Functional significance of unique sequences in Mycobaterium smegmatis Ku proteins

Ku is central to the non-homologous end-joining pathway of DNA double strand break repair, first discovered in eukaryotes and more recently in prokaryotes and archaea. This study concerns the importance of two unique sequence features of Ku protein from Mycobacterium smegmatis that include a lysine-rich extension at the C-terminus and a zinc-binding motif in the DNA-binding bridge-region. The unique C-terminal tail of M. smegmatis Ku contains several lysine-rich low-complexity PAKKA repeats that are absent from homologs encoded by obligate parasitic mycobacteria, but present in other mycobacterial proteins such as histone-like proteins. Removal of the lysine-rich extension from Ku decreased thermal stability and abolished DNA end-joining. The tail contacts the core DNA binding domain of Ku and hinders DNA-protein interaction as evidenced by an increase in DNA binding affinity upon removal of the lysine-rich extension. In contrast to Ku lacking the C-terminus, full-length Ku can directly bind DNA without free ends and form multiple complexes with a short stem-loop-containing DNA previously designed to accommodate only one Ku dimer, suggesting that these properties are conferred by its C-terminus. My study suggests that low-complexity lysine-rich sequences have evolved repeatedly to modulate the function of unrelated DNA-binding proteins and that extensions beyond the shared core domain may have independently evolved to expand Ku function. An in vitro metal binding assay showed zinc binding to a predicted zinc-binding motif in the bridge-region of M. smegmatis Ku, an event that stabilizes the protein and prevents cysteine oxidation, but has little effect on DNA binding. In vivo, zinc induced significant upregulation of the gene encoding Ku as well as a divergently oriented gene encoding a predicted zinc-dependent MarR family transcription factor. In addition, overexpression of Ku conferred zinc tolerance on E. coli. I speculate that zinc binding sites in Ku proteins from M. smegmatis and other mycobacterial species have been evolutionarily retained to provide protection against zinc toxicity. In all, my study identifies novel properties conferred by unique sequences present in M. smegmatis Ku protein, which suggests that the retention and evolution of unique sequences within a protein provides an adaptive advantage to microorganisms against environmental stress

An efficient high-order Nystr\"om scheme for acoustic scattering by inhomogeneous penetrable media with discontinuous material interface

This text proposes a fast, rapidly convergent Nystr\"{o}m method for the solution of the Lippmann-Schwinger integral equation that mathematically models the scattering of time-harmonic acoustic waves by inhomogeneous obstacles, while allowing the material properties to jump across the interface. The method works with overlapping coordinate charts as a description of the given scatterer. In particular, it employs "partitions of unity" to simplify the implementation of high-order quadratures along with suitable changes of parametric variables to analytically resolve the singularities present in the integral operator to achieve desired accuracies in approximations. To deal with the discontinuous material interface in a high-order manner, a specialized quadrature is used in the boundary region. The approach further utilizes an FFT based strategy that uses equivalent source approximations to accelerate the evaluation of large number of interactions that arise in the approximation of the volumetric integral operator and thus achieves a reduced computational complexity of $O(N \log N)$ for an $N$-point discretization. A detailed discussion on the solution methodology along with a variety of numerical experiments to exemplify its performance in terms of both speed and accuracy are presented in this paper

