Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
This study analyzed variation in heat shock protein (Hsp) genes between populations of the copepod Tigriopus californicus along the California coast to identify potential functional differences related to local adaptation. The researchers found amino acid variation in two Hsp genes, Hsp70 and Hsp-β, between northern and southern populations. Heterologous expression of the different alleles in E. coli found that the southern Hsp-β allele conferred greater thermotolerance than the northern allele, suggesting functional divergence between populations.
The document compares the efficiency of five commercial DNA extraction kits for extracting DNA from faecal samples. Two students, Maria Carolina Rave Aguirre and Maria Isabel Palacio, conducted experiments extracting DNA from stool samples using the five kits. They evaluated the DNA yield, purity, and integrity produced by each kit. Quantitative PCR was also used to analyze the extraction of three common gut bacteria. The students found that some kits produced higher DNA yields and purity than others. They concluded that different techniques can be used to extract DNA from stool with varying effectiveness, and that analyzing gut microbiota is important for understanding diseases.
This study analyzed genetic diversity in indigenous chicken populations from Iraq. Fifty-six samples were collected from four locations and sequenced to identify mitochondrial DNA haplogroups. Eleven haplotypes belonging to three haplogroups were found. Haplogroup D was most common, seen in 50 chickens, while haplogroups A and B occurred at low frequencies. Genetic diversity varied between locations. The high frequency of haplogroup D supports an origin in the Indian subcontinent for Iraqi village chickens. Rare haplogroup B may result from recent introgression with commercial chickens, while haplogroup A could be linked to historical visitors rather than coastal trade.
EWMA 2014 - EP422 CHRONIC WOUND-DERIVED BACTERIA IN BIOFILM FORM SHOWS HIGH L...EWMA
Louise Suleman conducted a study assessing the proteolytic activity of bacteria isolated from human and equine chronic wounds. Bacteria were tested in both planktonic and biofilm forms. The results showed that Pseudomonas aeruginosa displayed higher proteolytic activity than Staphylococcus aureus. Human-derived P. aeruginosa had significantly higher activity in biofilm form compared to planktonic. Collagen zymography identified a 55kDa protease secreted by human P. aeruginosa biofilms and equine P. aeruginosa in both forms. Differences in proteolytic profiles between human and equine bacteria may be due to wound environment factors. Further research is needed to determine if this protease acts as a virulence factor in chronic wound progression.
Survival of the weakest: is evolution on our side?SMACC Conference
The 1%. Jeremy Cohen examines what makes us unique. Are there observable genetic traits that will determine how we respond to severe illness and can we measure them?
Genetic and Molecular Characterization of a Dental Pathogen Using a Genome-Wi...shabeel pn
This document discusses genetic and molecular characterization of Actinobacillus actinomycetemcomitans (A.a.), a dental pathogen, using genomic approaches. Key points include:
1) A.a.'s genome has been sequenced which will help study its iron acquisition systems, Fur and iron regulons, and virulence factors.
2) A rat model has been used to study A.a. pathogenesis and induced colonization, immune response, and bone loss similar to human infections.
3) Future studies aim to use genomics and DNA microarrays to better understand A.a. biology, host-pathogen interactions, and develop new therapies.
This study identified Chiriya 7 as a resistant wheat genotype against Bipolaris sorokiniana, the causal agent of spot blotch disease in wheat. Differentially expressed genes in the resistant Chiriya 7 and susceptible Sonalika genotypes were identified using suppression subtractive hybridization. Over 1500 clones were obtained from the cDNA library, of which more than 150 were sequenced. Twelve genes were categorized as defense-related genes. Real-time PCR analysis confirmed the role of the TaDSPK gene in the defense response against B. sorokiniana in wheat. Chiriya 7 is a promising source of resistance genes against this important wheat pathogen.
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
This study analyzed variation in heat shock protein (Hsp) genes between populations of the copepod Tigriopus californicus along the California coast to identify potential functional differences related to local adaptation. The researchers found amino acid variation in two Hsp genes, Hsp70 and Hsp-β, between northern and southern populations. Heterologous expression of the different alleles in E. coli found that the southern Hsp-β allele conferred greater thermotolerance than the northern allele, suggesting functional divergence between populations.
The document compares the efficiency of five commercial DNA extraction kits for extracting DNA from faecal samples. Two students, Maria Carolina Rave Aguirre and Maria Isabel Palacio, conducted experiments extracting DNA from stool samples using the five kits. They evaluated the DNA yield, purity, and integrity produced by each kit. Quantitative PCR was also used to analyze the extraction of three common gut bacteria. The students found that some kits produced higher DNA yields and purity than others. They concluded that different techniques can be used to extract DNA from stool with varying effectiveness, and that analyzing gut microbiota is important for understanding diseases.
This study analyzed genetic diversity in indigenous chicken populations from Iraq. Fifty-six samples were collected from four locations and sequenced to identify mitochondrial DNA haplogroups. Eleven haplotypes belonging to three haplogroups were found. Haplogroup D was most common, seen in 50 chickens, while haplogroups A and B occurred at low frequencies. Genetic diversity varied between locations. The high frequency of haplogroup D supports an origin in the Indian subcontinent for Iraqi village chickens. Rare haplogroup B may result from recent introgression with commercial chickens, while haplogroup A could be linked to historical visitors rather than coastal trade.
