Through genetic barcoding of the tufA gene, an unknown green algae specimen was identified as belonging to the Ulva compressa clade. DNA was isolated from the specimen and the tufA gene was amplified via PCR. The gene was cloned and the nucleotide sequence analyzed and compared to sequences in GenBank. Phylogenetic analysis indicated the specimen was most similar to Ulva sp. BER-2007, but could not be identified to the species level. While in the U. compressa clade, further testing is needed to confirm its identity as a potential new species of Ulva in Narragansett Bay.
Hypothesis: The 4 factors which can affect the strength of an electromagnet are the type of core used, the number of turns of wire, the magnitude of the current used and the shape of the solenoid.
Aim: To investigate the factors which affect the strength of an electromagnet.
ESTIMATION OF SODIUM IN TAP WATER SAMPLE BY FLAME EMISSION SPECTROPHOTOMETER ...Sadia Rahat
The document describes a procedure to estimate the concentration of sodium in a tap water sample using flame emission spectrophotometry. The procedure involves preparing standard sodium chloride solutions of known concentrations, measuring their emissions using the spectrophotometer, and generating a calibration curve. The tap water sample's emission is also measured and its sodium concentration is determined using the calibration curve. The estimated sodium concentration in the tap water sample was 1.45 ppm.
The document discusses three allotropes of carbon: diamond, graphite, and buckminsterfullerence. Diamond has a rigid structure of carbon atoms bonded together, giving it properties of hardness and high melting point. Graphite has layers of carbon atoms bonded weakly, making it softer and able to conduct electricity. Buckminsterfullerence is a spherical cluster of 60 carbon atoms that is a dark solid.
Adhesion is the force of attraction between molecules of different substances, such as water molecules being attracted to a glass plate or cotton cloth. Cohesion is the force of attraction between molecules of the same substance, causing mercury to form spherical drops and not wet a glass plate. The force of cohesion depends on factors like molecular weight and properties, with polar molecules having stronger cohesive forces than non-polar molecules of similar mass.
This lab experiment investigated ligand exchange reactions involving copper (II) ions. Anhydrous copper (II) sulfate was reacted with water, ammonia, and hydrochloric acid. When water was added, the copper (II) sulfate dissolved with a color change from pale to dark blue. Ammonia caused no further change, but hydrochloric acid resulted in a color shift to green and gas release, demonstrating ligand exchange between chloride and the original sulfate and water ligands.
In complexometric titrations, initially the indicator forms a metal indicator complex with metal ions which is less stable compared to the metal-EDTA complex. Hexadentate ligand like EDTA acts as a chelating agent that complex with the metal ions in the solution. When all the metal ions form a complex with a chelating agent, the original colour of the indicator in the buffer is observed which reflects the endpoint of the titration
The document outlines how to write a plan and design experiment for testing which color of lime (yellow or green) has a higher level of acidity. It includes sections for the problem statement, hypothesis, aim, apparatus and materials, method, variables, expected results, treatment of results, chemical principles, and sources of errors/assumptions/limitations. The hypothesis is that yellow limes have the highest acidity. The aim is to measure and compare the pH levels of lime juice from each color lime. Yellow lime juice is expected to give a lower pH reading, supporting the hypothesis that it has a higher acidity.
Hypothesis: The 4 factors which can affect the strength of an electromagnet are the type of core used, the number of turns of wire, the magnitude of the current used and the shape of the solenoid.
Aim: To investigate the factors which affect the strength of an electromagnet.
ESTIMATION OF SODIUM IN TAP WATER SAMPLE BY FLAME EMISSION SPECTROPHOTOMETER ...Sadia Rahat
The document describes a procedure to estimate the concentration of sodium in a tap water sample using flame emission spectrophotometry. The procedure involves preparing standard sodium chloride solutions of known concentrations, measuring their emissions using the spectrophotometer, and generating a calibration curve. The tap water sample's emission is also measured and its sodium concentration is determined using the calibration curve. The estimated sodium concentration in the tap water sample was 1.45 ppm.
The document discusses three allotropes of carbon: diamond, graphite, and buckminsterfullerence. Diamond has a rigid structure of carbon atoms bonded together, giving it properties of hardness and high melting point. Graphite has layers of carbon atoms bonded weakly, making it softer and able to conduct electricity. Buckminsterfullerence is a spherical cluster of 60 carbon atoms that is a dark solid.
Adhesion is the force of attraction between molecules of different substances, such as water molecules being attracted to a glass plate or cotton cloth. Cohesion is the force of attraction between molecules of the same substance, causing mercury to form spherical drops and not wet a glass plate. The force of cohesion depends on factors like molecular weight and properties, with polar molecules having stronger cohesive forces than non-polar molecules of similar mass.
This lab experiment investigated ligand exchange reactions involving copper (II) ions. Anhydrous copper (II) sulfate was reacted with water, ammonia, and hydrochloric acid. When water was added, the copper (II) sulfate dissolved with a color change from pale to dark blue. Ammonia caused no further change, but hydrochloric acid resulted in a color shift to green and gas release, demonstrating ligand exchange between chloride and the original sulfate and water ligands.
In complexometric titrations, initially the indicator forms a metal indicator complex with metal ions which is less stable compared to the metal-EDTA complex. Hexadentate ligand like EDTA acts as a chelating agent that complex with the metal ions in the solution. When all the metal ions form a complex with a chelating agent, the original colour of the indicator in the buffer is observed which reflects the endpoint of the titration
The document outlines how to write a plan and design experiment for testing which color of lime (yellow or green) has a higher level of acidity. It includes sections for the problem statement, hypothesis, aim, apparatus and materials, method, variables, expected results, treatment of results, chemical principles, and sources of errors/assumptions/limitations. The hypothesis is that yellow limes have the highest acidity. The aim is to measure and compare the pH levels of lime juice from each color lime. Yellow lime juice is expected to give a lower pH reading, supporting the hypothesis that it has a higher acidity.
