Optimization of Conditions for Studies of Protein Unfolding by Hydrogen Exchange/Mass Spectrometry

Understanding the forces driving protein folding and aggregation is an essential step in developing means for controlling these important processes. Amide hydrogen exchange, coupled with mass spectrometry, has become an important method for studying protein unfolding and refolding. To extend procedures developed to study unfolding of relatively soluble proteins to less soluble, aggregation-prone proteins requires special considerations. This publication describes a general strategy developed using yeast transaldolase, which aggregates easily under conditions required to study its unfolding. Results presented here show that reducing the protein concentration to the nanomolar range is essential for managing aggregation of transaldolase. In addition, the present results point to use of relatively high concentrations of denaturants and short incubation times to, minimize aggregation. These results also show how amide hydrogen exchange, coupled with mass spectrometry, ran be used to study soluble aggregates

Counting proofs in propositional logic

We give a procedure for counting the number of different proofs of a formula in various sorts of propositional logic. This number is either an integer (that may be 0 if the formula is not provable) or infinite

Establishing RNAi in a non-model organism: The Antarctic nematode Panagrolaimus sp. DAW1

The Antarctic nematode Panagrolaimus sp. DAW1 is one of the only organisms known to survive extensive intracellular freezing throughout its tissues. Although the physiological mechanisms of this extreme adaptation are partly understood, the molecular mechanisms remain largely unknown. RNAi is a method that allows the examination of gene function in a direct, targeted manner, by knocking out specific mRNAs and revealing the effects on the phenotype. In this study we have explored the viability of RNAi in Panagrolaimus sp. DAW1. In the first trial, nematodes were fed E. coli expressing Panagrolaimus sp. DAW1 dsRNA of the embryonic lethal genes rps-2 and dhc, and the blister gene duox. Pd-rps-2(RNAi)-treated nematodes showed a significant decrease in larval hatching. However, qPCR showed no significant decrease in the amount of rps-2 mRNA in Pd-rps-2(RNAi)-treated animals. Several soaking protocols for dsRNA uptake were investigated using the fluorescent dye FITC. Desiccation-enhanced soaking showed the strongest uptake of FITC and resulted in a significant and consistent decrease of mRNA levels of two of the four tested genes (rps-2 and tps-2a), suggesting effective uptake of dsRNA-containing solution by the nematode. These findings suggest that RNAi by desiccation-enhanced soaking is viable in Panagrolaimus sp. DAW1 and provide the first functional genomic approach to investigate freezing tolerance in this non-model organism. RNAi, in conjunction with qPCR, can be used to screen for candidate genes involved in intracellular freezing tolerance in Panagrolaimus sp. DAW1

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

A geometric discretisation scheme applied to the Abelian Chern-Simons theory

We give a detailed general description of a recent geometrical discretisation scheme and illustrate, by explicit numerical calculation, the scheme's ability to capture topological features. The scheme is applied to the Abelian Chern-Simons theory and leads, after a necessary field doubling, to an expression for the discrete partition function in terms of untwisted Reidemeister torsion and of various triangulation dependent factors. The discrete partition function is evaluated computationally for various triangulations of $S^3$ and of lens spaces. The results confirm that the discretisation scheme is triangulation independent and coincides with the continuum partition functionComment: 27 pages, 5 figures, 6 tables. in late

Multiplicity in Supersymmetric Spin Chains

We discuss a simple procedure for obtaining new integrable spin chains from old by replacing each single state of the original model by some collection of states. This works whenever the Lax matrix of the chain has a certain form. The simplest example is the su(n) XX model. We apply the techniques of the nested algebraic Bethe ansatz to solve such systems, in the bosonic and supersymmetric cases.Comment: 14 pages. v2: Added references and minor corrections; v3: Acknowledgement adde

Enrollment in community based health insurance schemes in rural Bihar and Uttar Pradesh, India

This paper assesses insurance uptake in three community based health insurance (CBHI) schemes located in rural parts of two of India’s poorest states and offered through women’s self-help groups (SHGs). We examine what drives uptake, the degree of inclusive practices of the schemes, and the influence of health status on enrollment. The most important finding is that a household’s socio-economic status does not appear to substantially inhibit uptake. In some cases Scheduled Caste/ Scheduled Tribe (SC/ST) households are more likely to enroll. Second, households with greater financial liabilities find insurance more attractive. Third, access to the hospital insurance scheme (RSBY) does not dampen CBHI uptake, suggesting that the potential for greater development of insurance markets and products beyond existing ones would respond to a need. Fourth, recent episodes of illness and selfassessed health status do not influence uptake. Fifth, insurance coverage is prioritized within households, with the household head, the spouse of the household head and both male and female children of the household head, more likely to be insured as compared to other relatives. Sixth, offering insurance through women’s SHGs appears to mitigate concerns about the inclusiveness and sustainability of CBHI schemes. Given the pan-Indian spread of SHGs, offering insurance through such groups offers the potential to scale-up CBHI

Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi

Isolated and established in culture from the Antarctic in 1988, the nematode Panagrolaimus davidi has proven to be an ideal model for the study of adaptation to the cold. Not only is it the best-documented example of an organism surviving intracellular freezing but it is also able to undergo cryoprotective dehydration. As part of an ongoing effort to develop a molecular understanding of this remarkable organism, we have assembled both a transcriptome and a set of genomic scaffolds. We provide an overview of the transcriptome and a survey of genes involved in temperature stress. We also explore, in silico, the possibility that P. davidi will be susceptible to an environmental RNAi response, important for further functional studies

The Partonic Nature of Instantons

In both Yang-Mills theories and sigma models, instantons are endowed with degrees of freedom associated to their scale size and orientation. It has long been conjectured that these degrees of freedom have a dual interpretation as the positions of partonic constituents of the instanton. These conjectures are usually framed in d=3+1 and d=1+1 dimensions respectively where the partons are supposed to be responsible for confinement and other strong coupling phenomena. We revisit this partonic interpretation of instantons in the context of d=4+1 and d=2+1 dimensions. Here the instantons are particle-like solitons and the theories are non-renormalizable. We present an explicit and calculable model in d=2+1 dimensions where the single soliton in the CP^N sigma-model can be shown to be a multi-particle state whose partons are identified with the ultra-violet degrees of freedom which render the theory well-defined at high energies. We introduce a number of methods which reveal the partons inside the soliton, including deforming the sigma model and a dual version of the Bogomolnyi equations. We conjecture that partons inside Yang-Mills instantons hold the key to understanding the ultra-violet completion of five-dimensional gauge theories.Comment: 28 pages. v3: extra references and comments. Mathematica notebooks for the figures can be downloaded from http://www.damtp.cam.ac.uk/user/dt281/parton.htm

An integrated information management model for proactive prevention of struck-by-falling-object accidents on construction sites

The construction industry is one of the most hazardous industries in many countries. Struck-by-falling-object accidents are not given adequate attention even though they are of great importance on construction sites. The objective of this paper is to analyze the proactively preventive information requirement of struck-by-falling-object accidents and propose an integrated information management model using a ZigBee RFID sensor network to fulfill these requirements. First, the frequency of particular type of objects is analyzed based on vast historical accident cases. Next, this paper analyzes the proactively preventive information requirement of struck-by-falling-object accidents and brought forth an integrated information management model. Furthermore, considering the crucial and controllable objects, an integrated information management model is proposed. This study would provide a possible approach for tracking struck-by-falling-object accidents based on real-time information for proactive prevention and could serve as a foundation for further study. © 2012 Elsevier B.V. All rights reserved