Methods to improve gene signal : Application to cDNA microarrays

Microarrays are high throughput biological assays that allow the screening of thousands of genes for their expression. The main idea behind microarrays is to compute for each gene a unique signal that is directly proportional to the quantity of mRNA that was hybridized on the chip. A large number of steps and errors associated with each step make the generated expression signal noisy. As a result, microarray data need to be carefully pre-processed before their analysis can be assumed to lead to reliable and biologically relevant conclusions. This thesis focuses on developing methods for improving gene signal and further utilizing this improved signal for higher level analysis. To achieve this, first, approaches for designing microarray experiments using various optimality criteria, considering both biological and technical replicates, are described. A carefully designed experiment leads to signal with low noise, as the effect of unwanted variations is minimized and the precision of the estimates of the parameters of interest are maximized. Second, a system for improving the gene signal by using three scans at varying scanner sensitivities is developed. A novel Bayesian latent intensity model is then applied on these three sets of expression values, corresponding to the three scans, to estimate the suitably calibrated true signal of genes. Third, a novel image segmentation approach that segregates the fluorescent signal from the undesired noise is developed using an additional dye, SYBR green RNA II. This technique helped in identifying signal only with respect to the hybridized DNA, and signal corresponding to dust, scratch, spilling of dye, and other noises, are avoided. Fourth, an integrated statistical model is developed, where signal correction, systematic array effects, dye effects, and differential expression, are modelled jointly as opposed to a sequential application of several methods of analysis. The methods described in here have been tested only for cDNA microarrays, but can also, with some modifications, be applied to other high-throughput technologies. Keywords: High-throughput technology, microarray, cDNA, multiple scans, Bayesian hierarchical models, image analysis, experimental design, MCMC, WinBUGS.Tarkastellaan menetelmiä, joilla voidaan parantaa geneetisiä signaaleja ja hyödyntää vahvistetun signaalin käyttöä myöhemmissä analyyseissä

A Review Paper on PAPR Reduction in OFDM using SLM and Adaptive Clipping

Orthogonal Frequency division Multiplexing (OFDM) is an effectual technique of data transmission for high speed communication schemes. However, the main drawback of OFDM system is the high Peak to Average Power Ratio (PAPR) of the communicated signals. OFDM contain of large number of independent subcarriers, as a result of which the amplitude of such a signal can have high peak values. Coding, phase rotation and clipping are between many PAPR reduction schemes that have been proposed to overcome this problem. Here in this paper we survey on two different PAPR reduction methods adaptive clipping and selective mapping (SLM) are used to reduce PAPR. Important reduction in PAPR has been achieved using these techniques

Surgical Bone Adhesives with Potential Maxillofacial Applications A Systematic Review

The reduction and stabilisation of fractured bone fragments have always been a challenging task for thesurgeon. A micro-platesystem for maxillofacial fracture treatment provides excellent results. However, plates and screws are difficult toadapt to the thin bone, and small fragments often lead to the weakening of bone causing secondary fractures. Surgical bone adhesives promise as a viable alternative for issues with micro-plates, but a lotremains desired for successful usefor clinical application. The present systematic review aims to identify the bone adhesive materials available at various stages in animal or human models in the last decade and enumerate their characteristics for potential use in non-load bearing maxillofacial fractures. PubMed electronic database searched using a combination of keywords to identify English language articles between January 2011 and December 2020 yielded a total of 1204 records, of which 15 were included for final review after applying PRISMA guidelines. Cyanoacrylate was the commonly used adhesive material followed by fibrin glue and calcium phosphate-based materials. Although encouraging, results with each material still lack human randomised control trials thus presenting inconclusive evidence. Studies on these lines are suggested along with the development of newer materials to overcome the shortcomings in the currently available systems

Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan

Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan

Ex-vivo skin permeation studies of sumatriptan succinate using different solvent systems and its comparison with PLGA nanoparticles