This experiment aims to identify alkanes and alkenes by their reactions with different substances and determine their properties. Cyclohexane and cyclohexene are used as representative alkanes and alkenes, respectively. A series of tests are conducted including bromine, potassium permanganate, sulfuric acid and sodium hydroxide tests. The results show that cyclohexene is more reactive than cyclohexane due to the presence of a carbon-carbon double bond, undergoing addition reactions, while cyclohexane only undergoes substitution reactions. This supports the hypothesis that alkenes are much more reactive than alkanes.
Coulometry and electrogravimetric analysis are analytical techniques that involve completely oxidizing or reducing an analyte through electrolysis. In coulometry, the quantity of electrical charge passed is measured and related to the amount of analyte present. In electrogravimetry, the analyte is converted electrolytically into a product that is weighed to determine the analyte amount. Both techniques are accurate and precise, but require ensuring all current passed results in analyte oxidation/reduction. Controlled-potential coulometry uses a constant potential, while controlled-current coulometry applies a constant current, each with their own experimental considerations to achieve complete analyte conversion.
This document discusses three main types of chemical bonding: ionic bonds, covalent bonds, and metallic bonds. Ionic bonds form between metals and nonmetals through the transfer of electrons from one atom to another, producing charged ions. Covalent bonds form between nonmetals of similar electronegativity through the sharing of electron pairs. Metallic bonds form between metallic elements through a shared "electron cloud" that holds the atoms together strongly.
This document discusses molecular geometry and hybridization. It begins by explaining how the shape of a molecule is determined by electron pair repulsions. It then discusses different types of hybridization including sp, sp2, sp3, sp3d, sp3d2, and sp3d3 hybridization. For each type of hybridization it provides details on the number and orientation of the hybridized orbitals and their characteristics. It concludes by summarizing the number of electron pairs, hybridization, and molecular geometry for different compounds.
This document provides guidance on formulating a research topic and question for an Extended Essay. It discusses the differences between a research topic and question, with topics being more general and questions being focused and answerable. Good research questions are interesting, new, researchable within the allowed timeframe and resources, and neither too broad nor narrow in scope. Examples of effective and ineffective topics and questions are provided. Students are encouraged to develop questions around their own interests and passions. Question starters are suggested to help narrow topics into focused questions, such as "To what extent...", "How successful...", and "What is the impact of...". The document concludes by walking through narrowing a subject into a focused research question.
Estimation of sodium bicarbonate and carbonate in mixtureMithil Fal Desai
This document provides instructions for estimating the amounts of sodium carbonate and sodium bicarbonate present in a mixture. The experiment involves titrating a sample of the mixture against a standardized hydrochloric acid solution using the pH indicators phenolphthalein and methyl orange to determine the endpoints of the reactions of carbonate and bicarbonate ions with hydrogen ions. Phenolphthalein can be used to detect only the reaction of carbonate ions, while methyl orange is needed to detect the complete neutralization of both carbonate and bicarbonate ions.
This document summarizes two biology lab reports by a student. The first lab involved classifying 10 organisms found around the student's school into their scientific kingdoms, phyla, and classes. The second lab investigated interdependence between organisms by constructing food chains and a food web of 10 organisms and their food sources. Key findings were that organisms can be classified into taxonomic groups and that living things rely on each other through predator-prey relationships and the transfer of energy up the food chain from producers to consumers.
Valence shell electron pair repulsion (VSEPR) theory is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. It is also named the Gillespie-Nyholm theory after its two main developers, Ronald Gillespie and Ronald Nyholm
Ppt1 Introduction To Qa & Tests For Gasessitinurbaiyah
The document discusses qualitative analysis, which is a process chemists use to identify unknown substances. It involves performing chemical tests to determine the cations and anions present, allowing identification of the substance. Common tests include observing the appearance of solids and solutions, determining solubility, observing gases produced from heating or adding acids/alkalis. Gases can be identified using tests like their reaction with litmus, ability to relight a glowing splint, or forming precipitates with reagents. The goal is to perform experiments and make inferences to identify an unknown salt or mixture.
CSEC Physics Lab - Mapping the magnetic fields of a bar magnet Ronaldo Degazon
The magnetic field lines of a bar magnet were mapped in a physics experiment. The field lines formed curved loops from the north to south pole of the magnet. The field was strongest near the poles where the lines were closest together, and weakened farther away as the lines spread out. Potential sources of error included inaccurate placement of dots, shifting of the magnet or paper, and incorrectly drawn field line directions. Precautions were taken to accurately place dots, prevent shifting, draw the right directions for lines, and precisely trace the field lines.
Elements are substances made of only one type of atom, while compounds are made of two or more elements that are chemically bonded together. The chemical formula of a compound shows which elements it contains. Compounds have different properties than their constituent elements. Common table salt, or NaCl, is a compound formed from the elements sodium and chlorine bonding together, even though on their own sodium is a metal and chlorine is a gas. Compounds form when atoms bond by sharing, gaining or losing electrons.
dish and heat gently. NH4Cl will sublime leaving behind NaCl.
Filter the remaining NaCl through the funnel. The filtrate will
contain the sublimed NH4Cl.
This separates the mixture using the technique of sublimation
based on the fact that NH4Cl sublimes but NaCl does not.