EWMA 2014 - EP422 CHRONIC WOUND-DERIVED BACTERIA IN BIOFILM FORM SHOWS HIGH L...EWMA
Louise Suleman conducted a study assessing the proteolytic activity of bacteria isolated from human and equine chronic wounds. Bacteria were tested in both planktonic and biofilm forms. The results showed that Pseudomonas aeruginosa displayed higher proteolytic activity than Staphylococcus aureus. Human-derived P. aeruginosa had significantly higher activity in biofilm form compared to planktonic. Collagen zymography identified a 55kDa protease secreted by human P. aeruginosa biofilms and equine P. aeruginosa in both forms. Differences in proteolytic profiles between human and equine bacteria may be due to wound environment factors. Further research is needed to determine if this protease acts as a virulence factor in chronic wound progression.
Survival of the weakest: is evolution on our side?SMACC Conference
The 1%. Jeremy Cohen examines what makes us unique. Are there observable genetic traits that will determine how we respond to severe illness and can we measure them?
Genetic and Molecular Characterization of a Dental Pathogen Using a Genome-Wi...shabeel pn
This document discusses genetic and molecular characterization of Actinobacillus actinomycetemcomitans (A.a.), a dental pathogen, using genomic approaches. Key points include:
1) A.a.'s genome has been sequenced which will help study its iron acquisition systems, Fur and iron regulons, and virulence factors.
2) A rat model has been used to study A.a. pathogenesis and induced colonization, immune response, and bone loss similar to human infections.
3) Future studies aim to use genomics and DNA microarrays to better understand A.a. biology, host-pathogen interactions, and develop new therapies.
This study identified Chiriya 7 as a resistant wheat genotype against Bipolaris sorokiniana, the causal agent of spot blotch disease in wheat. Differentially expressed genes in the resistant Chiriya 7 and susceptible Sonalika genotypes were identified using suppression subtractive hybridization. Over 1500 clones were obtained from the cDNA library, of which more than 150 were sequenced. Twelve genes were categorized as defense-related genes. Real-time PCR analysis confirmed the role of the TaDSPK gene in the defense response against B. sorokiniana in wheat. Chiriya 7 is a promising source of resistance genes against this important wheat pathogen.
1) The document describes a study investigating the epigenetic regulation of induced pluripotent stem cell (iPSC) reprogramming through genome-wide analysis of histone X localization using next-generation sequencing and computational analysis with Python.
2) The study found that histone X enrichment occurs near stem cell-specific gene promoters, such as Pou5f1 and Nanog, at the early stages of cell reprogramming, prior to full gene activation.
3) Gene ontology analysis revealed histone X is involved in biological processes important for stem cell pluripotency, such as embryonic development and stem cell maintenance. This suggests histone X participates in activating stem cell genes during the initiation
Presentation at COMBIO 2016 in the small ORF/peptide symposium. hew I talk about our work on ascorbate (vitamin C) and out identification and characterisation of a small uORF that regulate translation on ascorbic acid and the relevance of this to Iron deficiency anemia.
Development of Monoclonal Antibodies -Creative BiolabsCreative-Biolabs
This document discusses several methods for developing monoclonal antibodies: hybridoma technology which fuses B cells and myeloma cells to produce hybridomas; surface display technology which uses genetic engineering to display antibody fragments on surfaces like phage, bacteria or yeast for screening; and transgenic technology which uses transgenic mice to produce monoclonal antibodies. It also describes Creative Biolabs' services for monoclonal antibody development including hybridoma generation and screening as well as in vitro surface display technologies.
Welcome to Creative Biolabs. As a new preparation technology for genetically engineered antibodies, antibody library technology has important theoretical and practical value in the cloning of human antibodies, antibody performance modification, and antibody gene research. Here, we will explore the de novo antibody library screening technologies and the corresponding services.
This document provides a catalog of DNA purification kits from a supplier, including kits for cleaning up and extracting DNA from various sources like PCR reactions, agarose gels, blood, bacteria, plants, and more. It lists the product names, descriptions, catalog numbers, available sizes, and prices in Euros. Various kit types are designed for different sample sizes and volumes, and include options for increased efficiency, gravity flow columns, or 96-well plate formats.
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.
New technologies for manufacturing recombinant products in embryonated eggsEluemuno R Blyden
New non-GMO vector technologies for expressing recombinant proteins in hen eggs offer a novel development and production platform for biologics and vaccines. By upgrading egg-based manufacturing, these technologies bring a wealth of experience and resources to the 21st Century fight against emerging diseases. The AdCEV(TM) vector technology developed by AfriVax and the Sendai Virus vector technologies can potentially improve manufacturing in eggs by increasing yields, expanding the repertoire of possible products, and increasing biosafety. With AdCEV(TM) technology, eggs can be used as miniature bioreactors for rapidly manufacturing a wide range of high-value biopharmaceuticals. The speed with which recombinant products can be developed, scaled and manufactured with these technologies offers a unique competitive advantage compared to other industrial technologies like cell culture and plants.
