Bio lab - Final Soil Presentation Poster, PDF
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This study analyzed soil samples from around the University of Pittsburgh campus to isolate bacteria with potential antibiotic properties against drug-resistant pathogens. Two isolates were found to produce zones of inhibition against specific pathogens - Bacillus funiculus inhibited E. coli and Enterobacter aerogenes, while Paenibacillus xylanexedens inhibited Staphylococcus epidermis. Both isolates were characterized through biochemical tests and DNA analysis. While the antibiotic compounds themselves could not be extracted, the study showed soil contains diverse microbes with potential for developing new antibiotics.
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Temperature tolerance
Being sessile, plants are constantly exposed to changes in temperature and other abiotic stress factors. The temperature stress experienced by plants can be classified into three types: those occurring at (a) temperature below freezing (b) low temperature above freezing and (c) high temperature. The plants must adapt to them in other ways. The biological substances that are deeply related to these stresses, such as heat shock proteins, glycine betaine as a compatible solute, membrane lipids etc.and also detoxifiers of active oxygen species, contribute to temperature stress tolerance in plants. Rapid advances in Molecular Genetic approaches have enabled genes to be cloned, both from prokaryotes and directly from plants themselves, that are thought to provide the key to the mechanism of temperature adaptation (Iba et al., 2002).
The accumulation of heat shock proteins under the control of heat stress transcription factors is assumed to play a central role in the heat stress response and in acquired thermotolerance in plants (Kotak et al., 2007). The pattern of protein synthesis during cold acclimation is very dissimilar to the heat shock proteins in many ways. Different low temperature stress proteins, such as Anti-freeze proteins or thermal hysteresis proteins (THPs) and cold shock domain proteins etc. are accumulated in plant cell and are frequently correlated with enhanced cold tolerance ( Guy, 1999).
The heat stress-induced dehydrin proteins (DHNs) expression and their relationship with the water relations of sugarcane (Saccharum officinarum L.) leaves were studied to investigate the adaptation to heat stress in plants (Wahid and Close, 2007). In order to get an in vitro evidence of Hsc70 functioning as a molecular chaperone during cold stress, a cold-inducible spinach cytosolic Hsc70 was subcloned into a protein expression vector and the recombinant protein was expressed in bacterial cells. Results suggest that the molecular chaperone Hsc70 may have a functional role in plants during low temperature stress (Zhang and Guy, 2006). To analyze the least and most strongly interacting stress with Hsps and Hsfs, a transcriptional profiling of Arabidopsis Hsps and Hsfs has been done (Swindell et al., 2007).
As plants receive complex of stress factors together, therefore in future research, emphasis should be placed on such cases where tolerance is attempted to different stress factors simultaneously by employing sophisticated techniques.
Chemicals used in pcr
Polymerase chain reaction, PCR, chemicals used in PCR, Ingredients used in PCR, Deionized water, PCR Buffer, MgCl2, dNTPS, types of dNTPS, Taq DNA polymerase, Primers, Amplicon, Molecular method.
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This presentation gives the insight idea about drought and its effect on the plant system also talks about development of drought-tolerant variety for ensuring food security.
Gene pyramiding
Gene pyramiding or stacking can be defined as a process of combining two or more genes from multiple parents to develop elite lines and varieties.
Mechanisms of Biological Control
Biological control is the suppression of one organism by another. There are two modes of mechanisms namely direct and indirect. Here I focused on the direct mechanisms such as parasitism, predatism, antibiotic-mediated suppression, lytic enzymes and unregulated-waste products. with the help of these various direct mechanisms, the bio-control agents will compete the pathogen's activity.
Epigenetics mediated gene regulation in plants
Epigenetics mediated gene regulation in plants describes how epigenetic mechanisms like DNA methylation and histone modification can regulate gene expression without changing the underlying DNA sequence. The document discusses various epigenetic mechanisms in plants including DNA methylation, histone modifications, and RNA interference. It also outlines applications of epigenetics like improving plant stress tolerance and yield as well as evolutionary studies.
Fungal Identification method by RDNA sequence analysis: Molecular approach to...
This document describes a study that used PCR and DNA sequencing to identify four fungal species - Aspergillus flavus, A. fumigatus, Alternaria alternata, and A. terreus - found in vermicompost produced from floral waste. Genomic DNA was isolated from fungal mycelium and the internal transcribed spacer region of ribosomal DNA was amplified by PCR using universal primers. The PCR products were sequenced and compared to identify the fungal species based on their ITS sequences. The molecular identification method was able to reliably distinguish between the four fungal species and provides insights into the role of microbes in the vermicomposting process.
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Temperature tolerance
Being sessile, plants are constantly exposed to changes in temperature and other abiotic stress factors. The temperature stress experienced by plants can be classified into three types: those occurring at (a) temperature below freezing (b) low temperature above freezing and (c) high temperature. The plants must adapt to them in other ways. The biological substances that are deeply related to these stresses, such as heat shock proteins, glycine betaine as a compatible solute, membrane lipids etc.and also detoxifiers of active oxygen species, contribute to temperature stress tolerance in plants. Rapid advances in Molecular Genetic approaches have enabled genes to be cloned, both from prokaryotes and directly from plants themselves, that are thought to provide the key to the mechanism of temperature adaptation (Iba et al., 2002).
The accumulation of heat shock proteins under the control of heat stress transcription factors is assumed to play a central role in the heat stress response and in acquired thermotolerance in plants (Kotak et al., 2007). The pattern of protein synthesis during cold acclimation is very dissimilar to the heat shock proteins in many ways. Different low temperature stress proteins, such as Anti-freeze proteins or thermal hysteresis proteins (THPs) and cold shock domain proteins etc. are accumulated in plant cell and are frequently correlated with enhanced cold tolerance ( Guy, 1999).
