A bioinformatics framework for RNA structure mining, motif discovery and polyadenylation analysis

The RNA molecules play various important roles in the cell and their functionality depends not only on the sequence information but to a large extent on their structure. The development of computational and predictive approaches to study RNA molecules is extremely valuable. In this research, a tool named RADAR was developed that provides a multitude of functionality for RNA data analysis and research. It aligns structure annotated RNA sequences so that both the sequence as well as structure information is taken into consideration. This tool is capable of performing pair-wise structure alignment, multiple structure alignment, database search and clustering. In addition, it provides two salient features: (i) constrained alignment of RNA secondary structures, and (ii) prediction of consensus structure for a set of RNA sequences. This tool is also hosted on the web and can be freely accessed and the software can be downloaded from http://datalab.njitedu/biodata/rna/RSmatch/server.htm . The RADAR software has been applied to various datasets (genomes of various mammals, viruses and parasites) and our experimental results show that this approach is capable of detecting functionally important regions. As an application of RADAR, a systematic data mining approach was developed, termed GLEAN-UTR, to identify small stem loop RNA structure elements in the Untranslated regions (UTRs) that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This study resulted in 90 distinct RNA structure groups containing 748 structures, with 3\u27 Histone stem loop (HSL3) and Iron Response element (IRE) among the top hits. Further, the role played by structure in mRNA polyadenylation was investigated. Polyadenylation is an important step towards the maturation of almost all cellular mRNAs in eukaryotes. Studies have identified several cis-elements besides the widely known polyadenylation signal (PAS) element (AATAAA or ATTAAA or a close variant) which may have a role to play in poly(A) site identification. In this study the differences in structural stability of sequences surrounding poly(A) sites was investigated and it was found that for the genes containing single poly(A) site, the surrounding sequence is most stable as compared with the surrounding sequences for alternative poly(A) sites. This indicates that structure may be providing a evolutionary advantage for single poly(A) sites that prevents multiple poly(A) sites from arising. In addition the study found that the structural stability of the region surrounding a polyadenylation site correlates with its distance from the next gene. The shortest distance corresponding to a greater structural stability

Study of Carbon Materials and Effect of its Ball Milling, on Capacitance of Supercapacitor

AbstractThe various forms of energy are available in nature, however the electrical energy is the most convenient form of energy for any application. Due to this reason, day by day the demand of electrical energy is rapidly growing in this decade. There is always mismatch in time zone between availability of energy especially from renewable energy sources and demand. Thus, the storage of electrical energy is now becoming important. However, amount of electrical energy which can be stored is again a critical issue in many renewable energy systems. Supercapacitor can be a new technology for the storage of electrical energy. Supercapacitors are currently a prominent area of research for energy storage devices as they have high power density, long cycling time, and short charging time. Due to a short charging time feature of supercapacitor, in future it can have application in hybrid cars. Supercapacitor is similar to a regular capacitor in operation, however it offers a very high capacitance in a small package for achieving the requirement of power supplies. Capacitance, internal resistance, self discharge, ageing, pulse current, size, shape are some of the parameters in selection of supercapacitor in various applications. Capacitance value of capacitor is very important in energy storage system as amount of energy stored by capacitor is directly proportional to its capacitance value. The capacitance value of supercapacitor depends on types of carbon material and method of construction of supercapacitor. Various kinds of activated carbon materials are available with different pore size, pore density and specific surface area, are found more suitable to get higher values of capacitor. In this research work, the properties of various carbons are studied to select appropriate carbon material to construct the supercapacitor. Supercapacitor along with fuel cell can address many issues related to effective electrical energy storage and it can have number of applications in future. This research work also presents the effect of ball milling of an electrode material on the value of capacitance of an aqueous metal oxide based supercapacitor

Satellite observed wind forcing over the southwest equatorial Indian ocean during Indian summermonsoon

In this paper, satellite-observed wind forcing in the form of strong surge of cold air through Mozambique channel and along east African coast, under the influence of eastward propagating baroclinic wave disturbances over southwest Indian ocean has been studied during various summer monsoon seasons. Further, its impact on the intensification of monsoon systems over the Arabian sea through the excitation of low-level jet and associated cross-equatorial flow has been illustrated. For this purpose, satellite-observed cloud imagery, obtained from TIROS-N, NOAA, DMSP, GOES and INSAT satellites during 1979 and 1988-95,have been utilized for finding latitudinal positions of the cold fronts across south African-Malgassy region (i.e. 30°S, I -40°E), GOES(IO) and INSAT derived low level cloud drift winds in the domain 2.5°S to 2.5°N and 40°50°E have been used to observe the triggering of low level jet and associated cross equatorial flow. Daily rainfall of ten stations viz. Tiruvananthapuram, Alleppy, Cochin, Kozikhode, Mangalore, Karwar, Goa, Ratnagiri, Bombay and Dahanu have been used for finding the modulation of the rainfall activity along the west coast of India. From the results of the study it is inferred that there is an abrupt increase in the strength of low-level wind flow along east African coast 2 to 3 days after the first appearence of northward propagating cold front across south African-Malgassy region. This is followed by intensification of the rainbearing monsoon systems (e.g. ITCZ, lows, off shore troughs etc.) over the Arabian sea giving increase in rainfall activity along the west coast of India. Therefore it is suggested that above association between northward-propagating cold front across south African-Malgassy region and excitation of low-level cross-equatorial flow can be linked to forecast increase in rainfall activity alone the west coast of India 5-7 days in advance

