1) The study aimed to determine environmental sources of variation in reproductive lifespan using genetically identical fruit fly lines. 2) While the lines were genetically identical, substantial variation was found between individuals' reproductive lifespans. 3) The study compared differences between treated and untreated lines, infected and cured lines, and results from different experimental sections, but no single environmental factor consistently explained the observed variation.
A lot of sequence data are getting accumulated with the increase in affordability to technology coupled with decreasing cost. But 'Pangenome' concept could help in efficient understanding and thereby practical utilization of sequence data
1) The study found Extended Spectrum Beta-Lactamase (ESBL) antibiotic resistant bacteria on packaged fruit samples, indicating that unwashed fruit can be a vector for these bacteria to enter the human food chain.
2) Of the 58 fruit samples tested, 10.3% of isolated bacteria were found to be ESBL producers carrying genes such as TEM, SHV, and CTXM that code for beta-lactamase enzymes which break down beta-lactam antibiotics.
3) Specifically, samples of strawberries, apples, and red grapes were found to contain ESBL bacteria carrying TEM, SHV, and CTXM genes, showing that fresh produce can be a source
This document describes the development of a multiplex PCR assay targeting the cgcA gene, which encodes a diguanylate cyclase, to differentiate between species within the genus Cronobacter. Analysis of 12 Cronobacter genomes identified 7 conserved diguanylate cyclase-encoding genes, one of which, cgcA, showed species-specific divergence that matched known phylogenetic relationships between Cronobacter species. Primers were designed for this gene and tested in a multiplex PCR assay on 305 Cronobacter isolates representing 6 species. The assay correctly identified the species of all isolates tested and did not identify any of 20 non-Cronobacter species, demonstrating high specificity and sensitivity for rapid identification of Cronobacter.
Elucidating changes in gene expression in Tryp susceptible and resistant cattle during progression of tryp infection using Affymetrix gene expression Micro arrays
characterization of FQ Non-susceptible S. Pyogenescamilomesa22
The aim of this study was to investigate the frequency, mechanism, and epidemiological association of FQ non susceptibility in S.pyogenes during 2011 and 2016 from Shanghai, China.
identification and characterization of FQ-non-susceptable S. Pyogenescamilomesa22
The aim of this study was to investigate the frequency, mechanism, and epidemiological association of FQ non susceptibility in S.pyogenes during 2011 and 2016 from Shanghai, China.
Chasing a Unicorn for Model Host-Microbiome-Systems Jonathan Eisen
This document summarizes a presentation given by Jonathan Eisen on his research into the rice microbiome. Some key points:
- Eisen studies how the rice plant and its genotype influence the microbial communities that colonize its roots (rhizosphere, rhizoplane, endosphere).
- In greenhouse experiments, rice genotype explained a significant amount of variation in root microbial communities. Certain microbes were enriched or depleted across root compartments.
- Field experiments also found the rice cultivation site and farming practices influenced root microbiome composition.
- Dynamics studies showed microbes rapidly colonize roots within 24 hours of transplantation, with shifts in community composition over time.
- Network analysis revealed microbial modules involved in methane cycling that varied across
A lot of sequence data are getting accumulated with the increase in affordability to technology coupled with decreasing cost. But 'Pangenome' concept could help in efficient understanding and thereby practical utilization of sequence data
1) The study found Extended Spectrum Beta-Lactamase (ESBL) antibiotic resistant bacteria on packaged fruit samples, indicating that unwashed fruit can be a vector for these bacteria to enter the human food chain.
2) Of the 58 fruit samples tested, 10.3% of isolated bacteria were found to be ESBL producers carrying genes such as TEM, SHV, and CTXM that code for beta-lactamase enzymes which break down beta-lactam antibiotics.
3) Specifically, samples of strawberries, apples, and red grapes were found to contain ESBL bacteria carrying TEM, SHV, and CTXM genes, showing that fresh produce can be a source
This document describes the development of a multiplex PCR assay targeting the cgcA gene, which encodes a diguanylate cyclase, to differentiate between species within the genus Cronobacter. Analysis of 12 Cronobacter genomes identified 7 conserved diguanylate cyclase-encoding genes, one of which, cgcA, showed species-specific divergence that matched known phylogenetic relationships between Cronobacter species. Primers were designed for this gene and tested in a multiplex PCR assay on 305 Cronobacter isolates representing 6 species. The assay correctly identified the species of all isolates tested and did not identify any of 20 non-Cronobacter species, demonstrating high specificity and sensitivity for rapid identification of Cronobacter.
Elucidating changes in gene expression in Tryp susceptible and resistant cattle during progression of tryp infection using Affymetrix gene expression Micro arrays
characterization of FQ Non-susceptible S. Pyogenescamilomesa22
The aim of this study was to investigate the frequency, mechanism, and epidemiological association of FQ non susceptibility in S.pyogenes during 2011 and 2016 from Shanghai, China.
identification and characterization of FQ-non-susceptable S. Pyogenescamilomesa22
The aim of this study was to investigate the frequency, mechanism, and epidemiological association of FQ non susceptibility in S.pyogenes during 2011 and 2016 from Shanghai, China.
Chasing a Unicorn for Model Host-Microbiome-Systems Jonathan Eisen
This document summarizes a presentation given by Jonathan Eisen on his research into the rice microbiome. Some key points:
- Eisen studies how the rice plant and its genotype influence the microbial communities that colonize its roots (rhizosphere, rhizoplane, endosphere).
- In greenhouse experiments, rice genotype explained a significant amount of variation in root microbial communities. Certain microbes were enriched or depleted across root compartments.
- Field experiments also found the rice cultivation site and farming practices influenced root microbiome composition.
- Dynamics studies showed microbes rapidly colonize roots within 24 hours of transplantation, with shifts in community composition over time.
- Network analysis revealed microbial modules involved in methane cycling that varied across
This study investigated the nasopharyngeal microbiome of 45 Malawian children who carried Streptococcus pneumoniae. The microbiome was characterized using 16S rRNA gene sequencing. The results showed a shift in microbial diversity with HIV infection, with Moraxella and Streptococcus influencing diversity. Multiple carriage of pneumococcal serotypes did not significantly impact microbial diversity. The major limitation was that only pneumococcal carriers were studied. Further research on non-carriers is recommended to better understand implications on pneumococcal colonization.