129 andrew z. fire - 8283329 - genetic inhibition of double-stranded rnaMello_Patent_Registry
Andrew Z. Fire, Stephen A. Kostas, Mary K. Montgomer, Lisa Timmons, SiQun Xu, Hiroaki Tabara, Samuel E. Driver, Craig C. Mello - Genetic Inhibition of Double-Stranded RNA
Recombinant Antibody Overview II - Creative BiolabsCreative-Biolabs
It is created by Creative Biolabs who is specialized in providing recombinant antibodies and engineered antibodies. The part two of recombinant antibody overview, we will explain introduction of recombinant antibody ant recombinant antibody expression.
The one-step RT-qPCR assay developed by Exopol S.L. was able to detect a wide variety of ruminant pestiviruses with excellent specificity and good sensitivity down to 102 copies per reaction. Testing on 272 clinical samples identified BVDV/BDV in 17.1% of cattle and 16.7% of sheep samples, with most positive cases in reproductive swabs and blood/serum. The assay provides a reliable and sensitive diagnostic tool for routine detection of pestiviruses in ruminants.
09 elisa kits for hemangioma of bone researchElabscience
Hemagioma can occurs in all parts of the body, and it may also occurs
in bone, but the latter is more rare than the others parts of body.
Hemangioma of bone sometimes exists with hemangioma of other parts at
the same time, it is a common tumor of benign tumor attached in bone
tissue.More info visit: http://www.elabscience.com
Updates on the ACP v3 genome and annotation from USDA NIFA project meetingSurya Saha
ACP version 3 genome, official gene set version 3 and Isoseq transcriptome
Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha
5th Annual Meeting
Indian River State College
Fort Pierce, FL
IRJET- Effect of Various Factors on Growth and L- Asparaginase Production...IRJET Journal
The article discusses international issues. It mentions that globalization has increased economic interdependence between nations while also raising tensions over immigration and trade. Solutions will require cooperation and compromise and a recognition that isolationism is not a viable strategy in an interconnected world.
Dr. Randy Prather - Porcine Reproductive and Respiratory Syndrome Virus Resis...John Blue
Porcine Reproductive and Respiratory Syndrome Virus Resistant Pigs - Dr. Randy Prather, University of Missouri, from the 2015 North American PRRS Symposium, December 4 - 5, 2015, Chicago, IL, USA.
More presentations at http://www.swinecast.com/2015-north-american-prrs-symposium
Mining Saccharomyces diversity and experimental evolution for cellulosic biofuelDavid Peris Navarro
This document summarizes research on using yeast diversity and experimental evolution to develop yeast strains for cellulosic biofuel production. Key points include:
- There is genetic diversity within the Saccharomyces genus that can be exploited, including species with better tolerance to toxins produced during biomass hydrolysis.
- Hybridization of tolerant non-S. cerevisiae species with engineered S. cerevisiae strains can combine beneficial traits.
- Experimental evolution of hybrid strains under hydrolysis conditions leads to strains with improved growth and xylose consumption.
- Genome sequencing shows adaptations involve new mutations, chromosomal rearrangements, and changes in gene copy number.
The rise of the yeast genus Saccharomyces: biodiversity and evolutionDavid Peris Navarro
The document discusses the rise of the yeast genus Saccharomyces, focusing on its biodiversity and evolution. It summarizes research showing that Saccharomyces yeasts are geographically structured and phenotypically diverse. While nuclear gene flow between species is limited, mitochondrial and 2μm plasmid gene flow is more common. Gene flow can impact phenotypes, and mitochondrial inheritance influences temperature tolerance. The origin of the parental S. eubayanus donor for lager yeast strains remains unknown.
Reticulate evolution in yeasts and its industrial applicationsDavid Peris Navarro
This document summarizes research on reticulate evolution in yeasts and its industrial applications. Reticulate evolution refers to evolution occurring through hybridization and introgression rather than strictly vertical descent. The document discusses how hybridization has contributed to the diversification and domestication of yeasts like Saccharomyces cerevisiae. It also explores how mining genomic diversity through hybridization could enable new industrial applications, such as developing yeast strains capable of growth at lower temperatures or utilizing additional carbon sources.
IN-SILICO CHARACTERISATION OF PROTEIN CODED BY CYT-B GENE OF Radopholus simil...Amit Yadav
Of the more than 30 species in the genus Radopholus, the burrowing nematode, Radopholus similis, is the only pathogen of widespread economic importance (Duncan and Moens, 2006). Radopholus similis is a migratory endoparasitic nematode that is known to be a destructive pest of citrus crops, pepper and, most importantly, banana, on which it causes toppling disease. The nematode causes economic problems throughout the world, most notably in warmer regions, including South America, the Caribbean, Africa, Asia and the Pacific.
Saccharomyces genus as a model of evolution and industrial applicationsDavid Peris Navarro
Saccharomyces genus offers a huge diversity that can be mined for different industrial applications (wine, beer, biofuels, and others). MITOGRESSION seeks to develop new strains via hybridization and different mitochondrial-nuclear combinations.
