Phylogenetic Analysis of Cell Types using Histone Modifications

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Harmonic Nature of Maddalam : - A Study

 The sound samples of different strokes of maddalam are analysed using MIR toolbox. The frequency spectrum, attack and decay parameters are studied. The reasons for the harmonic nature of maddalam are identified

Corneal Characteristics in Myopic Patients

INTRODUCTION: Myopia is a significant public health problem, affecting 33% of individuals over the age of 12 years in the United States and a much higher percentage in parts of Asia such as Taiwan and Singapore and the prevalence may be increasing over time. Single vision spectacle lenses and contact lenses are commonly prescribed for myopia and more recently refractive surgery has become a popular option. While these treatments correct the myopic refractive error, they do not slow the accompanying eye growth or retard the physiological changes associated with excessive axial elongation. The World Health Organization has set a goal to eliminate preventable blindness in the world by the year 2020, with refractive error, including myopia, as one of its top five priorities. The high prevalence of myopia and its prominence as a public health problem emphasize the importance of gaining increased understanding of the mechanisms of eye growth and of finding effective treatments that slow progression and axial elongation. AIM AND OBJECTIVE: To evaluate corneal and refractive characteristics of Indian myopic patients seeking refractive surgery at a tertiary care eye centre. MATERIALS AND METHODS: Study Design: A retrospective study of 910 eyes in 455 patients who were screened by Orbscan topography (Bausch and Lomb) before undergoing myopic refractive surgery (LASIK / ZYOPTIX) from April 2011 to October 2011 in Aravind Eye Hospital, Madurai. Inclusion crIteria: • Age group between 21-40 years both male and female. • Myopia with at least-0.25 sphere and astigmatism of-0.25 cylinder. • Refractive power has been constant for at least 1 year. • Cylindrical power not more than 5 D. Exclusion Criteria: • Keratoconus / subclinical/ Forme Fruste. • Ocular surface disease including severe dry eye. • Other Ethnic groups. METHODOLOGY: • A detailed history is taken, including history of contact lens wear. • Undilated subjective refraction and auto refractometry is done. • A complete pre-operative work up is done in all patients including slit lamp- bio microscopy. • Schirmer’s 1 test in Contact Lens wearers and symptomatic patients to rule out dry eye. • The Orbscan Topography (Bausch & Lomb) was used to evaluate the corneal diameter, corneal curvature, corneal thickness, angle kappa and AC depth. • An Indirect Ophthalmoscopic examination was done with a dilated pupil for periphery examination of the posterior segment. • A dilated subjective refraction is done. • If all parameters are normal, the patients is advised LASIK. CONCLUSION: Characteristics of cornea in a sample of an Indian population showed. • The percentage of females was marginally more than males with the percentage of 53% to 47% respectively. • The results showed that 61.3% of the people were in the age group from 21-25 years. • 35% of people had mild (6D) refractive error. • The mean manifest refraction (spherical equivalent) was 3.90D±2.28 diopters (ranging from -0.25 to -14.00D). • K- Maximum had a Mean (SD) of 44.52 D ±1.34 D ranging from 41.0 D to 48.1 D. • K- Minimum had a Mean (SD) of 43.62 D ±1.29 D ranging from 40.2 D to 47.5 D. • Mean (SD) of the corneal diameter is 11.75± 0.4mm ranging from 10.6mm to 13mm. • Mean (SD) of AC depth is 3.04± 0.27mm ranging from 2.27mm to a Maximum of 3.74mm. • The Mean (SD) of the thickness of the corneal is 557.43±29.72μm and the range is a Minimum of 496μm to a Maximum of 665μm. • The thinnest areas of the cornea were found to be predominantly temporal with 21%, followed by Infero-temporal and Supero-temporal with 18%. • There was no statistically significant difference between the findings of the right and left eye. A larger population based study may help us to further understand the corneal characteristics of Indian population. This has important implication in surgical planning and this will enable the surgeon to screen patients more appropriate both for LASIK and for Phakic IOL’s

Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta

Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants

Warming and elevated CO\u3csub\u3e2\u3c/sub\u3e alter the suberin chemistry in roots of photosynthetically divergent grass species

