDW designed experiments, created databases, wrote code, analyzed and interpreted data and wrote the manuscript. RLD and JJG supervised the project, designed experiments, interpreted data, and critically revised the manuscript. Standard conformations for the canonical structures of immunoglobulins.
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The Gene Ontology Consortium. Nature genetics. Semisynthetic combinatorial antibody libraries: a chemical solution to the diversity problem. Announcing the worldwide Protein Data Bank. Nat Struct Biol. Monoclonal antibody therapeutics: history and future. Curr Opin Pharmacol. Canonical structures for the hypervariable regions of immunoglobulins. Conformations of immunoglobulin hypervariable regions. WebLogo: a sequence logo generator. Genome Res. Antibody-antigen complexes.
Annu Rev Biochem. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. The Pfam protein families database. Nucleic Acids Res. The promise and challenge of high-throughput sequencing of the antibody repertoire. LoopWeaver: loop modeling by the weighted scaling of verified proteins.
J Comput Biol.
Most services for CDR’s credentialed practitioners remain uninterrupted. CDR staff members are available by telephone at /, ext. , by email at [email protected] or by live chat from am until pm CST. If you recently mailed physical items of timely importance, please contact CDR. For a staff list click derbattmogegefilykornorolsoftcat.xyzinfog: Blue Potential. Jul 01, · We describe an antibody optimization strategy that seeks to overcome the restrictive nature of existing affinity-maturation methods, by rapidly exploring a vast sequence space in an unbiased manner through application of PCR techniques and ribosome display. We exemplified the significance of this method by contrasting the crystal structure of the parent and optimized antibodies bound to. Jul 01, · The light blue shading in the Market Cap column shows micro-cap REITs. The other colors separate the REITs by debt ratio. Green shows. in both situations chimes are cdr/mr/hphe is good at counterganking and generally breaking up fights. and putting enemy jun behind. skill order. start q- max last. e second w third. max w, but occasionally drop point into e so mid game is like. 1/2/2or 1/3/2/1. between w and e. It also contains extra CDR, helping you to reach cap together with blue buff. Not widely used, yet pretty good item for any kind of player that likes to gamble a bit. It proved to be really good, whenever you have good early and you know, that enemy team don't really have too many tools to get on your face. CDR Gary Thomas (Ret.) talks deploying into heavy seas as a cutter swimmer to rescue a man overboard, commanding a Key West patrol boat during the tragic sinking of a Haitian ferry, working to support LORANimals, and how these events illustrate the servicewide impacts individuals can have in the Coast Guard. He also discusses his work with the National Coast Guard Museum Association and the Missing: Blue Potential. Mar 20, · CDR provides a nearly direct offset of CO 2 emissions by removing the CO 2. Other climate impacts from CDR are indirect: surface albedo may be changed through changes in vegetation required for some CDR strategies (e.g., afforestation); soil moisture, river runoff, nutrient cycles, etc.,may be changed to support some kinds of CDR (e.g., biochar). Blizzard has announced they will be fixing a bug with Ineffable Truth, so that flat cooldown reduction effects will not benefit from effects that increase your cooldown rate. The Blue Post specifically mentions Paladin's Hand of Justice talent but this will nerf any class that uses Ineffable Truth and has an ability that reduces the cooldown of another ability by a flat amount. Track listing: A. The Bells (original version) taken from “Kat Moda” EP (PM) () B1. The Bells (Blue Potential version) with Montpellier Philharmonic Orchestra taken from “Blue Potential” DVD+CD () / Classical arrangement by Thomas Roussel B2. The Homosapien Sapiens (previously unreleased) “Looking back in hindsight to the activity and accomplishments of Axis is with much. Feb 03, · The range of structural variation in the CDR H3 LATs is significantly more constrained than that of the non-antibody set from the PDB (Fig. S1 shows residue loops), which is a result of having selected H3 definitions extending to a structurally conserved position of the F V (to facilitate comparisons among such loops).After confirming that the degrees of freedom have a negligible .
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