Midterm Environmental Sampling and Analysis
Conducting Research: (1) Sampling Uncertainty - Sample Collection: Grab Sample
Uncertainty - Sample Collection: Grab Sample
Conducting Research: (1) Sampling Uncertainty - Sample Collection: Integrated Sample
Uncertainty - Sample Collection: Integrated Sample
Conducting Research: (1) Sampling Uncertainty - Sample Preservation and Storage
Uncertainty - Sample Preservation and Storage
Microbiology: Viruses and Prions
Viruses - are small pieces of genetic material wrapped in a protein coat. - have some, but not all, of the characteristics of life: • Not made of cells • Reproduce only within a host cell • Have genes • Evolve - may have genes made of DNA or RNA. - have genes that mutate quickly. - are responsible for many human diseases, as well as those of other species.
Hazard
implies a probability of adverse effects in a particular situation.
Microbiology: Rotifiers
(Animals - microscopic) Rotifers are microscopic aquatic animals of the phylum Rotifera. Rotifers can be found in many freshwater environments and in moist soil, where they inhabit the thin films of water that are formed around soil particles
Risk Perception: It's all how you look at it!
- Engineers vs Population *Not in my back yard (NIMBY) *A term for a person who resists unwanted development, such as manufacturing plants, prisons, power companies, or chemical companies in his or her own neighborhood or town. - Less concerned with "known" or what is more comfortable. *Gas stations vs nuclear power plants * Gas stations are just as harmful but doesn't get as much recognition like a nuclear power plant. - Accept Natural Risks * Tornadoes, hurricanes, etc. -Permanent vs Temporary Effect - Familiarity vs Exotic * Common Cold and Flu vs Swine Flu, SARS, MRSA. There are many other factors that contribute to varied risk perception: Scientists vs. Other Stakeholders: A scientist or engineer may think there is an acceptable risk placing a wind farm off-shore in a bay; however, property owners may feel they are at risk from decreased home revenues, noise pollution, etc. A classic example of this issue is NIMBY (or Not In My Backyard) where the population may accept that there must be landfills and therefore there is an acceptable risk to landfills, but individuals are not willing to accept that risk in their vicinity. Knowns vs. Unknowns: The population tends to be more accepting of things they "known" rather than things that are more mysterious. For example, people are less concerned with a proposed gas station being built on a corner than they would be of a nuclear power plant despite the fact that there are more acute and chronic risks associated with living in proximity to a gas station compared to a nuclear power plant. Natural vs. Man-made: People are more willing to accept natural risks such as tornadoes, hurricanes, etc. as compared to man-made risks like the nuclear power plant example above. Permanent vs. Temporary Effect: While temporary effects may be more acute and pose more of a threat, the population tends to be more willing to accept those risks as compared to a lower-risk yet permanent effect. Familiar vs. Exotic: This is similar to #2 above. People tend to be more concerned with things that are considered "exotic" or unique. For example, the population was more risk adverse to the Swine Flu, SARS, MRSA, etc. than they are to Influenza. SARS dominated the news during its peak in 2003 despite the fact that 8 people in the U.S. were documented to have had SARS. In contrast, about 36,000 people die each year from influenza and another 200,000 are hospitalized from the flu.
Risk: Why is it controversial?
- Models are frequently conflicting. - High Uncertainty - Data: *Ambiguous * Extrapolated from animals, high dose to low dose. - Highly Overestimated - Diverse Populations = Diverse Responses. * Ex: Drinking water in Mexico has a different risk for individuals that live there vs tourists. Models are frequently conflicting: Depending on your inputs and assumptions into your statistical model, you can get a wide variety of answers. In fact, it is not uncommon for models to vary on orders of magnitude. High Uncertainty: Because data has to be inferred and assumptions made, there is typically a high level of uncertainty in the actual response. Extrapolation: This is very related to number 2 above, but because toxicity data is derived from extrapolating from animal testing, human response is based on an educated estimate of how humans will respond from animal dosing. There are also varying responses from high dose and lose dose which also have to be extrapolated to humans. Highly Overestimated: Because we are dealing with human hazards, the conclusions scientists draw tend to be highly conservative and potentially detrimental to manufacturers and industry Diverse Populations = Diverse Responses: Risk models assume certain factors (i.e., male, 70 kg, 70 year life span) and may not apply to all populations. For example about 15% of the population are immune to the effects of poison ivy (lucky!). Since our genetic make-up is diverse, our responses will be different and risk aims for some "law of averages." Another example is that an American drinking tap water while traveling in Mexico will have a completely different risk than a local drinking the water.
Conducting Research: (1) Sampling
- Population: Collection of all possible observations that might exist. - Sample: Collection of observations actually taken.
