Anharmonicity and self-similarity of the free energy landscape of protein G

The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence of salient thermodynamical features. While the quasi-harmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.Comment: revtex, 6 pages, 5 figure

Influence of coral bleaching on the fauna of Tutia Reef, Tanzania

In 1998, coral reefs of Tanzania were severely affected by bleaching. The coral mortality that followed caused a concern for coral reef degradation and overall resource depletion. In this study, we investigated coral bleaching effects on the coral reef fauna at Tutia Reef in Mafia Island Marine Park, Tanzania. Corals from adjacent reef patches of the species Acropora formosa were transplanted into plots, and reef structure and associated fish assemblages were examined before and after the bleaching event. Following the coral bleaching, 88% of all corals died. A year after the event, a large proportion of the dead corals was still standing. As surviving and dead corals were from different clones, results suggested that genetic variation might influence bleaching tolerance. After the bleaching event, a change in fish community composition, with an increase in fish abundance, could be seen. Species diversity, however, was less affected. There was a correlation between structural complexity and fish densities after disturbance. This indicates that the reef may uphold an abundant fish population as long as the architectural structure is intact. The impact that the coral beaching event may have on fisheries is difficult to anticipate. The Tutia Reef supports a multi-species fishery and a variety of techniques are used. As a broad range of species are targeted, including smaller fishes, catches may not be reduced as long as the reef structure is sustained. If reef degradation follows, however, fish abundance is likely to decrease

Usage of FTA (R) Classic Cards for Safe Storage, Shipment, and Detection of Arboviruses

Infections caused by arthropod-borne RNA viruses are overrepresented among emerging infectious diseases. Effective methods for collecting, storing, and transporting clinical or biological specimens are needed worldwide for disease surveillance. However, many tropical regions where these diseases are endemic lack analytical facilities and possibility of continuous cold chains, which presents challenges from both a biosafety and material preservation perspective. Whatman (R) FTA (R) Classic Cards may serve as an effective and safe option for transporting hazardous samples at room temperature, particularly for RNA viruses classified as biosafety level (BSL) 2 and 3 pathogens, from sampling sites to laboratories. In this study, we investigated the biosafety and perseverance of representative alpha-and flaviviruses stored on FTA (R) cards. To evaluate the virus inactivation capacity of FTA (R) cards, we used Sindbis virus (SINV), chikungunya virus (CHIKV), and Japanese encephalitis virus (JEV). We inoculated susceptible cells with dilution series of eluates from viral samples stored on the FTA (R) cards and observed for cytopathic effect to evaluate the ability of the cards to inactivate viruses. All tested viruses were inactivated after storage on FTA (R) cards. In addition, we quantified viral RNA of JEV, SINV, and tick-borne encephalitis virus (TBEV) stored on FTA (R) cards at 4 degrees C, 25 degrees C, and 37 degrees C for 30 days using two reverse transcriptase quantitative PCR assays. Viral RNA of SINV stored on FTA (R) cards was not reduced at either 4 degrees C or 25 degrees C over a 30-day period, but degraded rapidly at 37 degrees C. For JEV and TBEV, degradation was observed at all temperatures, with the most rapid degradation occurring at 37 degrees C. Therefore, the use of FTA (R) cards provides a safe and effective workflow for the collection, storage, and analysis of BSL 2- and 3-virus RNA samples, but there is a risk of false negative results if the cards are stored at higher temperatures for long periods of time. Conscious usage of the cards can be useful in disease surveillance and research, especially in tropical areas where transportation and cold chains are problematic

Maximizing Laboratory Production of Aflatoxins and Fumonisins for Use in Experimental Animal Feeds

Warm and humid climatic conditions coupled with poor agricultural practices in sub-Saharan Africa favor the contamination of food and feed by Aspergillus flavus and Fusarium verticillioides fungi, which subsequently may produce aflatoxins (AFs) and fumonisins (FBs), respectively. The growth of fungi and the production of mycotoxins are influenced by physical (temperature, pH, water activity, light and aeration), nutritional, and biological factors. This study aimed at optimizing the conditions for the laboratory production of large quantities of AFs and FBs for use in the animal experiments. A. flavus and F. verticillioides strains, previously isolated from maize in Kenya, were used. Levels of AFB1 and total FBs (FB1, FB2, and FB3) in different growth substrates were screened using ELISA methods. Maize kernels inoculated with three different strains of A. flavus simultaneously and incubated at 29 degrees C for 21 days had the highest AFB1 level of 12,550 +/- 3397 mu g/kg of substrate. The highest level of total FBs (386,533 +/- 153,302 mu g/kg of substrate) was detected in cracked maize inoculated with three different strains of F. verticillioides and incubated for 21 days at temperatures of 22-25 degrees C in a growth chamber fitted with yellow light. These two methods are recommended for the mass production of AFB1 and FBs for animal feeding trials

Detection of Asynchronous Message Passing Errors Using Static Analysis

Concurrent programming is hard and prone to subtle errors. In this paper we present a static analysis that is able to detect some commonly occurring kinds of message passing errors in languages with dynamic process creation and communication based on asynchronous message passing. Our analysis is completely automatic, fast, and strikes a proper balance between soundness and completeness: it is effective in detecting errors and avoids false alarms by computing a close approximation of the interprocess communication topology of programs. We have integrated our analysis in dialyzer, a widely used tool for detecting software defects in Erlang programs, and demonstrate its effectiveness on libraries and applications of considerable size. Despite the fact that these applications have been developed over a long period of time and are reasonably well-tested, our analysis has managed to detect a significant number of previously unknown message passing errors in their code

Strong pressure-energy correlations in van der Waals liquids

Strong correlations between equilibrium fluctuations of the configurational parts of pressure and energy are found in the Lennard-Jones liquid and other simple liquids, but not in hydrogen-bonding liquids like methanol and water. The correlations, that are present also in the crystal and glass phases, reflect an effective inverse power-law repulsive potential dominating fluctuations, even at zero and slightly negative pressure. In experimental data for supercritical Argon, the correlations are found to be approximately 96%. Consequences for viscous liquid dynamics are discussed.Comment: Phys. Rev. Lett., in pres

Trans-phonon effects in ultrafast nano-devices

We report a novel phenomenon in carbon nanotube (CNT) based devices, the transphonon effects, which resemble the transonic effects in aerodynamics. It is caused by dissipative resonance of nanotube phonons similar to the radial breathing mode, and subsequent drastic surge of the dragging force on the sliding tube, and multiple phonon barriers are encountered as the intertube sliding velocity reaches critical values. It is found that the transphonon effects can be tuned by applying geometric constraints or varying chirality combinations of the nanotubes