Researchers used zinc-finger nucleases (ZFNs) to generate knockout rats by targeting three genes - green fluorescent protein (GFP), Immunoglobulin M (IgM), and Rab38. ZFNs were microinjected into rat embryos to induce mutations in the target genes. Of 295 founder animals screened, 35 (12%) contained targeted mutations, including full knockout of the GFP transgene in some animals. Mutations were transmitted to offspring, demonstrating the ability of ZFNs to disrupt genes and induce heritable mutations in the rat genome. This technique allows for targeted genetic modification of the rat, an important model for studying human disease.
The influence of reduced oxygen availability on gene expression in laboratory...Santhi Devasundaram
Virtually all dormant
models against tuberculosis tested in animals used laboratory strain H37Rv or Erdman strain. But major
outbreaks of tuberculosis (TB) occur with the strains that have widely different genotypes and phenotypes
compared to H37Rv. In this study, we used a custom oligonucleotide microarray to determine the overall
transcriptional response of laboratory strain (H37Rv) and most prevalent clinical strains (S7 and S10) of
M. tuberculosis from South India to hypoxia.
EcoTILLING is a method for identifying natural mutations and polymorphisms in populations using TILLING techniques. It allows for the detection of point mutations and small insertions/deletions in DNA in a high-throughput but low-cost manner using gel electrophoresis. EcoTILLING has been used to identify allelic variants in genes related to powdery mildew resistance (mlo and Mla) in barley. It has also been applied to identify natural variation in 196 Arabidopsis ecotypes and 41 cottonwood trees. The method shows potential for discovering alleles relevant to salt tolerance in rice varieties and resistance to potato virus Y in pepper varieties.
When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.
Deleterious Alleles in maize, talk from PAGXXIIjrossibarra
This document discusses deleterious alleles in maize and their implications. It finds that:
1) Maize accumulates around 90 new mutations per meiosis, most of which are deleterious. Studies have found many new mutations of large effect in maize.
2) Genes show signatures of purifying selection, with deleterious variants found at lower frequencies compared to non-genic regions. These deleterious variants likely contribute to inbreeding depression.
3) Analysis of a panel of 282 maize inbreds found that genes containing deleterious alleles were enriched in genome-wide association studies hits for traits related to heterosis.
4) The patterns observed are consistent with a model of complementation playing
Deploying genome sequence information for pigeonpea improvementICARDA
This document discusses the deployment of genome sequencing information to improve pigeonpea, an important food legume crop. It outlines constraints on pigeonpea production including diseases and loss of genetic diversity. The author details efforts to use specialized genetic stocks, whole genome resequencing, and phenotyping to understand genetic diversity and identify alleles controlling traits like flowering time, shattering, and ligule development. Marker-trait associations have been found that can enable marker-assisted breeding to improve yield and other important traits. Overall, harnessing genetic diversity and the genome sequence is facilitating genetic gains in pigeonpea.
1) Researchers inoculated soil microcosms with switchgrass and tracked changes in microbial communities over 62 transfers.
2) Initial diversity decreased from 30 phyla to mainly Firmicutes (>99%) despite rare OTUs accounting for most diversity.
3) A stable yet specialized community developed, maintaining high species diversity among closely related organisms.
2015. Patrik Schnable. Trait associated SNPs provide insights into heterosis...FOODCROPS
1) Trait-associated SNPs provide insights into the genetic basis of heterosis or hybrid vigor in maize. GWAS identified over 1,000 associations between SNPs and seven yield-related traits.
2) Including dominance effects in models explains more of the observed heterosis and genetic variation than additive effects alone. The ratio of SNPs exhibiting positive versus negative dominance is correlated with heterosis for a given trait.
3) Field-based phenotyping using sensors on robots and UAVs can study dynamic traits influenced by environment and GxE interactions, overcoming limitations of endpoint traits in controlled conditions. This will improve predictive models for plant breeding and variety recommendations.
Fast forward genetic mapping provides candidate genes for resistance to fusar...ICRISAT
This document summarizes a study that used a combination of whole genome sequencing and bulk segregant analysis to identify candidate genes for fusarium wilt and sterility mosaic disease resistance in pigeonpea. Researchers developed resistant and susceptible bulks from a mapping population and sequenced these along with a resistant parent. They identified over 35,000 SNPs between the bulks and found four candidate genes on two chromosomes associated with initiating defense mechanisms against fungal and viral diseases. This approach combined fast genetic mapping with genome sequencing to efficiently identify targeted genomic regions controlling important traits.
This study investigated antibiotic resistance in urinary tract E. coli isolates from hospitalized patients in India. Urine samples were collected from 73 patients with urinary tract infections and E. coli was isolated from 35 samples (48%). The E. coli isolates showed high resistance to novobiocin, vancomycin, and co-trimaxazole. 80% of isolates were biofilm producers, with over 50% producing strong biofilms. 51% of isolates were beta-lactamase producers. The results indicate that biofilm-producing E. coli strains with beta-lactamase activity exhibited the highest antibiotic resistance.
Phage adhere more strongly to mucus layers than surrounding environments across diverse animal species. In vitro experiments show that phage adhere specifically to mucin glycoproteins in mucus via interactions between Ig-like domains on phage capsids and glycan residues on mucins. Pretreating mucus-producing cells with phage reduces subsequent bacterial attachment and infection, protecting the underlying epithelium. The presence of Ig-like protein domains in phages from many environments suggests a widespread symbiotic relationship between phages and metazoans, whereby phage adherence to mucus provides a non-host-derived antimicrobial defense of mucosal surfaces.
This document summarizes a study that analyzed samples from infants, children, and adults in Kolkata, India with acute gastroenteritis between 2007-2009. The study found 5 novel genetic variants and 12 recombinant strains of human astroviruses infecting the patients. Analysis of two conserved genomic regions, ORF1a and ORF2, showed that the recombinant strains contained ORF1a from genotypes G2 or G8, and ORF2 from genotypes G1, G2, or G3. The predominant recombinants detected were HAstV_G8_G1 (n=10) and HAstV_G2_G3 (n=1).
