Bacillus pumilus SAFR-032 isolate

The present invention relates to discovery and isolation of a biologically pure culture of a Bacillus pumilus SAFR-032 isolate with UV sterilization resistant properties. This novel strain has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus. The GenBank accession number for the 16S rDNA sequence of the Bacillus pumilus SAFR-032 isolate is AY167879

Molecular Technique to Understand Deep Microbial Diversity

Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample

Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem

Method bacterial endospore quantification using lanthanide dipicolinate luminescence

A lanthanide is combined with a medium to be tested for endospores. The dipicolinic acid released from the endospores binds the lanthanides, which have distinctive emission (i.e., luminescence) spectra, and are detected using photoluminescence. The concentration of spores is determined by preparing a calibration curve generated from photoluminescence spectra of lanthanide complex mixed with spores of a known concentration. A lanthanide complex is used as the analysis reagent, and is comprised of lanthanide ions bound to multidentate ligands that increase the dipicolinic acid binding constant through a cooperative binding effect with respect to lanthanide chloride. The resulting combined effect of increasing the binding constant and eliminating coordinated water and multiple equilibria increase the sensitivity of the endospore assay by an estimated three to four orders of magnitude over prior art of endospore detection based on lanthanide luminescence

Intrusion Detection Systems for Community Wireless Mesh Networks

Wireless mesh networks are being increasingly used to provide affordable network connectivity to communities where wired deployment strategies are either not possible or are prohibitively expensive. Unfortunately, computer networks (including mesh networks) are frequently being exploited by increasingly profit-driven and insidious attackers, which can affect their utility for legitimate use. In response to this, a number of countermeasures have been developed, including intrusion detection systems that aim to detect anomalous behaviour caused by attacks. We present a set of socio-technical challenges associated with developing an intrusion detection system for a community wireless mesh network. The attack space on a mesh network is particularly large; we motivate the need for and describe the challenges of adopting an asset-driven approach to managing this space. Finally, we present an initial design of a modular architecture for intrusion detection, highlighting how it addresses the identified challenges

‘I don’t talk about my distress to others; I feel that I have to suffer my problems..’ Voices of Indian women with breast cancer: a qualitative interview study

Background: Breast cancer is the commonest form of cancer among women globally, including in India. The rising incidence in the developing world is thought to be due to increased life expectancy, urbanization and adoption of western lifestyles. A recent systematic review found that Indian women living in India or as immigrants in Canada experienced a range of psychological distresses both ameliorated and exacerbated by cultural issues personally, within the family, their community and in the context of faith and only two of the five qualitative studies explored the experience of women with breast cancer living in India. Distress may also affect treatment compliance. Aim: The aim of the study was to explore the psychological distresses experienced by Indian women with breast cancer living in Kerala, South India during and after treatment and to understand better what helped to relieve or increase these distresses.Methods: In-depth interviews were conducted with 20 consenting women undergoing treatment for breast cancer. Purposive sampling was used to obtain maximum variation in socio-demographic and clinical characteristics. Interviews were verbatim transcribed, translated into English and back translated to Malayalam to ensure that the meaning had not been lost. English data were analyzed using thematic frame work analysis and synthesized to provide a deeper understanding of the individuals’ experience.Results: Three major themes emerged from the data. The first major theme was “far-reaching psychological distress”. This included anxiety, guilt, anger and depression in response to the disease and physical side effects of treatment and issues relating to body image, especially hair loss and sexuality. The second major theme was “getting on with life”. Women tried to make sense of the disease, by actively seeking information, the role of medical professionals, and their practical adaptations. Many found a new future and a new way to live normal. The third major theme was the “support system” strongly based on family, friends, faith and the community which affect them positively as well as negatively.Conclusion: Psychological concerns related to disease and treatment is common in Indian women with particular emphasis on body image issues associated with hair loss. Family and faith were key support systems for almost all the women although could also be causes of distress

Extreme Ionizing-Radiation-Resistant Bacterium

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing microorganisms. Eradification techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation- based sterilization processes. Due to their resistance to a variety of perturbations, the non-spore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-spore-forming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/sq m), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination

A fully non-linear optimization approach to acousto-electric tomography

This paper considers the non-linear inverse problem of reconstructing an electric conductivity distribution from the interior power density in a bounded domain. Applications include the novel tomographic method known as acousto-electric tomography, in which the measurement setup in Electrical Impedance Tomography is modulated by ultrasonic waves thus giving rise to a method potentially having both high contrast and high resolution. We formulate the inverse problem as a regularized non-linear optimization problem, show the existence of a minimizer, and derive optimality conditions. We propose a non-linear conjugate gradient scheme for finding a minimizer based on the optimality conditions. All our numerical experiments are done in two-dimensions. The experiments reveal new insight into the non-linear effects in the reconstruction. One of the interesting features we observe is that, depending on the choice of regularization, there is a trade-off between high resolution and high contrast in the reconstructed images. Our proposed non-linear optimization framework can be generalized to other hybrid imaging modalities