The heat stress-induced dehydrin proteins (DHNs) expression and their relationship with the water relations of sugarcane (Saccharum officinarum L.) leaves were studied to investigate the adaptation to heat stress in plants (Wahid and Close, 2007). In order to get an in vitro evidence of Hsc70 functioning as a molecular chaperone during cold stress, a cold-inducible spinach cytosolic Hsc70 was subcloned into a protein expression vector and the recombinant protein was expressed in bacterial cells. Results suggest that the molecular chaperone Hsc70 may have a functional role in plants during low temperature stress (Zhang and Guy, 2006). To analyze the least and most strongly interacting stress with Hsps and Hsfs, a transcriptional profiling of Arabidopsis Hsps and Hsfs has been done (Swindell et al., 2007).
As plants receive complex of stress factors together, therefore in future research, emphasis should be placed on such cases where tolerance is attempted to different stress factors simultaneously by employing sophisticated techniques.
Chemicals used in pcr
Polymerase chain reaction, PCR, chemicals used in PCR, Ingredients used in PCR, Deionized water, PCR Buffer, MgCl2, dNTPS, types of dNTPS, Taq DNA polymerase, Primers, Amplicon, Molecular method.
Hormone crosstalk in plant disease and defense
Phytohormones are small molecules produced within plants that govern diverse physiological processes, including plant defense. Hormonal interactions collectively form hormone signaling networks, which mediate immunity as well as growth and abiotic stress responses.
Drought tolerance in crops
This presentation gives the insight idea about drought and its effect on the plant system also talks about development of drought-tolerant variety for ensuring food security.
Gene pyramiding
Gene pyramiding or stacking can be defined as a process of combining two or more genes from multiple parents to develop elite lines and varieties.
Mechanisms of Biological Control
Biological control is the suppression of one organism by another. There are two modes of mechanisms namely direct and indirect. Here I focused on the direct mechanisms such as parasitism, predatism, antibiotic-mediated suppression, lytic enzymes and unregulated-waste products. with the help of these various direct mechanisms, the bio-control agents will compete the pathogen's activity.
Epigenetics mediated gene regulation in plants
Epigenetics mediated gene regulation in plants describes how epigenetic mechanisms like DNA methylation and histone modification can regulate gene expression without changing the underlying DNA sequence. The document discusses various epigenetic mechanisms in plants including DNA methylation, histone modifications, and RNA interference. It also outlines applications of epigenetics like improving plant stress tolerance and yield as well as evolutionary studies.
Fungal Identification method by RDNA sequence analysis: Molecular approach to...
This document describes a study that used PCR and DNA sequencing to identify four fungal species - Aspergillus flavus, A. fumigatus, Alternaria alternata, and A. terreus - found in vermicompost produced from floral waste. Genomic DNA was isolated from fungal mycelium and the internal transcribed spacer region of ribosomal DNA was amplified by PCR using universal primers. The PCR products were sequenced and compared to identify the fungal species based on their ITS sequences. The molecular identification method was able to reliably distinguish between the four fungal species and provides insights into the role of microbes in the vermicomposting process.
Muhammad usman
The document discusses the phosphorus cycle and transformations of phosphorus within soil. It notes that phosphorus is essential for life but cannot exist as a gas, and its cycle is the slowest. Within soil, microbes play an important role in mineralizing organic phosphorus compounds into a form plants can absorb through enzymes. They also solubilize insoluble phosphates and precipitate phosphorus compounds. The transformations involve acids, gases, chelators and are impacted by pH, calcium, magnesium, iron and aluminum levels.
Root excudates and their role in nutrition
Root exudates play an important role in plant nutrition by interacting with soil microbes and influencing the rhizosphere. Root exudates include primary metabolites like amino acids, carbohydrates, organic acids, and secondary metabolites like flavonoids, lignins, coumarins, and fatty acids. These exudates are released from the root tip through passive diffusion and active transport processes. They function to attract beneficial microbes, chelate nutrients, and defend against pathogens in the rhizosphere. The composition and concentration of root exudates varies depending on plant species and environmental conditions like nutrient availability.
Signal transduction in plant defense responses
Signal transduction a Process by which a cell converts one kind of signal into another. Plant disease resistance and susceptibility are gov¬erned by the combined genotypes of host and pathogen and depend on a complex exchange of signals and responses occurring under given environmental con¬ditions. During the long process of host-pathogen co-evolution, plants have developed various elaborate mechanisms to ward off pathogen attack. Whereas some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection, others are induced only after pa¬thogen attack. Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection. They do not have immune system and locomotary organs to escape environmental challenges and biotic stresses. In plant, nature has provided them some preformed and inducible defense resistance. Host recognition of invading pathogen is often determined by the so called “gene for gene” interaction between avirulence (avr) gene of pathogen and corresponding resistance (R) gene of host (Flor, 1971) which encode receptor for the recognition of specific elicitor or ligand encoded directly or indirectly by pathogen avr gene. Recent studies have revealed intriguing parallels between animal and plant defense responses as demonstrated by the structural and functional conservation of some of their signal transduction processes. Furthermore, signaling components such as G proteins, NADPH oxidase, H202, salicylic acid (SA, and aspirin), mitogen-activated protein kinases (MAPK), and transcription factors have been shown to be associated with or participate in both animal and plant defense responses, suggesting the presence of con¬served signaling pathways for host defenses in diverse higher eukaryotes.
Seed Priming
“Seed priming is a controlled hydration technique in which seeds are soaked in water or low osmotic potential solution to a point where germination related metabolic activities begin in the seeds but radical emergence does not occur.”
Marker-Assisted Backcrossing in breeding
Marker-assisted backcrossing can improve the efficiency of backcross breeding in three ways:
1) Markers can be used for early-generation selection when phenotyping traits is difficult.
2) Markers enable selection against the donor parent genome outside of the target region to minimize linkage drag.
3) Markers allow selection of rare recombinants near the target gene.