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIjrossibarra
1) The document discusses how population bottlenecks during domestication can reduce genetic diversity and influence patterns of variation across the genome.
2) Bottlenecks are shown to increase the number of rare variants, affect site frequency spectra, and influence the effects of purifying selection. They can also mimic signals of positive selection.
3) Studies of maize domestication estimate a weaker bottleneck than previously thought, with rapid recent population growth increasing diversity from resequencing data. However, selection still reduces diversity more in genic regions relative to intergenic regions.
AMR Collaborative Grants at the University of Bristolwarwick_amr
The document discusses various topics relating to antibiotic resistance (AMR) transmission in real world settings. It mentions that dairy farming uses cephalosporins extensively and explores potential links between this usage and cephalosporin resistant E. coli infections in humans. The document also discusses using proteomics to identify mechanisms of antibiotic resistance and finding new antibiotic lead compounds through comparative studies.
This document describes a study that used profile hidden Markov models (HMMs) to identify genes that differentiate pathogenic and non-pathogenic Pseudomonas isolates. The researchers examined 27 Pseudomonas isolates and identified three genes with significantly different score distributions between pathogenic and non-pathogenic isolates. These three genes - 4-aminobutyrate aminotransferase, outer membrane efflux protein, and bacterioferritin - correctly discriminated between pathogenic and non-pathogenic isolates in the test group and may help classify new organisms. The profile HMM method captures amino acid frequency and indel information to provide a score indicating how mutations might affect gene function.
This document summarizes a study that used multilocus sequence typing (MLST) to analyze the evolutionary history and origins of major methicillin-resistant Staphylococcus aureus (MRSA) clones. The researchers analyzed 912 MRSA and methicillin-susceptible S. aureus isolates from 20 countries. They identified 11 major MRSA clones within 5 groups of related genotypes. Analysis of the methicillin resistance genes and the most parsimonious patterns of descent identified the likely ancestral genotype and MSSA progenitor of each major MRSA clone. Major MRSA clones have repeatedly emerged from successful epidemic MSSA strains through acquisition of the methicillin resistance gene. Isolates with decreased susceptibility to vancomycin,
This document summarizes a study on the evolutionary dynamics of human influenza B virus. The study analyzed complete genome sequences of influenza B viruses collected over 30 years to determine rates of evolution, patterns of reassortment between gene segments, and evidence of natural selection. Key findings include:
1. Influenza B viruses evolve at lower rates than influenza A viruses but the hemagglutinin (HA) gene evolves more rapidly, suggesting positive selection through antigenic drift.
2. Analysis of phylogenetic patterns revealed sporadic reassortment events between gene segments over the study period.
3. Sites under positive selection were detected in the HA and neuraminidase (NA) genes, which encode surface proteins targeted by
This document outlines the schedule and requirements for a genomics course consisting of 9 sessions over March and May. Students are required to attend all sessions and give one 20-minute seminar and write one essay. Seminars will be 15% of the final grade and essays will also be 15%, with a final exam making up the remaining 70% of the grade. Topics for the seminars and essays will be assigned.
Alpha-1 Antitrypsin (α-1 AT) deficiency is a common genetic disorder that affects 1 in 2,000 individuals in the USA. Additionally, over 20 million people have been identified as carriers for this genetic disorder. In severe cases, α-1 AT deficiency can cause substantial lung and liver damage, which if left untreated could result in death and there are no current available treatments. Alpha-1 protein is produced in the liver, travels in the bloodstream and utilized in the lungs to protect healthy lung tissue from harmful destruction by elastase. A common single amino acid substitution, located at E342K (ATZ) was identified in α-1 AT deficient humans. When this specific mutation occurs two phenotypes can result: 1) ATZ can polymerize in the liver causing cellular toxicity 2) inhibits alpha-1 antitrypsin from inhibiting elastase which can result in lung disease. Currently; little is known about the cellular mechanisms that clear the accumulated proteins in the liver. Therefore, an investigative study utilizing C. elegans model of ATZ was performed in order to help determine the cellular mechanisms that dispose of accumulated proteins. Specifically RNA interference was utilized to knockdown expression of specific genes. This investigation examined genes involved in the heat-shock pathway (HSP), unfolded protein response (UPR), and insulin signaling pathway (IS). Phenotypic analysis including: embryonic lethality, protein aggregation expression, and longevity, was completed after knockdown of genes to determine effect on ATZ accumulation. Currently with our preliminary data suggests that the heat-shack pathway may play a role in ATZ accumulation. Determining the mechanism of protein accumulation in the investigation of C. elegans may lead to possible drug targets and therefore the development of a treatment which may alleviate those diagnosed with this disorder.
This study investigated the nasopharyngeal microbiome of 45 Malawian children who carried Streptococcus pneumoniae. The microbiome was characterized using 16S rRNA gene sequencing. The results showed a shift in microbial diversity with HIV infection, with Moraxella and Streptococcus influencing diversity. Multiple carriage of pneumococcal serotypes did not significantly impact microbial diversity. The major limitation was that only pneumococcal carriers were studied. Further research on non-carriers is recommended to better understand implications on pneumococcal colonization.
Researchers used zinc-finger nucleases (ZFNs) to generate knockout rats by targeting three genes - green fluorescent protein (GFP), Immunoglobulin M (IgM), and Rab38. ZFNs were microinjected into rat embryos to induce mutations in the target genes. Of 295 founder animals screened, 35 (12%) contained targeted mutations, including full knockout of the GFP transgene in some animals. Mutations were transmitted to offspring, demonstrating the ability of ZFNs to disrupt genes and induce heritable mutations in the rat genome. This technique allows for targeted genetic modification of the rat, an important model for studying human disease.
