Sequence analysis of a salt tolerant metagenomic clone

Metagenome represent an unlimited resource for discovery of novel genes. Here we report, sequence analysis of a salt tolerant metagenomic clone (6B4) from a pond water metagenomic library. Clone 6B4 had an insert of 2254 bp with G+C composition of 64.06%. DNA sequence from 6B4 showed homology to DNA sequences from proteobacteria indicating origin of 6B4 metagenomic insert from a yet uncharacterized proteobacteria. Two encoded proteins from clone 6B4 showed match with ATP-dependent Clp protease adaptor protein (ClpS) and phasin, while two truncated encoded proteins showed match with poly-3-hydroxybutyrate synthase and permease. Clp complex is known to play a role in stress tolerance. Expression of ClpS from metagenomic clone is proposed to be responsible for salt tolerance of the metagenomic clone 6B4.

Identification of expressed HSP`s in blacklip abalone (Haliotis rubra Leach) during heat and salinity stresses

Both prokaryotes and eukaryotes express a set of highly conserved proteins in response to external and internal stress. The stressors include tissue trauma,anoxia, heavy metal toxicity, infection, changed salinity, and the mmost characterized, heat shock. The result is an expression of stress proteins or heat shock proteins (HSP's) which lead to protection of protein integrity, and also to tolerance under continued heat stress conditions. The Australian backflip abalone (Haliotis rubra) is found principally in southern coastal water and also in estuarine/bay environments. Esturaine/bay environments have greater fluctuations in environmental conditions, especially those of salinity and water temperature, than they are found along oceanic coasts. Abalone from esturaine/bay and oceanic coastal environments were subjected to either increased temperature (2° C/day for a total of 10°C) or hyposalinity (80% seawater). Esturaine/bay abolone were less affectes than the oceanic animals by temperature increase and also demonstrated the ability to volume regualte 3 h after the initial salinity shock. SDS-PAGE and Western blotting techniques, together with dot blots of total protein, using HSP70 specific antibodies, were used to detect HSP70s in the foot muscle of the animals and indicated an expression of HSP70 in response to heat shock in abalone, but not following hyposalinity shock. RT-PCR yeilded a partial cDNA clone of HSP70 from the foot muscle.

A custom-built insulin resistance gene chip

Objectives/Aim—Microarray (gene chip) technology offers a powerful new tool for analyzing the expression of large numbers of genes in many experimental samples. The aim of this study was to design, construct, and use a gene chip to measure the expression levels of key genes in metabolic pathways related to insulin resistance.
Methods—We selected genes that were implicated in the development of insulin resistance, including genes involved in insulin signaling; glucose uptake, oxidation, and storage; fat uptake, oxidation, and storage; cytoskeletal components; and transcription factors. The key regulatory genes in the pathways were identified, along with other recently identified candidate genes such as calpain-10. A total of 242 selected genes (including 32 internal control elements) were sequence-verified, purified, and arrayed on aldehyde-coated slides.
Results—Where more than 1 clone containing the gene of interest was available, we chose those containing the genes in the 5' orientation and an insert size of around 1.5 kb. Of the 262 clones purchased, 56 (21%) were found to contain sequences other than those expected. In addition, 2 (1%) did not grow under standard conditions and were assumed to be nonviable. In these cases, alternate clones containing the gene of interest were chosen as described above. The current version of the Insulin Resistance Gene Chip contains 210 genes of interest, plus 48 control elements. A full list of the genes is available at http://www.hbs.deakin.edu.au/mru/research/gene_chip_tech/genechip_three.htm/.
Conclusions—The human Insulin Resistance Gene Chip that we have constructed will be a very useful tool for investigating variation in the expression of genes relevant to insulin resistance under various experimental conditions. Initially, the gene chip will be used in studies such as exercise interventions, fasting, euglycemic-hyperinsulinemic clamps, and administration of antidiabetic agents

An parallel information retrieval method for e-commerce

An online transaction always retrieves a large amount of information before making decisions. Currently, the parallel methods for retrieving such information can only provide a similar performance to serial methods. In this paper we first perform an analysis to determine the factors that affect the performance of exiting methods, i.e., HQR and EHQR, and show that the several of these factors are not considered by these methods. Motivated by this, we propose a new dispatch scheme called AEHQR, which takes into account the features of parallel dispatching. In addition, we provide cost models that determine the optimal performance achievable by any parallel dispatching method. Using experimental comparison, we illustrate that the AEHQR is significantly outperforms the HQR and EHQR under all conditions.

