# NISER GeneralActivities DNA 082407

(Difference between revisions)
 Revision as of 01:21, 24 August 2007 (view source)IvoDinov (Talk | contribs)← Older edit Revision as of 01:32, 24 August 2007 (view source)IvoDinov (Talk | contribs) Newer edit → Line 1: Line 1: - == [[NISER_EduMaterials_GeneralActivities | NISER General Activities]] - Mercury Contamination in Fish: A multi-disciplinary Activity == + == UNDER Construction!!!== + + ==[[NISER_EduMaterials_GeneralActivities | NISER General Activities]] - The Biology, Chemistry and Physics of DNA and the Mathematical Methods for DNA Modeling, Analysis and Visualization == ==Summary== ==Summary== - Visualization, understanding and interpreting real data may be challenging because of noise in the data, data complexity, multiple variables, hidden relations between variables and large variation. This [[Main_Page |NISER]] activity demonstrates how to use free Internet-based IT-tools and resources to solve problems that arise in the areas of biological, chemical, medical and social research. + This is an interactive hands-on educational activity that described the fundamentals of [http://en.wikipedia.org/wiki/DNA DNA] (DeoxyriboNucleic Acid), its importance for all living species and its implications for the diversity of life on [http://en.wikipedia.org/wiki/Earth Earth]. Specifically, this multi-disciplinary [[NISER]] activity discusses DNA structure, half-time life, mutation rate and variability across species. ==Goals== ==Goals== - This [[Main_Page | NISER]] activity has the following specific goals: + This [[NISER]] activity has the following specific goals: - * to demonstrate the typical research investigation pipeline - from problem formulation, to data collection, visualization, analysis and interpretation; + * TBD; - * to illustrate the variety of portable freely available Internet-based Java tools, computational resources and learning materials for solving practical problems; + * TBD; - * to provide a hands-on example of interdisciplinary training, cross-over of research techniques, data, models and expertise to enhance contemporary science education; + * TBD. - * to promote interactions between different science education areas and stimulate the development of new and synergistic learning materials and course curricula across disciplines. + ==Motivation/Problem== ==Motivation/Problem== [[Image:Largemouth_Bass.jpg|150px|thumbnail|right| [http://en.wikipedia.org/wiki/Largemouth_Bass Largemouth Bass] ]] [[Image:Largemouth_Bass.jpg|150px|thumbnail|right| [http://en.wikipedia.org/wiki/Largemouth_Bass Largemouth Bass] ]] - Mercury contamination of edible freshwater fish poses a direct threat to human health. [http://en.wikipedia.org/wiki/Largemouth_Bass Largemouth bass] is a fresh water fish that was studied in 53 different Florida lakes to examine the factors that influence the level of mercury contamination. Water samples were collected from the surface of the middle of each lake in August 1990 and then again in March 1991. The '''pH level''', the '''amount of chlorophyll''', '''calcium''', and '''alkalinity''' were measured in each sample. Also, samples of fish were taken from each lake with sample sizes ranging from 4 to 44 fish. The age of each fish and mercury concentration in the muscle tissue was measured. Since [http://en.wikipedia.org/wiki/Mercury_(element)#Mercury_in_fish fish absorb mercury over time], older fish will tend to have higher concentrations. [http://en.wikipedia.org/wiki/Mercury_(element)#Safety Here is a detailed discussion] of why mercury accumilates in muscle tissues and why is it toxic in larger amounts. + TBD ==[[NISER_081107_ID_Data | Data]]== ==[[NISER_081107_ID_Data | Data]]== [[Image:NISER_081107_ID_Fig10.png|150px|thumbnail|right| [[NISER_081107_ID_Data | Data Spreadsheet]] ]] [[Image:NISER_081107_ID_Fig10.png|150px|thumbnail|right| [[NISER_081107_ID_Data | Data Spreadsheet]] ]] - [[NISER_081107_ID_Data | Largemouth bass were studied in 53 different Florida]] lakes to examine the factors that influence the level of mercury contamination. Water samples were collected from the surface of the middle of each lake in August 1990 and then again in March 1991. The pH level, the amount of chlorophyll, calcium, and alkalinity were measured in each sample. The average of the August and March values were used in the analysis. Next, a sample of fish was taken from each lake with sample sizes ranging from 4 to 44 fish. The age of each fish and mercury concentration in the muscle tissue was measured. + TBD. ==Challenge== ==Challenge== [[Image:WarningMercurySign.jpg|150px|thumbnail|right|Common risks with eating fish.]] [[Image:WarningMercurySign.jpg|150px|thumbnail|right|Common risks with eating fish.]] - To make a fair comparison of the fish in different lakes using a regression estimate of the expected mercury concentration in a three-year-old fish as the standardized value for each lake. Determine the age of the individual fish in some lakes and correlate this with the average mercury concentration of the sampled fish. + TBD. - Florida has set a standard of 1/2 part per million as the unsafe level of mercury concentration in edible foods. 