Experiment 1 demonstrates sublimation as a method of separating mixtures where one component sublimes and the other does not.
Syllabus requirement met: describe the separating methods of simple distillation , fractional distillation , filtration , layer separation and identify sublimation as a method of separating mixtures based on their composition.
Spectroscopic methods in Inorganic ChemistryChris Sonntag
This document provides an overview of spectroscopic methods in inorganic chemistry, focusing on infrared (IR) spectroscopy. It discusses key concepts like dipole moments, factors that influence bond vibrational frequencies, and using symmetry to determine vibration modes. Specific applications covered include identifying functional groups, distinguishing between cis and trans transition metal carbonyl complexes using IR spectra, and analyzing metal-ligand vibrations in complexes. The document also lists several online resources for IR spectral simulation, prediction, and reference databases.
The document discusses the key concepts of elements, compounds, atoms, and molecules. It defines elements as pure substances that cannot be broken down further, and compounds as substances made of two or more elements bonded chemically. Atoms are the smallest particles of an element, with a nucleus containing protons and neutrons surrounded by electrons. Molecules are formed when two or more atoms of elements share electrons to achieve a stable electron configuration.
Biosynthesis and characterisation of copper oxide nanoparticle from papaya plantTDMNS College T.Kalikulam
The document describes the biosynthesis and characterization of copper oxide nanoparticles from papaya plant extracts. Copper oxide nanoparticles were synthesized using fruit, peel, and leaf extracts of papaya by mixing the extracts with copper sulfate solution. The nanoparticles were characterized using UV-Vis spectroscopy, FTIR, XRD, TEM, SEM, and AFM. UV-Vis analysis showed absorption peaks around 300nm. XRD analysis revealed the crystalline nature of the particles with sizes ranging from 10-20nm. TEM and SEM images showed the spherical morphology of the particles. FTIR showed the presence of functional groups involved in nanoparticle synthesis. The copper oxide nanoparticles exhibited good antimicrobial activity against M. luteus and E. coli.
Rutherford's experiment involved firing alpha particles at a thin gold foil. Most passed straight through, showing the atom is mostly empty space. Some were deflected, showing a small, dense central nucleus. Very few bounced straight back, showing the nucleus is very small compared to the atom. This led to the discovery of the nuclear model of the atom, with a small, dense nucleus surrounded by electrons.
Universal and rapid salt extraction of high quality genomic dna for pcr-based...CAS0609
This document describes a simple and universal method for extracting high-quality genomic DNA from a variety of organisms including plants, fungi, insects, and shrimp. The method uses a salt-based homogenizing buffer and SDS to extract DNA from as little as 50mg of fresh tissue. The extracted DNA is of sufficient quality and quantity to be used in PCR, restriction digestion, and other molecular techniques. The method is fast, inexpensive, and does not require expensive equipment, making it suitable for laboratories with limited resources. Test results demonstrated the method successfully extracted high molecular weight DNA from many diverse organisms without modification, indicating its universal applicability.
This document summarizes information from a student's assignment on plant genome sequencing techniques. It discusses early phenotypic selection methods and their limitations. It then summarizes different sequencing strategies used for important crop plants like rice, poplar, and Arabidopsis. These include BAC-by-BAC, whole genome shotgun, and various next-generation sequencing platforms. The document also summarizes applications of sequencing including identifying genes related to rice yield and flowering time and using sequencing to improve potato and maize varieties.
This experiment aims to identify alkanes and alkenes by their reactions with different substances and determine their properties. Cyclohexane and cyclohexene are used as representative alkanes and alkenes, respectively. A series of tests are conducted including bromine, potassium permanganate, sulfuric acid and sodium hydroxide tests. The results show that cyclohexene is more reactive than cyclohexane due to the presence of a carbon-carbon double bond, undergoing addition reactions, while cyclohexane only undergoes substitution reactions. This supports the hypothesis that alkenes are much more reactive than alkanes.
Coulometry and electrogravimetric analysis are analytical techniques that involve completely oxidizing or reducing an analyte through electrolysis. In coulometry, the quantity of electrical charge passed is measured and related to the amount of analyte present. In electrogravimetry, the analyte is converted electrolytically into a product that is weighed to determine the analyte amount. Both techniques are accurate and precise, but require ensuring all current passed results in analyte oxidation/reduction. Controlled-potential coulometry uses a constant potential, while controlled-current coulometry applies a constant current, each with their own experimental considerations to achieve complete analyte conversion.
This document discusses three main types of chemical bonding: ionic bonds, covalent bonds, and metallic bonds. Ionic bonds form between metals and nonmetals through the transfer of electrons from one atom to another, producing charged ions. Covalent bonds form between nonmetals of similar electronegativity through the sharing of electron pairs. Metallic bonds form between metallic elements through a shared "electron cloud" that holds the atoms together strongly.
This document discusses molecular geometry and hybridization. It begins by explaining how the shape of a molecule is determined by electron pair repulsions. It then discusses different types of hybridization including sp, sp2, sp3, sp3d, sp3d2, and sp3d3 hybridization. For each type of hybridization it provides details on the number and orientation of the hybridized orbitals and their characteristics. It concludes by summarizing the number of electron pairs, hybridization, and molecular geometry for different compounds.
This document provides guidance on formulating a research topic and question for an Extended Essay. It discusses the differences between a research topic and question, with topics being more general and questions being focused and answerable. Good research questions are interesting, new, researchable within the allowed timeframe and resources, and neither too broad nor narrow in scope. Examples of effective and ineffective topics and questions are provided. Students are encouraged to develop questions around their own interests and passions. Question starters are suggested to help narrow topics into focused questions, such as "To what extent...", "How successful...", and "What is the impact of...". The document concludes by walking through narrowing a subject into a focused research question.