Microbiology: Macromolecules Needed for Life
- Proteins (carries out all functions of organisms). - Carbohydrates (Short term energy sources, sugars needed for cellular respiration) - Lipids (fatty acid genes, do not dissolve in water, give shape to our cells). - Nucleic Acids (DNA and RNA) Carbon Oxygen Nitrogen Phosphorus Hydrogen
Risk Vocabulary
- Risk Perception *Ones judgment about the characteristics and/or severity of risk. - One challenge for scientists and policymakers prior to analyzing risk is the issue of risk perception (i.e., a personal belief about relative risks of given activities. When asked what is riskier -- eating a steak or skiing -- most people would indicate the latter. That being said, there is a much higher likelihood (> 1000x) of dying from heart disease compared to skiing (Figure 3). That being said, your risk of getting cancer living in Denver is much higher than the cancer risk from eating charbroiled steak once a week for 1 year (increased radiation from elevation and radon levels) (Figure 4). - Risk Assessment *Calculating risk, or the degree of likelihood that a person will become ill upon exposure to a toxin or pathogen. - Risk assessment is a systematic process of evaluating the potential probability of an adverse effect or hazard that may be involved in a projected activity or undertaking. In the context of environmental science, it is an empirically based, scientific evaluation of potential harm from pollutants, activities, substances, natural environments, etc. - Risk Tolerance * The degree, amount, or volume of risk that an organization or individual will withstand.
Human Research and IRB: Triangle Test
- Three samples are given where one of the samples is different from the rest. Tester is asked to identify the odd sample. - Used to find out if the difference between two similar samples can be detected. Ex: Tester is asked to identify the odd sample. Sample code = 642 Reasons = this sample is sweeter. Why triangle test is most preferred method? Triangle tests are often preferred, as they require fewer tasters, and there is a greater likelihood that a result will be genuine and not due to a chance effect. The triangle test uses three samples to determine if an overall difference exists between two products.
Conducting Research
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Human Research and IRB
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Microbiology
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Risk Analysis
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4 steps of risk assessment
1. Hazard identification - determining whether or not a particular chemical is casually linked to particular health effects. such as cancer or birth defects. Human data difficult to obtain. Focuses on whether a chemical is toxic in animals or other test organisms. - Hazard Identification To identify the potential hazard, scientists must gather and analyze site-specific data to identify substances of health interest/concern and develop a preliminary assessment of potential human and ecosystem exposures. In this step, it is necessary to identify: 1. Possible contaminants. 2. Contaminant concentrations in the air, soil, and water. 3. Site characteristics that could affect contaminant fate, transport, and persistence. 2. Dose-response assessment -Characterizing the relationship between dose of an agent administered or received and the incidence of an adverse heath effect. Low dose and high dose. - Dose-Response Assessment The purpose of this step is to determine the relationship between the quantity of toxicant a person is exposed to and the unhealthy exposure level. First, scientists must establish the dose (i.e., mass of chemical received by an animal or exposed individual). This is assessed using animal studies and extrapolated to human doses. Typically, a dose is measured in mg of chemical/kg of animal. Through animal studies a dose-response curve can be developed (Figure 5). - Based on the dose-response curve and toxicity data, scientists will report a LD50 or the lethal dose for half of the population. - Once the LD50 has been established and exposure has been analyzed, scientists can create a new dose-response curve with a proposed reference dose acceptable to humans 3. Exposure assessment - determining the size and the nature of the population that has been exposed to the toxicant under consideration and the length of time and toxicant concentration to which they have been exposed. - To conduct an exposure assessment, we need to evaluate: 1. The factors that control the production of the hazardous agent and its subsequent release into the environment. 2. The quantities of the agent released and the location and timing of the release. 3. The environmental fate of the agent after release. - Movement Persistence. Degradation pathways - Human contact with the agent. - Size and distribution of vulnerable populations. - When considering human effects, there are three modes of exposure that are considered: 1) inhalation, 2) skin contact, and 3) ingestion (Figure 8). - After the mode of exposure is identified, the exposure must be characterized (i.e., how long was exposure? what was the amount of exposure? etc.) For example, maybe you are analyzing the risk of inhalation of chlorine from a swimming pool. You would need to characterize the amount inhaled (Figure 9) per exposure. There are also default values that can be used for general exposure (Figure 10). 4. Risk characterization - integration of the first three steps, which results in an estimate of the magnitude of the public health problem. - Risk Characterization After these values have been determined, risk scientists combine information gained from Hazard Identification, Dose-Response Assessment, and Exposure Assessment to determine the likelihood that humans will experience any of the various forms of toxicity associated with a substance. There are three characterizations that are typically made with risk: 1) relative risk, 2) odds ratio and 3) attributable risk
Microbiology: 6 Characteristics of All Living Things
1. Made of Cells 2. Obtain and use energy 3. Grow and Develop 4. Reproduce 5. Respond to environment. 6. Adapt to environment
Microbiology: Pathogens
A pathogen is defined as an organism causing disease to its host. or organisms that make individuals sick Sources: 1.) Water Bourne: - Drinking Water with pathogens. - Possible diseases = diarrhea, cholera, typhoid, shigellosis, hepatitis A and E. - How to stop getting sick = improve drinking water quality by removing or killing pathogens. 2.) Water Washed: - Pathogens touch the skin or eye. - possible diseases = Trachoma, scabies. - How to stop getting sick = provide enough water needed for basic hygiene. Improve basic hygiene practices. 3.) Water Based: - Pathogens go through the skin. like swimming, etc. - Possible diseases = Schistosomiasis, guinea worm. - How to stop getting sick = Do not bath or swim in water that is known to be contaminated. Improve water quality by removing or killing source of pathogens. 4.) Water insect vector: - Pathogens are passed on by insects that breed or live in water, such as mosquitoes. - Possible diseases = Malaria, dengue, yellow fever, filariasis, river blindness, sleeping sickness. - How to stop getting sick = Prevent insects from breeding in water. Use pesticides to control insects. Prevent insects from biting by using bed nets and wearing long clothes.