Using markers at multiple stages of selection, including for the target gene, recombinant selection around the gene, and background selection, can accelerate the recovery of the recurrent parent genome and potentially save 2-4 backcross generations.
induce systemic resistance
This document discusses induced systemic resistance (ISR) in plants. It provides historical context on studies of induced resistance dating back to the late 1800s. ISR is defined as a phenomenon where treatment with certain chemicals or pathogens activates a plant's defenses throughout the plant. Key findings include:
- ISR is activated by rhizobacteria and involves jasmonic acid and ethylene signaling rather than salicylic acid signaling as in systemic acquired resistance.
- Several bacteria, fungi, chemicals, and elicitors are reported to induce ISR through different signaling pathways and defense responses.
- Further research is needed to fully understand ISR signaling and apply it effectively in fields to control plant diseases.
Genome wide association studies seminar
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Molecular tagging
Molecular tagging of genes involves identifying existing DNA or introducing new DNA to function as a tag or label for the gene of interest. There are four main strategies for gene tagging: marker-based tagging, transposon tagging, T-DNA tagging, and epitope tagging. Marker-based tagging uses molecular markers tightly linked to important traits to assist in plant breeding programs. Transposon tagging relies on transposons, which can move within the genome, to provide a DNA tag that can then be used to identify adjacent DNA sequences and genes.
Loop Mediated Isothermal Amplification
The document summarizes Loop-mediated Isothermal Amplification (LAMP), a sensitive and efficient nucleic acid amplification technique. LAMP uses 4-6 primers that recognize 6 distinct regions on the target gene. The reaction proceeds at a constant temperature without thermal cycling. It produces billions of copies of target DNA in less than an hour. LAMP has applications in rapid diagnosis of diseases and identification of parasites due to its low cost, simplicity and speed compared to PCR.
Estimation of proline
This document describes a method for estimating proline content in plants. Proline acts as an osmolyte and protects cell structures under abiotic stress. It is extracted from plant tissues using sulphosalicylic acid and reacts with acid ninhydrin to form a red chromophore, whose absorbance at 520nm is used to determine proline concentration based on a standard curve. The method involves tissue extraction, reaction with reagents, measurement of absorbance, and calculation of proline content from the standard curve.
Variability in fungi
1. What is pathogen variability?
2. Significance of pathogen Variability
3. Stages of variation
4. Mechanism of Variability in fungi
5. Characterization of variability among plant pathogens
Root Exudates :Functions in plant-microbe interaction
Root exudates are chemicals exuded by plant roots that influence the surrounding soil environment and microbiome. They regulate microbial communities, encourage beneficial symbiotic relationships, and change soil chemical and physical properties. Root exudates are composed of low and high molecular weight compounds, including organic acids, amino acids, sugars, phenolics, proteins, and polysaccharides. They mediate both positive and negative interactions between plant roots and other organisms such as communication between roots and microbes or inhibition of competing plant species. The rate and composition of root exudates can be influenced by microorganisms, soil properties, and plant characteristics.
SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENS
This document discusses serological methods for detecting plant pathogens. It explains that serodiagnosis involves inducing an immune response in an animal to produce antibodies against a pathogen's antigens. These antibodies can then be used to detect the presence of the pathogen. The document describes several serological testing methods including ring interface tests, microprecipitin tests, double diffusion tests, ELISA, immunosorbent electron microscopy, and immunofluorescent staining. It concludes that serodiagnosis is a sensitive tool for identifying pathogens, detecting infections, and quantifying crop diseases.
Resistance_Mechanism_and_Molecular_Responses_to_the_Salinity.pptx
In this presentation, I would like to provide the Resistance Mechanism and Molecular Responses to the Salinity.
There are two types of plants Halophytes and Glycophytes (categories on the basis of their responses to the salinity) examples are Thellungiella halophila and Arabidopsis thaliana, respectively.
Earlier Arabidopsis was considered as Model organism incase of plants but it can't tolerate high saline condition that's the reason for the limited study of plant towards salinity responses. But in the year 2004 the discovery of new plant Thellungiella halophila generates new knowledge about the tolerance mechanism of plants towards salinity responses because it's a halophytes which can tolerate extreme saline condition.
And also it has very similarity with the Arabidopsis so it's considered as the Model organism for the study of Salt stress physiology.
There are major two pathways involved in response to Salt stress (described in presentation).
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The document summarizes molecular diagnostic techniques for detecting plant pathogens. It discusses several techniques including polymerase chain reaction (PCR), molecular hybridization, molecular markers, nucleic acid sequencing, and microarrays. PCR is described as a sensitive technique that can amplify DNA from pathogens. Molecular hybridization uses probes to detect complementary DNA or RNA sequences from pathogens. Molecular markers like RFLP and RAPD can identify pathogens by detecting DNA polymorphisms. Nucleic acid sequencing techniques like NASBA and LAMP can detect and amplify RNA from pathogens. Microarrays allow simultaneous detection of multiple pathogens using DNA probes spotted onto a chip.
Molecular markers
Molecular markers are DNA sequences that can be used to identify differences between individuals. They are found at specific locations in the genome and can be used to track inheritance of traits. Common types include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs detect differences in fragment lengths after restriction enzyme digestion and probing. RAPDs use random PCR primers to amplify polymorphic loci. AFLPs combine restriction digestion and PCR to detect multiple loci. SSRs are co-dominant markers based on differences in repeated microsatellite sequences. Molecular markers are powerful tools for genetic mapping, diversity analysis, fingerprinting, and marker-assisted selection.
Virus induced gene silencing
Virus-induced gene silencing (VIGS) is a technique that uses a viral vector carrying a fragment of a plant gene of interest to induce gene silencing. When the virus infects the plant, double-stranded RNA is produced from the viral genome and plant gene fragment, which is cleaved by the plant's dicer enzyme into siRNAs. These siRNAs are incorporated into the RISC complex and guide mRNA degradation of the targeted endogenous gene. Examples discussed were using tobacco rattle virus for VIGS in Nicotiana benthamiana and silencing tomato genes involved in the GABA pathway to study their roles in salt tolerance.