The influence of reduced oxygen availability on gene expression in laboratory...Santhi Devasundaram
Virtually all dormant
models against tuberculosis tested in animals used laboratory strain H37Rv or Erdman strain. But major
outbreaks of tuberculosis (TB) occur with the strains that have widely different genotypes and phenotypes
compared to H37Rv. In this study, we used a custom oligonucleotide microarray to determine the overall
transcriptional response of laboratory strain (H37Rv) and most prevalent clinical strains (S7 and S10) of
M. tuberculosis from South India to hypoxia.
EcoTILLING is a method for identifying natural mutations and polymorphisms in populations using TILLING techniques. It allows for the detection of point mutations and small insertions/deletions in DNA in a high-throughput but low-cost manner using gel electrophoresis. EcoTILLING has been used to identify allelic variants in genes related to powdery mildew resistance (mlo and Mla) in barley. It has also been applied to identify natural variation in 196 Arabidopsis ecotypes and 41 cottonwood trees. The method shows potential for discovering alleles relevant to salt tolerance in rice varieties and resistance to potato virus Y in pepper varieties.
When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.
Deleterious Alleles in maize, talk from PAGXXIIjrossibarra
This document discusses deleterious alleles in maize and their implications. It finds that:
1) Maize accumulates around 90 new mutations per meiosis, most of which are deleterious. Studies have found many new mutations of large effect in maize.
2) Genes show signatures of purifying selection, with deleterious variants found at lower frequencies compared to non-genic regions. These deleterious variants likely contribute to inbreeding depression.
3) Analysis of a panel of 282 maize inbreds found that genes containing deleterious alleles were enriched in genome-wide association studies hits for traits related to heterosis.
4) The patterns observed are consistent with a model of complementation playing
Deploying genome sequence information for pigeonpea improvementICARDA
This document discusses the deployment of genome sequencing information to improve pigeonpea, an important food legume crop. It outlines constraints on pigeonpea production including diseases and loss of genetic diversity. The author details efforts to use specialized genetic stocks, whole genome resequencing, and phenotyping to understand genetic diversity and identify alleles controlling traits like flowering time, shattering, and ligule development. Marker-trait associations have been found that can enable marker-assisted breeding to improve yield and other important traits. Overall, harnessing genetic diversity and the genome sequence is facilitating genetic gains in pigeonpea.
1) Researchers inoculated soil microcosms with switchgrass and tracked changes in microbial communities over 62 transfers.
2) Initial diversity decreased from 30 phyla to mainly Firmicutes (>99%) despite rare OTUs accounting for most diversity.
3) A stable yet specialized community developed, maintaining high species diversity among closely related organisms.
2015. Patrik Schnable. Trait associated SNPs provide insights into heterosis...FOODCROPS
1) Trait-associated SNPs provide insights into the genetic basis of heterosis or hybrid vigor in maize. GWAS identified over 1,000 associations between SNPs and seven yield-related traits.
2) Including dominance effects in models explains more of the observed heterosis and genetic variation than additive effects alone. The ratio of SNPs exhibiting positive versus negative dominance is correlated with heterosis for a given trait.
3) Field-based phenotyping using sensors on robots and UAVs can study dynamic traits influenced by environment and GxE interactions, overcoming limitations of endpoint traits in controlled conditions. This will improve predictive models for plant breeding and variety recommendations.
Fast forward genetic mapping provides candidate genes for resistance to fusar...ICRISAT
This document summarizes a study that used a combination of whole genome sequencing and bulk segregant analysis to identify candidate genes for fusarium wilt and sterility mosaic disease resistance in pigeonpea. Researchers developed resistant and susceptible bulks from a mapping population and sequenced these along with a resistant parent. They identified over 35,000 SNPs between the bulks and found four candidate genes on two chromosomes associated with initiating defense mechanisms against fungal and viral diseases. This approach combined fast genetic mapping with genome sequencing to efficiently identify targeted genomic regions controlling important traits.
This study investigated antibiotic resistance in urinary tract E. coli isolates from hospitalized patients in India. Urine samples were collected from 73 patients with urinary tract infections and E. coli was isolated from 35 samples (48%). The E. coli isolates showed high resistance to novobiocin, vancomycin, and co-trimaxazole. 80% of isolates were biofilm producers, with over 50% producing strong biofilms. 51% of isolates were beta-lactamase producers. The results indicate that biofilm-producing E. coli strains with beta-lactamase activity exhibited the highest antibiotic resistance.
Phage adhere more strongly to mucus layers than surrounding environments across diverse animal species. In vitro experiments show that phage adhere specifically to mucin glycoproteins in mucus via interactions between Ig-like domains on phage capsids and glycan residues on mucins. Pretreating mucus-producing cells with phage reduces subsequent bacterial attachment and infection, protecting the underlying epithelium. The presence of Ig-like protein domains in phages from many environments suggests a widespread symbiotic relationship between phages and metazoans, whereby phage adherence to mucus provides a non-host-derived antimicrobial defense of mucosal surfaces.
This document summarizes a study that analyzed samples from infants, children, and adults in Kolkata, India with acute gastroenteritis between 2007-2009. The study found 5 novel genetic variants and 12 recombinant strains of human astroviruses infecting the patients. Analysis of two conserved genomic regions, ORF1a and ORF2, showed that the recombinant strains contained ORF1a from genotypes G2 or G8, and ORF2 from genotypes G1, G2, or G3. The predominant recombinants detected were HAstV_G8_G1 (n=10) and HAstV_G2_G3 (n=1).
Bottlenecks -- some ramblings and a bit of data from maize PAGXXIIjrossibarra
1) The document discusses how population bottlenecks during domestication can reduce genetic diversity and influence patterns of variation across the genome.
2) Bottlenecks are shown to increase the number of rare variants, affect site frequency spectra, and influence the effects of purifying selection. They can also mimic signals of positive selection.
3) Studies of maize domestication estimate a weaker bottleneck than previously thought, with rapid recent population growth increasing diversity from resequencing data. However, selection still reduces diversity more in genic regions relative to intergenic regions.
AMR Collaborative Grants at the University of Bristolwarwick_amr
The document discusses various topics relating to antibiotic resistance (AMR) transmission in real world settings. It mentions that dairy farming uses cephalosporins extensively and explores potential links between this usage and cephalosporin resistant E. coli infections in humans. The document also discusses using proteomics to identify mechanisms of antibiotic resistance and finding new antibiotic lead compounds through comparative studies.
