A novel method for prokaryotic promoter prediction based on DNA stability

Background: In the post-genomic era, correct gene prediction has become one of the biggest challenges in genome annotation. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. This work presents a novel prokaryotic promoter prediction method based on DNA stability.Results: The promoter region is less stable and hence more prone to melting as compared to other genomic regions. Our analysis shows that a method of promoter prediction based on the differences in the stability of DNA sequences in the promoter and non-promoter region works much better compared to existing prokaryotic promoter prediction programs, which are based on sequence motif searches. At present the method works optimally for genomes such as that of Escherichia coli, which have near 50% G+C composition and also performs satisfactorily in case of other prokaryotic promoters.Conclusions: Our analysis clearly shows that the change in stability of DNA seems to provide a much better clue than usual sequence motifs, such as Pribnow box and -35 sequence, for differentiating promoter region from non-promoter regions. To a certain extent, it is more general and is likely to be applicable across organisms. Hence incorporation of such features in addition to the signature motifs can greatly improve the presently available promoter prediction programs

Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes

Background: Horizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.Results: Simulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.Conclusion: The majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation

Large Magnetic Moments of Arsenic-Doped Mn Clusters and their Relevance to Mn-Doped III-V Semiconductor Ferromagnetism

We report electronic and magnetic structure of arsenic-doped manganese clusters from density-functional theory using generalized gradient approximation for the exchange-correlation energy. We find that arsenic stabilizes manganese clusters, though the ferromagnetic coupling between Mn atoms are found only in Mn$_2$As and Mn$_4$As clusters with magnetic moments 9 $\mu_B$ and 17 $\mu_B$, respectively. For all other sizes, $x=$ 3, 5-10, Mn$_x$As clusters show ferrimagnetic coupling. It is suggested that, if grown during the low temperature MBE, the giant magnetic moments due to ferromagnetic coupling in Mn$_2$As and Mn$_4$As clusters could play a role on the ferromagnetism and on the variation observed in the Curie temperature of Mn-doped III-V semiconductors.Comment: 4 Pages, 3 Figures[1 EPS and 2 JPG files], RevTeX

Ab initio Molecular Dynamical Investigation of the Finite Temperature Behavior of the Tetrahedral Au19_{19} and Au20_{20} Clusters

Density functional molecular dynamics simulations have been carried out to understand the finite temperature behavior of Au$_{19}$ and Au$_{20}$ clusters. Au$_{20}$ has been reported to be a unique molecule having tetrahedral geometry, a large HOMO-LUMO energy gap and an atomic packing similar to that of the bulk gold (J. Li et al., Science, {\bf 299} 864, 2003). Our results show that the geometry of Au$_{19}$ is exactly identical to that of Au$_{20}$ with one missing corner atom (called as vacancy). Surprisingly, our calculated heat capacities for this nearly identical pair of gold cluster exhibit dramatic differences. Au$_{20}$ undergoes a clear and distinct solid like to liquid like transition with a sharp peak in the heat capacity curve around 770 K. On the other hand, Au$_{19}$ has a broad and flat heat capacity curve with continuous melting transition. This continuous melting transition turns out to be a consequence of a process involving series of atomic rearrangements along the surface to fill in the missing corner atom. This results in a restricted diffusive motion of atoms along the surface of Au$_{19}$ between 650 K to 900 K during which the shape of the ground state geometry is retained. In contrast, the tetrahedral structure of Au$_{20}$ is destroyed around 800 K, and the cluster is clearly in a liquid like state above 1000 K. Thus, this work clearly demonstrates that (i) the gold clusters exhibit size sensitive variations in the heat capacity curves and (ii) the broad and continuous melting transition in a cluster, a feature which has so far been attributed to the disorder or absence of symmetry in the system, can also be a consequence of a defect (absence of a cap atom) in the structure.Comment: 7 figure

Size--sensitive melting characteristics of gallium clusters: Comparison of Experiment and Theory for Ga17+_{17}{}^{+} and Ga20+_{20}{}^{+}

Experiments and simulations have been performed to examine the finite-temperature behavior of Ga$_{17}{}^{+}$ and Ga$_{20}{}^{+}$ clusters. Specific heats and average collision cross sections have been measured as a function of temperature, and the results compared to simulations performed using first principles Density--Functional Molecular--Dynamics. The experimental results show that while Ga$_{17}{}^{+}$ apparently undergoes a solid--liquid transition without a significant peak in the specific--heat, Ga$_{20}{}^{+}$ melts with a relatively sharp peak. Our analysis of the computational results indicate a strong correlation between the ground--state geometry and the finite--temperature behavior of the cluster. If the ground--state geometry is symmetric and "ordered" the cluster is found to have a distinct peak in the specific--heat. However, if the ground--state geometry is amorphous or "disordered" the cluster melts without a peak in the specific--heat.Comment: 6 figure

Technical note: Facilitating laparoscopic liver biopsy by the use of a single-handed disposable core biopsy needle

Despite the use of advanced radiological investigations, some liver lesions cannot be definitely diagnosed without a biopsy and histological examination. Laparoscopic Tru-Cut biopsy of the liver lesion is the preferred approach to achieve a good sample for histology. The mechanism of a Tru-Cut biopsy needle needs the use of both hands to load and fire the needle. This restricts the ability of the surgeon to direct the needle into the lesion utilising the laparoscopic ultrasound probe. We report a technique of laparoscopic liver biopsy using a disposable core biopsy instrument (BARD (R) disposable core biopsy needle) that can be used single-handedly. The needle can be positioned with laparoscopic graspers in order to reach posterior and superior lesions. This technique can easily be used in conjunction with laparoscopic ultrasound.M. I. Trochsler, Q. Ralph, F. Bridgewater, H. Kanhere, and Guy J. Madder

A unified framework for data integrity protection in people-centric smart cities

© 2019, Springer Science+Business Media, LLC, part of Springer Nature. With the rapid increase in urbanisation, the concept of smart cities has attracted considerable attention. By leveraging emerging technologies such as the Internet of Things (IoT), artificial intelligence and cloud computing, smart cities have the potential to improve various indicators of residents’ quality of life. However, threats to data integrity may affect the delivery of such benefits, especially in the IoT environment where most devices are inherently dynamic and have limited resources. Prior work has focused on ensuring integrity of data in a piecemeal manner and covering only some parts of the smart city ecosystem. In this paper, we address integrity of data from an end-to-end perspective, i.e., from the data source to the data consumer. We propose a holistic framework for ensuring integrity of data in smart cities that covers the entire data lifecycle. Our framework is founded on three fundamental concepts, namely, secret sharing, fog computing and blockchain. We provide a detailed description of various components of the framework and also utilize smart healthcare as use case

Is Privacy Regulation Slowing Down Research on Pervasive Computing?

Privacy legislation has often been identified as a roadblock for advanced context-aware applications. The feedback collected from more than 150 researchers in pervasive computing reveals a different attitude. Has pervasive computing\u2019s privacy challenge been solved

Spin-Charge Separation in Two Dimensions - A Numerical Study

The question of spin-charge separation in two-dimensional lattices has been addressed by numerical simulations of the motion of one hole in a half-filled band. The calculations have been performed on finite clusters with Hubbard and t-J models. By comparing the time evolution of spin and charge polarisation currents in one and two dimensions, evidence in favor of spin-charge separation in two dimensions is presented. In contrast with this, spin-charge separation is absent in a highly doped, metallic, system.Comment: RevTeX 3.0, 10 Pages, 6 PostScript Figures (on request