Agrobacterium
Common information about Agrobacterium tumefaciens, Rhizobium rhizogenes and plant diseases caused by them.
Rosenbloom_PosterAntibiotics
This study aimed to isolate antibiotic-producing soil bacteria to discover new antibiotics. Researchers collected a soil sample from Connecticut and isolated the bacterium Lysobacter antibioticus based on its zones of inhibition against pathogens. Sequence analysis identified the isolate as L. antibioticus. An ethyl acetate extract of L. antibioticus inhibited the growth of Bacillus subtilis but not the fungus Candida albicans, indicating antibiotic activity. L. antibioticus is known to produce beta-lactams and other antibiotics active against both gram-positive and gram-negative bacteria.
SWI antibiotic producers presentation at NU Fall Assembly
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Muhammad usman
The document discusses the phosphorus cycle and transformations of phosphorus within soil. It notes that phosphorus is essential for life but cannot exist as a gas, and its cycle is the slowest. Within soil, microbes play an important role in mineralizing organic phosphorus compounds into a form plants can absorb through enzymes. They also solubilize insoluble phosphates and precipitate phosphorus compounds. The transformations involve acids, gases, chelators and are impacted by pH, calcium, magnesium, iron and aluminum levels.
Root excudates and their role in nutrition
Root exudates play an important role in plant nutrition by interacting with soil microbes and influencing the rhizosphere. Root exudates include primary metabolites like amino acids, carbohydrates, organic acids, and secondary metabolites like flavonoids, lignins, coumarins, and fatty acids. These exudates are released from the root tip through passive diffusion and active transport processes. They function to attract beneficial microbes, chelate nutrients, and defend against pathogens in the rhizosphere. The composition and concentration of root exudates varies depending on plant species and environmental conditions like nutrient availability.
Signal transduction in plant defense responses
Signal transduction a Process by which a cell converts one kind of signal into another. Plant disease resistance and susceptibility are gov¬erned by the combined genotypes of host and pathogen and depend on a complex exchange of signals and responses occurring under given environmental con¬ditions. During the long process of host-pathogen co-evolution, plants have developed various elaborate mechanisms to ward off pathogen attack. Whereas some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection, others are induced only after pa¬thogen attack. Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection. They do not have immune system and locomotary organs to escape environmental challenges and biotic stresses. In plant, nature has provided them some preformed and inducible defense resistance. Host recognition of invading pathogen is often determined by the so called “gene for gene” interaction between avirulence (avr) gene of pathogen and corresponding resistance (R) gene of host (Flor, 1971) which encode receptor for the recognition of specific elicitor or ligand encoded directly or indirectly by pathogen avr gene. Recent studies have revealed intriguing parallels between animal and plant defense responses as demonstrated by the structural and functional conservation of some of their signal transduction processes. Furthermore, signaling components such as G proteins, NADPH oxidase, H202, salicylic acid (SA, and aspirin), mitogen-activated protein kinases (MAPK), and transcription factors have been shown to be associated with or participate in both animal and plant defense responses, suggesting the presence of con¬served signaling pathways for host defenses in diverse higher eukaryotes.
Seed Priming
“Seed priming is a controlled hydration technique in which seeds are soaked in water or low osmotic potential solution to a point where germination related metabolic activities begin in the seeds but radical emergence does not occur.”
Marker-Assisted Backcrossing in breeding
Marker-assisted backcrossing can improve the efficiency of backcross breeding in three ways:
1) Markers can be used for early-generation selection when phenotyping traits is difficult.
2) Markers enable selection against the donor parent genome outside of the target region to minimize linkage drag.
3) Markers allow selection of rare recombinants near the target gene.
Using markers at multiple stages of selection, including for the target gene, recombinant selection around the gene, and background selection, can accelerate the recovery of the recurrent parent genome and potentially save 2-4 backcross generations.
induce systemic resistance
This document discusses induced systemic resistance (ISR) in plants. It provides historical context on studies of induced resistance dating back to the late 1800s. ISR is defined as a phenomenon where treatment with certain chemicals or pathogens activates a plant's defenses throughout the plant. Key findings include:
- ISR is activated by rhizobacteria and involves jasmonic acid and ethylene signaling rather than salicylic acid signaling as in systemic acquired resistance.
- Several bacteria, fungi, chemicals, and elicitors are reported to induce ISR through different signaling pathways and defense responses.
- Further research is needed to fully understand ISR signaling and apply it effectively in fields to control plant diseases.
Genome wide association studies seminar
This document provides an overview of genome-wide association studies (GWAS). It defines key terms related to GWAS such as linkage disequilibrium, minor allele frequency, and odds ratio. It compares linkage mapping and association mapping. It describes the methodology of GWAS including identifying population structure, selecting case and control subjects, genotyping samples, and determining associated SNPs. It discusses challenges such as multiple hypothesis testing and population structure. It provides examples of successful GWAS in crops like maize and Arabidopsis. Overall, the document provides a comprehensive introduction and overview of GWAS.
Genome Editing in Fruit Crops
This document discusses genome editing in fruit crops using CRISPR/Cas9 technology. It provides examples of using CRISPR to edit genes involved in fruit ripening, pigmentation, and flowering time regulation in strawberry, banana, apple, and kiwifruit. Specifically, it describes using CRISPR to increase beta-carotene levels in banana, induce early flowering in apple and pear, and generate dwarf kiwifruit plants. The document concludes that integrating biotechnology like CRISPR with conventional breeding is a promising strategy for fruit crop improvement.
Molecular tagging
Molecular tagging of genes involves identifying existing DNA or introducing new DNA to function as a tag or label for the gene of interest. There are four main strategies for gene tagging: marker-based tagging, transposon tagging, T-DNA tagging, and epitope tagging. Marker-based tagging uses molecular markers tightly linked to important traits to assist in plant breeding programs. Transposon tagging relies on transposons, which can move within the genome, to provide a DNA tag that can then be used to identify adjacent DNA sequences and genes.