This document describes a study that used profile hidden Markov models (HMMs) to identify genes that differentiate pathogenic and non-pathogenic Pseudomonas isolates. The researchers examined 27 Pseudomonas isolates and identified three genes with significantly different score distributions between pathogenic and non-pathogenic isolates. These three genes - 4-aminobutyrate aminotransferase, outer membrane efflux protein, and bacterioferritin - correctly discriminated between pathogenic and non-pathogenic isolates in the test group and may help classify new organisms. The profile HMM method captures amino acid frequency and indel information to provide a score indicating how mutations might affect gene function.
This document summarizes a study that used multilocus sequence typing (MLST) to analyze the evolutionary history and origins of major methicillin-resistant Staphylococcus aureus (MRSA) clones. The researchers analyzed 912 MRSA and methicillin-susceptible S. aureus isolates from 20 countries. They identified 11 major MRSA clones within 5 groups of related genotypes. Analysis of the methicillin resistance genes and the most parsimonious patterns of descent identified the likely ancestral genotype and MSSA progenitor of each major MRSA clone. Major MRSA clones have repeatedly emerged from successful epidemic MSSA strains through acquisition of the methicillin resistance gene. Isolates with decreased susceptibility to vancomycin,
This document summarizes a study on the evolutionary dynamics of human influenza B virus. The study analyzed complete genome sequences of influenza B viruses collected over 30 years to determine rates of evolution, patterns of reassortment between gene segments, and evidence of natural selection. Key findings include:
1. Influenza B viruses evolve at lower rates than influenza A viruses but the hemagglutinin (HA) gene evolves more rapidly, suggesting positive selection through antigenic drift.
2. Analysis of phylogenetic patterns revealed sporadic reassortment events between gene segments over the study period.
3. Sites under positive selection were detected in the HA and neuraminidase (NA) genes, which encode surface proteins targeted by
This document outlines the schedule and requirements for a genomics course consisting of 9 sessions over March and May. Students are required to attend all sessions and give one 20-minute seminar and write one essay. Seminars will be 15% of the final grade and essays will also be 15%, with a final exam making up the remaining 70% of the grade. Topics for the seminars and essays will be assigned.
Alpha-1 Antitrypsin (α-1 AT) deficiency is a common genetic disorder that affects 1 in 2,000 individuals in the USA. Additionally, over 20 million people have been identified as carriers for this genetic disorder. In severe cases, α-1 AT deficiency can cause substantial lung and liver damage, which if left untreated could result in death and there are no current available treatments. Alpha-1 protein is produced in the liver, travels in the bloodstream and utilized in the lungs to protect healthy lung tissue from harmful destruction by elastase. A common single amino acid substitution, located at E342K (ATZ) was identified in α-1 AT deficient humans. When this specific mutation occurs two phenotypes can result: 1) ATZ can polymerize in the liver causing cellular toxicity 2) inhibits alpha-1 antitrypsin from inhibiting elastase which can result in lung disease. Currently; little is known about the cellular mechanisms that clear the accumulated proteins in the liver. Therefore, an investigative study utilizing C. elegans model of ATZ was performed in order to help determine the cellular mechanisms that dispose of accumulated proteins. Specifically RNA interference was utilized to knockdown expression of specific genes. This investigation examined genes involved in the heat-shock pathway (HSP), unfolded protein response (UPR), and insulin signaling pathway (IS). Phenotypic analysis including: embryonic lethality, protein aggregation expression, and longevity, was completed after knockdown of genes to determine effect on ATZ accumulation. Currently with our preliminary data suggests that the heat-shack pathway may play a role in ATZ accumulation. Determining the mechanism of protein accumulation in the investigation of C. elegans may lead to possible drug targets and therefore the development of a treatment which may alleviate those diagnosed with this disorder.
The document summarizes an experiment that studied the effects of natural selection on core promoter regions (CPRs) of gene regulatory regions in Drosophila melanogaster. Researchers obtained sequence and transcriptome data from 29 lines of D. melanogaster from the Drosophila Genetic Reference Panel. They analyzed single nucleotide polymorphisms, gene expression levels, and linkage between CPRs and surrounding regions. The results showed that nucleotide changes in CPRs caused gene expression variation and were influenced by both positive and balancing selection. Sex-biased gene expression was also common but CPRs were not dependent on sex-specific expression. In conclusion, CPRs are a source of natural selection and gene expression variation within populations of D. melanogaster.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
An Experimental Study of Natural Selection and Relative Fitness .docxamrit47
An Experimental Study of Natural Selection and Relative Fitness
Introduction (2/3 or 2/4)
Biological evolution is a fundamental concept in biology that helps us understand the natural world i.e., the history and diversity of life on Earth. At the most basic definition, biological evolution is descent with modification. That is, subsequent generations change over time. Biological evolution can be subdivided into microevolution and macroevolution. Microevolution involves small-scale changes in allele frequencies in a population from one generation to the next. Macroevolution encompasses large-scale changes that produces different species from common ancestors over many generations. Since macroevolution requires an extensive period of time (most are beyond human lifetimes), macroevolutionary studies are largely observational. In other words, we cannot create experiments to test macroevolutionary hypotheses. Instead, we observe patterns and infer the processes from those patterns. Alternatively, microevolution studies require a relatively short period of time such that hypotheses testing can be observational or experimentational (we can create experiments).
Performing microevolution experiments requires an understanding of the Hardy-
Weinberg equilibrium principle. Hardy-Weinberg equilibrium is a simple mathematical model
that assumes a single population’s gene pool does not change in frequency from one generation
to the next. The model is represented by two algebraic equations: the allele frequency equation (p
+ q = 1) and the genotype frequency equation (p2 + 2pq + q2 = 1). To illustrate these equations,
let’s consider a simple dominant/recessive relationship of a character (mouse fur color,
represented by the letter “b”) with two traits (brown and white). This means we will have two
alleles and three genotypes. The lower-case b allele represents the white fur trait and the upper-
case B allele represents the brown fur trait, while the white fur phenotype is represented by the
ww genotype and the brown fur phenotype is represented by the WW and Ww genotypes. With
respect to the frequencies, f(w) is represented by q and f(W) is represented by p, while ww is 22
represented by q , Ww is represented by pq and WW is represented by p . This lab consists of using these equations to determine whether microevolution has occurred, so make sure you understand them.
