Evolution2014 desert mouse talk
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This document discusses research on the desert rodent Peromyscus eremicus and its adaptation to desert conditions. Genome sequencing and analysis revealed signals of positive selection in genes related to water balance and osmoregulation. Physiological experiments showed changes in electrolyte levels and weight in response to water deprivation. RNA sequencing of kidneys identified differential expression of genes involved in extracellular matrix and solute transport. Correlation of gene expression with physiology supported roles for aquaporin 2, solute carrier 2a9, and solute carrier 22a11 in osmoregulation. The research aims to combine genomics, physiology and natural selection to understand P. eremicus' adaptations to desert environments.
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Real-time phylogenomics or 'Some interesting problems in genomic big data' discusses the opportunities and challenges presented by rapidly increasing genomic data. The author details their experiences field sequencing plant genomes and shows how partial and real-time data can still enable species identification. Evolution is complex with gene duplications, inversions, hybridization and horizontal gene transfer common. With thousands of sequencing machines producing billions of base pairs daily, managing and analyzing the "genomic big data" will require scalable tools and models to connect the data and enable reproducible and sustainable research.
9 27-2012 -long
This document summarizes research on the effects of temperature on longevity in C. elegans. Microarray analysis identified lysosomal protease genes that are differentially expressed at 15°C vs 25°C. Follow up experiments showed that lysosome structure and number are altered at elevated temperatures. RNAi of temperature-regulated proteases caused progressive paralysis specifically at 15°C, indicating a role in neuronal health. Further experiments traced this paralysis to dysfunction of motor neurons rather than muscles. The research suggests that proteostasis, particularly lysosomal function, is important for neuronal health under cool temperatures and influences longevity.
Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison
This document discusses domestication, polyploidy, and genomics of crops and weeds. It notes that most major crop species were domesticated around 10,000 years ago, with a few more recently. Polyploidy, or whole genome duplication events, have also played an important role in crop evolution. The document examines genome sizes and components of various crop species, and notes that repetitive elements like transposons can make up large proportions of plant genomes. Differences in repetitive sequences between microspecies of dandelion are also discussed.
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Nowadays, PCR is an indispensable technique used in medical and biological Research labs. Developed in 1983, PCR is a versatile technique that allows a wide spectrum of applications. From the simplest applications, an amplification using plasmid or genomic sequences as template, to the Diagnosis of Hereditary or infectious diseases, the identification of Genetic fingerprints for Cloning, Mutagenesis, Sequencing or the analysis of Gene function.
Canvax™ offers a complete range of high quality PCR products with a proven track record of greatest performance in most common applications, like Routine PCR, Hot Start & Real Time PCR, High Fidelity PCR, Ultra High Fidelity, and more related Polymerases and Enzymes. Our Horse-Power™ and FastPANGEA™ products are specially designed to enhance the results of your research.
Tissue Culture and Cloning Work
This document summarizes work done on culturing crocodile cell lines and cloning the parc gene from Pseudomonas keratitis. Primary crocodile cell lines were established from various organs and immortalized using hTERT. The parc gene was cloned from mutant and wild-type Pseudomonas strains and will be expressed and crystallized to study its role in quinolone antibiotic resistance.
Roberts Insight
This document summarizes research on how environmental stressors and changes impact the expression of genes in oysters. The summary is:
[1] The research program examines how environmental stressors such as pathogens, carbon dioxide, mechanical stress, and anthropogenic activities affect the oyster stress response at the transcriptome, proteome, and epigenome levels.
[2] Studies found that multiple environmental stressors can interact to reduce an oyster's ability to respond to stress, and that characterizing gene expression in natural oyster populations exposed to different human impacts provided insight into their biology and adaptation.
[3] DNA methylation is an important mechanism in oysters for transcriptional control that can be impacted
Lec.1 Introduction Prokaryote_and_Eukaryote
This document summarizes Lecture 1 of the Wet-Lab course which covers prokaryotic and eukaryotic cells using bacteria and yeast as examples. It introduces the central dogma of biology and compares the structures and gene expression of prokaryotic cells like bacteria and eukaryotic cells like yeast. Specific topics covered include the structures of E. coli and B. subtilis, bacterial operons, the lac operon, and how yeast undergo fermentation.
Molecular_bilogy_lab_report_2
This laboratory report summarizes an experiment exploring RNA splicing in Drosophila melanogaster. Genomic DNA and total RNA were extracted from fruit flies and used to study the rngo gene. PCR and RT-PCR were performed on the genomic DNA and cDNA samples. The genomic PCR product was cloned and sequenced. Bioinformatics analysis showed the genomic sequence was longer, containing introns absent from the cDNA, indicating splicing of the rngo pre-mRNA. Future work could investigate other splicing sites and homology to human genes.
6 26-2012
This document summarizes research on mechanisms of longevity and aging in C. elegans. Key findings include:
- 23-26% of longevity is genetic, with the remaining 75% due to environmental factors.
