The document summarizes research on identifying stress-related genes in gray whales and fin whales. It provides background information on the species and describes objectives to isolate specific genes involved in responses to pollution, climate change, and disease. Results showed portions of interleukin 17, prostaglandin-endoperoxide synthetase-2, and glutathione S-transferase A4 genes were isolated from both whale species and had high similarity to gene sequences in other organisms.
Toll-like receptors (TLRs) are a family of pattern recognition receptors that play a key role in the innate immune system as the first line of defense against pathogens. TLR2 and TLR4 have received significant attention in cardiovascular research. This document summarizes evidence that TLR2 and TLR4 activation by exogenous ligands from bacteria and viruses as well as endogenous ligands highly expressed in atherosclerotic plaques can induce inflammation, plaque instability, and vascular remodeling through pathways involving cytokines, matrix metalloproteinases and other mediators. Modulation of TLR signaling may be a potential therapeutic strategy for cardiovascular diseases.
Cybr is a cytokine-inducible protein that binds to cytohesin-1. [The study] purified Cybr, cytohesin-1, and other related proteins. It found that Cybr binds directly to cytohesin-1 using a GST pull-down assay. The regions of Cybr and cytohesin-1 responsible for their interaction are being investigated using mutants. This protein may regulate cytohesin-1's activity and signaling pathways.
This document summarizes a study that analyzed the frequency of the CYP4F2 rs2108622 genetic variant among 90 healthy Jordanian volunteers. The study found:
- The frequency of the C allele was 0.55 and of the T allele was 0.45.
- The most common genotype was heterozygous CT at 0.55 frequency.
- The frequencies in Jordanians were similar to Caucasians but different from other groups like Africans.
- This variant may influence cardiovascular diseases and warfarin response in Jordanians.
This document describes arylphthalazines as potent inhibitors of VEGFR-2 (Vascular Endothelial Growth Factor Receptor 2), an important target for inhibiting angiogenesis. A series of arylphthalazine derivatives were synthesized in two steps from commercially available starting materials. Compound IM-094482 57 was found to be a potent inhibitor of VEGFR-2 and VEGFR-1 in enzymatic, cellular, and mitogenic assays, comparable to ZD-6474. Compound 57 also showed good oral bioavailability in mice. Structure-activity relationship studies around the 1-anilino group and 4-aryl group of the arylphthalazine core identified substituents that improved inhibitory potency against VEGFR-2.
Presentation of Fridtof Lund-Johansen in 1st International Antibody Validatio...St John's Laboratory Ltd
Fridtjof Lund-Johansen is an MDPhD who has worked for 30 years with antibodies and flow cytometry. He took his degree at the University of Bergen in Norway. He then did post-docs in California, first at Becton Dickinson in San Jose and then at DNAX instiute of Immunology in Palo Alto. He is now a PI at the Institute of Immunology at Oslo University Hospital where he leads an effort to develop antibody-based proteomics. His technology is called MAP for microsphere affinity proteomics. He will talk about how MAP can be used to test thousands of antibodies in parallel.
For more details about 1st international antibody validation forum please check on http://www.stjohnslabs.com/ac_cms/blog
The importance of high quality reference genome assemblies to personal and me...kmsteinberg
This document discusses improvements to the human reference genome through new long-read genome assemblies of the hydatidiform mole sample CHM13. A new PacBio-based assembly of CHM13 was constructed and integrated with BioNano optical maps to improve contiguity. This hybrid assembly revealed structural variants like collapses in the original assembly due to segmental duplications. Integration of the improved CHM13 assembly into GRCh38 helped resolve previously problematic regions and improved read mapping and variant calling compared to the older GRCh37 reference. Continued improvement of reference genomes is important for advancing personal and medical genomics.
The document discusses ways to improve the diagnostic yield of exome sequencing by addressing limitations in analytical and clinical validity. It notes that standard exomes do not fully cover the exome or reference genomes, and clinical interpretation is limited by incomplete knowledge in the literature and databases. Improving coverage, integrating more information sources, and enhancing data processing could help uncover more diagnostic variants.
Toll-like receptors (TLRs) are a family of pattern recognition receptors that play a key role in the innate immune system as the first line of defense against pathogens. TLR2 and TLR4 have received significant attention in cardiovascular research. This document summarizes evidence that TLR2 and TLR4 activation by exogenous ligands from bacteria and viruses as well as endogenous ligands highly expressed in atherosclerotic plaques can induce inflammation, plaque instability, and vascular remodeling through pathways involving cytokines, matrix metalloproteinases and other mediators. Modulation of TLR signaling may be a potential therapeutic strategy for cardiovascular diseases.
Cybr is a cytokine-inducible protein that binds to cytohesin-1. [The study] purified Cybr, cytohesin-1, and other related proteins. It found that Cybr binds directly to cytohesin-1 using a GST pull-down assay. The regions of Cybr and cytohesin-1 responsible for their interaction are being investigated using mutants. This protein may regulate cytohesin-1's activity and signaling pathways.
This document summarizes a study that analyzed the frequency of the CYP4F2 rs2108622 genetic variant among 90 healthy Jordanian volunteers. The study found:
- The frequency of the C allele was 0.55 and of the T allele was 0.45.
- The most common genotype was heterozygous CT at 0.55 frequency.
- The frequencies in Jordanians were similar to Caucasians but different from other groups like Africans.
- This variant may influence cardiovascular diseases and warfarin response in Jordanians.
This document describes arylphthalazines as potent inhibitors of VEGFR-2 (Vascular Endothelial Growth Factor Receptor 2), an important target for inhibiting angiogenesis. A series of arylphthalazine derivatives were synthesized in two steps from commercially available starting materials. Compound IM-094482 57 was found to be a potent inhibitor of VEGFR-2 and VEGFR-1 in enzymatic, cellular, and mitogenic assays, comparable to ZD-6474. Compound 57 also showed good oral bioavailability in mice. Structure-activity relationship studies around the 1-anilino group and 4-aryl group of the arylphthalazine core identified substituents that improved inhibitory potency against VEGFR-2.
Presentation of Fridtof Lund-Johansen in 1st International Antibody Validatio...St John's Laboratory Ltd
Fridtjof Lund-Johansen is an MDPhD who has worked for 30 years with antibodies and flow cytometry. He took his degree at the University of Bergen in Norway. He then did post-docs in California, first at Becton Dickinson in San Jose and then at DNAX instiute of Immunology in Palo Alto. He is now a PI at the Institute of Immunology at Oslo University Hospital where he leads an effort to develop antibody-based proteomics. His technology is called MAP for microsphere affinity proteomics. He will talk about how MAP can be used to test thousands of antibodies in parallel.
For more details about 1st international antibody validation forum please check on http://www.stjohnslabs.com/ac_cms/blog
The importance of high quality reference genome assemblies to personal and me...kmsteinberg
This document discusses improvements to the human reference genome through new long-read genome assemblies of the hydatidiform mole sample CHM13. A new PacBio-based assembly of CHM13 was constructed and integrated with BioNano optical maps to improve contiguity. This hybrid assembly revealed structural variants like collapses in the original assembly due to segmental duplications. Integration of the improved CHM13 assembly into GRCh38 helped resolve previously problematic regions and improved read mapping and variant calling compared to the older GRCh37 reference. Continued improvement of reference genomes is important for advancing personal and medical genomics.