In simpler terms, this means that if 60% of a population of mice have the white fur trait and 40% have the brown fur trait, this proportion will be the same in the next generation regardless of population size. There may be more individuals in the next generation, but the ratio remains the same (three white fur traits to two brown fur traits). As a principle, this expectation makes sense. However, there are mechanisms of evolutionary change that violate this Hardy- Weinberg equilibrium principle that need to be understood.
There are five recognized mechanisms that disrupt the Ha.
This document summarizes the findings of a comparative genomic analysis of 627 bacteriophages (viruses that infect bacteria) that infect Mycobacterium smegmatis. The analysis revealed dramatic variation in genome structures and relationships among the phages. The phages were grouped into 20 clusters and 8 singletons based on genome similarities. However, the degree of genetic diversity and connectivity to other phages varied greatly between clusters. Some clusters were discrete with few shared genes, while others shared many genes. This indicates the phage population spans a continuum of relationships rather than representing discrete populations. The mosaic genomic architectures of many phages complicate classification. Overall, the analysis revealed a highly diverse global phage population with unequal representation of
The document discusses linkage and crossing over in genetics. It defines linkage as two or more genes staying together on the same chromosome during inheritance. Crossing over refers to the exchange of genetic material between non-sister chromatids during meiosis. There are two main types of linkage - complete linkage where no crossing over occurs, and incomplete linkage where crossing over does occur, resulting in both parental and recombinant offspring types. The document also outlines the mechanism of crossing over and factors that can influence its frequency.
Understanding the origin and evolution of the eukaryotic cell and the full diversity of eukaryotes is relevant to many biological disciplines.
However, our current understanding of eukaryotic genomes is extremely biased, leading to a skewed view of eukaryotic biology.
We argue that a phylogeny-driven initiative to cover the full eukaryotic diversity is needed to overcome this bias.
•
◦There is an important bias in eukaryotic knowledge, affecting cultures and genomes.
Eukaryotic genomics are biased towards multicellular organisms and their parasites.
◦A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.
◦We propose to sequence neglected cultures and increase culturing efforts.
◦Single-cell genomics should be embraced as a tool to explore eukaryotic diversity
Comparing the Amount and Quality of Information from Different Sequencing Str...jembrown
This document compares the amount and quality of phylogenetic information from six amniote phylogenomic datasets. It finds that while median support for major relationships is often strong, there is wide variance in support, both for and against known relationships. This suggests a minimum level of systematic error. Support for turtle placement varies the most between datasets, indicating relatively little phylogenetic information about turtles compared to other amniote groups. Overall, the analysis demonstrates that phylogenomic datasets can differ substantially in information content and reliability.
The document discusses the topic of phylogenetics. It begins with definitions of key terms like phylogeny, phylogenetic tree, clade, and orthologous genes. It then provides examples of how phylogenetic methods are used in fields like epidemiology, conservation biology, and pharmaceutical research. The document also discusses choosing appropriate genetic sequences to use in phylogenetic analysis and introduces molecular clock models.
Genomic gene expression changes resulting from Trypanosomiasis: a horizontal study Examining expression changes elucidated by micro arrays in seminal tissues associated with the pathophysiology of Trypanosomiasis during disease progression
Variable transcriptional adaptation between the laboratory (H37Rv) and clinic...Santhi Devasundaram
The remarkable success of M. tuberculosis as a pathogen is largely due to its ability to
persist within the host for long periods. To develop the effective intervention strategies, understanding the biology
of persistence is highly required. Accumulating evidences showed oxygen deprivation (hypoxia) as a potential
stimulus for triggering the transition of M. tuberculosis to a non-replicating persistent state analogous to
latency in vivo. To date, in vitro hypoxia experimental models used the laboratory adapted isolate H37Rv and
very little is known about the behavior of clinical isolates that are involved during disease outbreaks. Hence,
we compared the transcription profiles of H37Rv and two south Indian clinical isolates (S7 and S10) under hypoxia
to find differences in gene expression pattern.
Sarah's INBRE poster updated Aug 11 LL FINAL-2Sarah Sanders
1) Vibrio vulnificus (Vv) is an opportunistic human pathogen found in the Great Bay Estuary (GBE) of New Hampshire. While cases of Vv infection have increased in the Gulf of Maine, there have been no reported cases from GBE strains.
2) The study analyzed 37 Vv isolates from GBE using short read genome sequencing and multilocus sequence typing (MLST). Most isolates contained novel sequence types not in databases, suggesting genetic diversity.
3) Analysis of virulence genes and a phylogenetic marker showed GBE isolates were more similar to environmental strains and different from known pathogenic strains, supporting the hypothesis that GBE strains are non-pathogenic.
This document discusses a study that found significant differences in gene expression variability between knockout and wild-type mice using microarray data from 25 publicly available datasets. The study found that knockouts exhibited either significantly increased or decreased variability compared to wild-types in virtually every dataset analyzed. Examination of the data distributions indicated that these differences were due to broad changes in variability across most genes, rather than being driven by outliers. The findings suggest that changes in gene expression variability due to gene knockouts may have important phenotypic consequences.
The document summarizes a study that used nested PCR and gel electrophoresis to analyze DNA samples from birds in Peru in order to determine the prevalence of avian Plasmodium infection and investigate how climate change may affect infection rates. The results showed bands for the positive control but no bands for the bird samples, likely because few samples were actually infected based on information from collaborators, and differences in sample preparation or protocols may have affected the ability to detect infections. The document discusses limitations and avenues for future investigation.
Isolation and Evaluation of bacteriophages against Salmonella TyphiShubaBalakrishnan
This slides consists of the result of isolation of bacteriophages against Salmonella Typhi and the evaluation of Salmonella Typhi in bioinformatics method which is online based.
1) The document presents a new method for synchronizing proliferating mammalian cells in the G1 phase of the cell cycle using standard optical flow cytometry to separate cells by size.
2) Current methods for synchronizing cells rely on chemical agents that arrest the cell cycle, which can introduce unwanted variables and decouple cell growth from the cell cycle.
3) The new method exploits the correlation between cell size and age, sorting for the smallest cells using light scattering parameters as a proxy for size, which yields a highly purified population of over 90% G1 cells without chemical treatment.
