Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (similar to 80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of similar to 2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water < dM(W) (0)delta M-W (t) > is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (similar to 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. (C) 2014 AIP Publishing LLC.

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.

Keys to success in an example of inter-competitor cooperation: The case of the "Big Seven" basque chefs

The case of the top chefs relates the two areas that are apparently most distant, nutrition and health technology. It is the element that binds[3] the four, making them into a single whole. The results achieved by our chefs, in terms of their individual and collective success and their international projection of the image of the Basque Country comprise a goal to which other industries in the region should aspire. It is therefore our plan to apply the keys to this successful inter-competitor cooperation to development of the health technology industry. At the same time, we want to fulfil one of the aims that have been established for the food area: to make use of the country’s gastronomy-related assets.

Distribution of Atlantic menhaden, Brevoortia tyrannus, purse-seine sets and catches from southern New England to North Carolina, 1985-96

Sets and catches of Atlantic menhaden, Brevoortia tyrannus, made in 1985-96 by purse-seine vessels from Virginia and North Carolina were studied by digitizing and analyzing Captain's Daily Fishing Reports (CDFR's), daily logs of fishing activities completed by captains of menhaden vessels. 33,674 CDFR's were processed, representing 125,858 purse-seine sets. On average, the fleet made 10,488 sets annually. Virginia vessels made at least one purse-seine set on 67%-83% of available fishing days between May and December. In most years, five was the median number of sets attempted each fishing day. Mean set duration ranged from 34 to 43 minutes, and median catch per set ranged from 15 to 30 metric tons (t). Spotter aircraft assisted in over 83% of sets overall. Average annual catch in Chesapeake Bay (149,500 t) surpassed all other fishing areas, and accounted for 52% of the fleet's catch. Annual catch from North Carolina waters (49,100 t) ranked a distant second. Fishing activity in ocean waters clustered off the Mid-Atlantic states in June-September, and off North Carolina in November-January. Delaware Bay and the New Jersey coast were important alternate fishing grounds during summer. Across all ocean fishing areas, most sets and catch occurred within 3 mi. of shore, but in Chesapeake Bay about half of all fishing activity occurred farther offshore. In Virginia, areas adjacent to fish factories tended to be heavily fished. Recent regulatory initiatives in various coastal states threaten the Atlantic menhaden fleet's access to traditional nearshore fishing grounds. (PDF file contains 26 pages.)

Drying of fish--factors to consider

Although one of the best possibilities for raising the animal protein of the diets of Nigerian is to increase the consumption of fish; particularly through the use of several methods of long term preservation techniques, such as drying, no radical approach has yet emerged. Although, a great deal of the artisanal fish catch is dried for the huge consumer and distant markets, the traditional methods of fish preservation need improvements to cope with demand for increased quantity, shelf-stable, and improved quality of fish products. The paper discusses drying requirements, heat and mass transfer, consumer acceptance, fuel sources, storage and marketing of dried fish products; and suggest ways and means of structurally transforming the artisanal technology of fish drying

Magnetospheric access of solar particles and the configuration of the distant geomagnetic field

The access of 1.2-40 MeV protons and 0.4-1.0 MeV electrons from interplanetary space to the polar cap regions has been investigated with an experiment on board a low altitude, polar orbiting satellite (OG0-4).

A total of 333 quiet time observations of the electron polar cap boundary give a mapping of the boundary between open and closed geomagnetic field lines which is an order of magnitude more comprehensive than previously available.

Persistent features (north/south asymmetries) in the polar cap proton flux, which are established as normal during solar proton events, are shown to be associated with different flux levels on open geomagnetic field lines than on closed field lines. The pole in which these persistent features are observed is strongly correlated to the sector structure of the interplanetary magnetic field and uncorrelated to the north/south component of this field. The features were observed in the north (south) pole during a negative (positive) sector 91% of the time, while the solar field had a southward component only 54% of the time. In addition, changes in the north/south component have no observable effect on the persistent features.