- Genes involved in proteostasis and the unfolded protein response are differentially regulated by temperature and genotype. Inhibition of certain proteostasis genes increases lifespan at 25°C but decreases it at 15°C.
- Neurodegeneration caused by RNAi of proteostasis genes starts in motor neurons with fewer synaptic connections. This suggests impaired neuronal maintenance or function at cooler temperatures.
- In wild type worms, RNAi of UPR genes hsp-3 and hsp-4
Sfnge array poster
This study examined how chronic physical restraint stress alters gene expression in mouse spleens. Mice were subjected to restraint stress for 12 hours per day for two days. Microarray analysis found that 48 out of 225 apoptosis- and p53 signaling-related genes showed significant expression changes in stressed mice compared to unstressed controls. Four genes (Fas, FADD, p53, p21) were validated with real-time PCR. The results provide evidence that apoptotic pathways contribute to stress-induced lymphopenia and identify potential stress response biomarkers.
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This study aimed to clone homologous genes of SND1, a key regulator of secondary cell wall biosynthesis, from Populus trichocarpa. The researcher amplified four SND1 homologs from P. trichocarpa cDNA using PCR. The amplified genes were cloned into E. coli and sequenced. Two colonies were found to contain the correct SND1 sequence insert, while others were false positives. Further work will express and quantify the proteins and determine their effects on other genes and phenotypes.
Reducing off-target events in CRISPR genome editing applications with a novel...
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The CRISPR-Cas9 system demonstrates unparalleled genome editing efficiency in a broad range of species and cell types, but it suffers from concerns related to target specificity. Modified guide RNAs and mutant Cas9 proteins have been developed to reduce off-target editing but, in many cases, the alterations also significantly reduce on-target editing performance. In this presentation, Dr Chris Vakulskas discusses a novel, high-fidelity Cas9 protein that reduces off-target gene editing, while maintaining high on-target activity. Dr Vakulskas presents data from the development of the new Alt-R® S.p. HiFi Cas9 Nuclease 3NLS and describes its usefulness in mitigating unwanted off-target gene editing, without the issues associated with transfection of plasmid DNA.Principles of DNA isolation, PCR and LAMP
1. The document discusses principles of DNA isolation and purification as well as polymerase chain reaction (PCR). It describes how cells are broken to release DNA and the components of extraction buffers used to isolate DNA.
2. The three main steps of PCR - denaturation, annealing, and elongation - are explained. Denaturation separates DNA strands, annealing attaches primers, and elongation duplicates the DNA. Required PCR reagents and their roles are also outlined.
3. Loop-mediated isothermal amplification (LAMP) is introduced as an alternative to PCR that amplifies DNA at a constant temperature. LAMP uses multiple primers and has advantages like lower cost and faster results. The mechanism and applications of LAMP are summarized.
DNA Analysis - Basic Research : A Case Study
The document discusses using the QIAxcel system for analyzing DNA fragments from genetic analyses like genotyping and mapping mutant genes. It provides examples of using the QIAxcel to genotype Arabidopsis thaliana plants with CAPS markers for a pks3 mutant allele. The system allows accurate sizing of DNA fragments in a high-throughput manner to unambiguously identify genotypes. It also discusses using the QIAxcel to analyze alternative splicing patterns regulated by the Tra2β protein to identify roles of its domains. The system provides rapid, sensitive and reproducible analysis of splicing patterns.
The biodegradation of Polystyrene
This document summarizes a research study on the biodegradation of polystyrene foam by microorganisms found in a landfill in Thailand. Samples of microbes were taken from polystyrene foam and contaminated soil in the landfill. The microbes were cultured with polystyrene as the sole carbon source to identify those capable of degrading it. Analysis of the cultures over time found shifts in the dominant microbial species. Selected species were identified through molecular techniques as known aromatic compound degraders, including Herbaspirillum seropedicae and Ochrobactrum sp. Scanning electron microscopy was used to observe physical changes to polystyrene exposed to the cultures, indicating biodegradation
Arnab kumar de
This document discusses methods for analyzing transgenic plants, including determining if a plant is transgenic and if transgenes are expressed. It describes established methods like PCR, Southern blots, and Northern blots. Southern blots are used to confirm transgene insertion into the genome by detecting fragments of different sizes after restriction enzyme digestion and gel electrophoresis. Northern blots detect RNA transcripts to confirm transgene expression. Proper experimental design and controls are important to avoid false positives and obtain conclusive evidence of stable transgene integration and expression.
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Genetics Presentation - Meiping Sun and Jason Dillon - works cited
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Domestication, polyploidy and genomics of crops #PAGXXV Heslop-Harrison
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The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
ESR spectroscopy in liquid food and beverages.pptx
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
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The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
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Equivariant neural networks and representation theory
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
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mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
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Evolution2014 desert mouse talk
- 1. Understanding Adaptation to Deserts in Peromyscus eremicus Matthew MacManes University of New Hampshire ! Twitter: @PeroMHC macmanes@gmail.com
- 2. How do desert animals survive???