The document discusses ways to improve the diagnostic yield of exome sequencing by addressing limitations in analytical and clinical validity. It notes that standard exomes do not fully cover the exome or reference genomes, and clinical interpretation is limited by incomplete knowledge in the literature and databases. Improving coverage, integrating more information sources, and enhancing data processing could help uncover more diagnostic variants.
1) The study evaluated the effects of two growth hormone receptor (GHR) mutations (p.R229H and c.899dupC) found in a patient with GH insensitivity.
2) Functional studies showed that the p.R229H mutation did not impair GHR signaling or function. However, the c.899dupC mutation resulted in a truncated GHR protein that was unable to activate downstream signaling pathways in response to GH.
3) When coexpressed, the c.899dupC mutation dominantly inhibited the normal signaling of wild-type GHR and the p.R229H variant. This dominant negative effect explains the patient's GH insensitivity phenotype.
Clinical Variant Analysis with VSClinical: Virtus Diagnostics Case Study and ...Golden Helix
It is our pleasure to announce the following speakers for our Golden Helix webcast for the Asia-Pacific region:
Val Hyland, Molecular Genetics Chief Scientist, BA(Mod) PhD, Virtus Diagnostics
Peter Field, Molecular Genetics Supervisor, Virtus Diagnostics
Gabe Rudy, VP of Product & Engineering, Golden Helix
Val Hyland and Peter Field from Virtus Diagnostics (Brisbane) discuss two cases from their cohort of 1095 patients that were screened for inherited diseases using the Illumina 552 genes Inherited Disease screening panel. They found 637 different pathogenic/likely pathogenic variants in 252 genes using a combination of software tools from Golden Helix, including VSClinical, Sentieon and Illumina. This presentation is based on a poster first presented at the HGSA Wellington Conference in 2019 which can be referenced here.
Gabe Rudy from Golden Helix discusses how VSClinical can be used to follow the ACMG & AMP guidelines for the interpretation of germline and somatic variants, respectively. By incorporating new algorithms and annotation sources, detailed variant scoring, classification, and interpretation can occur right within VarSeq without the need for additional, external tools or resources. These capabilities are designed to improved throughput while allowing the lab to maintain consistent quality.
View the webcast recording to learn more about these powerful capabilities:
Streamline germline variant interpretation using the ACMG scoring guidelines with automatic criteria recommendations and incorporated historical data
Quickly determine the oncogenicity of somatic mutations using our automated oncogenicity scoring system
Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
Mitochondrial ND-1 gene-specific primer polymerase chain reaction to determin...UniversitasGadjahMada
A specificity method to detect mice meat contamination in beef meatballs using specific primer-polymerase chain reaction (PCR) technique has been developed. The primer ND1-P1 primers were designed using primer-BLAST software using mtDNA of mice as a template. The Primer ND1-P1 forward (5’-CGGCATCCTACAACCATTTGC-3’) and reverse (5’-CGGCTCGTAAAGC-TCCGAA-3’) was able to amplify a 294 bp fragment of ND1 gene in mice mtDNA. The primers have been proven precise with only amplify the target fragment in mice meatball but not in another meatball including beef meatball, chicken meatball, pork meatball, horse meatball, and goat meatball. The present of mice meat in meatballs can be detected at a concentration as low as 5% (w/w). The ND1-P1 primer is potentially used as a specific marker for detection of mice meat in the meat products.
Building a platinum human genome assembly from single haplotype human genomes...kmsteinberg
This document summarizes research to build a platinum human genome assembly from long read sequencing of single haplotype human genomes. Last year, a study generated a high quality assembly of CHM1. This year, the researchers generated a new assembly of CHM13 using PacBio sequencing with an N50 of 12.9 Mb. However, analysis with BioNano and Illumina data revealed collapsed regions in the PacBio assembly due to segmental duplications. By integrating the PacBio assembly with BioNano maps, they generated hybrid scaffolds with fewer, larger contigs and resolved the collapsed regions. Comparing the new CHM13 assembly to CHM1 found they were highly consistent with only 13 variant sites, demonstrating the quality
N-methyl-D-aspartate receptors (NMDARs) mediate a slow component of excitatory synaptic transmission that plays important roles in normal brain function and development. A large number of disease-associated variants in the GRIN gene family encoding NMDAR GluN subunits have been identified in patients with various neurological and neuropsychiatric disorders. Many of these variants reduce the function of NMDARs by a range of different mechanisms, including
reduced glutamate potency, reduced glycine potency, accelerated deactivation time course, reduced current response amplitude, decreased surface expression, and/or reduced open probability. This talk will focus on three positive allosteric modulators of NMDAR receptor function (24(S)-hydroxycholesterol, pregnenolone sulfate, tobramycin) and two co-agonists (D-serine and D-cycloserine) on their ability to mitigate the diminished function of NMDARs harboring GRIN variants. We examined the effects of these modulators on NMDARs that contained 24 different loss-of-function missense variants in GRIN1, GRIN2A, or GRIN2B. The clinical phenotypes of the patients hosting these variants include epilepsy/seizures and/or developmental delay/intellectual disability. Some patients have autistic behavior or show symptoms of ADHD. For all variants, some aspect of the
reduced function was partially restored. Moreover, some variants showed enhanced sensitivity to positive allosteric modulators compared to wild type receptors. These results raise the possibility that enhancement of NMDAR function by positive allosteric modulators may be a useful therapeutic strategy.
This document provides information about affinity purified secondary antibodies and bulk human anti-mouse antibody (HAMA) reagents from ImmunoReagents. It lists several affinity purified secondary antibodies for various species. It also notes that ImmunoReagents manufactures primary antibodies and antigens using cGMP and QSR compliant procedures and that primary antibodies are used in FDA approved diagnostic assays. Finally, it lists bulk HAMA reagents for several species.
The document summarizes the targeted disruption of the citrinin synthase gene in Monascus purpureus through Agrobacterium tumefaciens-mediated transformation. Key steps include construction of targeting vectors containing homologous regions of the citrinin synthase gene for homologous recombination, transformation of M. purpureus conidia using A. tumefaciens, and selection of transformants using hygromycin resistance. Analysis by PCR, Southern blotting, and two-dimensional electrophoresis confirmed disruption of the citrinin synthase gene.
This document discusses the use of effector proteins in cereal rust fungi to discover new rust resistance genes and accelerate plant breeding. It provides background on known rust resistance genes in wheat and outlines three approaches - bioinformatics, expression profiling, and proteomics - to identify candidate effector proteins. The genomes of cereal rust fungi contain large families of small secreted proteins that may function as effectors. Comparing genomes of different rust races can reveal differences in effector repertoires that explain variations in virulence. Effector proteins can be used to rapidly screen germplasm and assist in cloning resistance genes. This strategy may help develop more durable resistance by targeting highly conserved or fitness-costly effectors.