Observations of events associated with co-rotating regions of enhanced proton flux in interplanetary space are used to establish the characteristics of the 1.2 - 40 MeV proton access windows: the access window for low polar latitudes is near the earth, that for one high polar latitude region is ~250 R_⊕ behind the earth, while that for the other high polar latitude region is ~1750 R_⊕ behind the earth. All of the access windows are of approximately the same extent (~120 R_⊕). The following phenomena contribute to persistent polar cap features: limited interplanetary regions of enhanced flux propagating past the earth, radial gradients in the interplanetary flux, and anisotropies in the interplanetary flux.

These results are compared to the particle access predictions of the distant geomagnetic tail configurations proposed by Michel and Dessler, Dungey, and Frank. The data are consistent with neither the model of Michel and Dessler nor that of Dungey. The model of Frank can yield a consistent access window configuration provided the following constraints are satisfied: the merging rate for open field lines at one polar neutral point must be ~5 times that at the other polar neutral point, related to the solar magnetic field configuration in a consistent fashion, the migration time for open field lines to move across the polar cap region must be the same in both poles, and the open field line merging rate at one of the polar neutral points must be at least as large as that required for almost all the open field lines to have merged in 0 (one hour). The possibility of satisfying these constraints is investigated in some detail.

The role played by interplanetary anisotropies in the observation of persistent polar cap features is discussed. Special emphasis is given to the problem of non-adiabatic particle entry through regions where the magnetic field is changing direction. The degree to which such particle entry can be assumed to be nearly adiabatic is related to the particle rigidity, the angle through which the field turns, and the rate at which the field changes direction; this relationship is established for the case of polar cap observations.

Tão próximos e tão distantes: indivíduo e pessoa nas relações dentro de um edifício residencial

Essa dissertação é um estudo de antropologia urbana sobre as relações entre moradores e entre moradores e empregados em dois edifícios residenciais nos bairros do Maracanã e Grajaú. O objetivo foi demonstrar os sentidos subjacentes ao uso das noções de indivíduo e de pessoa, de individualismo e de hierarquia, em cada um desses contextos de relacionamento. Foram realizadas sete entrevistas semi-estruturadas com homens e mulheres de camadas médias urbanas. Os sentidos sugeridos pelos moradores apontaram para a existência de uma tensão entre as noções de público e privado, cordialidade e impessoalidade nos modos de classificar a si mesmo e aos outros nas interações sob diferentes circunstâncias dentro do edifício. Os depoimentos dos entrevistados concederam maior destaque às relações que mantinham com suas empregadas domésticas do que com as empregadas de outros condôminos. Nesse caso concedeu-se destaque para a operação de classificações em que pravaleciam a hierarquização e a subordinação, da parte dos moradores, e expedientes de agenciamento, por parte dos empregados.

The Fisheries for Mangrove Cockles,Anadaraspp., from Mexico to Peru, With Descriptions of Their Habitats and Biology, the Fishermen’s Lives, and the Effects of Shrimp Farming