Risk Analysis: Human Exposure Assessment
An estimate of the number of people exposed and the magnitude, duration, and timing of their exposure to a chemical. 1. Pathways that allow toxic agents to be transported from the source to the point of contact with people must be evaluated. 2. an estimate must be made of the amount of contact that is likely to occur between people and those contaminants.
Microbiology: Protozoa - Eukaryotic Protists
Animal like (heterotrophic) protists that have different structures for movement. Protozoa (singular protozoon or protozoan, plural protozoa or protozoans) is an informal term for a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris. Bane of water treatment world. can go into cyst form, hard to kill. Ex: Giardia and Cryptosporidium
Microbiology: The three domains of life
Bacteria Archaea Eukarya
Microbiology: Animal and Plant Eukaryotic Cells
Eukaryotic Cell Have Nucleus Cell membrane (animal) Cell Wall (Plant)
Risk Analysis: Risk Management
Examine the results of risk assessment in the context of social concerns: - Socioeconomic conditions - Political pressures - Economic concerns Figure: Risk management balances costs (social, political and economic) with human health and ecology risks.
Conducting Research: (1) Sampling Uncertainty - Sample Collection: Autosampler
Uncertainty - Sample Collection: Autosampler
Conducting Research: (5) Experimental Unit
Experimental Unit- smallest division of experimental material to which a treatment (or combination of factorial treatments) can be assigned in a single act of randomization. experimental unit, in an experimental study, a physical entity that is the primary unit of interest in a specific research objective. Generally, the experimental unit is the person, animal, or object that is the subject of the experiment. EX: Consider a situation where someone wants to evaluate polluted stream water for its effect on fish lesions. They set up 2 aquaria, each with 50 fish. They randomly assign a water treatment (polluted vs. control) to each of the aquaria. After 30 days, they catch 10 fish from each aquarium and count the number of lesions. Here we have 4 treatments (colored rectangles), and 10 plots within each. What is the experimental unit? Fish What is the replication (Replication of a study is repeating a study's procedure and observing if the prior findings repeat in similar conditions)? 0 independent variable = It is a variable that stands alone and isn't changed by the other variables you are trying to measure. Response Variable = lesions Control Variable = Water not treated
Risk Analysis: Relative Risk
Figure 12: The relative risk is the incident rates of disease for those exposed to the risk and those non-exposed to the risk.
Risk Analysis: Attributable Risk
Figure 13: The attributable risk is the amount of disease that can be associated with a given exposure. It eliminates the background risk.
Risk Analysis: Carcinogens and Thresholds Graph
Figure 4.8: Hypothetical dose response curves. Dose response curves for carcinogens are assumed to have no threshold, that is any exposure produces some chance for causing cancer. Threshold Dose: the maximum dose that has no measurable effect. - Below which there will be no response.
Risk Analysis Lab
Finding CDI = (C mg/L * Intake rate L/day * Exposure days/yr * Exposure Duration) / (70kg * 70 yr/life * 365 days/y) Cancer Risk = CDI*PF Expected Cancers = Risk * (Population/Life Span) Expected All Cancers = Population * Cancer rate (198/10000) Finding MCGL = Inverse CDI equation with multiplication of Risk on top and multiplication of PF on bottom. (Risk * 70 kg * 70 yr/life * 365 days) / (Intake rate L/day * Exposure days/yr * Exposure Duration * PF) * Rember to convert either multiply or divide by 1000 to get Mg/L *m3= 20= 20*1000 = 20000mg/L 0r 0.10 ug/L = .10/1000 = 0.0001 mg/L or C= 6785 ug/L = 6785/1000 = 6.785 mg/L How can risk analysis be used in solving environmental problems in real tie such as spills and contaminant breaches? You can use risk analysis to calculate and predict the risk of exposure to individuals that live in areas that are contaminated. Also, can use this analysis to set and enforce standards for public health hazards. What are some limitations of using risk analysis? Models are conflicting and there is high uncertainty because data is inferred, and assumptions are made. When calculating risk, we assume all sorts of information about individuals (like their weight, sex, average life span, etc.) which limits the accuracy and certainty of the risk analysis.