This document summarizes research on the bile acid receptor GP-BAR1 (TGR5). It finds that GP-BAR1 gene deletion in mice alters intestinal structure and function, increasing intestinal damage and inflammatory markers in colitis models. Activation of GP-BAR1 by bile acids and oleanolic acid protects against gastrointestinal injury caused by non-steroidal anti-inflammatory drugs like aspirin and ciprofloxacin in mice by reducing inflammation and promoting mucosal healing. The findings suggest GP-BAR1 is a potential therapeutic target for treating intestinal inflammation and injury.
Mmc1 2 The Lancet - Supplementary appendix 10/15/2014John Redaelli
This appendix formed part of the original submission and has been peer reviewed.
We post it as supplied by the authors.
Supplement to: Schwartz SD, Regillo CD, Lam BL, et al. Human embryonic stem
cell-derived retinal pigment epithelium in patients with age-related macular degeneration
and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet
2014; published online Oct 15. http://dx.doi.org/10.1016/S0140-6736(14)61376-3.
The loss of other HtrA family members reduces the severity of the Parkinsonian phenotype observed in HtrA2 knockout mice. Multiple HtrA gene knockout mice show a rescue of OPA1 processing, improved mitochondrial respiration, and reduced severity of Parkinsonian phenotypes compared to HtrA2 knockout mice. Deletion of an additional HtrA gene leads to increased mitochondrial activity, improved neuromuscular strength, and modulation of the Parkinsonian phenotype presented in HtrA2 knockout mice.
1) Oxidative stress and mitochondrial dysfunction play a key role in neuronal apoptosis following acute brain injuries like spinal cord injury and traumatic brain injury. 2) The STAT3 transcription factor regulates the expression of the mitochondrial antioxidant enzyme MnSOD (SOD2) which reduces oxidative stress. 3) Activating the IL-6/STAT3/MnSOD pathway may be neuroprotective by reducing mitochondrial oxidative stress and neuronal death following brain injuries.
Fiorucci presents research on the role of bile acids and their activation of nuclear receptors such as FXR in regulating gastrointestinal mucosa integrity. Bile acids are endogenous ligands for FXR and other receptors that modulate inflammation. Activation of FXR was shown to reduce markers of colitis and inflammation in mouse models of inflammatory bowel disease. FXR deficient mice had increased inflammation and tissue damage compared to controls in response to colitis induction. Pharmacological FXR activation also reduced inflammation. This suggests FXR plays an important role in innate immunity and protection of the GI tract from inflammation.
This document summarizes an SNP workshop that discussed challenges with NGS and SNP discovery. It then describes a study that used 454 transcriptome sequencing to discover SNPs in Pacific herring. Researchers sequenced liver and testes tissues separately, assembling over 1.7 million reads into 47,267 contigs. They identified over 16,000 SNPs between tissues and annotated corresponding genomic features. The study provides a workflow and pipeline for targeted SNP discovery.
The Internet provides many educational opportunities for kids, but parents must take steps to protect their children online. Set clear rules for appropriate websites and monitor your child's activity to prevent exposure to inappropriate content. Discuss Internet safety with your kids, teach them not to share personal information with strangers, and use parental control features of browsers and devices to restrict access to certain sites and applications.
The document discusses using various DNA dyes like SYTO 13 for real-time PCR and how dye concentration and DNA sequence composition can affect DNA amplification and melting temperatures. It also briefly mentions topics like myostatin, yeast two-hybrid, BLAST, oysters, abalone, and spiders but provides no context or connections between these terms.
This document provides an overview of dependency relationships, interfaces, and basic behavior modeling in UML. It defines dependencies as relationships between model elements where one element requires the other. Dependency relationships can be further specified using keywords or stereotypes. Interfaces specify a subset of operations and attributes for classifiers to implement. Basic behavior in UML includes state machines, activities, interactions, and use cases, and behavior is always associated with an owning classifier or operation.
The document describes research characterizing how changes in the environment influence the physiology of Vibrio tubiashii. The researchers assessed alterations in V. tubiashii physiology by measuring changes in expression of genes and proteins when exposed to different conditions. They extracted RNA and proteins from V. tubiashii exposed to environments with or without the presence of adult oysters and under varying pH levels. Their results showed that exposure to adult oysters upregulated a chitinase gene in V. tubiashii and expression of the vthB gene increased at two hours then decreased. Changes in pH also altered gene expression patterns. Protein expression analysis identified several virulence-associated pathways in V. tubiash
The document summarizes research from the University of Washington on pathogens affecting shellfish species and genomics research on the Pacific oyster and other shellfish. It describes work identifying the pathogen Vibrio tubiashii, sequencing its genome, and finding genes related to disease tolerance. It also discusses genomics research on Crassostrea gigas and other species looking at responses to Vibrio challenge and disease resistance related to prostaglandins.
1) The study evaluated the effects of two growth hormone receptor (GHR) mutations (p.R229H and c.899dupC) found in a patient with GH insensitivity.
2) Functional studies showed that the p.R229H mutation did not impair GHR signaling or function. However, the c.899dupC mutation resulted in a truncated GHR protein that was unable to activate downstream signaling pathways in response to GH.
3) When coexpressed, the c.899dupC mutation dominantly inhibited the normal signaling of wild-type GHR and the p.R229H variant. This dominant negative effect explains the patient's GH insensitivity phenotype.
Clinical Variant Analysis with VSClinical: Virtus Diagnostics Case Study and ...Golden Helix
It is our pleasure to announce the following speakers for our Golden Helix webcast for the Asia-Pacific region:
Val Hyland, Molecular Genetics Chief Scientist, BA(Mod) PhD, Virtus Diagnostics
Peter Field, Molecular Genetics Supervisor, Virtus Diagnostics
Gabe Rudy, VP of Product & Engineering, Golden Helix
Val Hyland and Peter Field from Virtus Diagnostics (Brisbane) discuss two cases from their cohort of 1095 patients that were screened for inherited diseases using the Illumina 552 genes Inherited Disease screening panel. They found 637 different pathogenic/likely pathogenic variants in 252 genes using a combination of software tools from Golden Helix, including VSClinical, Sentieon and Illumina. This presentation is based on a poster first presented at the HGSA Wellington Conference in 2019 which can be referenced here.
Gabe Rudy from Golden Helix discusses how VSClinical can be used to follow the ACMG & AMP guidelines for the interpretation of germline and somatic variants, respectively. By incorporating new algorithms and annotation sources, detailed variant scoring, classification, and interpretation can occur right within VarSeq without the need for additional, external tools or resources. These capabilities are designed to improved throughput while allowing the lab to maintain consistent quality.
View the webcast recording to learn more about these powerful capabilities:
Streamline germline variant interpretation using the ACMG scoring guidelines with automatic criteria recommendations and incorporated historical data
Quickly determine the oncogenicity of somatic mutations using our automated oncogenicity scoring system
Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation
Mitochondrial ND-1 gene-specific primer polymerase chain reaction to determin...UniversitasGadjahMada
A specificity method to detect mice meat contamination in beef meatballs using specific primer-polymerase chain reaction (PCR) technique has been developed. The primer ND1-P1 primers were designed using primer-BLAST software using mtDNA of mice as a template. The Primer ND1-P1 forward (5’-CGGCATCCTACAACCATTTGC-3’) and reverse (5’-CGGCTCGTAAAGC-TCCGAA-3’) was able to amplify a 294 bp fragment of ND1 gene in mice mtDNA. The primers have been proven precise with only amplify the target fragment in mice meatball but not in another meatball including beef meatball, chicken meatball, pork meatball, horse meatball, and goat meatball. The present of mice meat in meatballs can be detected at a concentration as low as 5% (w/w). The ND1-P1 primer is potentially used as a specific marker for detection of mice meat in the meat products.