Estimation of sodium bicarbonate and carbonate in mixtureMithil Fal Desai
This document provides instructions for estimating the amounts of sodium carbonate and sodium bicarbonate present in a mixture. The experiment involves titrating a sample of the mixture against a standardized hydrochloric acid solution using the pH indicators phenolphthalein and methyl orange to determine the endpoints of the reactions of carbonate and bicarbonate ions with hydrogen ions. Phenolphthalein can be used to detect only the reaction of carbonate ions, while methyl orange is needed to detect the complete neutralization of both carbonate and bicarbonate ions.
This document summarizes two biology lab reports by a student. The first lab involved classifying 10 organisms found around the student's school into their scientific kingdoms, phyla, and classes. The second lab investigated interdependence between organisms by constructing food chains and a food web of 10 organisms and their food sources. Key findings were that organisms can be classified into taxonomic groups and that living things rely on each other through predator-prey relationships and the transfer of energy up the food chain from producers to consumers.
Valence shell electron pair repulsion (VSEPR) theory is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. It is also named the Gillespie-Nyholm theory after its two main developers, Ronald Gillespie and Ronald Nyholm
Ppt1 Introduction To Qa & Tests For Gasessitinurbaiyah
The document discusses qualitative analysis, which is a process chemists use to identify unknown substances. It involves performing chemical tests to determine the cations and anions present, allowing identification of the substance. Common tests include observing the appearance of solids and solutions, determining solubility, observing gases produced from heating or adding acids/alkalis. Gases can be identified using tests like their reaction with litmus, ability to relight a glowing splint, or forming precipitates with reagents. The goal is to perform experiments and make inferences to identify an unknown salt or mixture.
CSEC Physics Lab - Mapping the magnetic fields of a bar magnet Ronaldo Degazon
The magnetic field lines of a bar magnet were mapped in a physics experiment. The field lines formed curved loops from the north to south pole of the magnet. The field was strongest near the poles where the lines were closest together, and weakened farther away as the lines spread out. Potential sources of error included inaccurate placement of dots, shifting of the magnet or paper, and incorrectly drawn field line directions. Precautions were taken to accurately place dots, prevent shifting, draw the right directions for lines, and precisely trace the field lines.
Elements are substances made of only one type of atom, while compounds are made of two or more elements that are chemically bonded together. The chemical formula of a compound shows which elements it contains. Compounds have different properties than their constituent elements. Common table salt, or NaCl, is a compound formed from the elements sodium and chlorine bonding together, even though on their own sodium is a metal and chlorine is a gas. Compounds form when atoms bond by sharing, gaining or losing electrons.
dish and heat gently. NH4Cl will sublime leaving behind NaCl.
Filter the remaining NaCl through the funnel. The filtrate will
contain the sublimed NH4Cl.
This separates the mixture using the technique of sublimation
based on the fact that NH4Cl sublimes but NaCl does not.
Experiment 1 demonstrates sublimation as a method of separating mixtures where one component sublimes and the other does not.
Syllabus requirement met: describe the separating methods of simple distillation , fractional distillation , filtration , layer separation and identify sublimation as a method of separating mixtures based on their composition.
Spectroscopic methods in Inorganic ChemistryChris Sonntag
This document provides an overview of spectroscopic methods in inorganic chemistry, focusing on infrared (IR) spectroscopy. It discusses key concepts like dipole moments, factors that influence bond vibrational frequencies, and using symmetry to determine vibration modes. Specific applications covered include identifying functional groups, distinguishing between cis and trans transition metal carbonyl complexes using IR spectra, and analyzing metal-ligand vibrations in complexes. The document also lists several online resources for IR spectral simulation, prediction, and reference databases.
The document discusses the key concepts of elements, compounds, atoms, and molecules. It defines elements as pure substances that cannot be broken down further, and compounds as substances made of two or more elements bonded chemically. Atoms are the smallest particles of an element, with a nucleus containing protons and neutrons surrounded by electrons. Molecules are formed when two or more atoms of elements share electrons to achieve a stable electron configuration.
Biosynthesis and characterisation of copper oxide nanoparticle from papaya plantTDMNS College T.Kalikulam
The document describes the biosynthesis and characterization of copper oxide nanoparticles from papaya plant extracts. Copper oxide nanoparticles were synthesized using fruit, peel, and leaf extracts of papaya by mixing the extracts with copper sulfate solution. The nanoparticles were characterized using UV-Vis spectroscopy, FTIR, XRD, TEM, SEM, and AFM. UV-Vis analysis showed absorption peaks around 300nm. XRD analysis revealed the crystalline nature of the particles with sizes ranging from 10-20nm. TEM and SEM images showed the spherical morphology of the particles. FTIR showed the presence of functional groups involved in nanoparticle synthesis. The copper oxide nanoparticles exhibited good antimicrobial activity against M. luteus and E. coli.
Rutherford's experiment involved firing alpha particles at a thin gold foil. Most passed straight through, showing the atom is mostly empty space. Some were deflected, showing a small, dense central nucleus. Very few bounced straight back, showing the nucleus is very small compared to the atom. This led to the discovery of the nuclear model of the atom, with a small, dense nucleus surrounded by electrons.