Standards/Dilutions Lab
Finding Molarity Molarity (M) = molecules of solute/Liters of solution Example 1: How would 500mL of a 0.6000 M NaCl solution be prepared? NaCl mass of 58.44 g/mol find the mass of the solute needed. Answer = 500 mL solution * (1 L solution/1000 mL solution) * (0.6000 mol NaCl / 1 L solution) * (58.44 NaCl / 1 mol NaCl) = 17.53 g NaCl Equation for finding amount of concentrated solution needed to carry out dilution: M1V1 = M2V2 or V1 = (M1*V2)/M2 Example 2: Suppose that an experiment required 500 mL of a 0.200 M NaCl solution be prepared from 0.6000 M NaCl what volume of the concentrated 0.6000 M solution would be needed? Answer = V1 = (0.200 M NaCl * 500mL) / 0.6000 M NaCl = 167 mL Example With Conversions: Prepare a 10 mL of a 0.050 M sucrose solution by dilution of 10 mL of stock solution. Answer = V1 = (0.050 M * 10 mL) / 0.10 = 5 mL 10mL to M = 0.01M (1 mL) 10*0.01 = 0.10 M More Example Problems: 1. Suppose you took 1.00 mL of 0.125 M KI and diluted it to 50 mL what would be the concertation of the new solution? Answer = (0.125 M KI * 1.00 mL) / 50mL = 0.0025 M KI 2. 25 mL of 0.50 M solution of NaOH was diluted to a final volume of 200mL. What is the new concentration of this solution? Answer = (0.50 M * 25mL)/ 200mL = 0.0625 M NaOH 3. Calculate the number of grams potassium iodide KI needed to prepare 500mL of a 0.125 M KI. With a molar mass of 166.0028 g/mol KI Answer = 500mL * (1 L/1000mL) * (0.125M KI/1 L) * (166.0028 g KI/ 1 mol/g) = 10.38 g KI What is the relationship between concentration and color intensity? The relationship between concentration and color intensity is that intensity of color is proportional to the concentration of the dissolved compound. Greater compound concentration, the darker or more intense the solutions color appears.
Data Mining/Excel Lab
Gathering Evidence -Data Mining EPA and USGS Water Quality Data Start here: htt://www.epa.sov/storet/index.html Explore the page. What kind of data can you get from this website? How might it be useful? The page tells you what water quality data is. It shows you the WQX vs. WQP, as well as three links to learn more about water quality data. This can be useful because you can decide what mechanism is best for your data, as well as learn how to understand water quality. Next, visit the Water Quality Portal: http://www.waterqualitydata.us/ Explore the "How to Use the WQP Page" to discover all the useful data and tools the USGS and EPA provide. Next, now explore the "About WQP" Section. What is the WQP? The WQP (Water Quality Portal) is a site that provides current and historical data of water quality from various water management groups. This program allows you to select certain countries or cities and provides you with data with the time frame of your choice. Who contributes to the WQP? The USGS (US Geological Survey), EPA (Environmental Protection Agency), and more than 400 state, federal, tribal, and local agencies contribute to the WQP. Three Sources: 1. NWIS (USGS) mapper provides access to over 1.5 million sites contained in the USGS National Water Information System., including sites where current and historical surface-water, groundwater, springs, and atmospheric data has been collected. The website serves current and historical data. The types of data collected are varied, but generally fit into the broad categories of surface water and groundwater. 2. STEWARDS (ARS) is a data delivery system with a geographic information system interface, using space, time, and topic as key fields for searching an extensive database of soil, water, climate, and land management data from multiple long-term watersheds. 3. WOX (EPA) is the nation's largest source for water quality monitoring data. The Quality Portal (WQ) uses the (WOP) data format to share over 380 million water quality data records from 900 federal, state, tribal, and other partners. Analyzing Evidence Your file will have a lot of information! Look at the columns. What type of information is listed? How might you want to organize this data to use for research? The data includes which organization conducted the sampling, the location and date of the samples, the merit characteristic name (substance) and its associated value, measurement units, and more. We might want to organize these data by characteristic names (ex: carbon dioxide, inorganic nitrogen, fluoride, etc.) if we want to research the specific characteristics of water. Alternatively, organizing the data by the result measure value (ex: 21 mg/L of carbon dioxide) could be useful if we want to research certain quantities of the characteristics of water. There is a lot of data, what we want to do is make it less cluttered and legible. Clean up the data that we will need and organize it so that it can be understood and clear. We organized our data by the characteristic name, result sample fraction text and the activity start date. Your data is now sorted! Why might it be helpfulto sort data in excel? It is helpful to sort data in excel because sometimes you get more data than you need, especially when there are multiple sources. By sorting data, you are weeding out what you don't need and looking at the targeted data you will use. It is helpful so that you get to see the data that is relevant for your research collection and analysis. Using Evidence and Reasoning How are repositories like this helpful for analyzing water data? Repositories like this are helpful for analyzing water data because they include a wide variety of information about water. There is a lot of data to choose and sort through, which is helpful for researchers and scientists because they need a lot of data to be able to draw valid conclusions. What major drawbacks might there be from a repository with so many different organizations contributing to it? A drawback of a repository with many different organizations contributing to it is that there may be too much data. At first, the amount of data may seem overwhelming and too vast to analyze.