Building a platinum human genome assembly from single haplotype human genomes...kmsteinberg
This document summarizes research to build a platinum human genome assembly from long read sequencing of single haplotype human genomes. Last year, a study generated a high quality assembly of CHM1. This year, the researchers generated a new assembly of CHM13 using PacBio sequencing with an N50 of 12.9 Mb. However, analysis with BioNano and Illumina data revealed collapsed regions in the PacBio assembly due to segmental duplications. By integrating the PacBio assembly with BioNano maps, they generated hybrid scaffolds with fewer, larger contigs and resolved the collapsed regions. Comparing the new CHM13 assembly to CHM1 found they were highly consistent with only 13 variant sites, demonstrating the quality
N-methyl-D-aspartate receptors (NMDARs) mediate a slow component of excitatory synaptic transmission that plays important roles in normal brain function and development. A large number of disease-associated variants in the GRIN gene family encoding NMDAR GluN subunits have been identified in patients with various neurological and neuropsychiatric disorders. Many of these variants reduce the function of NMDARs by a range of different mechanisms, including
reduced glutamate potency, reduced glycine potency, accelerated deactivation time course, reduced current response amplitude, decreased surface expression, and/or reduced open probability. This talk will focus on three positive allosteric modulators of NMDAR receptor function (24(S)-hydroxycholesterol, pregnenolone sulfate, tobramycin) and two co-agonists (D-serine and D-cycloserine) on their ability to mitigate the diminished function of NMDARs harboring GRIN variants. We examined the effects of these modulators on NMDARs that contained 24 different loss-of-function missense variants in GRIN1, GRIN2A, or GRIN2B. The clinical phenotypes of the patients hosting these variants include epilepsy/seizures and/or developmental delay/intellectual disability. Some patients have autistic behavior or show symptoms of ADHD. For all variants, some aspect of the
reduced function was partially restored. Moreover, some variants showed enhanced sensitivity to positive allosteric modulators compared to wild type receptors. These results raise the possibility that enhancement of NMDAR function by positive allosteric modulators may be a useful therapeutic strategy.
This document provides information about affinity purified secondary antibodies and bulk human anti-mouse antibody (HAMA) reagents from ImmunoReagents. It lists several affinity purified secondary antibodies for various species. It also notes that ImmunoReagents manufactures primary antibodies and antigens using cGMP and QSR compliant procedures and that primary antibodies are used in FDA approved diagnostic assays. Finally, it lists bulk HAMA reagents for several species.
The document summarizes the targeted disruption of the citrinin synthase gene in Monascus purpureus through Agrobacterium tumefaciens-mediated transformation. Key steps include construction of targeting vectors containing homologous regions of the citrinin synthase gene for homologous recombination, transformation of M. purpureus conidia using A. tumefaciens, and selection of transformants using hygromycin resistance. Analysis by PCR, Southern blotting, and two-dimensional electrophoresis confirmed disruption of the citrinin synthase gene.
This document discusses the use of effector proteins in cereal rust fungi to discover new rust resistance genes and accelerate plant breeding. It provides background on known rust resistance genes in wheat and outlines three approaches - bioinformatics, expression profiling, and proteomics - to identify candidate effector proteins. The genomes of cereal rust fungi contain large families of small secreted proteins that may function as effectors. Comparing genomes of different rust races can reveal differences in effector repertoires that explain variations in virulence. Effector proteins can be used to rapidly screen germplasm and assist in cloning resistance genes. This strategy may help develop more durable resistance by targeting highly conserved or fitness-costly effectors.
This document summarizes research on the bile acid receptor GP-BAR1 (TGR5). It finds that GP-BAR1 gene deletion in mice alters intestinal structure and function, increasing intestinal damage and inflammatory markers in colitis models. Activation of GP-BAR1 by bile acids and oleanolic acid protects against gastrointestinal injury caused by non-steroidal anti-inflammatory drugs like aspirin and ciprofloxacin in mice by reducing inflammation and promoting mucosal healing. The findings suggest GP-BAR1 is a potential therapeutic target for treating intestinal inflammation and injury.
Mmc1 2 The Lancet - Supplementary appendix 10/15/2014John Redaelli
This appendix formed part of the original submission and has been peer reviewed.
We post it as supplied by the authors.
Supplement to: Schwartz SD, Regillo CD, Lam BL, et al. Human embryonic stem
cell-derived retinal pigment epithelium in patients with age-related macular degeneration
and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet
2014; published online Oct 15. http://dx.doi.org/10.1016/S0140-6736(14)61376-3.
The loss of other HtrA family members reduces the severity of the Parkinsonian phenotype observed in HtrA2 knockout mice. Multiple HtrA gene knockout mice show a rescue of OPA1 processing, improved mitochondrial respiration, and reduced severity of Parkinsonian phenotypes compared to HtrA2 knockout mice. Deletion of an additional HtrA gene leads to increased mitochondrial activity, improved neuromuscular strength, and modulation of the Parkinsonian phenotype presented in HtrA2 knockout mice.
1) Oxidative stress and mitochondrial dysfunction play a key role in neuronal apoptosis following acute brain injuries like spinal cord injury and traumatic brain injury. 2) The STAT3 transcription factor regulates the expression of the mitochondrial antioxidant enzyme MnSOD (SOD2) which reduces oxidative stress. 3) Activating the IL-6/STAT3/MnSOD pathway may be neuroprotective by reducing mitochondrial oxidative stress and neuronal death following brain injuries.
Fiorucci presents research on the role of bile acids and their activation of nuclear receptors such as FXR in regulating gastrointestinal mucosa integrity. Bile acids are endogenous ligands for FXR and other receptors that modulate inflammation. Activation of FXR was shown to reduce markers of colitis and inflammation in mouse models of inflammatory bowel disease. FXR deficient mice had increased inflammation and tissue damage compared to controls in response to colitis induction. Pharmacological FXR activation also reduced inflammation. This suggests FXR plays an important role in innate immunity and protection of the GI tract from inflammation.
This document summarizes an SNP workshop that discussed challenges with NGS and SNP discovery. It then describes a study that used 454 transcriptome sequencing to discover SNPs in Pacific herring. Researchers sequenced liver and testes tissues separately, assembling over 1.7 million reads into 47,267 contigs. They identified over 16,000 SNPs between tissues and annotated corresponding genomic features. The study provides a workflow and pipeline for targeted SNP discovery.
The Internet provides many educational opportunities for kids, but parents must take steps to protect their children online. Set clear rules for appropriate websites and monitor your child's activity to prevent exposure to inappropriate content. Discuss Internet safety with your kids, teach them not to share personal information with strangers, and use parental control features of browsers and devices to restrict access to certain sites and applications.