This paper provides the first description of the mangrove cockle, Anadara spp., fisheries throughout their Latin American range along the Pacific coast from Mexico to Peru. Two species, A. tuberculosa and A. grandis, are found over the entire range, while A. similis occurs from El Salvador to Peru. Anadara tuberculosa is by far the most abundant, while A. grandis has declined in abundance during recent decades. Anadara tuberculosa and A. similis occur in level mud sediments in mangrove swamps, comprised mostly of Rhizophora mangle, which line the main-lands and islands of lagoons, whereas A. grandis inhabits intertidal mud flats along the edges of the same mangrove swamps. All harvested cockles are sexually mature. Gametogenesis of the three species occurs year round, and juvenile cockles grow rap-idly. Cockle densities at sizes at least 16–42 mm long ranged from 7 to 24/m2 in Mexico. Macrofaunal associates of cockles include crustaceans, gastropods, and finfishes. The mangrove swamps are in nearly pristine condition in every country except Honduras, Ecuador, and Peru, where shrimp farms constructed in the 1980’s and 1990’s have destroyed some mangrove zones. In addition, Hurricane Mitch destroyed some Honduran mangrove swamps in 1998. About 15,000 fishermen, including men, women, and children, harvest the cockles. Ecuador has the largest tabulated number of fishermen, 5,055, while Peru has the fewest, 75. Colombia has a large number, perhaps exceeding that in Ecuador, but a detailed census of them has never been made. The fishermen are poor and live a meager existence; they do not earn sufficient money to purchase adequate food to allow their full health and growth potential. They travel almost daily from their villages to the harvesting areas in wooden canoes and fiberglass boats at low tide when they can walk into the mangrove swamps to harvest cockles for about 4 h. Harvest rates, which vary among countries owing to differences in cockle abundances, range from about 50 cockles/fisherman/day in El Salvador and Honduras to 500–1,000/ fisherman/day in Mexico. The fishermen return to their villages and sell the cockles to dealers, who sell them mainly whole to market outlets within their countries, but there is some exporting to adjacent countries. An important food in most countries, the cockles are eaten in seviche, raw on the half-shell, and cooked with rice. The cockles are under heavy harvesting pressure, except in Mexico, but stocks are not yet being depleted because they are harvested at sizes which have already spawned. Also some spawning stocks lie within dense mangrove stands which the fishermen cannot reach. Consumers fortunately desire the largest cockles, spurning the smallest. Cockles are important to the people, and efforts to reduce the harvests to prevent overfishing would lead to severe economic suffering in the fishing communities. Pro-grams to conserve and improve cockle habitats may be the most judicious actions to take. Preserving the mangrove swamps intact, increasing their sizes where possible, and controlling cockle predators would lead to an increase in cockle abundance and harvests. Fishes that prey on juvenile cockles might be seined along the edges of swamps before the tide rises and they swim into the swamps to feed. Transplanting mangrove seedlings to suitable areas might increase the size of those habitats. The numbers of fishermen may increase in the future, because most adults now have several children. If new fishermen are tempted to harvest small, immature cockles and stocks are not increased, minimum size rules for harvestable cockles could be implemented and enforced to ensure adequate spawning.

Yellowfin Sole, Pleuronectes asper, of the Eastern Bering Sea: Biological Characteristics, History of Exploitation, and Management

Yellowfin sole, Pleuronectes asper, is the second most abundant flatfish in the North Pacific Ocean and is most highly concentrated in the eastern Bering Sea. It has been a target species in the eastern Bering Sea since the mid-1950's, initially by foreign distant-water fisheries but more recently by U.S. fisheries. Annual commercial catches since 1959 have ranged from 42,000 to 554,000 metric tons (t). Yellowfin sole is a relatively small flatfish averaging about 26 cm in length and 200 g in weight in commercial catches. It is distributed from nearshore waters to depths of about 100 m in the eastern Bering Sea in summer, but moves to deeper water in winter to escape sea ice. Yellowfin sole is a benthopelagic feeder. It is a longlived species (>20 years) with a correspondingly low natural mortality rate estimated at 0.12. After being overexploited during the early years of the fishery and suffering a substantial decline in stock abundance, the resource has recovered and is currently in excellent condition. The biomass during the 1980's may have been as high as, if not higher than, that at the beginning of the fishery. Based on results of demersal trawl surveys and two age structured models, the current exploitable biomass has been estimated to range between 1.9 and 2.6 million t. Appropriate harvest strategies were investigated under a range of possible recruitment levels. The recommended harvest level was calculated by multiplying the yield derived from the FOI harvest level (161 g at F = 0.14) hy an average recruitment value resulting in a commercial harvest of 276,900 t, or about 14% of the estimated exploitable biomass.

