Acidithiobacillus ferriphilus sp. nov.: a facultatively anaerobic iron- and sulfur-metabolising extreme acidophile

The genus Acidithiobacillus includes three species that conserve energy from the oxidation of ferrous iron, as well as reduced sulfur, to support their growth. Previous work, based on multi-locus sequence analysis, identified a fourth group of iron- and sulfur-oxidizing acidithiobacilli as a potential distinct species. Eleven strains of ‘Group IV’ acidithiobacilli, isolated from different global locations, have been studied. These were all shown to be obligate chemolithotrophs, growing aerobically by coupling the oxidation of ferrous iron or reduced sulfur (but not hydrogen) to molecular oxygen, or anaerobically by the oxidation of reduced sulfur coupled to ferric iron reduction. All strains were mesophilic, although some were also psychrotolerant. Strain variation was also noted in terms of tolerance to extremely low pH and to elevated concentrations of transition metals. One strain was noted to display far greater tolerance to chloride than reported for other iron-oxidizing acidithiobacilli. All of the strains were able to catalyse the oxidative dissolution of pyrite and, on the basis of some of the combined traits of some of the strains examined, it is proposed that these may have niche roles in commercial mineral bioprocessing operations, such as for low temperature bioleaching of polysulfide ores in brackish waters. The name Acidithiobacillus ferriphilus sp. nov. is proposed to accommodate the strains described, with the type strain being M20(T) ( = DSM 100412(T) = JCM 30830(T))

Speeding up shortest path algorithms

Given an arbitrary, non-negatively weighted, directed graph $G=(V,E)$ we present an algorithm that computes all pairs shortest paths in time $\mathcal{O}(m^* n + m \lg n + nT_\psi(m^*, n))$, where $m^*$ is the number of different edges contained in shortest paths and $T_\psi(m^*, n)$ is a running time of an algorithm to solve a single-source shortest path problem (SSSP). This is a substantial improvement over a trivial $n$ times application of $\psi$ that runs in $\mathcal{O}(nT_\psi(m,n))$. In our algorithm we use $\psi$ as a black box and hence any improvement on $\psi$ results also in improvement of our algorithm. Furthermore, a combination of our method, Johnson's reweighting technique and topological sorting results in an $\mathcal{O}(m^*n + m \lg n)$ all-pairs shortest path algorithm for arbitrarily-weighted directed acyclic graphs. In addition, we also point out a connection between the complexity of a certain sorting problem defined on shortest paths and SSSP.Comment: 10 page

The Peregrine High-Performance RPC System

The Peregrine RPC system provides performance very close to the optimum allowed by the hardware limits, while still supporting the complete RPC model. Implemented on an Ethernet network of Sun-3/60 workstations, a null RPC between two user-level threads executing on separate machines requires 573 microseconds. This time compares well with the fastest network RPC times reported in the literature, ranging from about 1100 to 2600 microseconds, and is only 309 microseconds above the measured hardware latency for transmitting the call and result packets in our environment. For large multi-packet RPC calls, the Peregrine user-level data transfer rate reaches 8.9 megabits per second, approaching the Ethernet’s 10 megabit per second network transmission rate. Between two user-level threads on the same machine, a null RPC requires 149 microseconds. This paper identifies some of the key performance optimizations used in Peregrine, and quantitatively assesses their benefits

Recovery in Distributed Systems Using Optimistic Message Logging and Checkpointing

Message logging and check pointing can provide fault tolerance in distributed systems in which all process communication is through messages. This paper presents a general model for reasoning about recovery in these systems. Using this model_ we prove that the set of recoverable system states that have occurred during any single execution of the system forms a lattice, and that therefore, there is always a unique maximum recoverable system state, which never decreases. Based on this model, we present an algorithm for determining this maximum recoverable state, and prove its correctness. Our algorithm utilizes all logged messages and checkpoints, and thus always finds the maximum recoverable state possible. Previous recovery methods using optimistic message logging and checkpointing have not considered the existing checkpoints, and thus may not find this maximum state. Furthermore, by utilizing the checkpoints, some messages received by a process before it was checkpointed may not need to be logged. Using our algorithm also adds less communication overhead to the system than do previous methods. Our model and algorithm can be used with any message logging protocol, whether pessimistic or optimistic, but their full generality is only required with optimistic logging protocols

Sender-Based Message Logging

Sender-based message logging, a low-overhead mechanism for providing transparent fault-tolerance in distributed systems, is described. It differs from conventional message logging mechanisms in that each message is logged in volatile memory on the machine from which the message is sent. Keeping the message log in the sender's local memory allows one to recover from a single failure at a time without the expense of synchronously logging each message to stable storage. The message log is then asynchronously written to stable storage, without delaying the computation, as part of the sender's periodic checkpoint. Maintaining the sender-based message log requires at most one extra network packet over non-fault-tolerant reliable message communication and imposes little additional synchronization delay. It can be applied transparently to existing distributed applications and does not required specialized hardware. It is currently being implemented on a network of Sun workstations

Effect of exogenous melatonin on antioxidant defense system and osmo-regulatory solutes of drought-stressed Morinda citrifolia

Morinda citrifolia is a small tropical tree that contains active natural metabolites in its leaves, stem, roots, and fruits. Despite these properties, drought stress has always been one of the limiting factors affecting its growth and productivity. This study investigated the role of melatonin in the regeneration of M. citrifolia in vitro under simulated drought stress. Nodal cuttings of six-month-old M. citrifolia were inoculated into Murashige and Skoog (MS) media supplemented with 2, 4-dichlorophenoxy-acetic acid (0.5 mg/L), indole acetic acid (0.5 mg/L) and varying concentrations of melatonin (0 μM, 50 μM and 100 μM) and polyethylene glycol (PEG) 6000 (0%, 20% and 40%). M. citrifolia experienced a significant increase in plant growth, stabilized chlorophyll contents, superoxide dismutase (SOD), and glutathione peroxidase (GPx) activities under drought stress possibly because it is a drought-tolerant plant. However, melatonin was involved in the accumulation of proline and ascorbic acid at 20% PEG. Osmoregulation of solutes stimulated and stabilized the production of catalase, GPx, and SOD activities. Upregulation of glutathione S-transferase augmented the biosynthesis of glutathione during drought stress. Also, a high accumulation of carotenoid function as photo-protectants and shields chlorophyll contents from drought-induced reactive oxygen species. Consequently, 40% of hydrogen peroxide was detoxified and plant growth was boosted. Therefore, melatonin acts as a stimulant of carotenoid, compatible solutes, enzymatic and non-enzymatic anti-oxidant defensive system, protects plants against oxidative injury, and boosted the growth of Morinda. citrifolia in vitro under drought stress

LOFT advanced densitometer for nuclear loss-of-coolant experiments

A ''nuclear hardened'' gamma densitometer, a device which uses radiation attenuation to measure fluid density in the presence of a background radiation field, is described. Data from the nuclear hardened gamma densitometer are acquired by time sampling the coolant fluid piping and fluid attenuated source energy spectrum. The data are used to calculate transient coolant fluid cross sectional average density to analyze transient mass flow and other thermal-hydraulic characteristics during the Loss-of-Fluid Test (LOFT) loss-of-coolant experiments. The nuclear hardened gamma densitometer uses a pulse height analysis or energy discrimination, pulse counting technique which makes separation of the gamma radiation source signal from the reactor generated gamma radiation background noise signal possible by processing discrete pulses which retain their pulse amplitude information