The document discusses using various DNA dyes like SYTO 13 for real-time PCR and how dye concentration and DNA sequence composition can affect DNA amplification and melting temperatures. It also briefly mentions topics like myostatin, yeast two-hybrid, BLAST, oysters, abalone, and spiders but provides no context or connections between these terms.
This document provides an overview of dependency relationships, interfaces, and basic behavior modeling in UML. It defines dependencies as relationships between model elements where one element requires the other. Dependency relationships can be further specified using keywords or stereotypes. Interfaces specify a subset of operations and attributes for classifiers to implement. Basic behavior in UML includes state machines, activities, interactions, and use cases, and behavior is always associated with an owning classifier or operation.
The document describes research characterizing how changes in the environment influence the physiology of Vibrio tubiashii. The researchers assessed alterations in V. tubiashii physiology by measuring changes in expression of genes and proteins when exposed to different conditions. They extracted RNA and proteins from V. tubiashii exposed to environments with or without the presence of adult oysters and under varying pH levels. Their results showed that exposure to adult oysters upregulated a chitinase gene in V. tubiashii and expression of the vthB gene increased at two hours then decreased. Changes in pH also altered gene expression patterns. Protein expression analysis identified several virulence-associated pathways in V. tubiash
The document summarizes research from the University of Washington on pathogens affecting shellfish species and genomics research on the Pacific oyster and other shellfish. It describes work identifying the pathogen Vibrio tubiashii, sequencing its genome, and finding genes related to disease tolerance. It also discusses genomics research on Crassostrea gigas and other species looking at responses to Vibrio challenge and disease resistance related to prostaglandins.
Bay Scallop Genetic Resources and Applicationssr320
This document discusses genomic resources for the bay scallop, including its use as a fishery and aquaculture product. It summarizes research on genes involved in scallop metamorphosis and muscle growth. Specifically, it examines differentially expressed genes during metamorphosis and the role of the myostatin gene in muscle growth, finding it is highly expressed in scallop adductor muscle tissue. The document also discusses using ESTs and markers for environmental response, population genetics, and restoration.
This study explores the wing phenotypes of crosses between male Drosophila melanogaster expressing RNAi targeting specific genes (RNAi driver lines) and female leon mutant flies. Various phenotypes were observed in the offspring wings, including rescue, deterioration, and distortion of wing veins and structures. A correlation between the wing phenotypes and physiological/metabolic functions of the targeted genes was found. Many of the genes are expressed in tissues like the brain, heart, and reproductive organs. The results provide insight into how knocking down gene expression can affect wing development and the roles of the genes studied.
Cloning of the c dna for thyroid stimulating hormone subunit and changes in a...rubycharlie
1) The researchers cloned the cDNA for the thyroid stimulating hormone beta subunit (TSHβ) of the Japanese eel (Anguilla japonica) and investigated changes in the pituitary-thyroid axis during silvering.
2) They found the TSHβ gene contains two introns and three exons, and the protein has a signal peptide and mature peptide. The TSHβ sequence is highly similar to other fish species.
3) In vitro, thyrotropin-releasing hormone increased while thyroxine decreased TSHβ mRNA expression in cultured pituitaries. TSHβ mRNA and serum thyroxine levels both increased during silvering in wild female eels, supporting the
This document reports on a study that sequenced and analyzed the small subunit ribosomal RNA (ssu-rRNA) genes of several protistan parasites - Dermocystidium salmonis, Dermocystidium sp., Ichthyophonus hoferi, and Psorospermium haeckelii. Phylogenetic analyses revealed that these parasites form a novel clade, along with the "rosette agent" parasite of fish. This clade, termed the DRIPs clade, diverges near the divergence of animals and fungi, and may constitute the earliest branching lineage within the animal kingdom based on the most parsimonious analyses. However, the precise phylogenetic position is unclear. This finding
Antarctic blackfin icefish genome reveals adaptations to extreme environments...JenithM
The Antarctic blackfin icefish has genetic adaptations that allow it to survive in extreme Antarctic environments. Its genome reveals that it lacks hemoglobin genes and has a less than 10% oxygen conduction ability, but has an enhanced vascular system and changes in mitochondria. It also produces antifreeze glycoproteins and has a genetic composition that varies depending on environmental exposures like radiation. Researchers constructed a genetic map of the blackfin icefish using RAD-tag sequencing of parents and offspring, identifying over 60,000 RAD-tags to localize markers and assign them to linkage groups corresponding to chromosomes.
The researchers analyzed a sea anemone collected from the East River in New York City. They obtained DNA sequence data from mitochondrial and nuclear genes to identify the species. Comparison to GenBank sequences showed it was Diadumene leucolena, not the initially identified Diadumene lineata. Phylogenetic analysis of mitochondrial cox3 gene sequences supported this finding. While D. leucolena is invasive, it does not appear to threaten local ecosystems. The researchers' molecular data resolved the incorrect initial identification based on morphology alone.
1. The document discusses biological markers of mental disorders that can be measured through post-mortem studies, such as neurotransmitters, related enzymes, and receptors.
2. It describes an experiment where patch clamp technique was used to measure serotonin receptor currents in human platelets, finding that D-serine increased the sensitivity of receptors in normal platelets but decreased it in schizophrenic patient platelets.
3. Preliminary data is presented showing higher levels of D-serine and increased coronary intima thickness in transient ischemic attack patients compared to controls, suggesting higher activity of the serine racemase enzyme.
Integrin V can form heterodimers with several subunits to mediate cell-cell and cell-extracellular matrix interactions. During zebrafish gastrulation, V is expressed maternally and zygotically. Here, we used a morpholino-mediated V knockdown strategy to study V function. Although V morphants displayed vascular defects, they also exhibited left-right body asymmetry defects affecting multiple visceral organs. This was preceded by mislocalization of dorsal forerunner cells (DFCs) and malformation of the Kupffer’s vesicle (KV) laterality organ
Barbaro et al, 2007. comparative study on extracts from the tissue covering thepryloock
1. The study compared properties of tissue extracts from the stingers of freshwater Potamotrygon falkneri and marine Dasyatis guttata stingrays.
2. By SDS-PAGE, the tissue extracts had similar protein bands above 80 kDa, but differences below this mass.
3. P. falkneri tissue extract displayed lethal, dermonecrotic, and myotoxic activities, while D. guttata did not. Both induced similar edema in mice. P. falkneri induced stronger nociception.
1) Rainbow trout were injected with somatostatin-14 (SS-14) or saline and transferred to 20 ppt seawater to examine the effects of SS-14 on the GH-IGF-1 axis and seawater adaptation.
2) SS-14 treated fish showed slightly elevated plasma chloride levels and reduced gill Na+,K+-ATPase activity compared to controls 12 hours after transfer.
3) Transfer to seawater increased mRNA levels of GH receptor 1, GH receptor 2, and IGF-1 in the liver and gills of control fish but SS-14 abolished or attenuated these increases, indicating SS-14 reduces seawater adaptability by inhibiting the GH-
Objective: To study the effects of resveratrol in neuronal structures in traumatic brain injury (TBI).