Universal and rapid salt extraction of high quality genomic dna for pcr-based...CAS0609
This document describes a simple and universal method for extracting high-quality genomic DNA from a variety of organisms including plants, fungi, insects, and shrimp. The method uses a salt-based homogenizing buffer and SDS to extract DNA from as little as 50mg of fresh tissue. The extracted DNA is of sufficient quality and quantity to be used in PCR, restriction digestion, and other molecular techniques. The method is fast, inexpensive, and does not require expensive equipment, making it suitable for laboratories with limited resources. Test results demonstrated the method successfully extracted high molecular weight DNA from many diverse organisms without modification, indicating its universal applicability.
This document summarizes information from a student's assignment on plant genome sequencing techniques. It discusses early phenotypic selection methods and their limitations. It then summarizes different sequencing strategies used for important crop plants like rice, poplar, and Arabidopsis. These include BAC-by-BAC, whole genome shotgun, and various next-generation sequencing platforms. The document also summarizes applications of sequencing including identifying genes related to rice yield and flowering time and using sequencing to improve potato and maize varieties.
This study aimed to clone homologous genes of SND1, a key regulator of secondary cell wall biosynthesis, from Populus trichocarpa. The researcher amplified four SND1 homologs from P. trichocarpa cDNA using PCR. The amplified genes were cloned into E. coli and sequenced. Two colonies were found to contain the correct SND1 sequence insert, while others were false positives. Further work will express and quantify the proteins and determine their effects on other genes and phenotypes.
In this research paper from the Spring 2015 semester, I described my analysis of certain genome scaffolds, or gaps within the Malaclemys terrapin genome. I examined seven of these scaffolds and determined their approximate sizes through Polymerase Chain Reaction (PCR) and Gel Electrophoresis. The DNA was then prepped to be sent for sequencing by an external source. The resulting chromatograms gave inconclusive results on the exact sequences of these scaffolds.
This lab report describes experiments to purify and express recombinant green fluorescent protein (rGFP) from E. coli using nickel affinity chromatography. rGFP with a His-tag was overexpressed in E. coli and purified using a nickel agarose column. The fraction with the highest elution (E3) had the highest rGFP levels and specific activity. Overall, the elution fractions contained most of the rGFP due to binding to nickel, while the wash fractions contained much less rGFP.
This document summarizes a study that used DNA barcoding to characterize Niphargus Kochianus Irlandicus, a tiny crustacean found in groundwater in Ireland. DNA was extracted from legs of specimens collected from two sites and amplified for the COI gene. Sequencing of the COI gene from four specimens revealed 72-84% homology with other Niphargus species, indicating molecular divergence within the species. A phylogenetic tree constructed from the COI sequences showed the existence of hidden diversity within Niphargus Kochianus Irlandicus.
This document describes a study that used polymerase chain reaction (PCR) to amplify 16S ribosomal DNA (rDNA) from various bacterial species for phylogenetic analysis. The researchers designed universal primers that could amplify nearly full-length 16S rDNA from many bacterial genera. They demonstrated that this method allowed phylogenetic analysis of fastidious or pathogenic bacteria directly from lyophilized cultures without requiring cultivation. As an example, they amplified, cloned, sequenced and phylogenetically analyzed the 16S rDNA of Anaplasma marginale, placing it within the genera Rickettsia and Ehrlichia.
Cloning and Characterization of Master Regulator of Systemic Acquired Resista...Akhilesh Rawat
The document describes research that cloned the npr1 gene, which encodes the non-expresser of PR proteins 1 protein and is a master regulator of systemic acquired resistance in plants. The researchers cloned the npr1 gene from mustard using PCR and sequenced it, finding 98% identity to reported npr1 genes. They transferred the cloned gene to tobacco through Agrobacterium-mediated transformation. The putative transgenic tobacco plants were confirmed using gene-specific PCR. Overexpression of npr1 has potential to provide broad-spectrum disease resistance in crops.
This study examines genetic variation in the Alabama hog sucker (Hypentelium etowanum) across river drainages in the southeastern United States using DNA sequencing of the mitochondrial cytochrome b gene. Tissue samples were collected from seven locations and DNA was extracted and amplified via PCR. Approximately 1150 base pairs of the cyt b gene were sequenced. Preliminary results found genetic variations between populations that are consistent with a previous study. The sequences from a new location in the Little Tallapoosa drainage were most closely related to those from the Chattahoochee drainage. This ongoing study aims to increase sampling to further resolve the genetic structure of H. etowanum across its range.
An Understanding Of Bacterial Transformation By Plasmid DnaGina Buck
Bacterial plasmids are small, circular DNA molecules within bacteria that are separate from the bacterial chromosome. Plasmids can contain genes that provide bacteria with useful traits like antibiotic resistance. During genetic transformation, the plasmid is introduced to recipient bacteria where it can be replicated independently of the bacterial chromosome. The foreign DNA from the plasmid is then expressed in the recipient bacteria, altering its genotype and phenotype. This allows bacteria to horizontally acquire new genes from plasmids and gain traits like antibiotic resistance without direct contact between bacterial cells.
The document summarizes several biology lab experiments conducted by the author:
1. They performed DNA extraction from samples, PCR, and Western blot techniques. For DNA extraction, their sample did not produce the expected results.
2. They learned aseptic technique and used Gram staining to identify bacteria samples as gram positive or negative.
3. PCR was used to amplify genomic DNA between primers over multiple cycles. Controls were included.
4. Nested PCR with more specific primers was used to further amplify portions of DNA. Exonuclease treated samples before nested PCR.
5. Gel electrophoresis separated DNA fragments by size. PCR products from two plant samples were analyzed, with one showing bands.