Loop Mediated Isothermal Amplification
The document summarizes Loop-mediated Isothermal Amplification (LAMP), a sensitive and efficient nucleic acid amplification technique. LAMP uses 4-6 primers that recognize 6 distinct regions on the target gene. The reaction proceeds at a constant temperature without thermal cycling. It produces billions of copies of target DNA in less than an hour. LAMP has applications in rapid diagnosis of diseases and identification of parasites due to its low cost, simplicity and speed compared to PCR.
Estimation of proline
This document describes a method for estimating proline content in plants. Proline acts as an osmolyte and protects cell structures under abiotic stress. It is extracted from plant tissues using sulphosalicylic acid and reacts with acid ninhydrin to form a red chromophore, whose absorbance at 520nm is used to determine proline concentration based on a standard curve. The method involves tissue extraction, reaction with reagents, measurement of absorbance, and calculation of proline content from the standard curve.
Variability in fungi
1. What is pathogen variability?
2. Significance of pathogen Variability
3. Stages of variation
4. Mechanism of Variability in fungi
5. Characterization of variability among plant pathogens
Root Exudates :Functions in plant-microbe interaction
Root exudates are chemicals exuded by plant roots that influence the surrounding soil environment and microbiome. They regulate microbial communities, encourage beneficial symbiotic relationships, and change soil chemical and physical properties. Root exudates are composed of low and high molecular weight compounds, including organic acids, amino acids, sugars, phenolics, proteins, and polysaccharides. They mediate both positive and negative interactions between plant roots and other organisms such as communication between roots and microbes or inhibition of competing plant species. The rate and composition of root exudates can be influenced by microorganisms, soil properties, and plant characteristics.
SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENS
This document discusses serological methods for detecting plant pathogens. It explains that serodiagnosis involves inducing an immune response in an animal to produce antibodies against a pathogen's antigens. These antibodies can then be used to detect the presence of the pathogen. The document describes several serological testing methods including ring interface tests, microprecipitin tests, double diffusion tests, ELISA, immunosorbent electron microscopy, and immunofluorescent staining. It concludes that serodiagnosis is a sensitive tool for identifying pathogens, detecting infections, and quantifying crop diseases.
Resistance_Mechanism_and_Molecular_Responses_to_the_Salinity.pptx
In this presentation, I would like to provide the Resistance Mechanism and Molecular Responses to the Salinity.
There are two types of plants Halophytes and Glycophytes (categories on the basis of their responses to the salinity) examples are Thellungiella halophila and Arabidopsis thaliana, respectively.
Earlier Arabidopsis was considered as Model organism incase of plants but it can't tolerate high saline condition that's the reason for the limited study of plant towards salinity responses. But in the year 2004 the discovery of new plant Thellungiella halophila generates new knowledge about the tolerance mechanism of plants towards salinity responses because it's a halophytes which can tolerate extreme saline condition.
And also it has very similarity with the Arabidopsis so it's considered as the Model organism for the study of Salt stress physiology.
There are major two pathways involved in response to Salt stress (described in presentation).
Bioherbicide and allelochemicals.ppt
Bioherbicide and allelochemicals.pptDR.Y.S. Parmar University of Horticulture and Forestry, Nauni,Solan - HP
This document discusses bio-herbicides and allelochemicals. It begins by defining weeds and their benefits and limitations. It then discusses different methods of weed control, focusing on biological methods like bio-herbicides and allelochemicals. Bio-herbicides are defined as biologically based weed control agents derived from microbes. Allelochemicals are secondary metabolites produced by plants that can inhibit other plants. Some examples of specific bio-herbicides and allelochemical sources are provided. The document discusses advantages and limitations of bio-herbicides, factors influencing allelopathy, and mechanisms of allelochemical action. It concludes by stating that while bio-herbicides and allelopathy show potentialmolecular approches
The document summarizes molecular diagnostic techniques for detecting plant pathogens. It discusses several techniques including polymerase chain reaction (PCR), molecular hybridization, molecular markers, nucleic acid sequencing, and microarrays. PCR is described as a sensitive technique that can amplify DNA from pathogens. Molecular hybridization uses probes to detect complementary DNA or RNA sequences from pathogens. Molecular markers like RFLP and RAPD can identify pathogens by detecting DNA polymorphisms. Nucleic acid sequencing techniques like NASBA and LAMP can detect and amplify RNA from pathogens. Microarrays allow simultaneous detection of multiple pathogens using DNA probes spotted onto a chip.
Molecular markers
Molecular markers are DNA sequences that can be used to identify differences between individuals. They are found at specific locations in the genome and can be used to track inheritance of traits. Common types include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs detect differences in fragment lengths after restriction enzyme digestion and probing. RAPDs use random PCR primers to amplify polymorphic loci. AFLPs combine restriction digestion and PCR to detect multiple loci. SSRs are co-dominant markers based on differences in repeated microsatellite sequences. Molecular markers are powerful tools for genetic mapping, diversity analysis, fingerprinting, and marker-assisted selection.
Virus induced gene silencing
Virus-induced gene silencing (VIGS) is a technique that uses a viral vector carrying a fragment of a plant gene of interest to induce gene silencing. When the virus infects the plant, double-stranded RNA is produced from the viral genome and plant gene fragment, which is cleaved by the plant's dicer enzyme into siRNAs. These siRNAs are incorporated into the RISC complex and guide mRNA degradation of the targeted endogenous gene. Examples discussed were using tobacco rattle virus for VIGS in Nicotiana benthamiana and silencing tomato genes involved in the GABA pathway to study their roles in salt tolerance.