Study Design: Thirty rats were categorized as (1) control group (n=10), saline solution administered i.p. for 14 days, (2) TBI group (n=10), trauma induced by weight-drop model on brain, and (3) TBI+Resveratrol group (n=10), 15 minutes after injury the rats were given resveratrol (10 μmoL/kg/i.p.) for 14 days. At the end of the experiment the cerebellum was excised for routine paraffin tissue protocol. Blood samples were tested for serum biochemical markers (MDA, SOD, CAT, and GSH-x).
Results: SOD, GPx, and CAT values were lowest in the TBI group. MDA and histological scores of dilations in vessels, inflammation, degeneration in neurons, apoptosis in microglia, ADAMTS8, and GFAP expressions were highest in the TBI group. Sections of the control group showed normal cerebellar histology. The trauma group showed degenerated ganglion layer, pyknotic and apoptotic Purkinje cell nuclei. Vascular thrombus was seen in the substantia alba and substantia grisea. In the Trauma+Resveratrol group, most pa- thologies observed in the TBI group were improved. In the control group, GFAP protein was expressed in granular cells, axons, dendrites, Purkinje cells, and microglia cells. In the trauma group, increased GFAP expression was observed in glial processes, neurons, and Purkinje cells. In the Trauma+Resveratrol group, GFAP was expressed in molecular layer and glial processes. In the control group, ADAMTS-4 activity was observed in granulosa layer, glial cells, and Purkinje cells. In the trauma group, ADAMTS-4 expression was positive in Purkinje cells and glial cells. In the Trauma+ Resveratrol group, ADAMTS-4 was expressed in Purkinje cells, granular cells, and glial cells.
Conclusion: GFAP and ADAMTS-4 proteins may be involved in regeneration of damaged astroglial cells and other glial cells, Purkinje cells, and synaptic extensions. We suggest that antioxidative drugs such as resveratrol may be alternative target agents in neurological disease.
Keywords: ADAMTS-4, brain, cerebellum, GFAP, rat, resveratrol, traumatic brain injury
This study investigated the effects of the angiotensin II type 1 receptor blocker losartan on cell apoptosis and blood-brain barrier integrity following craniectomy in a rat model of traumatic brain injury. Rats underwent craniectomy and were divided into three groups: a control group, a trauma group given saline, and a trauma group given losartan. Losartan treatment was found to decrease TUNEL staining, a marker of apoptosis, in neurons and glial cells compared to the saline group. Losartan also preserved the regular structure of astrocytes near blood vessels, whereas the saline group showed degenerative astrocyte processes. The results suggest losartan may reduce cellular apoptosis and help maintain blood
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Extracellular RNA (ex RNA) exists in nanoparticles called exosomes in human bodies. The document suggests that ex RNA is generated in the meridian, which is a proposed third circulatory system in addition to the blood and lymph systems. The author proposes identifying the meridian first using a specific dye, and then identifying and confirming ex RNA within it to understand the source of exosomes and ex RNA in the body.
The document summarizes research on testing 79 patients for mutations associated with hereditary spastic paraplegia. It finds that 24% of patients had a mutation in the SPG4 gene, while less than 1% had a mutation in the SPG3A gene. It also describes different types of mutations that were identified, such as missense, nonsense, and insertions/deletions. It outlines the methods used to detect known mutations in genes like SPG4 and SPG3A, as well as discover new mutations.
This document describes a technique for bioassaying histamine in the presence of prostaglandins using an Amberlite XAD-2 column. The column removes prostaglandins, rabbit aorta contracting substance, and possibly slow reacting substance of anaphylaxis, but allows histamine to pass through. Two banks of bioassay organs (rabbit aorta strip, rat stomach strip, guinea pig ileum) are used, with one bank above the column and one below. This allows accurate measurement of histamine levels in samples also containing prostaglandins and other substances that interfere with histamine bioassay. The method was tested using effluent from shocked, perfused guinea pig lungs and showed improved accuracy
1) The researchers used whole genome sequence data from 43 stickleback genomes to choose SNP markers for genotyping candidate genes involved in body size divergence. 2) Their criteria for choosing SNPs included a minor allele frequency over 20%, spacing of at least 30 base pairs from other SNPs, and preferentially choosing conserved and size-divergent SNPs. 3) They selected 30 SNPs across 14 candidate genes to genotype 500 stickleback specimens using TaqMan OpenArray. They will analyze associations between genotypes and growth phenotypes to identify genes underlying natural body size variation.
128 phillip d. zamore - 8232260 - in vivo production of small interfering r...Mello_Patent_Registry
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Genetic identity of proprioceptive sensory neuronsAnil Sharma
This document discusses research on proprioceptive sensory neurons (PSNs) which provide sensory feedback for motor control. There is a lack of definitive markers to study PSN subtypes. The researchers aimed to identify subtype markers through single-cell RNA sequencing of PSNs. They identified candidate markers for three PSN subtypes (Ia, Ib, II) through unbiased clustering of sequencing data. Validation experiments in mice, including tracing techniques, supported markers for distinguishing PSN subtypes. The research provides new genetic identifiers for developing and mature PSN populations.
1. Reconstitution of RNA interference (RNAi) in Saccharomyces cerevisiae by expressing RNAi components from other species. RNAi was successfully reconstituted using S. castellii Ago1 and Dcr1, but not human Ago2 and S. castellii Dcr1.
2. Inhibition of Hsp90 using geldanamycin did not reduce RNAi in the reconstituted S. cerevisiae strains, indicating Hsp90 is not required for RNAi in this system.
3. S. castellii Ago1 localized to P-bodies in S. cerevisiae independent of Dcr1, but the origin of small RNAs
Identifying Local Olympia Oyster Stocks Useful for Restorationsr320
Researchers conducted a reciprocal transplant experiment using Olympia oysters from four populations in Puget Sound to examine differences in mortality, growth, and reproduction. They found that oysters from Dabob Bay, which has harsh conditions, survived best when returned to their native site. Oysters from the more productive habitat at Oyster Bay reproduced earlier and more actively when placed in their home site. The results suggest that population of origin and local habitat conditions influence oyster performance, which is important to consider for restoration success in Puget Sound.
Does DNA methylation facilitate phenotypic plasticity in marine invertebrates?sr320
This document summarizes a presentation on whether DNA methylation facilitates phenotypic plasticity in marine invertebrates. The presentation notes that DNA methylation landscape and functions are different in non-vertebrates compared to vertebrates. Studies in the Pacific oyster show their genome is sparsely methylated, with methylation predominantly in transposable elements and gene bodies. Preliminary evidence suggests differentially methylated regions are most common in transposable elements. The presentation hypothesizes that DNA methylation may provide increased phenotypic diversity through transposable elements and response to environmental change, and the lab is beginning to test these hypotheses through studies on environmental impacts like ocean acidification.
Science Communication and Impact: A Researcher's Perspectivesr320
Presentation given at Special Libraries Association - Vancouver, Canada - June 2014. Part of the panel discussion - Staying in the Game: New Roles for Libraries in Research Support
Genomic approaches to assessing ecosystem healthsr320
This document discusses using genomic approaches to assess ecosystem health. It describes how DNA sequencing can generate large amounts of genetic data on variations, gene expression, proteins, and epigenetic alterations like DNA methylation. These biological indicators could then be used to monitor the health of ecosystems. The presentation focuses on a study examining the physiological response and DNA methylation of oysters in Puget Sound exposed to various environmental stressors like urban and agricultural runoff. While sequencing allows easy integration of omics into environmental studies, targeted assays would need to be used for practical applications. Epigenetics and its role in marine invertebrate responses to toxins requires more research but could significantly impact ecosystems.