45.3% of the lakes exceed this level. The smallest level of mercury concentration that the measuring instrument can detect is 40 parts per billion. Any level below that was set to 40 parts per billion. This, of course, "flattens out" the slope of the relationship at the low end as well as affecting the standardized values. These observations are usually on young fish. - - Logarithmic transformations on some of the variables may provide insights into the relationships among the other variables in the study. For instance, '''alkalinity level''' may be associated with mercury concentration, and may help account for the higher levels of mercury. ==Methods & Approaches== ==Methods & Approaches== [[Image:NISER_081107_ID_Fig11.png|150px|thumbnail|right| [http://www.falstad.com/qmatom/ Atomic structure]]] [[Image:NISER_081107_ID_Fig11.png|150px|thumbnail|right| [http://www.falstad.com/qmatom/ Atomic structure]]] - We now discuss varieties of scientific methods, models, tools and strategies for data modeling, understanding, inference and visualization of the data in this specific driving biological problem, as well as, discuss checking and affirming underlying model or technique assumptions. + There are varieties of scientific methods, models, tools and strategies for DNA representation, understanding, modeling, inference and visualization. ===Physics=== ===Physics=== - * What is an atom and what is the [http://environmentalchemistry.com/yogi/periodic/Hg.html#Atomic atomic structure of mercury]? + * TBD - * [http://environmentalchemistry.com/yogi/periodic/Hg.html#Physical Physical Properties of mercury]. + - * [http://environmentalchemistry.com/yogi/periodic/Hg-pg2.html#Nuclides Mercury nuclides and isotopes]. + - * How can [http://cobweb.ecn.purdue.edu/~epados/mercbuild/src/cleanup.htm small high-concentration mercury spills may be cleaned]? + ===Biology=== ===Biology=== [[Image:NISER_081107_ID_Fig9.png|150px|thumbnail|right| [http://www.rcsb.org/pdb/explore.do?structureId=2O01 Chlorophyll 3D Structure]]] [[Image:NISER_081107_ID_Fig9.png|150px|thumbnail|right| [http://www.rcsb.org/pdb/explore.do?structureId=2O01 Chlorophyll 3D Structure]]] - * Why is mercury (and other [http://en.wikipedia.org/wiki/Heavy_metals heavy metals]) accumulating in muscle tissue? + * TBD. - * What causes the [http://chem.sis.nlm.nih.gov/chemidplus/ProxyServlet?objectHandle=DBMaint&actionHandle=default&nextPage=jsp/chemidheavy/ResultScreen.jsp&ROW_NUM=0&TXTSUPERLISTID=007439976 toxicity of larger than normal amounts of mercury in the body]? + - * The [http://en.wikipedia.org/wiki/Chlorophyll Chlorophyll] molecule. + - * [http://www.rcsb.org/pdb/explore.do?structureId=2O01 3D structure of Chlorophyll] using [http://www.rcsb.org/pdb PDB/JMol viewer]. + - * [http://environmentalchemistry.com/yogi/periodic/Hg.html#Regulatory The biology and regulatory limits for mercury exposure]. + - * [http://en.wikipedia.org/wiki/Alkalinity Alkalinity] represents the ability of a solution to neutralize [http://en.wikipedia.org/wiki/Acid acids] to the equivalence point of carbonate or bicarbonate. Alkalinity is closely related to a solution's acid neutralizing capacity. However, the acid neutralizing capacity refers to the combination of the solution and solids present and the contribution of solids can dominate the acid neutralizing capacity. + - * Mercury uptake by plants + - ** Mercury uptake by plants is low (Jenkins, 1981; Paasivirta, 1991), however plants may be used for monitoring mercury contaminations. + - ** Trees uptake mercury through the xylem, from soil via the root system or from direct deposition via foliage and bark. + - * The Biology of mercury uptake: + - ** In fish, mercury appears  primarily as methylmercury and that's the most common form of mercury transfered through the food chain. + - ** The most conducive environmental conditions for the methylation and uptake of mercury into fish include: '''low pH (<7), low alkalinity (<20 mg/L), low calcium (<15 mg/L), high total organic carbon (TOC), low chlorophyll-a ([[Image:NISER_081107_ID_Fig3.png|300px]] [[Image:NISER_081107_ID_Fig4.png|300px]] + - ** We can also demonstrate the effect of using a wavelet decomposition of the column data (''avg_mercury''). The image below demonstrates the '''wavelet representation''' of this column vector data using Daubechies' 2 wavelet basis, where only the largest 10% of the wavelet coefficients were used to reconstruct/synthesize the (compressed) wavelet representation of the data. More information about [http://en.wikipedia.org/wiki/Wavelets wavelets] and [http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_GamesActivitiesWavelets wavelets-based activities may be found here]. You can use the [http://www.socr.ucla.edu/htmls/SOCR_Modeler.html SOCR Modeler] to fit is any of a number of wavelet models to data and observe the effect of wavelet shrinkage on the corresponding wavelet model fit. +