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Root Exudates :Functions in plant-microbe interaction
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SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENS
SEROLOGICAL METHODS FOR DETECTION OF PLANT PATHOGENS
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Similar to Bio lab - Final Soil Presentation Poster, PDF
Rosenbloom_PosterAntibiotics
This study aimed to isolate antibiotic-producing soil bacteria to discover new antibiotics. Researchers collected a soil sample from Connecticut and isolated the bacterium Lysobacter antibioticus based on its zones of inhibition against pathogens. Sequence analysis identified the isolate as L. antibioticus. An ethyl acetate extract of L. antibioticus inhibited the growth of Bacillus subtilis but not the fungus Candida albicans, indicating antibiotic activity. L. antibioticus is known to produce beta-lactams and other antibiotics active against both gram-positive and gram-negative bacteria.
SWI antibiotic producers presentation at NU Fall Assembly
These are the preliminary results of 5 antibiotic-producers isolated as part of the Small World Initiative implementation at National University.
Bacteria Project
This document summarizes a study conducted by researchers at the University of Puerto Rico at Cayey to identify soil bacteria capable of producing novel antibiotics. Soil samples were collected from two sites and diluted to isolate individual bacterial colonies. Colonies were purified, stained, and had their DNA analyzed. The isolated bacteria were tested for antibiotic resistance and their ability to inhibit the growth of other bacteria, which could indicate antibiotic production. The goal was to find bacteria producing compounds similar to teixobactin, a potent antibiotic discovered from uncultured soil bacteria.
Bacteria Report
This document describes a study conducted by researchers at the University of Puerto Rico at Cayey to identify soil-collected bacteria that could produce novel antibiotic compounds. Soil samples were collected from two sites and diluted to isolate individual bacterial colonies. Colonies showing growth were purified and analyzed using gram staining, freezing, electrophoresis, and tests for antibiotic resistance and production. Initial results identified distinct colony morphologies from the soil samples and showed growth from the undiluted, but not highly diluted, samples. Further analysis of purified colonies is planned to characterize the bacteria and determine their antibiotic properties.
ISOLATION AND IDENTIFICATION OF LACTIC ACID BACTERIA FROM PLANTS AND OTHER ...
ISOLATION AND IDENTIFICATION OF LACTIC ACID BACTERIA FROM PLANTS AND OTHER ...American Research Thoughts
This document describes a study that isolated lactic acid bacteria (LAB) from various plant and vegetable matrices. 22 LAB strains were isolated belonging to Lactobacillus, Lactococcus, and Enterococcus genera. The predominant species were Lactobacillus brevis (57%) and Lactobacillus delbrueckii subsp. bulgaricus (14%). The strains were tested for their ability to produce bacteriocin-like substances (BLS) with antimicrobial activity. A conjugation experiment was then successfully performed between Enterococcus faecium and Lactobacillus acidophilus to demonstrate horizontal gene transfer of BLS production.311241427655888
This document summarizes a study that isolated and characterized lactic acid bacteria from various environmental samples. 21 lactic acid bacteria isolates were obtained from milk, water, soil and plant samples. 10 were identified as Lactobacillus, 3 as Enterococcus, 2 as Staphylococcus, 5 as Lactococcus, and 1 as Leuconostoc based on biochemical and physiological tests. 6 of the isolates were found to harbor plasmids. Further characterization identified 3 isolates as Enterococcus faecium and 1 each as Weissella confusa, Pediococcus pentosaceus, and Staphylococcus epidermidis based on 16S rRNA gene sequencing. Some isolates showed inhibitory activity
Isolation and characterization of bacteria from tropical soils
The document describes a study that isolated and characterized bacteria from soils in Puerto Rico. Five bacteria were isolated from soils in Caguas, Santa Isabel, and Comerío. All five isolates were gram-positive bacilli. Two isolates showed resistance to tetracycline. One isolate had endospores and showed decreasing resistance when tested with bacterial clusters closer to antibiotics. Another isolate changed color from white to red with time, and also showed decreasing resistance with bacterial clusters. The isolates did not produce antibiotics against E. coli or M. luteus, though one was able to coexist with E. coli. Further experiments are needed to determine the causes of antibiotic resistance in the isolates.
Adina's Faculty Introduction - ISU ABE
Adina Howe presented on her research at the GERMS Lab which uses innovative scientific methods to understand global environmental change through studying microbes. The lab aims to develop quantitative tools to monitor microbial responses in complex environments like soils and water. Current projects analyze lake water quality using microbial genetic biomarkers, study soil microbes driving carbon cycling, and identify gut microbes influencing human health. Howe emphasized the importance of interdisciplinary collaboration and integrating diverse datasets to gain new insights.
Proposal seminar
This document outlines a proposed seminar that will conduct a comparative microbiological and physicochemical analysis of bottled water and water from treatment plants in Ondo State, Nigeria. The objectives are to determine the microbiological and mineral quality of the samples, compare their levels of purity, and assess antibiotic sensitivity of any isolates. Samples will be collected and tested for bacteria, fungi, coliforms, physicochemical properties. Results will provide information on the quality of bottled water and treated water distributed in Ondo State.
Isolation and Screening of Soil Actinomycetes for Antimicrobial Activity
Antimicrobial resistance in pathogens has greatly increased of late and now pose a serious public health problem globally. New antimicrobials are continuously needed to inhibit the growth of these resistant strains.
The aim of this study was to isolate and screen soil actinomycetes and evaluate their secondary metabolites for antimicrobial activities against selected pathogenic bacteria and fungi.
Comparative Study on Antimicrobial Activity and Microbial Load of Alternanthe...