Coastal States and Distant-water Fishing Nation Relations: An Economist's Perspective

The widespread implementation of Extended Fisheries Jurisdiction (EFJ) has confronted coastal states with several resource management problems. One of these consists of the economic relations, if any, that the coastal state should establish with distant-water fishing nations (DWFN's) seeking access to the coastal state's 200-mile zone. Several of the other papers presented here deal with specific aspects of the issue. This paper, on the other hand, will concern itself with the question of the analytical framework to be used by economists in studying this issue. It will offer some suggestions with respect to possible components of the framework. In doing so, the paper will restrict itself to the coastal state's perspective of EFJ and the management issues arising therefrom. It goes without saying, of course, that an enlightened coastal state will attempt to acquaint itself with the DWFN view of the world.

A U.S. Perspective on Access to Fisheries Resources

The passage of the Magnuson Fishery Conservation and Management Act of 1976 (MFCMA) and the establishment of a 200-mile exclusive economic zone (EEZ) in 1983 have resulted in a radical change in the pattern of foreign fishing operations off the U. S. coasts. Likewise, the extensions of 200-mile EEZ's by other nations have impacted U.S. distant-water fisheries. The result has been that a new international framework for fisheries is emerging and is continuing to evolve.

A report on the strategic fisheries stock assessment survey of the River Winster 1995 together with a coarse fish survey in 1994 and reference to the 1995 drought

This is the report on the strategic fisheries stock assessment survey of the River Winster 1995 together with a coarse fish survey in 1994 and reference to the 1995 drought, produced by the Environment Agency North West in 1996. Salmonid production within the Winster catchment was dominated by trout although good densities of salmon juveniles were found on some main river sites. Despite suffering drought conditions for much of 1995, only salmon fry production appeared to have been affected. Coarse fish populations once found in the lower reaches of the Winster appear to have declined to very low levels with no fish sampled. This may be partly due to broken tidal gates allowing saline intrusion. It seems that the lower river was suited to the development of a recreational coarse fishery, now that the gates have been repaired. This report completes the strategic stock assessment surveys planned for the period 1992-1995. It represents the last major catchment that was surveyed to determine the current status of fisheries in the South and South West Cumbria areas.

Reports of the ICSF seminar / workshop on the conditions of fishworkers on distant water vessels, Manila, Philippines, 1-3 February 1991

This ICSF Exchange Programme held in Manila is an offshoot of the Bangkok Conference on “Global Fisheries Trends and Future of Fishworkers” held on January 22–27, 1990. One of the issues raised in that conference was about the operation of Taiwanese fishing vessels outside its territorial waters and the impact of such operations on small fishermen from the countries concerned. The presence of a Taiwanese fishworker as well as an NGO supporter contributed to an enlightening discussion as the former shed light on the sad plight of Taiwanese fishworkers who are the victims of such structural problems. This meaningful exchange between groups of fishermen, particularly Taiwanese and Filipinos, resulted in the plan of the Taiwanese delegation to have some Taiwanese fishermen visit the Philippines and immerse in fishing communities.

Robust F0 estimation based on a multi-microphone periodicity function for distant-talking speech

This work addresses the problem of deriving F0 from distanttalking speech signals acquired by a microphone network. The method here proposed exploits the redundancy across the channels by jointly processing the different signals. To this purpose, a multi-microphone periodicity function is derived from the magnitude spectrum of all the channels. This function allows to estimate F0 reliably, even under reverberant conditions, without the need of any post-processing or smoothing technique. Experiments, conducted on real data, showed that the proposed frequency-domain algorithm is more suitable than other time-domain based ones.

The price of pain and the value of suffering.

Estimating the financial value of pain informs issues as diverse as the market price of analgesics, the cost-effectiveness of clinical treatments, compensation for injury, and the response to public hazards. Such valuations are assumed to reflect a stable trade-off between relief of discomfort and money. Here, using an auction-based health-market experiment, we show that the price people pay for relief of pain is strongly determined by the local context of the market, that is, by recent intensities of pain or immediately disposable income (but not overall wealth). The absence of a stable valuation metric suggests that the dynamic behavior of health markets is not predictable from the static behavior of individuals. We conclude that the results follow the dynamics of habit-formation models of economic theory, and thus, this study provides the first scientific basis for this type of preference modeling.