This laboratory report summarizes an experiment exploring RNA splicing in Drosophila melanogaster. Genomic DNA and total RNA were extracted from fruit flies and used to study the rngo gene. PCR and RT-PCR were performed on the genomic DNA and cDNA samples. The genomic PCR product was cloned and sequenced. Bioinformatics analysis showed the genomic sequence was longer, containing introns absent from the cDNA, indicating splicing of the rngo pre-mRNA. Future work could investigate other splicing sites and homology to human genes.
This document discusses Restriction Fragment Length Polymorphism (RFLP), a genetic marker technique. RFLP involves digesting genomic DNA with restriction enzymes, separating the fragments via gel electrophoresis, transferring the fragments to a membrane, and detecting variations in fragment lengths between individuals. The key steps are isolating DNA from samples, restriction enzyme digestion of the DNA, electrophoresis to separate fragments, Southern blotting to transfer DNA to a membrane, and autoradiography to detect polymorphisms. RFLP has advantages like using reliable genotypic characteristics and being co-dominant, but also disadvantages like being time-consuming and multi-step. RFLP can be applied to mapping chromosomes, assessing genetic diversity, and distinguishing
Cloning and sequence analysis of banana streak virus dna. harper 1998Paloma Susan
Banana streak virus (BSV) causes severe problems for banana cultivation. The researchers cloned and sequenced the genome of a Nigerian isolate of BSV. The genome was found to be 7,389 base pairs and organized similarly to other badnaviruses, with three open reading frames. Comparison showed BSV is distinct from but closely related to sugarcane bacilliform virus. PCR primers designed from the sequence data detected BSV sequences in banana plants, indicating portions of the BSV genome may integrate into the banana genome. The BSV sequence provides a basis for more sensitive PCR-based detection methods.
Induced Expression of CYP1A by Triclosan in Zebra Fish to measure toxicologic...Mujtaba Qureshi
1) The study examines the effects of triclosan exposure on zebrafish by observing changes in expression of the CYP1A and TCF3A genes.
2) Using qPCR, the study found a 250% increase in CYP1A expression in triclosan-treated zebrafish compared to controls, indicating triclosan exposure induces CYP1A expression. However, a 9% increase in TCF3A expression in treated fish was not statistically significant.
3) EROD assays were also used to measure CYP1A activity, showing triclosan exposure induces CYP1A enzyme activity in zebrafish. The study suggests further research is
Waksman Student Scholars Program PosterWesley Kwong
The document describes an experiment to sequence the DNA of the duckweed plant Landoltia punctata and analyze the protein encoded. Researchers used PCR to amplify duckweed DNA inserted into bacteria. Restriction digest isolated the duckweed DNA, which was sequenced. Analysis identified the protein as Mitogen-Activated Protein Kinase (MAPK), which regulates cellular responses to stimuli and contains conserved domains. The 3D structure of this protein is similar to the human MAPK protein, indicating an evolutionary advantage across kingdoms.
This document provides background information on genetic sequencing techniques. It begins with a brief history of Sanger sequencing and its role in decoding genetic sequences. It then discusses how DNA can be separated by size using gel electrophoresis, noting that polyacrylamide gels allow for greater resolution than agarose gels. The document goes on to explain how Sanger sequencing works and some improvements that were made over time. It also introduces next-generation sequencing techniques and discusses their advantages over Sanger sequencing in providing massively parallel sequencing at lower cost.
- The document discusses research on the cotton root-knot nematode (Meloidogyne incognita), an endoparasitic nematode that infects thousands of plant species and causes billions in crop damage worldwide.
- The research uses Arabidopsis thaliana plants, including mutant strains, to study the nematode's infection process. Mutant plants have mutations in an ABC transporter gene (At4g15320) involved in secreting chemicals that nematodes use to locate host plants.
- The goal is to see if the mutant transporter gene affects nematode infection rates compared to wild-type Arabidopsis. Results found the mutant was actually not a true mutant and showed similar nematode infection to the
1) The study analyzed genetic diversity in 66 finger millet accessions from Ethiopia and Eritrea using RAPD markers.
2) A total of 123 RAPD fragments were amplified using 15 primers, of which 89 (72%) were found to be polymorphic.
3) Genetic similarity between accessions ranged from 0.585 to 0.984. Cluster analysis grouped the 66 accessions into nine clusters at a similarity index of 0.83, showing high genetic variability among the accessions.
1. Genetic barcoding of Green Algae Ulva sp. for algal
inventory of Narragansett Bay
Benjamin Gibson
Abstract:
Through the use of DNA isolation, PCR amplification, plasmid cloning and
plasmid purification, the tufA gene from an unknown green algae underwent genetic
barcoding which allows for environmental biologists to assess the biodiversity of organisms
in a given ecosystem. The specimen was ultimately narrowed down to being a part of the
Ulva compressa clade, unable to determine the species of the specimen.
Introduction:
Genetic barcoding is one of the main ways used to assess biodiversity among
organisms, especially if those organisms are similar in appearance. Algae is a typical type of
organism that genetic barcoding is used for due to their characteristics being somewhat
similar to each other as the taxonomy specificity increases (Saunders G.W. 2005). In this
research project, the genetic composition of sea lettuce (Ulva spp.) is investigated to
determine the organism’s species. Ulva spp. have very similar visual characteristics; such as
their coloration, or their delicate blades. However their blades are broken down into two
subcategories: distromatic blades and monostromatic tubular structures. The identification of
the algal species Ulva is extremely difficult due to shared characteristics between species
(Hofmann et al. 2010).