Human Research and IRB: Exemptions
Human subjects research that is classified as "exempt" means that the research qualifies as no risk or minimal risk to subjects and is exempt from most of the requirements of the Federal Policy for the Protection of Human Subjects but is still considered research requiring an IRB review for an exemption determination. - Established or commonly accepted educational setting = any place where instruction would take place. - Normal educational practices = activities that typically occur in a classroom or other educational setting * Effectiveness of instructional strategies, classroom management, school activities. * Curriculum development and evaluation. *Assessment of attitudes about learning. *Test development. -Researchers using the student education records must meet FERPA requirements and must include information about data to be used must be included in application. - Studies that focus on personal characteristics of students or teachers (rather than the educational activity of interest) would most likely not qualify. - Surveys, interviews (includes focus groups), educational testing, or observation of public behavior *Public behavior is generally open to view by any member of the community and/or which would not involve special permission to observe, such as at a park, in a mall, or movie theatre. A classroom is not considered public. *Limitations for use with minors (under 18) - only educational tests or observation where investigator does not interact with kids. * Two Conditions: - data collected is not sensitive (criminal/civil liability, financial standing, employability or reputation OR - Data collected is anonymous. -Collection or study of existing data, documents, records, or specimens, if these are publicly available or subjects cannot be identified. *Primarily applies to projects where identifiable private information is accessed and viewed but is not recorded. * Example: Student data including personal identifiers is screened but data elements recorded for research analysis do not include identifiers.
Conducting Research: (2) Randomization
Humans who are observers and designers of experiments are biased. • Many of the biases are unconscious, thus unavoidable. • Only reliable way to eliminate bias in a sampling scheme is to have at least one, formal, randomization step. • When you claim a sample is random, you are making a specific mathematical claim. • Unless you have a protocol to create such randomness, followed fastidiously, what you have is indeed NOT random and should not be stated as such.
Microbiology: Prokaryote
Lack of a nucleus Lack of organelles *DO not have linear chromosomes, have circular chromosomes. No Mitochondria
Microbiology: MPN (Most Probable Number)
Most Probable Number (MPN) A statistical estimate of the number of coliform-group organisms per unit volume of sample water. Expressed as a density or population of organisms per 100 mL of sample water. Positive and Negative for Coliforms Based on the #s of positive and negatives. used mostly for .... looking for coliforms. *If the coliforms are digesting the lactose in the samples = drop in PH and Color Change. Advantages of MPN Ease of interpretation, either by observation or gas emission Sample toxins are diluted Effective method of analyzing highly turbid samples such as sediments, sludge, mud, etc. that cannot be analyzed by membrane filtration. Disadvantages of MPN It takes a long time to get the results Results are not very accurate Requires more hardware (glassware) and media Probability of false positives
Conducting Research: (5) Experimental Unit Pseudoreplication and others Example
Need replication of your experimental units, not subsamples within each of your experimental units. Here we have 4 treatments (colored rectangles), repeated 6 times each and have 10 plots within each. • What is the experimental unit? • What is the replication?
Microbiology: Drinking Water Nitrate
Nitrate Level (ppm) (Parts per million): - 0 to 10: Safe for humans and livestock. Concentrations of more than 4ppm are an indicator od possible pollution sources and could cause environmental problems. - 11 to 20: Generally safe for humans and livestock. Not safe for infants because their digestive systems cannot absorb and excrete nitrate. - 21 to 40: Should not be used as drinking water source but short term uses acceptable for adults and livestock unless food or feed sources are very high in nitrates. - 41 to 100: Risky for adults and young livestock. Probably acceptable for mature livestock if feed is low in nitrates. - Over 100: should not be used as drinking water for humans or livestock. * US Standards of 10 PPM. * Blue baby Syndrome = an illness that begins when large amounts of nitrates in water are ingested by an infant and converted to nitrate by the digestive. The nitrate then reacts with oxyhemoglobin (the oxygen carrying the blood protein) to form metheglobin, which cannot carry oxygen.
Microbiology: Model Biogeochemical Cycle: Pools, Fluxes, Residence and Cycling Time
Nutrient Cycle
Microbiology Lab
Pros and Cons of the 4 different methods of testing (HPC, MPN, P/A, etc.) HPC: Pros = Simple and fast, helps determine bacteria in water. Cons = time consuming, doesn't indicate specific pathogens or bacteria. Possible sources of error = too much or too little of samples were deposited onto the plates, human error when counting colonies that grew, etc. MPN: Pros = Great tool to determine presence of organisms or E. coli in samples. Quick and simple to make dilutions and deposit appropriate amount into the broth vials. Cons = Inaccurate measure, time consuming for results. Possible sources of errors = samples were contaminated, false positive results for Coliform. P/A: Pros = faster and cheaper to test adequacy of water. Cons = Doesn't test for specific pathogens. Possible sources or error = inaccurate dilutions, false positive or negative results if samples were contaminated.
Microbiology: Protists
Protists = Protozoa, Algae, and Fungus • Autotrophic protists: - Seaweed such as kelp, red algae, and green algae. -Make their own energy. - Urchins destroy kelp forests and algae. - Hydrogen and Phosphorous regularly tested.