Spectacle Compliance in Slum Population of Mumbai: Pilot

Background Mumbai Eye Care campaign was a mega refractive error project implemented for the slum population of Mumbai from 2009-15. The project was supported by Standard Chartered Bank’s CSR activity Seeing is Believing through Sightsavers. The project design and service delivery was implemented by Lotus College of Optometry. During the first 3 years of the project, spectacles were distributed free of cost to adults by only collecting case paper charge of Rs.10/-/ Hence a questionnaire based study was conducted to assess the spectacle compliance among this population. Methodology Spectacle Compliance questionnaire was designed, validated by Optometry faculty and the same was administered by an Optometry intern. The spectacle compliance and reasons for non compliance was analysed for 200 respondents. Results: Spectacle compliance was found to be 73.48%. Conclusion: Spectacle compliance was found to be high in this study and was single vision near spectacle design showed better compliance

Doppler study of middle cerebral artery and umbilical artery in biometrically suspected intra uterine growth restricted pregnancies

Background: Intra uterine growth restricted (IUGR) is when the expected foetal weight is less than 10th percentile for gestational age. The hemodynamics of the feotus takes into account both the umbilical-placental and cerebral vascular beds. Underlying etiology that results in the failure of a foetus to attain its expected growth may vary. However the final infliction is via uteroplacental insufficiency. It is highlighted that inadequate uteroplacental perfusion is the main and primary pathology in growth restriction resulting in an increased umbilical artery impedance. Following this step are the changes in the middle cerebral artery (MCA) which categorically set in as a secondary phenomenon.Methods: Duplex Doppler Sonography is a reliable, non- invasive and rapid diagnostic technique in IUGR patients. Grey scale findings together with colour Doppler characteristics help in the qualitative as well as quantitative evaluation of the Uteroplacental and Fetoplacental circulation. Hence ultrasonography (USG) has become the most widely used, standard and simple way of detecting and confirming IUGR. Ultrasound biometry is the gold standard for assessment of foetal size. Various criteria are used to label a feotus growth restricted; foetal weight less than 10th percentile for gestational age is mostly widely accepted criterion. Others like elevated HC/AC ratio, elevated FL/AC ratio, and presence of oligohydramnios without ruptured membranes, presence of advanced placental grade can also be used for improving the accuracy of diagnosis. After establishing the diagnosis of IUGR, Doppler imaging becomes a valuable investigating method for monitoring the pregnancy because it provides information about the hemodynamic status of the feotus. Uteroplacental system evaluation takes into account the flow pattern of uterine artery, reflecting any underlying Uteroplacental vascular ischemia. Umbilical artery Doppler waveforms reflect the status of the fetoplacental circulation and any underlying placental insufficiency.Results: Fourteen cases showed absent umbilical artery end diastolic flow and four patients showed reversal of end diastolic flow.: Twenty two patients showed elevated PI. Adverse perinatal outcome was observed in all patients with absent and reversal of end diastolic flow. Out of the twenty two with elevated PI fifteen showed adverse outcome. Thirty six cases showed low MCA PI and six showed a pseudonormalization. A cerebro -placental ratio of < 1.08 was observed in 16 patients, it was calculated in only those pregnancies that showed forward diastolic flow in umbilical artery (n= 22). Fifteen of them showed adverse perinatal outcome.Conclusions: Doppler imaging is of value for monitoring pregnancies complicated with IUGR because it can provide indirect evidence of foetal compromise and is known to improve outcome of high risk pregnancies. Doppler evaluation is complementary to all other surveillance modalities. Because the changes in umbilical, uterine & MCA strongly correlate with pregnancy outcome in growth restricted foetuses the use of foetal biometry & Doppler examination is recommended in all cases of suspected IUGR cases

Bilateral retrorenal colon-a case report

Ascending and descending colon normally lie in anterior pararenal space anterior to kidneys. Extension of colon behind kidney is rare. It is more frequently found on the left side behind lower pole of the left kidney. Bilateral retrorenal colon is rare. Its detection is important prior to Retrorenal, Percutaneous nephrolithotomy (PCNL) to avoid complications. We report a case of bilateral retrorenal colon detected incidentally in a case of obstructive jaundice

Investigation of features of May, 2001 tropical cyclone over the Arabian Sea through IRS-P4 and other satellite data