Sumatripatan succinate (SS) is a 5-HT1D agonist used in migraine therapy. Its low oral bioavailability (~15 %) is due to extensive pre-systemic metabolism and low biological half-life. The frequent administration of SS is required to maintain effective plasma concentration. In the present investigation, polymeric nanoparticles of SS (SS-NPs) were prepared by W1/O/W2 double emulsion solvent evaporation method followed by probe sonication. Poly-(lactide-co-glycolide) (PLGA) and poloxamer 188 were used as polymer and surfactant respectively to formulate SS-NPs. The particle size, polydispersity index, zeta potential, percent entrapment efficiency of SS-NPs were found to be 126 nm, 0.06, (-) 24.1 mV, 32.52 ± 2.34 % respectively. Characterization of lyophilized SS-NPs revealed formation of drug entrapped amorphous SS-NPs. Ex-vivo skin permeation studies of SS were conducted using distilled water, ethanol (EtOH), propylene glycol (PG) and their binary combinations. The lag time, flux, permeability and steady state permeability coefficient and enhancement ratio were determined. The ex-vivo permeation profiles of SS in different solvent systems were compared with SS-NPs in distilled water. The maximum flux of 345.8 µg.cm-2.h-1 was obtained with solvent system comprising 33% PG in EtOH. The minimum lag time and a comparable flux value was obtained in ex-vivo diffusion studies of SS-NPs. Hence, it can be concluded that SS-NPs can be administered in transdermal drug delivery system using a solvent system comprising 33%PG in EtOH. The present investigation indicated that using suitable solvent system and PLGA nanoparticles, the skin permeation of SS can be enhanced. Keywords: Migraine, sumatriptan succinate, poly-(lactide-co-glycolide), nanoparticles, transdermal patc

Bayesian integrated modeling of expression data: a case study on RhoG

Peer reviewe

Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post - transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack the ability to identify novel miRNAs and accurately determine expression at a range of concentrations. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts.</p> <p>Results</p> <p>The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 and HL60 are presented. In general K562 cells displayed overall low level of miRNA population and also low levels of DICER. Some of the highly expressed miRNAs in the leukocytes include several members of the let-7 family, miR-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 or HL60 cells revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Relative expression levels of individual miRNAs belonging to a cluster were found to be highly variable. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by Real-time RT-PCR and or RNase protection assay. Organization of some of the novel miRNAs in human genome suggests that these may also be part of existing clusters or form new clusters.</p> <p>Conclusions</p> <p>We conclude that about 904 miRNAs are expressed in human leukocytes. Out of these 370 are novel miRNAs. We have identified miRNAs that are differentially regulated in normal PBMC with respect to cancer cells, K562 and HL60. Our results suggest that post - transcriptional processes may play a significant role in regulating levels of miRNAs in tumor cells. The study also provides a customized automated computation pipeline for miRNA profiling and identification of novel miRNAs; even those that are missed out by other existing pipelines. The Computational Pipeline is available at the website: <url>http://mirna.jnu.ac.in/deep_sequencing/deep_sequencing.html</url></p

Hodgkin Lymphoma in a Case of Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitors

Chronic myeloid leukemia (CML) is characterized by increased and unregulated proliferation of granulocytic lineage in the bone marrow and presence of these immature myeloid cells in the peripheral blood with presence of Philadelphia (Ph) chromosome. Tyrosine kinase inhibitors are the most important drugs in the CML therapy and provide long disease-free survival. Due to the increased survival of CML patients with continual administration of these drugs, the chance of development of secondary malignancies may increase. The most common secondary malignancies are prostate, colorectal and lung cancer, non-Hodgkin lymphoma, malignant melanoma, non-melanoma skin tumors and breast cancer. Herein, we are describing a rare case of Hodgkin lymphoma in a patient of CML after ten year of primary disease presentation. Hodgkin lymphoma in a known case of CML is very rare and further studies are also needed to know the pathogenic relationship between the two entities and to assess the risk of secondary Hodgkin lymphoma in CML patients treated with tyrosine kinase inhibitors. CML itself is a risk factor for development of solid cancers and hematologic malignancies. In addition, patients on chemotherapy are immune-compromised and may be at greater risk of neoplasm driven by infectious agents such as Epstein-Barr virus

Advances in pulmonary drug delivery targeting microbial biofilms in respiratory diseases

The increasing burden of respiratory diseases caused by microbial infections poses an immense threat to global health. This review focuses on the various types of biofilms that affect the respiratory system and cause pulmonary infections, specifically bacterial biofilms. The article also sheds light on the current strategies employed for the treatment of such pulmonary infection-causing biofilms. The potential of nanocarriers as an effective treatment modality for pulmonary infections is discussed, along with the challenges faced during treatment and the measures that may be implemented to overcome these. Understanding the primary approaches of treatment against biofilm infection and applications of drug-delivery systems that employ nanoparticle-based approaches in the disruption of biofilms are of utmost interest which may guide scientists to explore the vistas of biofilm research while determining suitable treatment modalities for pulmonary respiratory infections. </jats:p