Saccharomyces has become a model genus for evolution and genomics. Improvements in genome sequencing and isolation protocols will allow us to produce high-quality genome sequences for all the major populations and lineages. In the mean time, multilocus phylogenetic and population genetic approaches are helping classify our strain collection for population genomic studies. In this talk, I will introduce some of the advances we have made in the description of populations of the newly discovered species S. eubayanus, the wild stock of lager-brewing hybrids. Using a combined pipeline of population and phylogenetic studies, we have described two well-differentiated populations in Patagonia (Argentina), indicating that S. eubayanus is native. Although S. eubayanus may not be endemic to South America, it is likely native. Lager-brewing hybrids isolated in Europe showed shared alleles with the S. eubayanus population P-B (L) and had low genetic diversity, suggesting the S. eubayanus alleles involved in hybridization were drawn from a small subpopulation derived from P-B (L). From our Wild YEAST Program, a yeast isolation project conducted by undergraduate students and citizen scientists from across the world, we identified three new S. eubayanus strains from Sheboygan, WI (USA). In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. To capture reticulation and summarize it in a phylogenetic framework, we combine state-of-the-art Bayesian methods with phylogenetic network analysis. Our findings support the hypothesis that genetically divergent microbes can produce rare but economically important hybrids when they migrate from their natural ecological context.
This study identified a novel gene, WHI2, that improves acetic acid resistance in Saccharomyces cerevisiae through overexpression. The key findings were:
1) A genomic library screen identified WHI2 overexpression as enhancing glucose and xylose fermentation under acetic acid stress.
2) WHI2-overexpressing strains showed 5-times-higher ethanol productivity compared to controls under acetic acid stress.
3) Endogenous WHI2 expression is induced by acetic acid, and WHI2 deletion strains are hypersensitive to acetic acid, indicating its role in the acetic acid response.
4) Overexpression of WHI2 and the phosphatase gene PSR
1) The document describes a study investigating the epigenetic regulation of induced pluripotent stem cell (iPSC) reprogramming through genome-wide analysis of histone X localization using next-generation sequencing and computational analysis with Python.
2) The study found that histone X enrichment occurs near stem cell-specific gene promoters, such as Pou5f1 and Nanog, at the early stages of cell reprogramming, prior to full gene activation.
3) Gene ontology analysis revealed histone X is involved in biological processes important for stem cell pluripotency, such as embryonic development and stem cell maintenance. This suggests histone X participates in activating stem cell genes during the initiation
Presentation at COMBIO 2016 in the small ORF/peptide symposium. hew I talk about our work on ascorbate (vitamin C) and out identification and characterisation of a small uORF that regulate translation on ascorbic acid and the relevance of this to Iron deficiency anemia.
Development of Monoclonal Antibodies -Creative BiolabsCreative-Biolabs
This document discusses several methods for developing monoclonal antibodies: hybridoma technology which fuses B cells and myeloma cells to produce hybridomas; surface display technology which uses genetic engineering to display antibody fragments on surfaces like phage, bacteria or yeast for screening; and transgenic technology which uses transgenic mice to produce monoclonal antibodies. It also describes Creative Biolabs' services for monoclonal antibody development including hybridoma generation and screening as well as in vitro surface display technologies.
Welcome to Creative Biolabs. As a new preparation technology for genetically engineered antibodies, antibody library technology has important theoretical and practical value in the cloning of human antibodies, antibody performance modification, and antibody gene research. Here, we will explore the de novo antibody library screening technologies and the corresponding services.
This document provides a catalog of DNA purification kits from a supplier, including kits for cleaning up and extracting DNA from various sources like PCR reactions, agarose gels, blood, bacteria, plants, and more. It lists the product names, descriptions, catalog numbers, available sizes, and prices in Euros. Various kit types are designed for different sample sizes and volumes, and include options for increased efficiency, gravity flow columns, or 96-well plate formats.
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.
New technologies for manufacturing recombinant products in embryonated eggsEluemuno R Blyden
New non-GMO vector technologies for expressing recombinant proteins in hen eggs offer a novel development and production platform for biologics and vaccines. By upgrading egg-based manufacturing, these technologies bring a wealth of experience and resources to the 21st Century fight against emerging diseases. The AdCEV(TM) vector technology developed by AfriVax and the Sendai Virus vector technologies can potentially improve manufacturing in eggs by increasing yields, expanding the repertoire of possible products, and increasing biosafety. With AdCEV(TM) technology, eggs can be used as miniature bioreactors for rapidly manufacturing a wide range of high-value biopharmaceuticals. The speed with which recombinant products can be developed, scaled and manufactured with these technologies offers a unique competitive advantage compared to other industrial technologies like cell culture and plants.
129 andrew z. fire - 8283329 - genetic inhibition of double-stranded rnaMello_Patent_Registry
Andrew Z. Fire, Stephen A. Kostas, Mary K. Montgomer, Lisa Timmons, SiQun Xu, Hiroaki Tabara, Samuel E. Driver, Craig C. Mello - Genetic Inhibition of Double-Stranded RNA
Recombinant Antibody Overview II - Creative BiolabsCreative-Biolabs
It is created by Creative Biolabs who is specialized in providing recombinant antibodies and engineered antibodies. The part two of recombinant antibody overview, we will explain introduction of recombinant antibody ant recombinant antibody expression.