Human Research and IRB: Flavor Rating Assessment (FRA)
Rating Test: - Rating of food samples according to a scale to find out the degree of preference for each food sample. *Not just food also the designated subject being tested. Example: 1 = dislike a lot 2= dislike immediately 3= neutral 4= like moderately 5= like a lot Sample Code and Degree of preference 315= 5 837= 3 642= 4
Risk Analysis: Non- Carcinogens and Thresholds Graph
Reference Dose (RfD): an estimate of daily exposure of the human population, including sensitive subgroups, to a substance that would not represent an appreciable risk of deleterious effects during a lifetime. RfD applies to non-carcinogens, while RSD applies to carcinogens. Lowest Observed effect level (LOEL): - The lowest dose administered, that results in a response. No observed effect level (NOEL): - the highest dose that does not create a response. *NOELS and LOELs are often further refined by noting a distinction between effects that are adverse to health and effects that are not. There is No observed adverse effect (NOAEL) and lowest observed adverse effect levels (LOAELS) The reference Dose (RfD) is the no-observed-adverse-effects-level (NOAEL) divided by an uncertainty factor, which is typically between 10 and 1000. The lowest-adverse-effects-levels (LOAEL) is also typically identified. This is the lowest dose at which measurable effects are noticed.
Conducting Research: (3) Replication & Error
Replication- assignment of more than one experimental unit to the same treatment. • Each replication is independent • More is better...and what is needed generally depends on the variation in the data set...i.e., how much experimental error is in the system. Error is all of the unaccounted-for variation within an experiment/study. • Some of this is likely natural variation based on the organism or study system...but can also include actual mistakes made by the observer (miss counting seeds in a dish). • Increasing replication generally improves accuracy and statistical power.
Conducting Research: Spikes
Spike sample - A sample to which known concentrations of specific analytes have been added in such a manner as to minimize the change in the matrix of the original sample. A spiked sample is a sample prepared by adding a known quantity of analyte to a matrix which is close to or identical to that of the sample of interest. Spiked samples may be used in method validation experiments to help identify matrix effects and determine the recovery of an analyte or the selectivity of the method.
Human Research and IRB: Human Taste Testing (Water Testing) and The Senses
Taste: Salty Bitter Sour Sweet Smell: Odorants Smell Receptors Olfaction Receptors The Senses: • Humans have more than 1000 different kinds of chemosensory cells for smells. These are triggered in different combinations, so we can detect over 10,000 different odors. • Taste cells are found in taste buds. The five basic tastes are sweet, salty, sour, bitter, and umami. • Flavor is a combination of taste and aroma.
Microbiology: The Carbon Cycle
The carbon cycle is nature's way of reusing carbon atoms, which travel from the atmosphere into organisms in the Earth and then back into the atmosphere over and over again. Most carbon is stored in rocks and sediments, while the rest is stored in the ocean, atmosphere, and living organisms. The carbon cycle is vital to life on Earth. Nature tends to keep carbon levels balanced, meaning that the amount of carbon naturally released from reservoirs is equal to the amount that is naturally absorbed by reservoirs. Maintaining this carbon balance allows the planet to remain hospitable for life. Inorganic to organic = photosynthesis. - the process by which green plants and some other organisms use sunlight to synthesize foods from carbon dioxide and water. Photosynthesis in plants generally involves the green pigment chlorophyll and generates oxygen as a byproduct. In ocean = Chemosynthesis *Abundant - The synthesis of organic compounds by bacteria or other living organisms using energy derived from reactions involving inorganic chemicals, typically in the absence of sunlight.
Microbiology: The Nitrogen Cycle
The nitrogen cycle is important because all living things require nitrogen. Explanation: Nitrogen is required for all living things. It is a component in DNA and RNA, proteins, ATP, and chlorophyll in plants. Disrupting the nitrogen cycle can lead to a range of negative effects. For example, eutrophication is caused by an excess of nitrogen in aquatic systems. An increase in atmospheric nitrogen can contribute to acid rain. Most ecosystems are well-adapted to low levels of nitrogen, because naturally most nitrogen is not biologically available. When humans drastically increase the amount of nitrogen available, though vehicle exhaust, fertilizers, and so forth, ecosystems are thrown off balance. - Denitrifying bacteria converts nitrates to molecular nitrogen. - Nitrates, ammonia, and ammonium absorbed by plants are used to make organic nitrogen compounds. Limited- Biological process Nitrite = very toxic and blue baby syndrome.
Risk Analysis: Odds Ratio
The odds ratio shows the relative rate of developing the disease from someone exposed to someone not exposed. If the odds ratio is > 1, than that means you have a greater chance of developing the disease from exposure compared to non-exposure. If the ratio is < 1 it means that your odds of developing the disease is likely independent from exposure.
Risk Analysis: Bioconcentration/Bioaccumulation
The tendency for a substance to accumulate in an organism.
Microbiology: Classifying Life
Thousands of years ago, Aristotle organized life into a "chain of being." Other scientists used this strategy to arrange living things from "simple" to "complex." Humans were at the top of the chain.
Human Research and IRB: American Society for Testing and Materials (ASTM), Threshold Testing
To detect threshold of taste. • 1 positive, 2 negative • Count correct responses using geometric mean of individual thresholds
Conducting Research: (1) Sampling Uncertainty - Sample Collection
Uncertainty - Sample Collection
Conducting Research: Common Blanks
What are blanks in lab? Blanks are artificial samples (made up of ultra-pure MilliQ water) used to trace sources of contamination which may be introduced to samples: During handling and transportation; During sampling in the field (from contaminated equipment); and. During laboratory preparation and analysis.