The present study analyses the antimicrobial activity and the microbial load of an edible plant Alternanthera philoxeroides (Mart.) Griseb growing in polluted and unpolluted site. The plants were collected and tested against various Gram positive, Gram negative bacteria and fungi. Antimicrobial activity was performed with acetone, aqueous, chloroform, ethanol and petroleum ether extracts of aerial parts A. philoxeroides collected from polluted and unpolluted site that showed significant antimicrobial activity against tested bacterial and fungal organisms. The extracts were compared with standards like Amoxicillin for antibacterial activity and Ketoconazole for antifungal activity. The extracts showed remarkable antimicrobial activity as measured from the zone of inhibition and results were comparable with that of standard drugs against the organisms tested. The microbial load is also enumerated in the cooked and cooked refrigerated samples from polluted and unpolluted site. In conclusion, plant extract of A. philoxeroides collected from polluted site showed less antimicrobial activity and higher antimicrobial activity in unpolluted site. The ethanol extract showed higher activity when compared to other extracts. The microbial load is higher in cooked refrigerated sample when compared to cooked sample.
Characterization of Bacteria Isolated from Tropical Soils of Puerto Rico
This document summarizes a student research project that aimed to characterize bacteria isolated from soils in Puerto Rico. Soil samples were collected and bacteria were isolated on agar plates before being purified through restreaking. Gram staining identified the bacteria as either gram-positive or gram-negative. Genomic DNA was extracted and amplified via PCR. However, when tested on indicator plates, the isolated bacteria did not show any antibiotic production against E. coli or M. luteus as hypothesized. While full characterization was not completed due to time constraints, the student plans future work identifying the bacteria through DNA sequencing.
JBK Soil Research
The document summarizes a research project aimed at discovering new antibiotics by culturing bacteria from unusual soil samples around the world. Soil samples are collected and bacteria isolated to find those that produce zones of inhibition against drug-resistant pathogens. One isolate, identified as Pseudomonas brassicacearum, showed inhibition of several drug-resistant bacteria but its extracted antibiotic was unsuccessful in further tests, possibly due to errors. The research highlights the need to find new antibiotics as pathogens grow more resistant.
7.ann&2.ramon bacteriareportofficial
This research aimed to characterize bacteria isolated from soils in Puerto Rico. Two soil samples were collected and various tests were performed on the isolated bacteria, including Gram staining, DNA purification and amplification, and testing for antibiotic production. One isolated bacterium (S15UPRC-RISEAMGP30SP01A1) was identified as a gram-positive cocci resembling Staphylococcus and did not produce antibiotics. The other (S15UPRC-RISERBCR30P01A2) was a gram-positive Bacillus but did not produce antibiotics. Neither bacterium could be fully characterized due to negative PCR results, failing to confirm the hypothesis of positive antibiotic production. Further tests are needed to fully characterize the
Antibiotic resistance and molecular characterization
This document reports on a study of antibiotic resistance and molecular characterization of Salmonella isolated from stool samples of diarrhoeal patients in Ile-Ife, Nigeria. A total of 69 Salmonella isolates (S. Typhimurium, S. Typhi, S. Paratyphi A) were obtained from 187 stool samples. The isolates showed high resistance to nitrofurantoin, ceftriazone, and augmentin. Sixty-seven isolates were resistant to at least two antibiotic classes, with resistance to combinations of four antibiotics being most common. Plasmid DNA analysis of resistant isolates identified multiple plasmids ranging from 1.46-23.13 kbp. Resistance genes blaCTX and
Antibiotic resistance and molecular characterization
This document reports on a study of antibiotic resistance and molecular characterization of Salmonella isolated from stool samples of diarrhoeal patients in Ile-Ife, Nigeria. A total of 69 Salmonella isolates (82.6% S. Typhimurium, 10.1% S. Typhi, 7.3% S. Paratyphi A) were obtained from 187 stool samples. The isolates showed high resistance to nitrofurantoin (100%), ceftriazone (97.2%), and gentamicin (94.2%). Sixty-seven isolates (97.1%) were resistant to at least two antibiotic classes, with 32 resistance patterns identified. Multiple plasmids ranging from 1.
13CSP
The document summarizes a study that assessed the antimicrobial activities of secondary metabolite extracts from three soil-inhabiting fungi - Trichoderma koningii, Rhizopus stolonifer, and Fusarium oxysporum. The fungi were cultured individually in Sabouraud broth for 21 days, after which ethyl acetate was used to extract secondary metabolites from the broth. Thin layer chromatography analysis indicated the extracts contained multiple compounds. The extracts were screened for antimicrobial activity against four microorganisms using a broth microdilution assay. The extracts displayed variable but low antimicrobial activity compared to standard antimicrobial drugs. This study provides a preliminary analysis of the antimicrobial potential of extracts from these under-explored
Pglo Lab Report
The document describes a lab experiment that tests how the addition of a pGLO plasmid affects the growth and characteristics of E. coli bacteria. The experiment involves transforming E. coli bacteria with the pGLO plasmid by adding it to a solution containing the bacteria. One solution receives the pGLO plasmid (+pGLO) while the other does not (-pGLO). The bacteria are then observed under UV light and incubated under various conditions to analyze effects on growth and gene expression.
Antimicrobial susceptibility of isolated E.coli from different water sources ...
This study tested the antimicrobial susceptibility of E.coli isolated from different water sources in Nyala Town, Sudan. E.coli was isolated from 50 water samples using standard methods and tested against 12 commonly used antimicrobial agents. The results showed that the E.coli strains were most sensitive to Ciprofloxacin, Co-Trimoxazole and Chloramphenicol and most resistant to Tetracycline and Ampicillin/Sulbactam. This indicates multiple antibiotic resistant E.coli exist in the water sources of the study area, making the water potentially unsafe for drinking.
Dr d p rajani
This document provides details of a study on screening, characterization, and antibiotic resistance testing of pathogens from various clinical specimens. Over 6,000 samples, including urine, blood, pus, sputum, and others, were collected and analyzed using microbiological techniques. Isolates were identified based on morphological and biochemical characteristics. Antibiotic susceptibility testing was performed using disk diffusion methods. Multiple drug-resistant organisms were detected. The study aimed to determine the prevalence and antibiotic resistance patterns of pathogens from different specimens to help guide treatment of infectious diseases.