Isolation of a gene preferentially expressed in mature anthers of rice (Oryza sativa L.)

Using monoclonal antibodies raised against pollen-specific proteins, we have isolated a cDNA clone, designatedOry-Cl from a rice anther cDNA expression library. A transcript corresponding to theOry-Cl gene showed preferential expression in anthers. This transcript was not detected in any vegetative tissues analysed. RNA gel blot analysis of different developmental stages of anthers showed that theOry-Cl gene is expressed at later stages of pollen development. In situ hybridisation showed that theOry-Cl transcript is only present in mature pollen.

Isolation of cDNA encoding a newly identified major allergenic protein of rye-grass pollen : intracellular targeting to the amyloplast

We have identified a major allergenic protein from rye-grass pollen, tentatively designated Lol pIb of 31kDa and with pI 9.0. A cDNA clone encoding Lol pIb has been isolated, sequenced, and characterized. Lol pIb is located mainly in the starch granules. This is a distinct allergen from Lol pI, which is located in the cytosol. Lol pIb is synthesized in pollen as a pre-allergen with a transit peptide targeting the allergen to amyloplasts. Epitope mapping of the fusion protein localized the IgE binding determinant in the C-terminal domain.

Involvement of rootstocks and their hydraulic conductance in the drought resistance of grafted rubber trees

Improving drought resistance of rubber trees has become a pressing issue with the extension of rubber plantations and the prevalence of seasonal drought. Root system is vital to water and nutrients uptake of all plants, therefore, rootstocks could play decisive roles in drought resistance of grafted rubber trees on a specific scion clone. To investigate the responses of different clone rootstocks and their grafted trees to water stress and find applicable methods for selecting drought resistant rootstocks, seven related parameters and root hydraulic properties of both seeds originated and grafted saplings of PB86, PR107, RRIM600 and GT1 were measured to assess their drought resistance. It was shown that the rootstock drought resistance and root hydraulic conductance may improve the drought resistance of the grafted rubber trees. Among the four clone rootstocks, GT1, which demonstrated more resistant to drought and higher root hydraulic conductance, was comparatively resistant to drought both for the seed propagation seedlings and grafted saplings. In addition, studies on the grafted saplings with different root hydraulic conductance further validated the possibility of selecting drought resistant rootstocks on the basis of rootstock hydraulic conductance using a high-pressure flow meter.

Mutations in the kissing-loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA packaging and dimerization

A stem-loop termed the kissing-loop hairpin is one of the most highly conserved structures within the leader of human immunodeficiency virus type 1 (HIV-1) and chimpanzee immunodeficiency virus genomic RNA. Because it plays a key role in the in vitro dimerization of short HIV-1 RNA transcripts (M. Laughrea and L. Jette, Biochemistry 35:1589-1598, 1996, and references therein; M. Laughrea and L. Jette, Biochemistry 35:9366-9374, 1996, and references therein) and because dimeric RNAs may be preferably encapsidated into the HIV-1 virus, alterations of the kissing-loop hairpin might affect the in vivo dimerization and encapsidation processes. Accordingly, substitution and deletion mutations were introduced into the kissing-loop hairpin of an infectious HIV-1 molecular clone in order to produce viruses by transfection methods. The infectivity of the resulting viruses was decreased by at least 99%, the amount of genomic RNA packaged per virus was decreased by 50 to 75%, and the proportion of dimeric genomic RNA was reduced from >80 to 40 to 50%, but the dissociation temperature of the genomic RNA was unchanged. There is evidence suggesting that the deletion mutations moderately inhibited CAp24 production but had no significant effect on RNA splicing. These results are consistent with the kissing-loop model of HIV-1 RNA dimerization. In fact, because intracellular viral RNAs are probably more concentrated in transfected cells than in cells infected by one virus and because the dimerization and encapsidation processes are concentration dependent, it is likely that much larger dimerization and encapsidation defects would have been manifested within cells infected by no more than one virus.

