86 research outputs found

    Computational Structural Analysis: Multiple Proteins Bound to DNA

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    BACKGROUND: With increasing numbers of crystal structures of proteinratioDNA and proteinratioproteinratioDNA complexes publically available, it is now possible to extract sufficient structural, physical-chemical and thermodynamic parameters to make general observations and predictions about their interactions. In particular, the properties of macromolecular assemblies of multiple proteins bound to DNA have not previously been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS: We have performed computational structural analyses on macromolecular assemblies of multiple proteins bound to DNA using a variety of different computational tools: PISA; PROMOTIF; X3DNA; ReadOut; DDNA and DCOMPLEX. Additionally, we have developed and employed an algorithm for approximate collision detection and overlapping volume estimation of two macromolecules. An implementation of this algorithm is available at http://promoterplot.fmi.ch/Collision1/. The results obtained are compared with structural, physical-chemical and thermodynamic parameters from proteinratioprotein and single proteinratioDNA complexes. Many of interface properties of multiple proteinratioDNA complexes were found to be very similar to those observed in binary proteinratioDNA and proteinratioprotein complexes. However, the conformational change of the DNA upon protein binding is significantly higher when multiple proteins bind to it than is observed when single proteins bind. The water mediated contacts are less important (found in less quantity) between the interfaces of components in ternary (proteinratioproteinratioDNA) complexes than in those of binary complexes (proteinratioprotein and proteinratioDNA).The thermodynamic stability of ternary complexes is also higher than in the binary interactions. Greater specificity and affinity of multiple proteins binding to DNA in comparison with binary protein-DNA interactions were observed. However, protein-protein binding affinities are stronger in complexes without the presence of DNA. CONCLUSIONS/SIGNIFICANCE: Our results indicate that the interface properties: interface area; number of interface residues/atoms and hydrogen bonds; and the distribution of interface residues, hydrogen bonds, van der Walls contacts and secondary structure motifs are independent of whether or not a protein is in a binary or ternary complex with DNA. However, changes in the shape of the DNA reduce the off-rate of the proteins which greatly enhances the stability and specificity of ternary complexes compared to binary ones

    Endourological Management of Forgotten Encrusted Ureteral Stents

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    PURPOSE: To present our experience and discuss the various endourological approaches for treating forgotten encrusted ureteral stents associated with stone formation. MATERIALS AND METHODS: From July 2006 to December 2008, 14 patients (11 men and 3 women) with encrusted ureteral stents were analyzed. The average indwelling time of the stent was 4.9 years (range 1 to 12). Plain-film radiography was used to evaluate encrustation, stone burden, and fragmentation of the stents. Intravenous urogram and a Tc99m diethylene triamine penta acetic-acid renogram was used to assess renal function. RESULTS: In seven patients, the entire stent was encrusted, in three patients the encrustation was confined to the ureteral and lower coil part of the stent, two patients had encrustation of the lower coil, and minimal encrustation was observed in two patients. Percutaneous nephrolithotomy was performed in 5 cases and retrograde ureteroscopy with intra-corporeal lithotripsy in 9 patients. Cystolithotripsy was used to manage the distal coil of the encrusted stent in eight patients. Simple cystoscopic removal of the stents with minimal encrustation was carried-out in two cases. Looposcopy and removal of the stent was performed in one patient with an ileal conduit and retained stent. Only one patient required open surgical removal of the stent. Thirteen out of 14 patients were rendered stone and stent free in one session. All except two stents were removed intact and stone analysis of encrustation and calcification revealed calcium oxalate and calcium phosphate in the majority of the cases. CONCLUSION: Endourological management of forgotten encrusted stents is highly successful and often avoids the need for open surgical techniques

    Chemical Composition and Insecticidal Activities of Essential Oils against the Pulse Beetle