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SWI antibiotic producers presentation at NU Fall Assembly
SWI antibiotic producers presentation at NU Fall Assembly
ISOLATION AND IDENTIFICATION OF LACTIC ACID BACTERIA FROM PLANTS AND OTHER ...
ISOLATION AND IDENTIFICATION OF LACTIC ACID BACTERIA FROM PLANTS AND OTHER ...
Isolation and characterization of bacteria from tropical soils
Isolation and characterization of bacteria from tropical soils
Isolation and Screening of Soil Actinomycetes for Antimicrobial Activity
Isolation and Screening of Soil Actinomycetes for Antimicrobial Activity
Comparative Study on Antimicrobial Activity and Microbial Load of Alternanthe...
Comparative Study on Antimicrobial Activity and Microbial Load of Alternanthe...
Characterization of Bacteria Isolated from Tropical Soils of Puerto Rico
Characterization of Bacteria Isolated from Tropical Soils of Puerto Rico
Antibiotic resistance and molecular characterization
Antibiotic resistance and molecular characterization
Antibiotic resistance and molecular characterization
Antibiotic resistance and molecular characterization
Antimicrobial susceptibility of isolated E.coli from different water sources ...
Antimicrobial susceptibility of isolated E.coli from different water sources ...
Bio lab - Final Soil Presentation Poster, PDF
- 1. Analysis of Soil Microbes for Antibiotic Properties Jake Kieserman & Linda Zheng There is an upcoming crisis in modern medicine in which pathogenic strains of bacteria are becoming resistant to the antibiotics that physicians commonly prescribe. Infections that were once commonly treatable are now developing into severe infections increasing the mortality rate of humans across the globe. In this study, bacterial isolates were cultured from soil samples around the University of Pittsburgh’s campus and were analyzed for antibiotic producing properties against ESKAPE pathogen (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) in hopes of developing new medications to combat this multi-drug resistant organisms. Introduction Objectives 1. To obtain bacterial samples from soil taken from around Pitt’s campus and culture the bacteria as single colonies to determine which bacterial specimens are antibiotic producers against ESKAPE pathogens 2. To analyze and characterize soil isolates by their physical and chemical properties 3. To contribute to the Small World Initiative database to work collaboratively toward addressing the antibiotic crisis Results Conclusions References Hernandez, S.A., et al. 2013. Introduction. In: The Small World Initiative Student Laboratory Manual. Yale University. 7. Reynolds, J. 2005. Small World Initiative Protocols. Yale University. 70- 106. Methods Flow Diagram Test Jake’s Sample Linda’s Sample Soil Type Silty loam Sandy clay loam pH of Soil (deionized water) 8 6 Percent Water Content 33.45% 30.7% Percent Organic Content (Wet Weight) 11% 8.16% Optimal Agar Medium NA R2A Optimal Dilution Ratio 1:1000 1:1000 CFU/g from Optimal Dilution 9.4x105 1.8x106 Test Jake’s Results Linda’s Results Starch Hydrolysis Positive for amylase Positive for amylase Catalase Reaction Negative for catalase Negative for catalase SIM (Sulfide /Indole/Motility) Negative for sulfide/indole, Positive for motility Negative for sulfide /indole, Positive for motility Fluid Thioglycollate Aerotolerant anaerobe Facultative anaerobe Triple Sugar Iron Ferments glucose, produces acid Ferments glucose/sucrose /lactose, produces acid MacConkey Agar No growth (Gram +) No growth (Gram +) DNA match (with BLAST) Bacillus funiculus (99% identity) Paenibacillus xylanexedens (99% identity) Table 2. Results of biochemical characterization testing Table 1. Results of soil characterization and optimization testing Our testing resulted in two antibiotic producers, one against Staphylococcus epidermis and the other against Escherichia coli and Enterobacter aerogenes, proving that antibiotic-producing microbes can be found and isolated from soil samples. From the various characterization testing, we see that the antibiotic producing bacterial isolates were diverse, exhibiting many different physical and chemical properties. Although we were not able to extract the antibiotic organic compounds, this may have been because the antibiotic compounds were not organic or difficulties with using ethyl acetate. Further testing may yield other antibiotic-producing microbes, such as if we continued to test other isolates from our soil samples using the same process. Acknowledgements Special thanks to Elia Crisucci and Jean Schmidt for their commitment and assistance to our research, our classmates for their continued encouragement and teamwork, and the University of Pittsburgh for funding and creating this opportunity for us to become part of the Small World Initiative. Identify antibiotic producers (zones of inhibition) Collect soil sample Analyze soil sample Serial dilution of soil Perform PCR reaction to amplify antibiotic- producing isolate DNA Gel electrophoresis to confirm PCR results Repeat if PCR unsuccessful ATGTCAATA Send DNA to be sequenced and identify isolate Test various agar types Isolate microbes Test against safe “ESKAPE” pathogen relatives Repeat if unsuccessful LB PDA R2A NA Perform gram staining on isolate Extract antibiotic organic compounds Biochemical characterization of isolates (e.g. starch hydrolysis test) • Two antibiotic-producing isolates found and identified, Bacillus funiculus produced a zone of inhibition against E. coli (Fig. 1) and E. aerogenes (Fig. 2), and Paenibacillus xylandexedens against S. epidermis (Fig. 3), although attempts to extract the antibiotic organic compounds were unsuccessful • Each soil sample was initially thoroughly analyzed (Table 1) and later biochemically characterized (Table 2) Figure 3. Results from spread /patch screen for soil isolate antibiotic production against S. epidermis, incubated at 30°C for seven days. Figure 2. Results from broad spectrum screen for soil isolate #1 antibiotic production against E. aerogenes, incubated at 30°C for two days. Figure 3. Results from spread/patch screen for soil isolate antibiotic production against E. coli, incubated at 30°C for five days.