Collaborative Genomic Data Analyses in the Cloudsr320
This document discusses collaborative genomic data analyses in the cloud. It promotes the benefits of open science such as freely sharing data and using open notebook science to make all research processes transparent. Challenges of open science include managing versioning, provenance, collaboration and ensuring work is discoverable. The document provides examples of using cloud computing for genomic analyses and joining annotation data, and acknowledges contributions from other researchers.
Genomics on the Half Shell: Making Science more Opensr320
Steven Roberts, an associate professor at the University of Washington School of Aquatic and Fishery Sciences, practices open notebook science by making all data and materials from his lab freely available online. This includes slides, data, and his lab notebook, which has evolved over time and is now hosted at sr320.info. He advocates transparency with limited effort to promote open science and sharing, beginning experiments openly from the start.
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This document summarizes research using short-read sequencing to characterize aquacultured shellfish at the genomic level. It describes studies that used RNA-seq to identify genes related to disease tolerance in the hard clam and genes affected by ocean acidification in oysters. It also discusses using MBD-seq and bisulfite sequencing to map DNA methylation sites in the Pacific oyster genome. The availability of shared genomic and transcriptomic data from short-read sequencing was highlighted as facilitating more applications of the technology.
This document discusses using short-read sequencing to characterize genomes in aquacultured shellfish. It presents research on (1) disease tolerance in hard clams using RNA-seq, (2) environmental stress response in Manila clams to ocean acidification through RNA-seq, and (3) DNA methylation patterns in the Pacific oyster using MBD-seq. The availability of shared genomic and transcriptomic sequences from short-read sequencing can help improve aquaculture production by facilitating increased application of the technology.
FISH441: Oysters, acidification and methylationsr320
This study examined the DNA methylation levels of Pacific oysters (Crassostrea gigas) exposed to varying acidified conditions. The researchers found that oysters exposed to low pH conditions exhibited higher levels of DNA methylation compared to oysters in control or high pH treatments. Both diploid and triploid oysters showed similar stress responses to ocean acidification through changes in DNA methylation levels. The results suggest that epigenetic modifications play a role in the phenotypic plasticity of oysters to environmental stressors like ocean acidification.
FISH441: Oyster acidification: gene and protein expression sr320
The document describes an experiment that examined the stress response of Pacific oysters (Crassostrea gigas) to acidification. The objectives were to determine if acidification would induce a stress response, by analyzing expression of genes and proteins involved in the stress response. Oysters of two ploidies (2n and 3n) were exposed to normal and low pH conditions. Results found no significant difference in expression of the heat shock protein HSP70 between pH conditions. Expression of the metalloprotein metallothionein was also analyzed and found to be lower in oysters exposed to low pH. This suggests acidification may induce a stress response in Pacific oysters.
This document summarizes a study on the impacts of hypoxia on gene expression in the Pacific oyster (Crassostrea gigas). The study found that: 1) Hsp70 expression was lower in oysters acclimated to low dissolved oxygen conditions, indicating an adaptive stress response; 2) HIF-1α expression was also lower in low oxygen acclimated oysters; and 3) hrIGF-1 expression was higher in oysters acclimated to low oxygen, suggesting it helps the oysters adapt, grow and survive in hypoxic conditions. The results demonstrate the oysters' ability to adapt their gene expression in response to low oxygen levels through phenotypic plasticity.
This document summarizes a study on the effects of ocean acidification on the development and physiology of Pacific oyster larvae. The study exposed oyster larvae to different levels of CO2 representing current and elevated future atmospheric CO2 levels. Results showed higher CO2 levels delayed development, decreased calcification and growth, and increased expression of stress response genes. The study suggests ocean acidification could negatively impact oyster larvae development and physiology.
This course will discuss innovations in sequencing technologies that have become major tools in aquatic sciences. The class will include presentations from researchers using these technologies, discussions of challenges working with non-model organisms, and a survey of available data analysis tools. Students will learn about applications of large-scale sequencing data to address issues in ecology and natural resource management. As technologies continue advancing rapidly, the course will also cover bioinformatics challenges.
The document summarizes a study that used an integrated molecular approach to examine the response of the Pacific oyster, Crassostrea gigas, to multiple stressors. The study exposed oysters to copper, a common pollutant, and Vibrio tubiashii, a bacterial pathogen. It measured the expression of genes involved in stress response, including heat shock protein 70 (Hsp70), metallothionein IV, and copper oxidase, at the mRNA and protein levels. The results showed that V. tubiashii inhibited the expression of metallothionein IV and copper oxidase, leaving the oysters more vulnerable to copper toxicity. The study demonstrated how one stressor can compromise an
This document summarizes research on how environmental stressors like ocean acidification and elevated temperatures affect Pacific oyster larvae physiology and survival when exposed to disease. The research examines the effects of these stressors individually and in combination on oyster larval development, temperature impacts on the oyster-Vibrio relationship, and an ongoing study on ocean acidification and Vibrio exposure.
The document summarizes research on DNA methylation patterns and epigenetic regulation in the Pacific oyster. Results showed DNA methylation occurs in stress-related genes and may play a regulatory role in immune and stress responses. Understanding genetic and epigenetic influences could increase predictability in selective breeding of oysters. Further evaluating epigenetic mechanisms in bivalves using new methods like whole genome bisulfite sequencing may provide insights with implications for selective breeding, hybrid vigor, and how nutrition affects gene expression through DNA methylation.
This document discusses research into the physiological processes that regulate senescence in sockeye salmon. It describes past research showing that senescence rate is influenced by environmental factors like temperature, climate, humans, salmon density, and stream toxins. Future research plans to focus on the cellular mechanisms of aging by fin clipping and tagging early and late arriving salmon in Hansen Creek, fin clipping daily, and sacrificing fish on days 6 and 7 post tagging to study physiological changes over time.
The document discusses using shellfish as bioindicators to study the impacts of environmental change, such as ocean acidification, on host-pathogen interactions and physiology through 'omic approaches like transcriptomics, proteomics, and investigating DNA methylation and the epigenome. It provides examples of research examining how changes in pH and other stressors influence immune response and pathogen virulence in oysters.
Strategies for Effective Upskilling is a presentation by Chinwendu Peace in a Your Skill Boost Masterclass organisation by the Excellence Foundation for South Sudan on 08th and 09th June 2024 from 1 PM to 3 PM on each day.
Chapter wise All Notes of First year Basic Civil Engineering.pptxDenish Jangid
Chapter wise All Notes of First year Basic Civil Engineering
Syllabus
Chapter-1
Introduction to objective, scope and outcome the subject
Chapter 2
Introduction: Scope and Specialization of Civil Engineering, Role of civil Engineer in Society, Impact of infrastructural development on economy of country.
Chapter 3
Surveying: Object Principles & Types of Surveying; Site Plans, Plans & Maps; Scales & Unit of different Measurements.