Microbiology: Coliforms
What are coliforms in microbiology? Coliforms are bacteria that are always present in the digestive tracts of animals, including humans, and are found in their wastes. They are also found in plant and soil material. Heterotrophic Bacteria: most bacteria in nature, includes pathogens. Total Coliforms: presence in water may indicate contamination. Thermotolerant Coliforms: found in intestines of warm-blooded animals. E. coli Coliforms: Indicator of fecal contamination.
Microbiology: Streak Plate Dilution - Isolating Colonies
What are the advantages of streak plate method? Agar streak plates are an essential tool in microbiology. They allow bacteria and fungi to grow on a semi-solid surface to produce discrete colonies. These colonies can be used to help identify the organism, purify the strain free of contaminants, and produce a pure genetic clone. What is a disadvantage of using the streak plate method? Syntrophic bacteria can't be purified by this method. It is unsuitable if the sample size is large and has a very high viable count. If we take heavy inoculum there may not be isolated colonies following the incubation
Microbiology: Helminths (Worms)
What do helminth parasites do? Helminths are worm-like parasites that survive by feeding on a living host to gain nourishment and protection, sometimes resulting in illness of the host Found in digestive tract can penetrate through skin to affect you.
Human Research and IRB: Institutional Review Board (IRB)
What does the Institutional Review Board do? Under FDA regulations, an Institutional Review Board is group that has been formally designated to review and monitor biomedical research involving human subjects. In accordance with FDA regulations, an IRB has the authority to approve, require modifications in (to secure approval), or disapprove research. When is IRB review required? - IRB review is required for projects that meet the regulatory definition of research with human subjects. - is the activity "research"? * a systematic investigation designed to contribute to generalizable knowledge. - Are there human subjects involved? * a living individual about whom an investigator conducting research obtains data through intervention or interaction with the individual or identifiable private information.
Microbiology: HPC - Potable Water - Spread Plate
What is an HPC water test? The HPC test (or Standard Plate Count), applied in many variants, is widely used to measure the heterotrophic microorganism population in drinking-water and other media. Heterotrophs are organisms, including bacteria, yeasts and Moulds, that require an external source of organic carbon for growth. The HPC method does not indicate the specific heterotrophic bacteria present or their sources. Instead, HPC testing indicates the culturable organisms present, which could be as low as 1% of the total bacteria present. There are several factors that affect the genera of bacteria and their level of presence recovered by HPC. These factors include the type of medium used to grow the bacteria, what temperature is used for incubation, how long the plates are incubated, where the water sample was collected, the time of year and the age of the sample. It is also important to note that the concentrations and types of bacteria that are recovered at the same sampling location can vary over time. Importance of HPC counts: High HPC counts indicate ideal conditions for bacterial regrowth and should be corrected. Bacterial regrowth can lead to pipe corrosion, encourage slime growth, increase the need for disinfectants, cause foul-tasting water, and harbour secondary respiratory pathogens (ex. Legionella). Thus, HPC can be used as a marker for the underlying causes of some aesthetic problems (WHO, 2002).
Microbiology: Bacteria and Protists
What is bacteria and its function? Bacteria are microscopic, single-celled organisms that exist in their millions, in every environment, both inside and outside other organisms. Some bacteria are harmful, but most serve a useful purpose. They support many forms of life, both plant and animal, and they are used in industrial and medicinal processes. Bacteria and Protists - C5H7O2N or C60H87O23N12P Bacteria is needed for ecosystem health. Can have negative effects. Bacterial Growth Curve: lag phase = linear growth log phase = exponential growth Declining Growth Phase = Declining
Microbiology: The Nitrogen Cycle and Nitrification and Denitrification
What is meant by nitrification and denitrification? The Formation of different organic nitrogen compounds from inorganic nitrogen compounds is called Nitrogen assimilation. Nitrification. Denitrification. The conversion of ammonia into nitrites is known as nitrification. The conversion of nitrates into nitrogen is known as denitrification.
Human Research and IRB: The Belmont Report
What is the Belmont Report Why is it important? Informed by monthly discussions that spanned nearly four years and an intensive four days of deliberation in 1976, the Commission published the Belmont Report, which identifies basic ethical principles and guidelines that address ethical issues arising from the conduct of research with human subjects. Ethical Principles: 1.) Respect for people - requirement to acknowledge autonomy. - Requirement to protect people with diminished autonomy. 2.) Beneficence - DO NO HARM - Maximize possible benefits and minimize possible harms. 3.) Social Justice - Justice - Injustice - Departures from equal distributions. - Selection of research subjects. Practical Applications: 1.) Informed Consent - Information - Comprehension - Voluntariness (No Coercion). 2.) Assessment of Risks and Benefits - Careful arrayal of relevant information. - Nature and scope of risks and benefits. - Systematic Assessment of risks and benefits. 3.) Selection of Subjects - Individual Justice - Social Justice - Burdened Classes - Vulnerable Subjects
Risk
a measure of probability associated with a given hazard.
Conducting Research: (5) Experimental Unit Pseudoreplication
a situation in which the various study sites or subjects do not represent truly independent samples. Pseudoreplication occurs when observations are not statistically independent but treated as if they are. This can occur when there are multiple observations on the same subjects, when samples are nested or hierarchically organized, or when measurements are correlated in time or space.