The importance of this research is because of the recent interest in assessing the
biodiversity of seaweed in certain environments. The most important reason why there is an
increased interest in the biodiversity of seaweed is to determine whether or not the species
present are invasive or endemic to that specific area. This is helpful in determining if the
ecosystem as a whole is doing well, as seaweed can be the determining factor on ecosystem
health. Specifically, Ulva spp. is a competitively dominant algae in their ecosystem, the
rocky intertidal zone, due to their fast growth and high reproductive capability (Skip
Pomeroy, personal communication, October 2014). They are also the main prey item for
species such as Littorina littorea, or the common periwinkle, who are predated on by larger
organisms; it can be extrapolated then, that the biodiversity of seaweed is an important aspect
of the environment as they impact the majority of the rocky intertidal zone (Watson &
Norton. 1985).
Materials and Methods:
Collection of specimens: The specimen collected for this genetic barcoding
project was Ulva spp. which was found in the lower rocky intertidal zone at low tide. This
took place on September 8th, 2014 at approximately 12:10pm. Using a technique called
specimen vouchering, the algae is preserved using various methods. In this case, the method
was through photography; specifically while it was on herbarium paper prior to the drying
process. The unique specimen ID number for the vouchering process is
BIO200.52.FA14.BJG33.
DNA isolation: A very small tissue sample (approximately the size of a dime) was
crushed up by adding liquid nitrogen to the sample in a mortar. After the mortar and pestle
was used to crush the sample, it had a paste-like texture to it. The DNA isolation technique
that was used utilized the Qiagen DNeasy Plant mini Kit.
2. After the DNA was isolated, the quality and quantity was observed using Agarose Gel
Electrophoresis which separates DNA fragments by size. The DNA was stained with ethidium
bromide which made the DNA fluoresce under UV light. Using the Agarose Gel Electrophoresis lab
handout the quality and quantity of the DNA was determined (Warren & Hagedorn. 2014).
PCR amplification: Using PCR amplification, the isolated DNA is able to be cloned and amplified
exponentially to ensure there is enough of the target segment. Due to the sample being a green algae,
this was done using the tufA forward primer #1 and the tufA reverse primer #2. The sequence of tufA
forward primer #1 is GGNGCNGCNCAAATGGAYGG and the sequence of tufA reverse primer #2
is CCTTCNCGAATMGCRAAWCGC. The amount of each primer added to the master mix was 0.25
ul. Other materials added to the master mix included the Buffer, MgCl2, dNTPs, Taq polymerase, and
water, which brings the volume per reaction up to 20 ul. The amount of DNA added to the volume of
master mix per reaction was 5 ul which brought the final volume up to 25 ul. The PCR amplification
was then put through agarose gel electrophoresis and it was determined whether or not the PCR
amplification worked (Warren and Hagedorn. 2014).
Gene cloning: The PCR product is then cloned into an E. coli vector using an Invitrogen
TOPO TA Cloning Kit, the PCR product was inserted into the plasmid successfully. After the cells
were incubated at 37°C for one hour, 100ul of the cells were placed on a plate that contained
ampicillin and X-gal which will help identify which colonies contain the plasmid that holds the PCR
insert. (Warren and Hagedorn. 2014).
Plasmid purification: After the cells were placed on a plate that contained ampicillin and
X-gal, colonies were grown in overnight cultures. Once there were enough colonies, one colony that
contained the plasmid was isolated using the Qiagen QIAprep Spin Miniprep kit. The entire
procedure can be found in the plasmid isolation and analysis lab handout and the QIAprep Miniprep
handbook published in 2003. Once the plasmid DNA was purified, it was analyzed by cutting the
insert out of the plasmid vector through the use of EcoRI restriction enzyme. The presence of the
tufA gene was determined using agarose gel electrophoresis (Warren and Hagedorn. 2014).
Sequence analysis: The plasmid DNA with the PCR insert was sent to University of
Rhode Island’s sequencing facility for automated sequencing. The returned sequence was then edited
by removing all N’s and all of the nucleotide sequence before the tufA forward primer #1. This newly
edited sequence was then entered into a number of databases, including a website that searches
GenBank for similar sequences, and a website that translates the nucleotide sequence into an amino
acid sequence. The nucleotide sequence was compared to two additional species sequences, both of
which were found in the list of sequences provided by Professors Kerri Warren and Tara Hagedorn.
Results:
Specimen collection: The specimen
was collected underneath the Roger
Williams University learning
platform in the lower intertidal zone
on September 8th, 2014 at
approximately 12:10pm which was
during low tide (fig. 1). At first
observation, the specimen appears to
be characteristically similar to Ulva
lactuca.
Figure 1. Preserved
green algae specimen.
3. DNA isolation: The isolated DNA was
intact and fairly abundant (fig. 2). There
was no need to dilute the DNA and there
were no additional steps to take to
increase DNA abundance. After isolating
the DNA, the target was amplified using
PCR amplification.
Figure 2. Agarose gel electrophoresis of total
genomic algal DNA. Gel 3, lane 7. Lane 2
contains the DNA ladder
PCR amplification: The PCR
amplification was a success, using
agarose gel electrophoresis. In the gel,
there was a single band that was slender
(fig. 3). The segment of DNA that was
amplified was the tufA gene which is a
common gene in all green algae.
Figure 3. (below) Agarose gel
electrophoresis of amplified PCR
product which was the tufA gene.
Gel 1, in the lane marked with an
arrow.