In this paper, utility of satellite derived atmospheric motion vectors and geophysical parameters is brought out to discern appropriate signals for improving short-range forecasts in respect of development/dissipation of tropical cyclones over the Indian region. Results of a particular case study of May, 2001 cyclone, which formed in the Arabian Sea are reported. Analysis of wind field with input of modified cloud motion vectors and water vapour wind vectors is performed utilizing Optimum Interpolation (OI) technique at 850 and 200 hPa for finding dynamical changes such as vorticity, convergence and divergence for the complete life period of this cyclone. Simultaneously, variations in geophysical parameters obtained from IRS-P4 and TRMM satellites in ascending and descending nodes are compared with dynamical variations for discerning some positive signals to improve short range forecasts over the Indian region. The enhancement of cyclonic vorticity at 200 hPa over larger area surrounding center of cyclone was observed from 26 to 28 May 2001 which gave a positive signal for dissipation of storm

Functional divergence of gene duplicates – a domain-centric view

Gene duplicates have been shown to evolve at different rates. Here we further investigate the mechanism and functional underpinning of this phenomenon by assessing asymmetric evolution specifically within functional domains of gene duplicates. Based on duplicate genes in five teleost fishes resulting from a whole genome duplication event, we first show that a Fisher Exact test based approach to detect asymmetry is more sensitive than the previously used Likelihood Ratio test. Using our Fisher Exact test, we found that the evolutionary rate asymmetry in the overall protein is largely explained by the asymmetric evolution within specific protein domains. Moreover, among cases of asymmetrically evolving domains, for the gene copy containing a fast evolving domain, the non-synonymous substitutions often cluster within the fast evolving domain. We found that rare substitutions were preferred within asymmetrically evolving domains suggestive of functional divergence. While overall ~32 % of the domains tested were found to be evolving asymmetrically, certain protein domains such as the Tyrosine and Ser/Thr Kinase domains had a much greater prevalence of asymmetric evolution. Finally, based on the spatial expression of Zebra fish duplicate proteins during development, we found that protein pairs containing asymmetrically evolving domains had a greater divergence in gene expression as compared to the duplicate proteins that did not exhibit asymmetric evolution. Taken together, our results suggest that the previously observed asymmetry in the overall duplicate protein evolution is largely due to divergence of specific domains of the protein, and coincides with divergence in spatial expression domains.https://doi.org/10.1186/1471-2148-12-12

Proper depiction of monsoon depression through IRS-P4 MSMR

In this paper, daily variations of satellite-derived geophysical parameters such as integrated water vapour (IWV), cloud liquid water content (CLW), sea surface temperature (SST) and sea surface wind speed (SSW) have been studied for a case of monsoon depression that formed over the Bay of Bengal during 19th-24th August 2000. For this purpose, IRS P4 MSMR satellite data have been utilized over the domain equator - 25°N and 40°-100°E. An integrated approach of satellite data obtained from IRS-P4, METEOSAT-5 and INSAT was made for getting a signal for the development of monsoon depression over the Indian region. Variations in deep convective activity obtained through visible, infrared and OLR data at 06 UTC was thoroughly analyzed for the complete life cycle of monsoon depression. Geophysical parameters obtained through IRS-P4 satellite data were compared with vorticity, convergence and divergence at 850 and 200 hPa levels generated through cloud motion vectors (CMVs) and water vapour wind vectors (WVWVs) obtained from METEOSAT-5 satellite. This comparison was made for finding proper consistency of geophysical parameters with dynamical aspects of major convective activity of the depression. From the results of this study it is revealed that there was strengthening of sea surface winds to the south of low-pressure area prior to the formation of depression. This indicated the possibility of increase in cyclonic vorticity in the lower troposphere. Hence, wind field at 850 hPa with satellite input of CMVs in objective analysis of wind field using optimum interpolation (OI) scheme was computed. Maximum cyclonic vorticity field at 850 hPa was obtained in the region of depression just one day before its formation. Similarly, with the same procedure maximum anticyclonic vorticity was observed at 200 hPa with WVWVs input. Consistent convergence and divergence at 850 and 200 hPa was noticed with respect to these vorticities. In association with these developments, we could get lowest values of OLR (120W/m 2) associated with major convective activity that was consistent with the maximum values of integrated water vapour (6-8 gm/cm 2) and cloud liquid water content (50-60 mg/cm 2) persisting particularly in the southwest sector of the monsoon depression

Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

<p>Abstract</p> <p>Background</p> <p>UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs have been experimentally identified, including the histone 3' UTR stem-loop structure (HSL3) and iron response element (IRE). These stem-loop structures are conserved among mammalian orthologs, and exist in a group of genes encoding proteins involved in the same biological pathways. It is not known to what extent RNA structures like these exist in all mammalian UTRs.</p> <p>Results</p> <p>In this paper we took a systematic approach, named GLEAN-UTR, to identify small stem-loop RNA structure elements in UTRs that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure.</p> <p>Conclusion</p> <p>Our result indicates that there may exist many conserved stem-loop structures in mammalian UTRs that are involved in coordinate post-transcriptional regulation of biological pathways.</p