Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Efficient Protocol for Authenticated Email Search

Executing authenticated computation on outsourced data is currently an area of major interest in cryptology. Large databases are being outsourced to untrusted servers without appreciable verification mechanisms. As adversarial server could produce erroneous output, clients should not trust the server's response blindly. Primitive set operations like union, set difference, intersection etc. can be invoked on outsourced data in different concrete settings and should be verifiable by the client. One such interesting adaptation is to authenticate email search result where the untrusted mail server has to provide a proof along with the search result. Recently Ohrimenko et al. proposed a scheme for authenticating email search. We suggest significant improvements over their proposal in terms of client computation and communication resources by properly recasting it in two-party settings. In contrast to Ohrimenko et al. we are able to make the number of bilinear pairing evaluation, the costliest operation in verification procedure, independent of the result set cardinality for union operation. We also provide an analytical comparison of our scheme with their proposal which is further corroborated through experiments.

Joint modeling of lithosphere and mantle dynamics: Evaluation of constraints from global tomography models

With the advances in technology, seismological theory, and data acquisition, a number of high-resolution seismic tomography models have been published. However, discrepancies between tomography models often arise from different theoretical treatments of seismic wave propagation, different inversion strategies, and different data sets. Using a fixed velocity-to-density scaling and a fixed radial viscosity profile, we compute global mantle flow models associated with the different tomography models and test the impact of these for explaining surface geophysical observations (geoid, dynamic topography, stress, and strain rates). We use the joint modeling of lithosphere and mantle dynamics approach of Ghosh and Holt (2012) to compute the full lithosphere stresses, except that we use HC for the mantle circulation model, which accounts for the primary flow-coupling features associated with density-driven mantle flow. Our results show that the seismic tomography models of S40RTS and SAW642AN provide a better match with surface observables on a global scale than other models tested. Both of these tomography models have important similarities, including upwellings located in Pacific, Eastern Africa, Iceland, and mid-ocean ridges in the Atlantic and Indian Ocean and downwelling flows mainly located beneath the Andes, the Middle East, and central and Southeast Asia.

Simulated long-term climate response to idealized solar geoengineering

Solar geoengineering has been proposed as a potential means to counteract anthropogenic climate change, yet it is unknown how such climate intervention might affect the Earth's climate on the millennial time scale. Here we use the HadCM3L model to conduct a 1000year sunshade geoengineering simulation in which solar irradiance is uniformly reduced by 4% to approximately offset global mean warming from an abrupt quadrupling of atmospheric CO2. During the 1000year period, modeled global climate, including temperature, hydrological cycle, and ocean circulation of the high-CO2 simulation departs substantially from that of the control preindustrial simulation, whereas the climate of the geoengineering simulation remains much closer to that of the preindustrial state with little drift. The results of our study do not support the hypothesis that nonlinearities in the climate system would cause substantial drift in the climate system if solar geoengineering was to be deployed on the timescale of a millennium.

Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http://bioserver1.physics.iisc.ernet.in/hbcs/.

Union Formation and Bargaining Rules in the Labor Market

This paper analyzes union formation in a model of bargaining between a firm and several unions. We address two questions: first, the optimal configuration of unions (their number and size) and, second, the impact of the bargaining pattern (simultaneous or sequential). For workers, grouping into several unions works as a price discrimination device which, at the same time, decreases their market power. The analysis shows that optimal union configuration depends on the rules that regulate the bargaining process (monopoly union, Nash bargaining or right to manage).

Whales, dolphins, and porpoises of the western North Atlantic: a guide to their identification

This is an identification guide for cetaceans (whales, dolphins, and porpoises). It was designed to assist laypersons in identifying cetaceans encountered in the western North Atlantic Ocean and was intended for use by ongoing cetacean observer programs. This publication includes sections on identifying cetaceans at sea as well as stranded animals on shore. Species accounts are divided by body size and presence or lack of a dorsal fin. Appendices cover tags used on cetacean species; how to record and report cetacean observations at see and for stranded cetaceans; and a list of contacts for reporting cetacean strandings. (Document pdf contains 183 pages - file takes considerable time to open)

Influence of the northeastern Atlantic oceano-meteorological variability on the northern hake ("merluccius merluccius"). Analysis of the 1978-2006 period

316 p. : il., graf., map.

The frequency of muscle protein polymorphism in Menidia menidia (Atherinidae) along the Atlantic coast

(PDF has 6 pages.)

Interactions between adult migratory striped bass (Morone saxatilis) and their prey during winter off the Virginia and North Carolina Atlantic coast from 1994 through 2007

The migratory population of striped bass (Morone saxatilis) (>400 mm total length[TL]) spends winter in the Atlantic Ocean off the Virginia and North Carolina coasts of the United States. Information on trophic dynamics for these large adults during winter is limited. Feeding habits and prey were described from stomach contents of 1154 striped bass ranging from 373 to 1250 mm TL, collected from trawls during winters of 1994-96, 2000, and 2002-03, and from the recreational fishery during 2005-07. Nineteen prey species were present in the diet. Overall, Atlantic menhaden (Brevoortia tyrannus) and bay anchovy (Anchoa mitchilli) dominated the diet by boimass (67.9%) and numerically (68.6%). The percent biomass of Atlantic menhaden during 1994-2003 to 87.0% during 2005-07. Demersal fish species such as Atlantic croaker (Micropogonias undulatus) and spot (Leiostomus xanthurus) represented <15% of the diet biomass, whereas alosines (Alosa spp.) were rarely observed. Invertebrates were least important, contributing <1.0% by biomass and numerically. Striped bass are capable of feeding on a wide range of prey sizes (2% to 43% of their total length). This study outlines the importance of clupeoid fishes to striped bass winter production and also shows that predation may be exerting pressure on one of their dominant prey, the Atlantic menhaden.