The one-step RT-qPCR assay developed by Exopol S.L. was able to detect a wide variety of ruminant pestiviruses with excellent specificity and good sensitivity down to 102 copies per reaction. Testing on 272 clinical samples identified BVDV/BDV in 17.1% of cattle and 16.7% of sheep samples, with most positive cases in reproductive swabs and blood/serum. The assay provides a reliable and sensitive diagnostic tool for routine detection of pestiviruses in ruminants.
09 elisa kits for hemangioma of bone researchElabscience
Hemagioma can occurs in all parts of the body, and it may also occurs
in bone, but the latter is more rare than the others parts of body.
Hemangioma of bone sometimes exists with hemangioma of other parts at
the same time, it is a common tumor of benign tumor attached in bone
tissue.More info visit: http://www.elabscience.com
Updates on the ACP v3 genome and annotation from USDA NIFA project meetingSurya Saha
ACP version 3 genome, official gene set version 3 and Isoseq transcriptome
Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha
5th Annual Meeting
Indian River State College
Fort Pierce, FL
IRJET- Effect of Various Factors on Growth and L- Asparaginase Production...IRJET Journal
The article discusses international issues. It mentions that globalization has increased economic interdependence between nations while also raising tensions over immigration and trade. Solutions will require cooperation and compromise and a recognition that isolationism is not a viable strategy in an interconnected world.
Dr. Randy Prather - Porcine Reproductive and Respiratory Syndrome Virus Resis...John Blue
Porcine Reproductive and Respiratory Syndrome Virus Resistant Pigs - Dr. Randy Prather, University of Missouri, from the 2015 North American PRRS Symposium, December 4 - 5, 2015, Chicago, IL, USA.
More presentations at http://www.swinecast.com/2015-north-american-prrs-symposium
Mining Saccharomyces diversity and experimental evolution for cellulosic biofuelDavid Peris Navarro
This document summarizes research on using yeast diversity and experimental evolution to develop yeast strains for cellulosic biofuel production. Key points include:
- There is genetic diversity within the Saccharomyces genus that can be exploited, including species with better tolerance to toxins produced during biomass hydrolysis.
- Hybridization of tolerant non-S. cerevisiae species with engineered S. cerevisiae strains can combine beneficial traits.
- Experimental evolution of hybrid strains under hydrolysis conditions leads to strains with improved growth and xylose consumption.
- Genome sequencing shows adaptations involve new mutations, chromosomal rearrangements, and changes in gene copy number.
The rise of the yeast genus Saccharomyces: biodiversity and evolutionDavid Peris Navarro
The document discusses the rise of the yeast genus Saccharomyces, focusing on its biodiversity and evolution. It summarizes research showing that Saccharomyces yeasts are geographically structured and phenotypically diverse. While nuclear gene flow between species is limited, mitochondrial and 2μm plasmid gene flow is more common. Gene flow can impact phenotypes, and mitochondrial inheritance influences temperature tolerance. The origin of the parental S. eubayanus donor for lager yeast strains remains unknown.
Reticulate evolution in yeasts and its industrial applicationsDavid Peris Navarro
This document summarizes research on reticulate evolution in yeasts and its industrial applications. Reticulate evolution refers to evolution occurring through hybridization and introgression rather than strictly vertical descent. The document discusses how hybridization has contributed to the diversification and domestication of yeasts like Saccharomyces cerevisiae. It also explores how mining genomic diversity through hybridization could enable new industrial applications, such as developing yeast strains capable of growth at lower temperatures or utilizing additional carbon sources.
IN-SILICO CHARACTERISATION OF PROTEIN CODED BY CYT-B GENE OF Radopholus simil...Amit Yadav
Of the more than 30 species in the genus Radopholus, the burrowing nematode, Radopholus similis, is the only pathogen of widespread economic importance (Duncan and Moens, 2006). Radopholus similis is a migratory endoparasitic nematode that is known to be a destructive pest of citrus crops, pepper and, most importantly, banana, on which it causes toppling disease. The nematode causes economic problems throughout the world, most notably in warmer regions, including South America, the Caribbean, Africa, Asia and the Pacific.
Saccharomyces genus as a model of evolution and industrial applicationsDavid Peris Navarro
Saccharomyces genus offers a huge diversity that can be mined for different industrial applications (wine, beer, biofuels, and others). MITOGRESSION seeks to develop new strains via hybridization and different mitochondrial-nuclear combinations.
Saccharomyces has become a model genus for evolution and genomics. Improvements in genome sequencing and isolation protocols will allow us to produce high-quality genome sequences for all the major populations and lineages. In the mean time, multilocus phylogenetic and population genetic approaches are helping classify our strain collection for population genomic studies. In this talk, I will introduce some of the advances we have made in the description of populations of the newly discovered species S. eubayanus, the wild stock of lager-brewing hybrids. Using a combined pipeline of population and phylogenetic studies, we have described two well-differentiated populations in Patagonia (Argentina), indicating that S. eubayanus is native. Although S. eubayanus may not be endemic to South America, it is likely native. Lager-brewing hybrids isolated in Europe showed shared alleles with the S. eubayanus population P-B (L) and had low genetic diversity, suggesting the S. eubayanus alleles involved in hybridization were drawn from a small subpopulation derived from P-B (L). From our Wild YEAST Program, a yeast isolation project conducted by undergraduate students and citizen scientists from across the world, we identified three new S. eubayanus strains from Sheboygan, WI (USA). In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. To capture reticulation and summarize it in a phylogenetic framework, we combine state-of-the-art Bayesian methods with phylogenetic network analysis. Our findings support the hypothesis that genetically divergent microbes can produce rare but economically important hybrids when they migrate from their natural ecological context.