This document discusses an experiment that measured the sublethal effects of antibiosis resistance in two Brachiaria hybrids on two important spittlebug pest species in Colombia. The experiment found that:
1) Nymphal survival of both spittlebug species was significantly lower and development time significantly longer when reared on the resistant hybrids compared to the susceptible genotype.
2) Median survival times of resulting adult spittlebugs did not differ based on whether nymphs were reared on resistant or susceptible plants, but reproductive biology was negatively impacted for adults from nymphs reared on the resistant hybrids.
3) The high nymphal mortality and sublethal effects on resulting adults caused by
1. Aging influences the physiology of all tissues in an organism. Many of the intrinsic and
extrinsic factors that affect function in aging are common to all cells and tissues. The male
reproductive system of the fruit fly, Drosophila melanogaster, offers an attractive model to study
influences of aging because it is not essential to viability and is highly active. It is established that
environmental factors, such as food quality, temperature, and humidity, influence Drosophila fertility.
However, little is known about the extrinsic factors that control reproductive maintenance during
aging. The goal of this project is to determine other environmental sources that cause variation in
reproductive lifespan. To identify these causes of variation, length of fertility was analyzed using
established strains of flies from the Drosophila Genetic Reference Panel (DGRP). The DGRP is a
collection of lines derived from wild caught females that have been inbred until all flies within a line
are genetically identical. This allows little to no genetic variation. This allows for the manipulation of
Wolbachia on the sex chromosomes. Because individuals within a line are genetically identical, it is
expected that any differences between animals in the same line should be due to environmental
effects. Wolbachia is an infection that can be inherited through the sex gene. More specifically, it is a
bacterial infection that can be treated with a simple antibiotic, Tetracycline. Part of the goal of this
experiment will be to se how Wolbachia and treatments for Wolbachia affect the variation of the data.
Of the environmental parameters, culturing conditions were also kept constant, including size and
type of container, food source, and temperature. However, because different individuals performed
experimental manipulations of animals with different equipment at different times of day, variability
could result from those parameters. Preliminary analysis indicates that there is substantial variation
in reproductive lifespan among individual males from the same line. Comparisons of the influences of
specific experimenters, equipment, and time of day will be presented. Environmental factors
identified as regulating reproductive lifespan may also have influences on other aging tissues.
In conclusion, no one environmental factor was found that can explain the variation in reproductive lifespan
of the fruit flies. Further research into other environmental factors (The amount of food in the vial and carbon
dioxide exposure amount) along with an expanded study to include more data points would be the next steps for this
research. Pinpointing the sources of variation in the reproductive lifespan of these genetically similar fly lines could
increase research quality for all research that uses the lines. It can allow for less question about the results that were
found and reduce error. It could also provide insight into how much of a role the environment plays in the life of a
fruit fly. That could then be extrapolated out to hypothesize the effect of the environment on other species, including
humans.
Contribution of experimental assay conditions to the measurement of
reproductive lifespan in Drosophila melanogaster
Mary Lee, Jalen Hickman, Mariah Koehler, Eileen Ramirez, Kiyana Hinton, Nicholas McVay, Autumn Conger, Macy Minix, Ebrima
Jarju, Nicaia Nash, Michelle Giedt, Peter Mirabito, Douglas Harrison
Department of Biology, University of Kentucky, Lexington, KY
Introduction
Conclusion
Results and Discussion
Figure 2: Variation in Fertility Length Between Sections- Variation can be seen between
sections even though the lines are genetically similar, demonstrating that there are environmental factors
affecting the reproductive cycle length. A)The mean for each line was calculated for each section of
students. The means are shown plotted beside each other with each section having its own color bar. B)
The standard deviation for each line was also calculated for each section. Standard deviations were then
graphed beside each other with each section having its own color bar.
Figure 3: Variation by Line of the Reproductive Lifespan Assay
Graphs A and B a strip plot of all of the data that was collected in the experiment. This figure is to show the variation that occurs between the lines of the Drosophila
melanogaster. A strip plot was chosen over a graph with the average because it shows the range and variability. A) Shows the variation in lines and the variation in
treated and untreated lines. B) Show the variation in lines and the variation in the Infected and cured. Both graphs A and B in figure 2 typically show a large amount of
variation no matter the treatment that was received. Graphs C and D show standard deviation, so the spread of the data could be observed. Graph C shows the spread
of the infected and cured flies by line. Graph D shows the spread of the treated and untreated flies by the line. There does not appear to be a significant difference
between the lines or the treatments. It is important to note that the populations vary widely throughout the data.
Each researcher had one station with a set of flies. The first trail was a set of 12 flies, and the
second trial was a set of 18 flies. Virgin females were anesthetized using carbon dioxide and then
placed in each vial with two females per vial. The students would then place one male in each vial
already containing virgin females. Then, as shown in Figure 1, the crosses were continued until each
male failed to produce offspring for two crosses or died before becoming infertile. There were
different treatments given to different lines of flies. The first two treatment types are Infected and
cured. The first fly of this category will have the Wolbachia infection, but the second line will not
because it will have been given a dose of Tetracycline to fight off the Wolbachia infection. The second
group is the treated and untreated group. This group will have lines that are treated with Tetracycline
to get rid or the Wolbachia infection. The untreated group will not have Wolbachia either, but will not
have received any Tetracycline treatments.
Reproduc ve Lifespan Assay
X
X
X
Original ♂
X
X
Reproduc ve
Lifespan
1♂
2 new♂
Original ♂ 2 new♂
Original ♂ 2 new♂
2 new♂Original ♂
Day 0
Day 2
Day 4
Day n
Day n+2
Fer le
Fer le
Fer le
X
X
2 ♂
Infer le
Fer le
Figure 1: In order to determine the reproductive
lifespan of the male flies, one male was mated
with two virgin females for every cross. The
original males flies were then transferred to a
new tube containing two new virgins, around
every two days. This process was repeated until
the original male fly was no longer fertile for two
consecutive crosses that were negative for a
week, or until death.