An Integrated Assessment of the Introduction of Lionfish (Pterois volitans/miles complex) to the Western Atlantic Ocean.

Lionfish (Pterois volitans/miles complex) are venomous coral reef fishes from the Indian and western Pacific oceans that are now found in the western Atlantic Ocean. Adult lionfish have been observed from Miami, Florida to Cape Hatteras, North Carolina, and juvenile lionfish have been observed off North Carolina, New York, and Bermuda. The large number of adults observed and the occurrence of juveniles indicate that lionfish are established and reproducing along the southeast United States coast. Introductions of marine species occur in many ways. Ballast water discharge, a very common method of introduction for marine invertebrates, is responsible for many freshwater fish introductions. In contrast, most marine fish introductions result from intentional stocking for fishery purposes. Lionfish, however, likely were introduced via unintentional or intentional aquarium releases, and the introduction of lionfish into United States waters should lead to an assessment of the threat posed by the aquarium trade as a vector for fish introductions. Currently, no management actions are being taken to limit the effect of lionfish on the southeast United States continental shelf ecosystem. Further, only limited funds have been made available for research. Nevertheless, the extent of the introduction has been documented and a forecast of the maximum potential spread of lionfish is being developed. Under a scenario of no management actions and limited research, three predictions are made: ● With no action, the lionfish population will continue to grow along the southeast United States shelf. ● Effects on the marine ecosystem of the southeast United States will become more noticeable as the lionfish population grows. ● There will be incidents of lionfish envenomations of divers and/or fishers along the east coast of the United States. Removing lionfish from the southeast United States continental shelf ecosystem would be expensive and likely impossible. A bounty could be established that would encourage the removal of fish and provide specimens for research. However, the bounty would need to be lower than the price of fish in the aquarium trade (~$25-$50 each) to ensure that captured specimens were from the wild. Such a low bounty may not provide enough incentive for capturing lionfish in the wild. Further, such action would only increase the interaction between the public and lionfish, increasing the risk of lionfish envenomations. As the introduction of lionfish is very likely irreversible, future actions should focus on five areas. 1) The population of lionfish should be tracked. 2) Research should be conducted so that scientists can make better predictions regarding the status of the invasion and the effects on native species, ecosystem function, and ecosystem services. 3) Outreach and education efforts must be increased, both specifically toward lionfish and more generally toward the aquarium trade as a method of fish introductions. 4) Additional regulation should be considered to reduce the frequency of marine fish introduction into U.S. waters. However, the issue is more complicated than simply limiting the import of non-native species, and these complexities need to be considered simultaneously. 5) Health care providers along the east coast of the United States need to be notified that a venomous fish is now resident along the southeast United States. The introduction and spread of lionfish illustrates the difficulty inherent in managing introduced species in marine systems. Introduced species often spread via natural mechanisms after the initial introduction. Efforts to control the introduction of marine fish will fail if managers do not consider the natural dispersal of a species following an introduction. Thus, management strategies limiting marine fish introductions need to be applied over the scale of natural ecological dispersal to be effective, pointing to the need for a regional management approach defined by natural processes not by political boundaries. The introduction and success of lionfish along the east coast should change the long-held perception that marine fish invasions are a minimal threat to marine ecosystems. Research is needed to determine the effects of specific invasive fish species in specific ecosystems. More broadly, a cohesive plan is needed to manage, mitigate and minimize the effects of marine invasive fish species on ecosystems that are already compromised by other human activities. Presently, the magnitude of marine fish introductions as a stressor on marine ecosystems cannot be quantified, but can no longer be dismissed as negligible. (PDF contains 31 pages)

Preliminary guide to the identification of the early life history stages of Priacanthid fishes of the Western Central Atlantic

The family Priacanthidae contains four genera and four species that occur in the western central North Atlantic (Starnes, 1988). Pristigenys alta is distributed in the Caribbean, Gulf of Mexico and along the east coast of North America. Although juveniles have been reported from as far north as southern New England waters, adults are not reported north of Cape Hatteras, NC. Priacanthus arenatus is distributed in tropical and tropically influenced areas of the western central North Atlantic in insular and continental shelf waters. Adult P. arenatus are distributed north to North Carolina and Bermuda, juveniles have been collected as far north as Nova Scotia. Cookeolus japonicus and Heteropriacanthus cruentatus are circumglobally distributed species and are both common in insular habitats. In the western central North Atlantic, C. japonicus ranges from New Jersey to Argentina; H. cruentatus from New Jersey and northern Gulf of Mexico to southern Brazil (Starnes, 1988). (PDF contains 6 pages)