This study identified a novel gene, WHI2, that improves acetic acid resistance in Saccharomyces cerevisiae through overexpression. The key findings were:
1) A genomic library screen identified WHI2 overexpression as enhancing glucose and xylose fermentation under acetic acid stress.
2) WHI2-overexpressing strains showed 5-times-higher ethanol productivity compared to controls under acetic acid stress.
3) Endogenous WHI2 expression is induced by acetic acid, and WHI2 deletion strains are hypersensitive to acetic acid, indicating its role in the acetic acid response.
4) Overexpression of WHI2 and the phosphatase gene PSR
The document summarizes genetic and mutational characterization of the relV gene of Vibrio cholerae, which encodes a small alarmone synthetase protein called RelV. Key findings include:
1) Site-directed mutagenesis identified five amino acid residues (K107, D129, R132, L150, E188) in the RelA-SpoT domain of RelV that are essential for its (p)ppGpp synthetase activity.
2) Progressive deletion analysis determined the functional N-terminal boundary of RelV to be amino acid 59 and the C-terminal boundary to be amino acid 248, indicating that flanking sequences of the RelA-SpoT
Genetic Dissection of Compositional & Anatomical Characteristics Associated w...Jonathan Clarke
- Biofuels and the Role of Maize
- Cell Wall Composition and Stalk Anatomical
Characteristics
- Tackling the Complexity of the Maize Genome
- Final Remarks
Plant Genetics and The Future of Food. Pam RonaldCIAT
Speaker: Pam Ronald, Professor in the Genome Center and the Department of Plant Pathology, and founding Faculty Director of the Institute for Food and Agricultural Literacy (IFAL), UC DavisFellow of the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”. http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
Swansea University (October-2020): Challenges of using GWAS in bacteriaBen Pascoe
Genome-wide association studies (GWAS) can help identify genetic factors associated with phenotypes in bacteria, but they face challenges due to differences from human GWAS. These include smaller bacterial genomes, clonal reproduction, and population structure effects. Early bacterial GWAS had limitations but new methods account for population structure and accessory genome differences. GWAS in Campylobacter have identified genes associated with host specificity, survival through poultry processing, biofilm formation, and oxygen tolerance. Results can be applied to vaccine design and predicting virulence. Larger datasets are needed but GWAS continue to provide insights into bacterial traits and opportunities for functional validation.
Hyaluronic acid (HA) is also known by the name hyaluronan. The necessity for
using this fabulous material lead to investigate non-pathogenic strains which produce
this material. The most non-pathogenic strain is S. thermophilus. The lack of literature
on microbial production of this substance by the strain prompted us to examine the
microbial production of HA from it and also to examine optimization of culture
conditions where HA is produced. The bacteria Streptococcus salivarius sub.
thermophilus was obtained from the Bank of Scientific and Industrial Research of Iran
(PTCC 1738). To separate S. thermophilus strains from yogurts, three types of yogurts
were used. They were cultured by pour-plate and surface methods on STA medium. To
identify the isolated strains, biochemical tests and Polymerase Chain Reaction (PCR)
were used. Bacterial strains isolated from yoghurts were identified as S. thermophilus
MN-BM-A02, S. thermophilus JIM8232 and S. thermophilus MN-ZLW-002. To separate
the capsule strains, each strain was cultured on STB medium and then they were
centrifuged. In order to purify the samples, ethanol and charcoal were used. To
optimize production, variety of sources of carbon, nitrogen, temperature and pH were
studied.
Genome-wide association mapping of canopy wilting in diverse soybean genotypesAvjinder (Avi) Kaler
Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified.
This study sequenced the carbonic anhydrase gene in Wabash pigtoe mussels to determine how they may respond to a proposed carbon dioxide barrier meant to prevent the spread of invasive Asian carp. RNA was extracted from mussel tissues and used to synthesize cDNA. Primers were designed based on a related species' gene sequence and used to amplify and sequence a 954 base pair region of the carbonic anhydrase gene. While real-time PCR was not performed due to time constraints, the researchers hypothesize expression of this gene, which is important for acid-base regulation and shell formation, would increase under elevated carbon dioxide levels.
Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maizePGS
This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
Upon the evolution brought about in the fermentation technology resulted out into various methodologies for optimization of the product yield by economical consumption of the substrates. Eventually, these ventures led for the development of technologies classified into as Submerged and Solid State technologies and the latter one being the concept of interest whose detailed view will be provided in the following presentation
CRISPR-Revolutionary Genome editing tools for Plants.....BHU,Varanasi, INDIA
CRISPR/Cas9 is a revolutionary genome editing tool discovered in bacterial immune systems. It provides acquired immunity against viruses and phages. CRISPR components include crRNA, tracrRNA, and Cas9 protein. There is an ongoing patent war over CRISPR between major scientists and institutions. CRISPR has been used to successfully edit plant genomes and develop disease resistant and drought tolerant crops like rice, cotton, wheat, and maize. It also shows promise for developing virus resistant varieties and removing unwanted plant species. CRISPR's applications extend to human health by potentially destroying cancer cells and disabling viruses like HIV.