Gene cloning: Once the PCR product
was placed into the plasmid of E. coli,
100 ul of the cells were placed on a plate
containing X-gal and ampicillin. The
blue colonies are blue because they make
a B-galactosidase enzyme that helps the
cells metabolize the X-gal. The only way
to acquire the enzyme is if they have the
Bgalactosidase gene. If the vector insert
is present, it will intercept the
Bgalactosidase gene which stops the
Bgalactosidase enzyme from being made
resulting in the white colored colonies.
The colonies that are blue do not contain
the vector insert, whereas the white
colonies contain the plasmid with the
inserted PCR product. There were a total
of 26 blue colonies and 74 white colonies
(fig. 4).
Figure 4. E. coli colonies. The white
colonies indicate that the PCR insert was
incorporated into the plasmid, and
transformed into the bacteria. The blue
colonies indicate that the PCR insert was not
incorporated into the plasmid.
4. Plasmid purification: Unfortunately
the plasmid from my specific sample
did not contain the expected gene,
however Nicholas Cmaylo and Cara
James both utilized the same
specimen and did have results. The
plasmid containing the gene is about
4,000 base pairs long (fig. 5).
Figure 5. (A) The DNA ladder used,
showing the amount of base pairs (bp) per
band level. (B) EcoRI gel plasmid
purification. Gel 2 Lane 3. (C) EcoRI gel
plasmid purification. Gel 1 Lane 7 labeled
with red arrow.
Sequence analysis of specimen (KW19BJG): The sequence of the original sample (KW19BJG)
confirmed that it was indeed a green algae. Using several sequences, the sequence of KW19BJG
was compared with the other tufA gene protein sequences provided by Professors Kerri Warren and
Tara Hagedorn (fig. 5).
Figure 5. Phylogenetic tree comparing the tufA gene protein sequences of several different species with the
original sample (KW19BJG).
The nucleotide BLAST results sent back a large quantity of sequences that the original specimen
was most closely related to. The number one sequence had an identical percentage of 99% and it
was Ulva sp. BER-2007 which doesn’t indicate the species name that the sequence belongs to.
However the most closely related sequence that had a species name associated with it was Ulva
compressa which had an identical percentage of 99% as well.
5. The nucleotide sequence of sample KW19BJG was compared to the sequences of two genetically
similar species of green algae deriving from nucleotide BLAST, two less similar species that are
common species found in this area, and two species of green algae that were found in the list of
sequences provided on bridges (fig. 6). The two species from the bridges list were chosen arbitrarily,
while the two less similar species were chosen based upon appearance. Ulva compressa is a tubular
type of sea lettuce whereas Ulva lactuca is a flat, more traditional type of sea lettuce.
Figure 6. Phylogenetic tree comparing the tufA gene nucleotide sequences of
several species of Ulva with the original sample (KW19BJG).
Discussion:
Using phylogenetic trees, KW19BJG was narrowed down to the Ulva compressa
clade. The clade contains two previously unknown species, Ulva sp. BER-2007 B125hi1 and
B25sm12, the former being the closest related species. The closest related species was found from a
sample that was isolated from the red alga Chondrus crispus collected from Sidmouth, South Devon,
England (Juliet Brodie, personal communication, November 19, 2014). Therefore, it is unlikely that
they are the exact same species. Using various reasons for process of elimination, it is determined
not to be any of the other species. Firstly, the location of the sampling site, being Narragansett Bay,
indicates that the specimen has to be native to the Atlantic Ocean. Secondly, through characterizing
the organism, dichotomous keys narrowed down the possibilities to Ulva fenestrata, Ulva fasciata
and Ulva lactuca. Using nucleotide sequence blasting, the most closely related species was one that
did not have a species name, as it was recently discovered: Ulva sp. BER-2007. It is most likely not
Ulva fenestrata because that is a pacific species of sea lettuce, which decreases the likelihood of it
being the mystery specimen; while Ulva fasciata and Ulva lactuca are not identical enough to the
sequence which makes either of them being the same species impossible. This leaves Ulva sp. BER-
2007 which is 99% identical to specimen KW19BJG. Therefore, this could represent an unidentified
species, but further testing with other molecular markers is required to confirm this. Without any
further testing using other genetic markers, such as the rbcL gene, the only conclusive evidence is
that the specimen is located within the Ulva compressa clade.
6. References
1. Guiry, M. D. & Guiry, G.M. 2014. AlgaeBase. World-wide electronic publication,
National University of Ireland, Galway. http://www.algaebase.org; searched on 09
November 2014.
2. Hofmann, L. C., Nettleton, J. C., Neefus, C. D. & Mathieson, C. Arthur. 2010. Cryptic
diversity of Ulva (Ulvales, Chlorophyta) in the Great Bay Estuarine System (Atlantic
USA): introduced and indigenous distromatic species, European Journal of Phycology,
45:3, 230-239
3. Rinkel, B. E., Hayes, P., Gueidan, C. & Brodie, J. 2012. a molecular phylogeny of
acrochaete and other endophytic green algae (ulvales, chlorophyta)1. J.
Phycol. 48:1020-7.
4. Saunders, G. W. 2005. Applying DNA barcoding to red macroalgae: a preliminary
appraisal holds promise for future applications Phil. Trans. R. Soc. B vol. 360 no. 1462
1879-1888
5. Warren, K. & Hagedorn, T. 2014. Lab handouts. This includes the: DNA Isolation,
Agarose Gel Electrophoresis, PCR, Bacteria plasmid cloning and transformation,
Bacterial colonies, plasmid DNA isolation, analyzing plasmid DNA and the
bioinformatics lab handouts.
6. Watson, D. & Norton, T. 1985. Dietary preferences of the common periwinkle,
Littorina littorea (L.). Journal of Experimental Marine Biology and Ecology.