Software similarity and classification

Software similarity and classification is an emerging topic with wide applications. It is applicable to the areas of malware detection, software theft detection, plagiarism detection, and software clone detection. Extracting program features, processing those features into suitable representations, and constructing distance metrics to define similarity and dissimilarity are the key methods to identify software variants, clones, derivatives, and classes of software. Software Similarity and Classification reviews the literature of those core concepts, in addition to relevant literature in each application and demonstrates that considering these applied problems as a similarity and classification problem enables techniques to be shared between areas. Additionally, the authors present in-depth case studies using the software similarity and classification techniques developed throughout the book.

Clonewise - detecting package-level clones using machine learning

Developers sometimes maintain an internal copy of another software or fork development of an existing project. This practice can lead to software vulnerabilities when the embedded code is not kept up to date with upstream sources. We propose an automated solution to identify clones of packages without any prior knowledge of these relationships. We then correlate clones with vulnerability information to identify outstanding security problems. This approach motivates software maintainers to avoid using cloned packages and link against system wide libraries. We propose over 30 novel features that enable us to use to use pattern classification to accurately identify package-level clones. To our knowledge, we are the first to consider clone detection as a classification problem. Our results show our system, Clonewise, compares well to manually tracked databases. Based on our work, over 30 unknown package clones and vulnerabilities have been identified and patched.

One-size-fits-all housing : an exploration of 6-star requirements in the volume builder sector

Energy consumption attributed to the residential sector makes up around 8% of the total consumption in Australia. Roughly a third of all houses built in Victoria are done so by the largest 20 builders. These volume builders keep costs down by offering a selection of ‘clone’ designs from which the client can choose, however they lose the site-specific customisation which is required for effective passive design in favour of a one-size-fits-all approach where designs are developed to a point where they can satisfy just the minimum requirements in a range of orientations and site locations. The Australian government has implemented regulations regarding the minimum efficiency standards for housing and these initiatives to limit the carbon emissions have brought the question of energy use to the table, yet are they enough? This paper will explore the concept of cloned house designs in terms of energy efficiency and optimal siting and through computer simulation, evaluate how a cloned house design performs under different site conditions in Victoria.

Doxycycline-inducible expression of SPARC/osteonectin/BM40 in MDA-MB-231 human breast cancer cells results in growth inhibition

SPARC (secreted protein acidic and rich in cysteine)/BM40/Osteonectin is a matricellular protein with multiple effects on cell behaviour. In vitro, its major known functions are anti-adhesive and anti-proliferative, and it is associated with tissue remodelling and cancer in vivo. SPARC is overexpressed in many cancers, including breast cancer, and the effects of SPARC seem to be cell type-specific. To study the effects of SPARC on breast cancer, we transfected SPARC into the MDA-MB-231 BAG, human breast cancer cell line using the Tet-On inducible system. By western analysis, we found low background levels in the MDA-MB-231 BAG and clone X parental cells, and prominent induction of SPARC protein expression after doxycycline treatment in SPARC transfected clones X5, X21, X24 and X75. Induction of SPARC expression did not affect cell morphology or adhesiveness to collagens type I and IV, but it slowed the rate of proliferation in adherent cultures. Cell cycle analysis showed that SPARC slowed the progression to S phase. Doxycycline induction of SPARC also slowed the rate of monolayer wound closure in the cultured wound healing assay. Thymidine inhibition of proliferation abrogated this effect, confirming that it was due to anti-proliferation rather than inhibition of migration. Consistent with this, we were unable to detect any differences in migration and Matrigel outgrowth analysis of doxycycline-stimulated cells. We conclude that SPARC is inhibitory to human breast cancer cell proliferation, and does not stimulate migration, in contrast to its stimulatory effects reported for melanoma (proliferation and migration) and glioma (migration) cells. Similar growth repression by SPARC has been reported for ovarian cancer cells, and this may be a common feature among carcinoma.