Microbiology: Biofilm Sampling
bacteria attached to pipes. if bacteria grows in the presence of chlorine, bacteria is in the biofilm rather than the natural water. Has adapted to the water. • Non-uniform: time and space • Random contamination • Limited access • Swab methods vary/ hard to replicate
Microbiology: The three domains of life
eukaryotic cells have a distinct nucleus containing the cell's genetic material. while prokaryotic cells don't have a nucleus and have free-floating genetic material instead. Eukaryotic cells are cells containing membrane-bound organelles and are the basis for both unicellular and multicellular organisms. In contrast, prokaryotic cells do not have any membrane-bound organelles and are always part of unicellular organisms.
Environmental Risk
first started thinking about risk in the 1980s. Highly controversial field Cost/Benefit Analysis - 0% risk = Infinite cost - when does the cost outweigh the public health/environmental concern? - Acceptable Risk = Acceptable Cost -Another reason risk can be controversial is that there is no such thing as a 0% risk. This risk would theoretically have infinite cost and is unreasonable. It is up to scientists and policy makers to determine some cost/benefit analysis and when the cost outweighs public health and/or environmental concern. Therefore, risk analysis has this central dogma: acceptable risk = acceptable cost. There are four steps to risk assessment followed by risk management.
Microbiology: BARTS
quantitative tests biological activity reactive test (BART). BART testers examine samples for whole communities of bacteria looking primarily for the quantification of the activity levels (population size) and reactions that are achieved (qualitative determination of the types of bacteria present).
Water Taste Test Lab
what are problems with taste test research? 1. The procedure of the tests are not precise and reproducible. The results are useful for local control and are difficult to compare from place to place. 2. Can be too time consuming and doesn't reflect consumer response. 3. Temperature can impact the intensity of the taste in the water. Who regulates tap water? Bottled water? which is more regulated? The US Environmental Protection Agency regulates tap water. The FDA regulates bottled water. Tap water is more regulated as it has tighter restrictions and inspection. Environmental impacts of using bottled water instead of tap water? Bottled water releases 2.5 million tons of CO2 into the atmosphere. Not every plastic bottle gets recycled and many end up in the ocean. Plastic bottles are a source of BPA which is harmful to humans and the environment. Let's say you are working in a municipality... How would you sell your water to the public? I would Sell my water by packaging the water in appealing metal bottles. I would push for refill stations and advertise how much waste we have reduced by using recyclable water bottles.
Conducting Research: (6) Statistical Hypotheses & Testing
• A hypothesis can be thought of as a restatement of the objective in statistical terms. • A hypothesis must state the response variable, the statistical under investigation, and the comparison of interest.
Conducting Research: (7) Treatment and Control
• An Experimental treatment is an impact that is intentionally enacted on a subset of the experimental units. - e.g., prescribed fire, herbicide treatment, dam removal. • In almost all cases an experiment needs to have a control. - Set of experimental units where treatment is withheld. • The control needs to be carefully considered when establishing an experiment and is a crucial part of most designs.
Human Research and IRB: Attribute Rating Test (ART)
• Compare intensity (> = <) (greater, less than, equal, etc.) (numerical order on intensity, etc.) Ranking Test Example: - Ranking of food samples according to a specific property e.g., sweetness. - Ranking of food samples according to the tester's preference to find out the popularity of each food sample. Sample Code and Ranking Order: 315 = ranking 2 837 = ranking 1 642 = ranking 3
Microbiology: Fungi
• Fungi are heterotrophs that release digestive enzymes over organic matter and then absorb the nutrients. • Many fungi are decomposers that obtain the bulk of their nutrients from dead organic matter. They play a crucial role in terrestrial ecosystems. • Fungi may be single-celled or multicellular. • Fungi are more closely related to animals than to plants.
Conducting Research: (2) Randomization
• In ecology the term "haphazard" is increasingly being used for processes in the field which are not mathematically random, but also are not systematic or "overtly intentional." Examples of things that are NOT random: • "I threw the quadrat over my head backward into the grassland thus established a random location" • "I selected flies from the container randomly" • "Shrubs were selected randomly along the trail" • "Random insects were collected from the petal of a flower" • "I selected random locations from the image • "Students were randomly selected from scrolling the list"
Microbiology: Classifying Life
• In the 18th century, Carolus Linnaeus developed a system for classification that emphasized the shared similarities of organisms. • The Linnaean system classified organisms using a series of hierarchical levels.
Microbiology: Total Coliform Rule - 1989
• PWSs monitor total coliforms in the distribution system at a frequency proportional to the number of people served. • Systems which serve fewer than 1,000 people may test once a month or less frequently. • systems with 50,000 customers test at least 60 times per month. • Systems with 2.5 million customers test at least 420 times per month. • >5 % positive must report.
Conducting Research: (4) Responsible Variable
• This is what you are measuring. • It is crucial that at the very start of the experiment the scientists figure out what this is, precisely, and that the study is designed based on this observation. • If this is an experiment, you will be applying treatments, the treatments must be constructed based on the response variable, and replication and randomization must be set based on the Experimental Unit.