!5#
0#
5#
10#
15#
20#
25#
30#
307#treated#307#untreated#391#treated#391#untreated#399#treated#399#untreated#765#treated#765#untreated#
Trial#1#
Trial#2#
!5#
0#
5#
10#
15#
20#
25#
30#
360#cured# 360#
infected#
380#cured# 380#
infected#
786#cured# 786#
infected#
820##cured# 820#
infected#
Trial#1#
Trial#2#
A B
A comparison be done between lines that were infected with Wolbachia and cured of the bacteria
infection. A strip plot of each of the data points can also be seen in Figure 2. Lines 360, 820, and
380 all have relatively similar amounts of variation regardless of the line being infected or
cured. Line 786 shows a large difference in variation with the infected version of the line having
data points clustered toward the low end. The treated version of the line, however, shows a large
spread in data points. These conclusions are upheld by a comparison of standard deviations
among the lines as shown by graph D in Figure 2. The standard deviations for lines 360, 820, and
380 are all similar when comparing the standard deviation of the cured and infected versions of the
lines. The standard deviations for line 786 were very different with the standard deviation of the
infected line being much lower than the standard deviation of the cured line. Because a large
difference in variation was only seen in one line, it cannot be concluded that the curing of Wolbachia
changes the variability of the reproductive lifespan of fruit flies.
A strip plot of the data reveals that between the untreated and treated version of lines 307, 391, and
399 there were differing levels of variation. For lines 307 and 391, the untreated version had more
variation in reproductive lifespan than the treated version as evidenced by more spread out data
points. In line 399, the treated version of the line had more variability than the untreated
version. Line 765 appears to have no noticeable difference in variation of reproductive lifespan
when examining the strip plot. So, although there seem to be obvious differences in the strip plot
there are not concrete patterns that can be observed. A comparison of the standard deviation of the
four lines further reveals this relationship for lines 307 and 399 by showing a difference in standard
deviation. The relationship is also confirmed as line 765 has similar standard deviations for both
versions of the line. Line 391, however, has very similar standard deviations, even though the strip
plot shows a large variation in data points. This similarity could be due to the clustering of the 391
untreated data points at the high and low ends of the reproductive lifespan length. This clustering
may have led to the standard deviation being more similar to the standard deviation of the more
compacted data of the treated version of the line. Because a decrease in variation with the use of
antibiotics was only seen in two of the four line comparisons, it is not certain that usage of antibiotics
to treat fruit flies decreases variation in reproductive lifespan among a line
.
Variation can also be examined by comparing the differing sections of classes that performed fly
crosses. As a result of each section meeting at a different time during the day, it is possible that this
factor affected variation in the reproductive lifespan of the fruit flies, so another comparison of the
mean reproductive lifespans of the same line of flies but with differing sections reveals that for line 307
untreated, 360 infected, 391 treated, 786 infected, and 820 infected there was a large difference in
means between sections. These differences can be seen in Figure 3, graph A. Further comparison of
the standard deviations of each line for each section reveals some differences between sections, but
no differences as large as the means. Because it is only the means that differ and not the standard
deviations, it is unlikely that there is much variation in reproductive lifespan among sections.
Another way to examine the variation among the lines is to look at the variation seen when comparing
the treated to untreated lines. As can be seen in Figure 2, there was definitely noticeable variation in
the length of the reproductive lifespan throughout the line. A strip plot of the data reveals that between
the untreated and treated version of lines 307, 391, and 399 there were differing levels of
variation. For lines 307 and 391, the untreated version had more variation in reproductive lifespan
than the treated version as evidenced by more spread out data points. In line 399, the treated version
of the line had more variability than the untreated version. Line 765 appears to have no noticeable
difference in variation of reproductive lifespan when examining the strip plot. A comparison of the
standard deviation of the four lines further reveals this relationship for lines 307 and 399 by showing a
difference in standard deviation. The relationship is also confirmed as line 765 has similar standard
deviations for both versions of the line. Line 391, however, has very similar standard deviations, even
though the strip plot shows a large variation in data points. This similarity could be due to the
clustering of the 391 untreated data points at the high and low ends of the reproductive lifespan
length. This clustering may have led to the standard deviation being more similar to the standard
deviation of the more compacted data of the treated version of the line. Because a decrease in
variation with the use of antibiotics was only seen in two of the four line comparisons, it is not certain
that usage of antibiotics to treat fruit flies decreases variation in reproductive lifespan among a line.
Although the lines of fruit flies were identical genetically, individuals in the lines showed sizeable differences in
reproductive lifespan. Since the genetic factor of variation was eliminated, only environmental factors were
causing the variation. By comparing the lines by treated and untreated, infected and cured, and by section we
hoped to find some evidence for possible causes of variation. Had the cured and treated lines been less variable
than the other lines, it would have been differing bacteria causing the variation. Had the variation been seen
when comparing lines across sections, it could have been caused by differences in time of day. However, neither
of these possible sources of variation were consistently seen in the data. Instead, only partial amounts of
variability can be contributed to these sources.
Figure 4: This figure shows the variation by trial. The bar graph represents the average life expectancy by trial per line.
The bars are to show the standard deviation in the data. This graph is to see if there was a learning curve in the fly
crossing to observe if human error could account for variation in the first trials. Graph A shows the variation between the
first two trials in the treated and untreated lines. Graph B shows the variation between the first two trials between the
cured and infected lines.
Another comparison was done in figure 4. This figure was to see if there was a learning curve at
the start of the experiment. If so, this could be a cause of variation. The graph does not appear to
favor either trial. In graph A the 307 treated line in trial one has a higher average lifespan than in
trial two, but Line 765 Treated has a much lower lifespan average in trial one than trial two. . The
same basic principle applies to graph B. In both graphs there is a wide variety of standard
deviation values, but there is no pattern. Line 399 treated had a large difference in the standard
deviation between the two trials. Trial 1 has a very low standard deviation, whereas the Trial 2 has
a high standard deviation. This would imply that the average may not be as accurate of a
representation for the second trial, as it was for the first. However, the bars of standard deviation
are higher on Graph B than on Graph A. Although, the bars do not vary more between trials , but
this could mean that the averages of graph B may not be as reliable as in Graph A because the
data is has more spread. There is not more standard deviation for one trials than another. One
way to interpret this data is to say that some people may have had more of a learning curve than
others, but because there was a different researcher for each of the trials the variation could be
accounted for because of the researcher, the station, or another variable.
A B