Community-onset Escherichia coli infection resistant to expanded- spectrum cephalosporins in low-prevalence countries

Background
By global standards the prevalence of community onset expanded-spectrum cephalosporin resistant Escherichia coli (ESC-R-EC) remains low in Australia and New Zealand. Of concern, our countries are in a unique position with high extramural resistance pressure from close population and trade links to Asia-Pacific neighbours with high ESC-R-EC rates. We aim to characterize the risks and dynamics of community onset ESC-R-EC in our low-prevalence region.

Methods
A case-control methodology was used. Patients with ESC-R-EC or susceptible E. coli isolated from blood or urine were recruited at six geographically dispersed tertiary hospitals in Australia and New Zealand. Epidemiological data was prospectively collected and bacteria were retained for analysis.

Results
In total, 182 patients (91 cases and 91 controls) were recruited. Multivariate logistic regression identified risk factors for ESC-R amongst E. coli including birth on the Indian subcontinent (OR=11.13, 2.17-56.98, p=0.003), urinary tract infection in the past year (per infection OR=1.430, 1.13-1.82, p=0.003), travel to South East Asia, China, Indian subcontinent, Africa and the Middle East (OR=3.089, 1.29-7.38, p=0.011), prior exposure to trimethoprim+/-sulfamethoxazole &/or an expanded-spectrum cephalosporin (OR=3.665, 1.30-10.35, p=0.014) and healthcare exposure in the previous six months (OR=3.16, 1.54-6.46, p=0.02).

Amongst our ESC-R-EC the blaCTX-M ESBLs was dominant (83% of ESC-R-EC), and the worldwide pandemic clone ST-131 was frequent (45% of ESC-R-EC).

Conclusion
In our low prevalence setting, ESC-R amongst community onset E. coli may be associated with both ‘export’ from healthcare facilities into the community and direct ‘import’ into the community from high-prevalence regions.

Variation of phloem turgor pressure in Hevea brasiliensis: An implication for latex yield and tapping system optimization

Phloem turgor pressure (PTP) is the initial driving force for latex flow after a rubber tree is tapped and therefore plays an important role in rubber tree latex production. Variation in PTP with rubber tree clone, age, yield potential and commonly used Ethrel (an ethylene releaser) stimulation have, however, not been comprehensively studied to date. The aim of this study was to investigate these relations and examine whether PTP can be used as an index for rubber tree clone assessment and tapping system optimization. The results showed that: (1) the daily change of PTP in the foliation season suggests that a high PTP can ensure a high latex yield and tapping could be moved forward to midnight or earlier in the night; (2) the decrease of PTP from the basal to distal stem indicates the benefit of a controlled upward tapping system; (3) the logarithmic increase in PTP with rubber tree planting age and age-based mean girth suggests that the preferred age for the commencement of rubber tree tapping is eight years; (4) the change of PTP with regenerated bark age suggests that the regenerated bark could be exploited again after the second year; (5) PTP is positively related to the yield potential of rubber tree clones; (6) although Ethrel stimulation could not significantly increase the initial PTP of a rubber tree, it delays the recovery of PTP after tapping. Therefore, PTP is an indicator of rubber tree latex yield and can be used for tapping system optimization. © 2014 Elsevier B.V.

Can we beat DDoS attacks in clouds?

Cloud is becoming a dominant computing platform. Naturally, a question that arises is whether we can beat notorious DDoS attacks in a cloud environment. Researchers have demonstrated that the essential issue of DDoS attack and defense is resource competition between defenders and attackers. A cloud usually possesses profound resources and has full control and dynamic allocation capability of its resources. Therefore, cloud offers us the potential to overcome DDoS attacks. However, individual cloud hosted servers are still vulnerable to DDoS attacks if they still run in the traditional way. In this paper, we propose a dynamic resource allocation strategy to counter DDoS attacks against individual cloud customers. When a DDoS attack occurs, we employ the idle resources of the cloud to clone sufficient intrusion prevention servers for the victim in order to quickly filter out attack packets and guarantee the quality of the service for benign users simultaneously. We establish a mathematical model to approximate the needs of our resource investment based on queueing theory. Through careful system analysis and real-world data set experiments, we conclude that we can defeat DDoS attacks in a cloud environment. © 2013 IEEE.