Application Specific Secure Grouping of Vehicles in Vehicular Ad-hoc Network

Providing efficient, secure and reliable communication among vehicles is complicated and challenging problem. Vehicles communicate with each other (V2V communication) and Road Side Infrastructure (V2X communication) unit to provide convenient, safety and commercial service to the travelers. Similar information shared by each vehicle within close proximity creates huge network congestion. Grouping of vehicles reduces dropping of packets due to collision of sending large number of duplicate packets. Grouping concept is used in our thesis to provide different applications of VANET in a better way. We have modified grouping of vehicles according to our applications requirement and proposed an approach for vehicles to select real-time adaptive path. Vehicles choose congestion free and shortest time path to their destination. In the next section, grouping of vehicles are used to transmit event-driven safety message in emergency situations. Grouping of vehicles is efficient in this case as it needed to be very fast and highly reliable. We have added different parameters for transmitting the message to neighbors which makes it more efficient. It uses decentralized environment as it needed to works both for highway and urban scenario of the city. It helps to improve security in the message and privacy of entities in an efficient manner which are major concern in achieving robust vehicular network. In testing phase, we evaluated the performance of our proposed approach with help of VANET simulators (OMNET++, SUMO, Veins) and compared ours proposed approach with other existing methods

Sequencing Closterium moniliferum: Future prospects in nuclear waste disposal

AbstractGenome sequencing can play a vital role in health and several other domains such as in nuclear outflow related environmental issues. The power of information derived out of sequencing has been used in the field of health care, evolutionary studies and for better understanding of the biological framework of life. Through the recent advancements in sequencing studies, now the researchers are aiming to use its power in non conventional areas. Here we have discussed on the importance of sequencing the Closterium moniliferum genome which will prove to be a future endeavour in nuclear cleanup and radioactive waste disposal

Human Machine Interface for Controlling a Robot Using Image Processing

This paper introduces a head movement based Human Machine Interface (HMI) that uses the right and left movements of head to control a robot motion. Here we present an approach for making an effective technique for real-time face orientation information system, to control a robot which can be efficiently used for Electrical Powered Wheelchair (EPW). Basically this project aims at application related to HMI. The system (machine) identifies the orientation of the face movement with respect to the pixel values of image in a certain areas. Initially we take an image and divide that whole image into three parts on the basis of its number of columns. On the basis of orientation of face, maximum pixel value of approximate same range of (R, G, and B value of a pixel) lie in one of divided parts of image. This information we transfer to the microcontroller through serial communication port and control the motion of robot like forward motion, left and right turn and stop in real time by using head movements

Role of magnetic resonance venogram, diffusion and susceptibility weighted imaging in diagnosis of cerebral venous thrombosis

Background: Cerebral venous thrombosis (CVT) is an uncommon and sometimes critical disease, especially in untreated patients. CVT is an elusive diagnosis because of its nonspecific presentation and its numerous predisposing causes. Accurate diagnosis is difficult but important because effective therapies, including anticoagulants and intrasinus thrombolysis are available. Patients with cerebral venous thrombosis often make dramatic recoveries after anticoagulation. For this reason, accurate diagnosis is important and critical. The aim was to study the extent of venous sinus involvement and associated cerebral parenchymal changes on magnetic resonance venogram (MRV); to study the pattern of diffusion weighted images and ADC (apparent diffusion coefficient) mapping in patients with cerebral venous thrombosis; to study the role of susceptibility weighted images in patients with cerebral venous thrombosis.Methods: Study was conducted on 34 patients diagnosed to have cerebral venous thrombosis on imaging.Results: Imaging analyses of 34 patients (19 females, 15 males, and age range 19-75 years) were done. Thrombus on MRV was seen as loss of high flow signal from the sinus in cases of complete occlusion of the sinus and frayed or patchy flow signal in the cases of non-occlusive thrombus. 16 patients with hemorrhagic infarct showed heterogeneous signal intensity on DWI (diffusion weighted imaging) and blooming on SWI (suseptibility weighted imaging) sequence. 13 patients with non-hemorrhagic infarct showed multifocal high signal intensities in DWI with variable ADC values and no blooming on SWI. 5 patients with intracerebral hematoma showed areas of heterogeneous signals on DWI with blooming on SWI, corresponding ADC values were variable.Conclusions: MRV, diffusion and susceptibility weighted imaging can be used to evaluate the extent of thrombus, discriminate between different types of edema, detect intracerebral hematoma, hemorrhagic and non-hemorrhagic infarcts, and deliver time-saving information for early diagnosis of CVT.