More Like this

1. Chromophore hydrolysis and release from photoactivated rhodopsin in native membranes

   https://doi.org/10.1073/pnas.2213911119  

   Hong, John D.; Salom, David; Kochman, Michał Andrzej; Kubas, Adam; Kiser, Philip D.; Palczewski, Krzysztof (November 2022, Proceedings of the National Academy of Sciences)

   For sustained vision, photoactivated rhodopsin (Rho*) must undergo hydrolysis and release of all- trans -retinal, producing substrate for the visual cycle and apo-opsin available for regeneration with 11- cis -retinal. The kinetics of this hydrolysis has yet to be described for rhodopsin in its native membrane environment. We developed a method consisting of simultaneous denaturation and chromophore trapping by isopropanol/borohydride, followed by exhaustive protein digestion, complete extraction, and liquid chromatography–mass spectrometry. Using our method, we tracked Rho* hydrolysis, the subsequent formation of N -retinylidene-phosphatidylethanolamine ( N -ret-PE) adducts with the released all- trans -retinal, and the reduction of all- trans -retinal to all- trans -retinol. We found that hydrolysis occurred faster in native membranes than in detergent micelles typically used to study membrane proteins. The activation energy of the hydrolysis in native membranes was determined to be 17.7 ± 2.4 kcal/mol. Our data support the interpretation that metarhodopsin II, the signaling state of rhodopsin, is the primary species undergoing hydrolysis and release of its all- trans -retinal. In the absence of NADPH, free all- trans -retinal reacts with phosphatidylethanolamine (PE), forming a substantial amount of N -ret-PE (∼40% of total all- trans -retinal at physiological pH), at a rate that is an order of magnitude faster than Rho* hydrolysis. However, N -ret-PE formation was highly attenuated by NADPH-dependent reduction of all- trans -retinal to all- trans -retinol. Neither N -ret-PE formation nor all- trans -retinal reduction affected the rate of hydrolysis of Rho*. Our study provides a comprehensive picture of the hydrolysis of Rho* and the release of all- trans -retinal and its reentry into the visual cycle, a process in which alteration can lead to severe retinopathies. 

   more » « less
2. Associations Among Cultivar Cropping Sequence, 2,4-Diacetlyphloroglucinol–Producing Pseudomonad Populations, and Take-All Disease of Winter Wheat in Oregon

   https://doi.org/10.1094/PDIS-02-24-0372-RE  

   Perkins, Evan M; Mundt, Christopher C (December 2024, Plant Disease)

   Take-all of wheat (Triticum aestivum L.), caused by Gaeumannomyces tritici (syn. G. graminis var. tritici), is perhaps the most important soilborne disease of wheat globally and can cause substantial yield losses under several cropping scenarios in Oregon. Although resistance to take-all has not been identified in hexaploid wheat, continuous cropping of wheat for several years can reduce take-all severity through the development of suppressive soils, a process called “take-all decline” (TAD). Extensive work has shown that TAD is driven primarily by members of the Pseudomonas fluorescens complex that produce 2,4-diacetlyphloroglucinol (DAPG), an antibiotic that is associated with antagonism and induced host resistance against multiple pathogens. Field experiments were conducted to determine the influence of agronomically relevant first-year wheat cultivars on take-all levels and ability to accumulate DAPG-producing pseudomonads within their rhizospheres in second-year field trials and in greenhouse trials. One first-year wheat cultivar consistently resulted in less take-all in second-year wheat and accumulated significantly more DAPG-producing pseudomonads than other cultivars, suggesting a potential mechanism for take-all reduction associated with that cultivar. An intermediate level of take-all suppression in other cultivars was not clearly associated with population size of DAPG-producing pseudomonads, however. The first-year cultivar effect on take-all dominated in subsequent plantings, and its impact was not specific to the first-year cultivar. Our results confirm that wheat cultivars may be used to suppress take-all when deployed appropriately over cropping seasons, an approach that is cost-effective, sustainable, and currently being used by some wheat growers in Oregon to reduce take-all. 

   more » « less
3. Universal knot diagrams

   https://doi.org/10.1142/S0218216519500317  

   Even-Zohar, Chaim; Hass, Joel; Linial, Nati; Nowik, Tahl (June 2019, Journal of Knot Theory and Its Ramifications)

   We study collections of planar curves that yield diagrams for all knots. In particular, we show that a very special class called potholder curves carries all knots. This has implications for realizing all knots and links as special types of meanders and braids. We also introduce and apply a method to compare the efficiency of various classes of curves that represent all knots. 

   more » « less
4. Heterogeneous Paxos

   Sheff, Isaac; Wang, Xinwen; van Renesse, Robbert; Myers, Andrew C. (January 2021, OPODIS: International Conference on Principles of Distributed Systems)

   null (Ed.)

   In distributed systems, a group of learners achieve consensus when, by observing the output of some acceptors, they all arrive at the same value. Consensus is crucial for ordering transactions in failure-tolerant systems. Traditional consensus algorithms are homogeneous in three ways: (1) all learners are treated equally, (2) all acceptors are treated equally, and (3) all failures are treated equally.These assumptions, however, are unsuitable for cross-domain applications, including blockchains, where not all acceptors are equally trustworthy, and not all learners have the same assumptions and priorities. We present the first algorithm to be heterogeneous in all three respects. Learners set their own mixed failure tolerances over differently trusted sets of acceptors. We express these assumptions in a novel Learner Graph, and demonstrate sufficient conditions for consensus. We present Heterogeneous Paxos, an extension of Byzantine Paxos. Heterogeneous Paxos achieves consensus for any viable Learner Graph in best-case three message sends, which is optimal. We present a proof-of-concept implementation and demonstrate how tailoring for heterogeneous scenarios can save resources and reduce latency. 

   more » « less
5. Snaking bifurcations of localized patterns on ring lattices

   https://doi.org/10.1093/imamat/hxab023  

   Tian, Moyi; Bramburger, Jason J; Sandstede, Björn (June 2021, IMA Journal of Applied Mathematics)

   null (Ed.)

   Abstract We study the structure of stationary patterns in bistable lattice dynamical systems posed on rings with a symmetric coupling structure in the regime of small coupling strength. We show that sparse coupling (for instance, nearest-neighbour or next-nearest-neighbour coupling) and all-to-all coupling lead to significantly different solution branches. In particular, sparse coupling leads to snaking branches with many saddle-node bifurcations, while all-to-all coupling leads to branches with six saddle nodes, regardless of the size of the number of nodes in the graph. 

   more » « less