Linear Measurements: Instruments used. Linear Measurement by Tape, Ranging out Survey Lines and overcoming Obstructions; Measurements on sloping ground; Tape corrections, conventional symbols. Angular Measurements: Instruments used; Introduction to Compass Surveying, Bearings and Longitude & Latitude of a Line, Introduction to total station.
Levelling: Instrument used Object of levelling, Methods of levelling in brief, and Contour maps.
Chapter 4
Buildings: Selection of site for Buildings, Layout of Building Plan, Types of buildings, Plinth area, carpet area, floor space index, Introduction to building byelaws, concept of sun light & ventilation. Components of Buildings & their functions, Basic concept of R.C.C., Introduction to types of foundation
Chapter 5
Transportation: Introduction to Transportation Engineering; Traffic and Road Safety: Types and Characteristics of Various Modes of Transportation; Various Road Traffic Signs, Causes of Accidents and Road Safety Measures.
Chapter 6
Environmental Engineering: Environmental Pollution, Environmental Acts and Regulations, Functional Concepts of Ecology, Basics of Species, Biodiversity, Ecosystem, Hydrological Cycle; Chemical Cycles: Carbon, Nitrogen & Phosphorus; Energy Flow in Ecosystems.
Water Pollution: Water Quality standards, Introduction to Treatment & Disposal of Waste Water. Reuse and Saving of Water, Rain Water Harvesting. Solid Waste Management: Classification of Solid Waste, Collection, Transportation and Disposal of Solid. Recycling of Solid Waste: Energy Recovery, Sanitary Landfill, On-Site Sanitation. Air & Noise Pollution: Primary and Secondary air pollutants, Harmful effects of Air Pollution, Control of Air Pollution. . Noise Pollution Harmful Effects of noise pollution, control of noise pollution, Global warming & Climate Change, Ozone depletion, Greenhouse effect
Text Books:
1. Palancharmy, Basic Civil Engineering, McGraw Hill publishers.
2. Satheesh Gopi, Basic Civil Engineering, Pearson Publishers.
3. Ketki Rangwala Dalal, Essentials of Civil Engineering, Charotar Publishing House.
4. BCP, Surveying volume 1
This document provides an overview of wound healing, its functions, stages, mechanisms, factors affecting it, and complications.
A wound is a break in the integrity of the skin or tissues, which may be associated with disruption of the structure and function.
Healing is the body’s response to injury in an attempt to restore normal structure and functions.
Healing can occur in two ways: Regeneration and Repair
There are 4 phases of wound healing: hemostasis, inflammation, proliferation, and remodeling. This document also describes the mechanism of wound healing. Factors that affect healing include infection, uncontrolled diabetes, poor nutrition, age, anemia, the presence of foreign bodies, etc.
Complications of wound healing like infection, hyperpigmentation of scar, contractures, and keloid formation.
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
How to Setup Warehouse & Location in Odoo 17 InventoryCeline George
In this slide, we'll explore how to set up warehouses and locations in Odoo 17 Inventory. This will help us manage our stock effectively, track inventory levels, and streamline warehouse operations.
This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.
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Leveraging Generative AI to Drive Nonprofit InnovationTechSoup
In this webinar, participants learned how to utilize Generative AI to streamline operations and elevate member engagement. Amazon Web Service experts provided a customer specific use cases and dived into low/no-code tools that are quick and easy to deploy through Amazon Web Service (AWS.)
Leveraging Generative AI to Drive Nonprofit Innovation
Research Presentation C. McLemore
1. Identification and Isolation
of Stress Related Gene in
Gray (Eschrichtius
robustus) and Fin Whales
(Balaenoptera physalus)
Christin McLemore
June 04, 2009
School of Aquatic and Fishery Science
University of Washington
Box 355020
Seattle, WA 98195
2. Background
• North Pacific is home to over 80 species of cetaceans
• Whales
• Dolphins
• Porpoises
• OrderCetacea
• Sub-Order Odontoceti
• Sub-Order Mysticeti
3. Gray Whale, Eschrichtius robustus
• Sub-Order Mysticeti
• Females are typically 11.7 and 15.2 m in length and males are 11.1 to 14.3
m (Evans 1987).
• Grey colored skin with barnacles (Cryptolepas rachianecti) and barnacle
scars
• Only large whale where the upper jaw extends over the lower jaw
(Reeves, 1987)
4. Fin Whale, Balaenoptera physalus
• Sub-Order Mysticeti
• Males and Females are typically 18 to 21 m, up to 27 m
• Clearly defined grey, white, brown and black, chevron-shaped coloration pattern on
the right side, behind the head and an asymmetrical coloration of the lower jaw:
white on right, dark on left
• The status of Atlantic and Pacific Fin Whale assigned by the Committee on the
Status of Endangered Wildlife in Canada (COSEWIC)
• April 1987 – “of special concern”
• May 2002 – Pacific Fin whale is classified as THREATENED
6. Environmental Factors
• Pollutant
• organochlorine compounds like
DDTs, hexachlorocyclohexanes
(HCHs), chlordane compounds (CHLs) and
polychlorinated biphenyls (PCBs) can disrupt
normal endocrine physiology in marine mammals
(Tanabe, 2002).
• Climate Change
• reduction of available habitat
•the acidification of the oceans as they absorb
growing quantities of CO2
• Disease
• Increased susceptibility of cetaceans to diseases
• reduced reproductive success
•body condition
•survival rates
(World Wide Fund, 2007)
7. Objectives
• Identification of genes of interest
•Glutathione S-transferase A4 (GStra)
• Superoxide dismutase [Cu-Zn] (SD)
• Heat shock 70kDa protein 6 (HSP6)
• Interleukin-2 precursor (IL-2)
• Interleukin 17 (IL17)
• Interleukin 13 precursor (IL13)
• Toll-like receptor 5 (TLR5)
• Cyclooxygenase (COX-2)
• Isolation of the expressed gene of interest
• Interleukin 17
• Prostaglandin-endoperoxide synthetase-2
• tRNA synthetase
• Glutathione S-transferase A4
• Homology of genes from other organisms with Grey and Fin Whale
8. Results
Figure 1: Row one: Lane (1)100 bp ladder, (2) Figure 2: Lane (1) 100 bp ladder, (2) Negative
Negative control Gstra, (3) Grey whale Gstra, (4) control IL17, (3) Grey whale IL17, (4) Fin whale
Fin whale Gstra, (5) Negative control HSP6, (6) IL17, (5) Negative control IL13, (6) Grey whale
Grey whale HSP6, (7) Fin whale HSP6, (8) Negative IL13, (7) Fin whale IL13, (8) Negative control
control SD, (9) Grey whale SD, (10) Fin whale SD. IL2, (9) Grey whale IL2, (10) Fin whale IL2, (11)
Row 2: Lane (1) 100 bp ladder, (2) Negative control Negative control TLR5, (12) Grey whale
COX2, (3) Grey whale COX2, (4) Fin whale COX2. TLR5, (13) Fin whale TLR5, (14) 100 bp ladder.
21. Acknowledgement
Dr. Steven Roberts
Research Scientist
Sam White
National Oceanic and Atmospheric Association
Seattle, Washington
Jina Ylitalo
Capstone Coordinator
Greg Jensen
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of endothelial cell tight junctions. Endothelium, 14:333-343.