- 3. Climate Change ! ! ! It’s getting hotter It’s getting drier IPCC 2007 Report on Climate Change
- 4. Peromyscus eremicus: model species for the study of adaptation
- 5. Adaptation • Anatomy/Physiology/Metabolism/Behavior • Genetics • Allelic diffs • Expression diffs • Pathway diffs • Epigenetics
- 6. Peromyscus eremicus as a model organism • Genome sequence • 2.6Gb - Illumina short insert + mate pair + PacBio • 89k scaffolds, CEGMA 85% core genes NG50 max 30kb 610kb
- 7. Peromyscus eremicus as a model organism • Annotation • Automated + manual curation • Informatics, RNAseq CpGi liver brain testes kidney CpGiZbt20 Slc27a5
- 8. Branch-site model of positive selection P. eremicus P. maniculatus Mus Rattus
- 9. Branch-site model of positive selection Prostaglandin R3 ω=237 Best1 ω=999 Slc36a1 ω=1.2 Slc38a8 ω=999 Slc2a9 ω=254 ABC9A ω=123 (80 others) P. eremicus P. maniculatus Mus Rattus
- 10. Branch-site model of positive selection Prostaglandin R3 ω=237 Best1 ω=999 Slc36a1 ω=1.2 Slc38a8 ω=999 Slc2a9 ω=254 ABC9A ω=123 (80 others) P. eremicus P. maniculatus Mus Rattus Aquaporins absent
- 11. Captive animals - Experimental Genomics
- 12. Experimental Genomics Cool - water Cool + water Hot - water Hot + water ]Cool + RH Hot + RH
- 13. Experimental Genomics Cool - water Cool + water Hot - water Hot + water ] ! •RNAseq •ChIPseq •BiSeq Cool + RH Hot + RH
- 14. Experimental Genomics Cool - water Cool + water Hot - water Hot + water ] ! •RNAseq •ChIPseq •BiSeq RNAi CRISPR-Cas9 Cool + RH Hot + RH
- 15. Winter: ± water Cool - water ! Weight: -35% Na: 165 K: 7.0 BUN: 55 Cr: 0.3 Cool + water ! Weight: ~20gm Na: 151 K: 8.1 BUN: 46 Cr: 0.2 !
- 16. RNAseq - kidneys • RNAseq • 10-20M reads per sample • Mapped reads to genome using STAR • eXpress -> filter low abundance transcripts • DESeq2
- 17. RNAseq - kidneys wet dry 1e−01 1e+01 1e+03 1e+05 −3−2−10123 mean of normalized counts log2foldchange
- 18. Number of genes GO:0004872 GO:0005488 GO:0005576 GO:0022610 GO:0031012 PC00102 0 20 40 60 80 Gene Ontology Enrichment Extracellular Matrix Protein Extracellular Matrix Biological Adhesion Extracellular Region Binding Receptor Activity
- 19. Number of genes GO:0004872 GO:0005488 GO:0005576 GO:0022610 GO:0031012 PC00102 0 20 40 60 80 Gene Ontology Enrichment Extracellular Matrix Protein Extracellular Matrix Biological Adhesion Extracellular Region Binding Receptor Activity
- 20. 350 400 450 500 155160165170 Na vs AQP2 AQP2 expression SerumSodium 350 400 450 500 105110115120125 Cl vs AQP2 AQP2 expression SerumChloride dry wet 350400450500 Aquaporin 2 FPMK PEER PEMA Mus Rattus ω=NS Combining Physiology, Expression, Nat. Selection
- 21. Combining Physiology, Expression, Nat. Selection 30 35 40 45 155160165170 Na vs Slc2a9 Slc2a9 expression SerumSodium 30 35 40 45 105110115120125 Cl vs Slc2a9 Slc2a9 expression SerumChloride dry wet 30354045 Slc2a9 FPMK PEER PEMA Mus Rattus ω=254
- 22. 10 20 30 40 50 60 70 155160165170 Na vs Slc22a11 Slc22a11 expression SerumSodium 10 20 30 40 50 60 70 105110115120125 Cl vs Slc22a11 Slc22a11 expression SerumChloride dry wet 10203040506070 Slc22a11 FPMK PEER PEMA Mus Rattus ω=NS Combining Physiology, Expression, Nat. Selection
- 23. Summary • Summary • Strong signal of lineage-specific positive selection. • Physiological differences with water deprivation • Differential gene expression • Solute carriers seem important • Aquaporins might be boring…
- 24. Questions? @PeroMHC macmanes@gmail.com Poster Tonight #120 Lindsay Havens:Ladybugs www.spotaladybug.com Lightning talk: Rm 304 9:10AM