A majority of soil carbon (C) is either directly or indirectly derived from fine roots, yet roots remain the least understood component of the terrestrial carbon cycle. The decomposability of fine roots and their potential to contribute to soil C is partly regulated by their tissue chemical composition. Roots rely heavily on heteropolymers such as suberins, lignins and tannins to adapt to various environmental pressures and to maximize their resource uptake functions. Since the chemical construction of roots is partly shaped by their immediate biotic/abiotic soil environments, global changes that perturb soil resource availability and plant growth could potentially alter root chemistry, and hence the decomposability of roots. However, the effect of global change on the quantity and composition of root heteropolymers are seldom investigated. We examined the effects of elevated CO2 and warming on the quantity and composition of suberin in roots of Bouteloua gracilis (C4) and Hesperostipa comata (C3) grass species at the Prairie Heating and CO2 Enrichment (PHACE) experiment at Wyoming, USA. Roots of B. gracilis exposed to elevated CO2 and warming had higher abundances of suberin and lignin than those exposed to ambient climate treatments. In addition to changes in their abundance, roots exposed to warming and elevated CO2 had higher ω-hydroxy acids compared to plants grown under ambient conditions. The suberin content and composition in roots of H. comata was less responsive to climate treatments. In H. comata, α,ω-dioic acids increased with the main effect of elevated CO2, whereas the total quantity of suberin exhibited an increasing trend with the main effect of warming and elevated CO2. The increase in suberin content and altered composition could lower root decomposition rates with implications for root-derived soil carbon under global change. Our study also suggests that the climate change induced alterations in species composition will further mediate potential suberin contributions to soil carbon pools

Climate Influences the Content and Chemical Composition of Foliar Tannins in Green and Senesced Tissues of \u3ci\u3eQuercus rubra\u3c/i\u3e

Environmental stresses not only influence production of plant metabolites but could also modify their resorption during leaf senescence. The production-resorption dynamics of polyphenolic tannins, a class of defense compound whose ecological role extends beyond tissue senescence, could amplify the influence of climate on ecosystem processes. We studied the quantity, chemical composition, and tissue-association of tannins in green and freshly-senesced leaves of Quercus rubra exposed to different temperature (Warming and No Warming) and precipitation treatments (Dry, Ambient, Wet) at the Boston-Area Climate Experiment (BACE) in Massachusetts, USA. Climate influenced not only the quantity of tannins, but also their molecular composition and cell-wall associations. Irrespective of climatic treatments, tannin composition in Q. rubra was dominated by condensed tannins (CTs, proanthocyanidins). When exposed to Dry and Ambient*Warm conditions, Q. rubra produced higher quantities of tannins that were less polymerized. In contrast, under favorable conditions (Wet), tannins were produced in lower quantities, but the CTs were more polymerized. Further, even as the overall tissue tannin content declined, the content of hydrolysable tannins (HTs) increased under Wet treatments. The molecular composition of tannins influenced their content in senesced litter. Compared to the green leaves, the content of HTs decreased in senesced leaves across treatments, whereas the CT content was similar between green and senesced leaves in Wet treatments that produced more polymerized tannins. The content of total tannins in senesced leaves was higher in Warming treatments under both dry and ambient precipitation treatments. Our results suggest that, though climate directly influenced the production of tannins in green tissues (and similar patterns were observed in the senesced tissue), the influence of climate on tannin content of senesced tissue was partly mediated by the effect on the chemical composition of tannins. These different climatic impacts on leaves over the course of a growing season may alter forest dynamics, not only in decomposition and nutrient cycling dynamics, but also in herbivory dynamics

Variation of CO Column over North Kerala by Exploring MOPITT Data

Carbon Monoxide (CO) is one of the prominent pollutant species mainly produced from of fossil fuel burning and motor vehicles. Being a toxic trace gas, it can considerably affect human health. The rapid increase in CO enhances the production of surface ozone which contributes to global warming. This is the first attempt to retrieve the increase in CO over a column of atmosphere up to 100 mb pressure from the surface using MOPITT version 3 of level 2 data. The increase in column abundance of CO observed is correlated with the increase in vehicles in this region and it gives a positive correlation for the four years of observation from 2004. The prominence of this location of north Kerala is that no major industries are sited within this region and the increase in pollution is solely due to anthropogenic activities.ÂÂ