[[Image:NISER_081107_ID_Fig7.png|400px]]
[[Image:NISER_081107_ID_Fig7.png|400px]]
===Statistics=== ===Statistics=== [[Image:NISER_081107_ID_Fig15.png|150px|thumbnail|right| [http://socr.ucla.edu Statistical Analysis]]] [[Image:NISER_081107_ID_Fig15.png|150px|thumbnail|right| [http://socr.ucla.edu Statistical Analysis]]] - * Are there associations in [[NISER_081107_ID_Data | these data]] between ''Alkalinity'', ''pH'', ''Calcium'' and ''Chlorophyll''? Using [http://www.socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] construct regression plots illustrating the relations between ''Calcium, Chlorophyll'' and '' Avg_Mercury'', as shown on the image below. + * TBD. -
[[Image:NISER_081107_ID_Fig2.png|400px]]
+ - * Generate some exploratory data analyses (EDA plots). For instance, the figure below demonstrates how you can use [http://www.socr.ucla.edu/htmls/SOCR_Charts.html SOCR Charts] to obtain the scatter plot of ''Alkalinity'' vs. ''pH''. What are some inferences about the bivariate relations between these variables? + -
[[Image:NISER_081107_ID_Fig1.png|400px]]
+ - * What is the distribution of the average amount of ''mercury'' in the entire sample? We can use [http://www.socr.ucla.edu/htmls/SOCR_Charts.html SOCR Charts] to construct the histogram of the ''avg_mercury'' column data. To learn how to use [http://www.socr.ucla.edu/htmls/SOCR_Charts.html SOCR Charts] see these [http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_ChartsActivities Charts Activities]. Notice the effect the bin-size parameter has on the shape of the data histogram (you can smoothly vary this parameter). Although, there are [http://en.wikipedia.org/wiki/Histogram many choices for determining the bin-size parameter], in general, the optimal choice of the histogram bin-size parameter may be determined by ${2\times(IQR)} \over {N^{1\over 3}}$, where the interquartile range $IQR= Q_3 - Q_1$, and $Q_3$ and $Q_1$ are the '''third''' and '''first''' [http://en.wikipedia.org/wiki/Quartiles quartiles] for the sample data, respectively. + -
[[Image:NISER_081107_ID_Fig8.png|400px]]
+ - * Is there evidence of statistical differences between the two groups (according to the ''age_data'' variable) in either ''Alkalinity'' or ''pH''? + - ** There does not seem to be a statistically significant difference in the ''pH'' levels between the two groups separated by the age_data varaible. A non-parametric [http://en.wikipedia.org/wiki/Mann-Whitney_U Wilcoxon Rank Sum test] did not produce significantly small p-value (see the image below showing the result of the calculations using [http://www.socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses].
[[Image:NISER_081107_ID_Fig5.png|400px]]
+ - ** Similarly, there does not seem to be a statistically significant difference in the ''Alkalinity'' levels between the two groups separated by the ''age_data'' variable. The same non-parametric [http://en.wikipedia.org/wiki/Mann-Whitney_U Wilcoxon Rank Sum test] did not produce significantly small p-value (see the image below showing the result of the calculations using [http://www.socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses]. + -
[[Image:NISER_081107_ID_Fig6.png|400px]]
+ ==Computational Resources== ==Computational Resources==

## Summary

This is an interactive hands-on educational activity that described the fundamentals of DNA (DeoxyriboNucleic Acid), its importance for all living species and its implications for the diversity of life on Earth. Specifically, this multi-disciplinary NISER activity discusses DNA structure, half-time life, mutation rate and variability across species.

## Goals

This NISER activity has the following specific goals:

• TBD;
• TBD;
• TBD.

TBD

TBD.

## Challenge

Common risks with eating fish.

TBD.

## Methods & Approaches

There are varieties of scientific methods, models, tools and strategies for DNA representation, understanding, modeling, inference and visualization.

• TBD

• TBD.

• TBD.

### Engineering

Engineering Thumbnail TBD
• [TBD.

• TBD.

• TBD.

## Hands-on activities

• TBD (Step-by-step practice problems).