The Tongue Biofilm Meta-transcriptome Identifies Metabolic Pathways Associate...Hajra Qayyum
This presentation is based on article titled "The Tongue Biofilm Meta-transcriptome Identifies Metabolic Pathways Associated with the Presence or Absence of Halitosis" as an application of transcriptomics in biomarkers discovery for halitosis.
Yeasts play an important role in fermented foods like bread, wine, and beer. Saccharomyces cerevisiae has been domesticated for brewing through both conscious and unconscious selection. Unconscious selection led to traits like efficient sugar consumption, good attenuation, and flocculation. Different types of beers use distinct yeasts adapted to variables like temperature and sugar utilization. Lager yeasts are adapted for low temperature fermentation through hybridization between S. cerevisiae and cold-tolerant yeasts. Traditional and industrial beers employ diverse yeasts that provide unique flavors through species differences and hybridization.
This document summarizes recent research on the reticulate evolution of yeast species in the Saccharomyces genus. It discusses several new genome sequences that have helped uncover the evolutionary history. Wild Saccharomyces species from bioprospecting projects are revealing new genetic diversity. There is evidence of introgressions between species in mitochondrial DNA and the 2μm plasmid. Phylogenetic trees show four main mitochondrial haplogroups and reticulation at the nuclear level. Gene flow appears to be more frequent between species for mitochondrial and plasmid genes than for nuclear genes, although incomplete lineage sorting also impacts nuclear phylogenies.
Yeast Biodiversity and Strategies for Industrial ApplicationsDavid Peris Navarro
This document summarizes David Peris's presentation on yeast biodiversity and strategies for industrial applications. It discusses the diversity of yeast species and strains, their phenotypic traits under different industrial conditions, and strategies for developing novel yeasts through hybridization. Specifically, it explores using hybridization between S. cerevisiae and other species like S. kudriavzevii or S. eubayanus to generate yeasts tolerant of industrial conditions for applications like brewing or biofuel production. The document presents data on growth profiles of many yeast strains under various conditions to identify promising candidates for further development.
Talk at VIII Biennial Conference of Society of Spanish Evolutionary Biology (SESBE).
MATB. Previous studies have revealed that species of the genus
Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system,
with multiple inferred alleles for MATA and MATB. We characterized the
chromosomal location of MAT loci, the molecular structure of MAT regions and their
allelic richness. We found multiple MAT alleles segregating in both multiple
Trichaptum specimens and non-Trichaptum species. Phylogenetic analyses and
various nucleotide statistics suggested that long-term balancing selection have
generated trans-species polymorphisms. Mating sequences were classified in
different allelic classes based on an identity threshold of higher than 86%. The
observed alleles could potentially generate 14,560 different mating types. The
inferred allelic information mirrored the outcome of in vitro crosses, thus allowing
us to estimate the degree of allelic divergence needed for successful mating. Even
with the high amount of divergence, key amino acids in functional domains are
conserved. We conclude that the genetic diversity of mating in Trichaptum loci is
due to long-term balancing selection that likely promote sexual outcrossing, with
limited recombination and duplication activity. Our large number of sequenced
specimens highlighted the importance of sequencing multiple individuals from
different species to clarify the mechanisms generating diversity and the
evolutionary forces maintaining them.
Este documento presenta la organización ECUSA-Midwest. Proporciona información sobre los objetivos, equipo de trabajo y comisiones de la organización. ECUSA-Midwest busca potenciar la visibilidad y networking de sus miembros en el Medio Oeste, así como integrarlos en las comisiones generales de ECUSA en áreas como comunicación, educación y divulgación profesional. El documento también invita a los miembros potenciales a unirse a la organización.
Els nostres amics microscòpics, els llevats: domesticació i aplicacions indus...David Peris Navarro
Xarrada impartida al IES Riu Túria de Quart de Poble el 13 de desembre de 2020. En ella parlarem de com els llevats han sigut domesticats per a la producció de pa i com podem redomesticar-les per atacar alguns dels reptes que la humanitat té per davant, com la reducció del consum de energies fòssils.
Developing your career with a MSCA IF - RI 2 years experienceDavid Peris Navarro
The talk presented in the Physiology of Yeasts & Filamentous Fungi was focused in my personal experience to develop a Marie Sklodowska Curie grant (time and contacts), previous results before writing and fellowship experience.
Slack is becoming an important tool for many research labs. I made a short introduction about what is slack and how it can be use for making your research day easier among your colleagues.
My introduction about how to send jobs in a HPC, create environments and install programs in CONDA, and make use of modules installed in SAGA (an HPC used by University of Oslo researchers).
Hibridación como mecanismo para generar nuevas cepas de levaduras industrialesDavid Peris Navarro
Este documento describe cómo la hibridación puede usarse como mecanismo para generar nuevas cepas de levaduras industriales. La hibridación permite combinar el genoma nuclear de diferentes especies de Saccharomyces con diferentes mitocondrias para generar mayor diversidad genética y así obtener cepas con nuevas propiedades como mayor tolerancia a la temperatura. El autor propone específicamente hibridar seis especies de Saccharomyces para lograr la máxima diversidad genómica posible a través de esta técnica.