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    Pulse beetles, Callosobruchus chinensis and Callosobruchus maculatus, are essential pests of cowpea, gram, soybean and pulses. Application of synthetic insecticides against the pulse beetle has led to insect resistance; insecticide residues on grains affect human health and the environment. Essential oils (EOs) are the best alternatives to synthetics due to their safety to the environment and health. The main objective of the investigation was to study the chemical composition and insecticidal activities of EOs, their combinations and compounds against the pulse beetle under laboratory. Neo-isomenthol, carvone and β-ocimene are the significant components of tested oils using GC-MS. Mentha spicata showed promising fumigant toxicity against C. chinensis (LC50 = 0.94 µL/mL) and was followed by M. piperita (LC50 = 0.98 µL/mL), whereas M. piperita (LC50 = 0.92 µL/mL) against C. maculatus. A combination of Tagetes minuta + M. piperita showed more toxicity against C. chinensis after 48 h (LC50 = 0.87 µL/mL) than T. minuta + M. spicata (LC50 = 1.07 µL/mL). L-Carvone showed fumigant toxicity against C. chinensis after 48 h (LC50 = 1.19 µL/mL). Binary mixtures of T. minuta +M. piperita and M. spicata showed promising toxicity and synergistic activity. EOs also exhibited repellence and ovipositional inhibition. The application of M. piperita can be recommended for the control of the pulse beetle

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    Not AvailableBovine respiratory disease (BRD) is a condition of severe pneumonia caused due to environmental stress followed by a multiple viral and bacterial pathogens.The present study aimed to detect the BRD agents such as Mannhaeimia haemolytica, Pasteurella multocida and Histophilus somni and IBR in yaks suffering from respiratory infections. For the study, 157 deep nasal and blood samples were collected from yak of Arunachal Pradesh and processed for isolation and PCR detection of respiratory bacterial pathogens such as M. haemolytica, P. multocida and H. somni and seroscreening of IBR. From 157 samples, one M. haemolytica and two H. somni isolates were recovered. This is the first report of H. somni and M. haemolytica isolation from yak nasal samples from India. In mPCR, 23 yak nasal samples (14.6%) amplified for M. haemolytica, two (1.2%) for P. multocida and six samples for H. somni (4.6%) by simplex PCR. Concurrence of H. somni and M. haemolytica in three samples, and M. haemolytica and P. multocida type B in two samples was also observed.Very high seroprevalence for IBR (37%) by Indirect ABELISA was recorded.The study concluded that highest number of samples were positive for M. haemolytica (14.6%) and emphasizes its role in respiratory infections along with high seroprevalence of IBR. It also reflected the diagnostic importance of mPCR/PCR in regions inaccessible for fresh sample collection and transportation as an alternate to isolation procedures.Not Availabl

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    Not AvailableRespiratory infections in yak(Bos grunniens): a pilot study on isolation and direct PCR diagnosis for pasteurellosis, mannheimiosis and histophilosis.Not Availabl

    Shock-wave processing of C60 in hydrogen

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    International audienceContext. Interstellar carbonaceous particles and molecules are subject to intense shocks in astrophysical environments. Shocks induce a rapid raise in temperature and density which strongly affects the chemical and physical properties of both the gas and solid phases of the interstellar matter.Aims. The shock-induced thermal processing of C60 particles in hydrogen has been investigated in the laboratory under controlled conditions up to 3900 K with the help of a material shock-tube.Methods. The solid residues generated by the exposure of a C60/H2 mixture to a millisecond shock wave were collected and analyzed using X-ray diffraction, scanning electron microscopy, transmission electron microscopy, Raman micro-spectroscopy, and infrared micro-spectroscopy. The gaseous products were analyzed by Gas Chromatography and Cavity Ring Down Spectroscopy. Results. Volatile end-products appear above reflected shock gas temperatures of ~2540 K and reveal the substantial presence of small molecules with one or two C atoms. These observations confirm the role played by the C2 radical as a major product of C60 fragmentation and less expectedly highlight the existence of a single C atom loss channel. Molecules with more than two carbon atoms are not observed in the post-shock gas. The analysis of the solid component shows that C60 particles are rapidly converted into amorphous carbon with a number of aliphatic bridges.Conclusions. The absence of aromatic CH stretches on the IR spectra indicates that H atoms do not link directly to aromatic cycles. The fast thermal processing of C60 in H2 over the 800–3400 K temperature range leads to amorphous carbon. The analysis hints at a collapse of the cage with the formation of a few aliphatic connections. A low amount of hydrogen is incorporated into the carbon material. This work extends the range of applications of shock tubes to studies of astrophysical interest
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