Automatic registration of microarray images. I. Rectangular grid

MOTIVATION: The analysis of high-throughput experiment data provided by microarrays becomes increasingly more and more important part of modern biological science. Microarrays allow to conduct genotyping or gene expression experiments on hundreds of thousands of test genes in parallel. Because of the large and constantly growing amount of experimental data the necessity of efficiency, robustness and complete automation of microarray image analysis algorithms is gaining significant attention in the field of microarray processing. RESULTS: The author presents here an efficient and completely automatic image registration algorithm (that is an algorithm for spots and blocks indexing) that allows to process a wide variety of microarray slides with different parameters of grid and block spacing as well as spot sizes. The algorithm scales linearly with the grid size, the time complexity is O(M), where M is number of rows x number of columns. It can successfully cope with local and global distortions of the grid, such as focal distortions and non-orthogonal transformations. The algorithm has been tested both on CCD and scanned images and showed very good performance-the processing time of a single slide with 44 blocks of 200 x 200 grid points (or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf     

Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.     

Hydrotropic polymeric micelles for enhanced paclitaxel solubility: in vitro and in vivo characterization

The purpose of this investigation was to characterize the in vitro stability and in vivo disposition of paclitaxel in rats after solubilization of paclitaxel into hydrotropic polymeric micelles. The amphiphilic block copolymers consisted of a micellar shell-forming poly(ethylene glycol) (PEG) block and a core-forming poly(2-(4-vinylbenzyloxy)-N,N-diethylnicotinamide) (P(VBODENA)) block. N,N-Diethylnicotinamide (DENA) in the micellar inner core resulted in effective paclitaxel solubilization and stabilization. Solubilization of paclitaxel using polymeric micelles of poly(ethylene glycol)-b-P(D,L-lactide) (PEG-b-PLA) served as a control for the stability study. Up to 37.4 wt % paclitaxel could be loaded in PEG-b-P(VBODENA) micelles, whereas the maximum loading amount for PEG-b-PLA micelles was 27.6 wt %. Thermal analysis showed that paclitaxel in the polymeric micelles existed in the molecularly dispersed amorphous state even at loadings over 30 wt %. Paclitaxel-loaded hydrotropic polymeric micelles retained their stability in water for weeks, whereas paclitaxel-loaded PEG-b-PLA micelles precipitated in a few days. Hydrotropic polymer micelles were more effective than PEG-PLA micelle formulations in inhibiting the proliferation of human cancer cells. Paclitaxel in hydrotropic polymer micelles was administered orally (3.8 mg/kg), intravenously (2.5 mg/kg), or via the portal vein (2.5 mg/kg) to rats. The oral bioavailability was 12.4% of the intravenous administration. Our data suggest that polymeric micelles with a hydrotropic structure are superior as a carrier of paclitaxel due to a high solubilizing capacity combined with long-term stability, which has not been accomplished by other existing polymeric micelle systems.     

Role of water molecules and ion pairs in Dps and related ferritin-like structures

A comparative study of water molecules and ion pairs in 11 Dps protein structures has been carried out. The invariant and common water molecules, the conserved residues interacting with them and the conserved ion pairs have been analyzed. Certain water molecules found on the interfaces between subunits are highly conserved and may be implicated in flexibility or continuing association of the subunits of the structure. It is possible that the water molecules, ion pairs and the special case of a water mediated charged network through a single water molecule are involved in maintaining the stability of the protein.     

The DNLS equation and parametric decay instability

A model that describes the interaction of nonlinear Alfvén packets propagating in opposite directions parallel to the ambient magnetic field is constructed. This model incorporates both (i) the parametric interaction of harmonics propagating in the same direction, which can be responsible for the transportation of the wave energy to the short-wavelength region of the spectrum, and (ii) the parametric interaction of Alfvén waves propagating in opposite directions, which can be responsible for the excitation of backward-propagating waves by the parametric decaylike instability of the forward-propagating fluctuations.     

Protective Ventilation of Preterm Lambs Exposed to Acute Chorioamnionitis Does Not Reduce Ventilation-Induced Lung or Brain Injury

Background

The onset of mechanical ventilation is a critical time for the initiation of cerebral white matter (WM) injury in preterm neonates, particularly if they are inadvertently exposed to high tidal volumes (V_T) in the delivery room. Protective ventilation strategies at birth reduce ventilation-induced lung and brain inflammation and injury, however its efficacy in a compromised newborn is not known. Chorioamnionitis is a common antecedent of preterm birth, and increases the risk and severity of WM injury. We investigated the effects of high V_T ventilation, after chorioamnionitis, on preterm lung and WM inflammation and injury, and whether a protective ventilation strategy could mitigate the response.

Methods

Pregnant ewes (n = 18) received intra-amniotic lipopolysaccharide (LPS) 2 days before delivery, instrumentation and ventilation at 127±1 days gestation. Lambs were either immediately euthanased and used as unventilated controls (LPS_UVC; n = 6), or were ventilated using an injurious high V_T strategy (LPS_INJ; n = 5) or a protective ventilation strategy (LPS_PROT; n = 7) for a total of 90 min. Mean arterial pressure, heart rate and cerebral haemodynamics and oxygenation were measured continuously. Lungs and brains underwent molecular and histological assessment of inflammation and injury.

Results

LPS_INJ lambs had poorer oxygenation than LPS_PROT lambs. Ventilation requirements and cardiopulmonary and systemic haemodynamics were not different between ventilation strategies. Compared to unventilated lambs, LPS_INJ and LPS_PROT lambs had increases in pro-inflammatory cytokine expression within the lungs and brain, and increased astrogliosis (p<0.02) and cell death (p<0.05) in the WM, which were equivalent in magnitude between groups.

Conclusions

Ventilation after acute chorioamnionitis, irrespective of strategy used, increases haemodynamic instability and lung and cerebral inflammation and injury. Mechanical ventilation is a potential contributor to WM injury in infants exposed to chorioamnionitis.     

Algorithm to find distant repeats in a single protein sequence

Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of importance to structural biologists, molecular biologists, biochemists and researchers involved in phylogenetic and evolutionary studies.     

Glaucoma Pred: Glaucoma prediction based on Myocilin genotype and phenotype information

Glaucoma is the second leading cause of blindness after cataract and is heterogeneous in nature. Employing a genetic approach for the detection of the diseased condition provides an advantage that the gene responsible for the disease can be identified by genetic test. The availability of predictive tests based on the published literature would provide a mechanism for early detection and treatment. The genotype and phenotype information could be a valuable source for predicting the risk of the disease. To this end, a web server has been developed, based on the genotype and phenotype of myocilin mutation, which were identified by familial linkage analysis and case studies. The proposed web server provides clinical data and severity index for a given mutation. The server has several useful options to help clinicians and researchers to identify individuals at a risk of developing the disease. Glaucoma Pred server is available at http://bioserver1.physics.iisc.ac.in/myocilin.