Polyploidy is a widespread phenomenon in biology, observed in plants, fungi, insects, and vertebrates. Polyploidy has been related with cellular differentiation in mammals and arthropods, and it promotes species diversification through evolutionary innovation. Additionally, polyploidy has important implications in tumorigenesis due to its implications in genome instability. Tools for testing polyploidy limits and their cellular consequences are lacking or scarce. Here, we have tested in an iterative way a methodology promoting Saccharomyces yeast hybridization, iHyPr (iterative Hybrid Production), for the generation of synthetic higher-order yeast hybrids. By using independent hybridization schemes, we have successfully generated multiple allotetraploid, allohexaploid hybrids, and four six-species synthetic hybrids (6-species hybrids) of Saccharomyces, a genus important for industrial applications (beer, wine, and biofuels). To test the potential future industrial applications of our synthetic hybrids, we evolved them in a medium containing xylose, a sugar not utilized well by wild Saccharomyces strains. By whole genome sequencing and kinetic analyses of ancestral and evolved six-species hybrids, we demonstrated how iHyPr is a useful tool for generating yeast diversity and better-adapted strains to new environments. We envision iHyPr as a tool to expand the Saccharomyces genus as a model to study the roles that polyploidy plays in organismal evolution, industry, and disease.
El documento presenta una charla sobre el cambio climático. Los objetivos de la charla son alfabetizar ecológicamente a la audiencia, mostrar las evidencias científicas que confirman el cambio climático, promover conversaciones privadas sobre el tema, y discutir posibles soluciones. La charla también cubre los efectos del cambio climático en España como sequías, pérdida de cultivos como el vino, y más plagas. Se discuten medidas para mitigar el cambio climático a nivel local y nacional.
El documento presenta la memoria anual 2015-2016 de la organización Españoles Científicos en USA (ECUSA). ECUSA tiene como objetivo establecer una red de científicos españoles en EEUU, mejorar la percepción social de la ciencia a través de eventos, y servir de enlace entre científicos y instituciones en España y EEUU. En el último año, ECUSA ha crecido exponencialmente, pasando de 10 a más de 60 voluntarios y estableciendo 5 secciones regionales. Sus programas de divulgación
Science description of some members of ECUSA@Midwest. ECUSA members participated on 21st and 22nd in the Wisconsin Science Festival in Madison.
Ciencia desarrollada por miembros de ECUSA@Midwest. Los miembros de ECUSA participaron durante el 21 y el 22 de octubre en el Festival de Ciencia de Wisconsin, Madison.
Mining Saccharomyces diversity and experimental evolution for cellulosic biof...David Peris Navarro
The document summarizes research on using experimental evolution and hybridization of Saccharomyces yeasts to develop strains for improved cellulosic biofuel production. Key points include:
- The diversity of Saccharomyces yeasts was mapped and certain lineages were selected for hybridization based on traits like tolerance.
- Hybrids were generated between S. cerevisiae (the chassis strain) and other species and then experimentally evolved over 50 generations.
- The evolved hybrid strains showed improved utilization of xylose compared to ancestor strains, producing similar ethanol levels without accumulating byproducts.
- Genome analysis found the evolved hybrids were mostly triploid and had chromosomal rearrangements replacing parent genes.
- Further work aims to
In the last decade, the application of new molecular techniques has helped to identify Saccharomyces species and suggested many types of reticulated evolutionary events, such as hybridization, interspecies recombination, introgression, horizontal gene transfer, and admixture. Many strains isolated from fermentative environments, such as S. bayanus, which was isolated from beer or fermented beverages, and S. pastorianus, used in making lager beer, have been misidentified as distinct species when they have chromosome contributions from two or more natural Saccharomyces species. These hybridization events likely occurred in the stressful conditions found in industrial environments where hybrids were better suited. These hybrids do not have unique origins, suggesting that hybridization has a clear selective advantage. We have recently described two well-differentiated Patagonian populations of S. eubayanus, the wild contributor to S. pastorianus (S. cerevisiae x S. eubayanus) lager-brewing strains. The application of the state-of-the-art phylogenetic methods (Supernetworks and Bayesian concordance factor analysis) illuminated many reticulation events in S. eubayanus outside of Patagonia and uncovered the relationship between one population of S. eubayanus from Patagonia and its counterpart in S. bayanus and S. pastorianus. We also recently isolated S. eubayanus strains from Sheboygan, WI that originated by intraspecific hybridization (admixture) of the two Patagonian populations, and we used supernetworks to graphically represent the hybridization and recombination in S. bayanus and S. pastorianus from the brewing industry. With the knowledge gained by understanding the process of hybrid evolution that occurred in winemaking and brewing environments, we are developing new methods to generate artificial hybrids to repeat the hybridization process for the bioethanol industry.
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...Sérgio Sacani
We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
+
53.13485
−
27.82088
with a host spectroscopic redshift of
2.903
±
0.007
. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
�
(
�
−
�
)
∼
0.9
) despite a host galaxy with low-extinction and has a high Ca II velocity (
19
,
000
±
2
,
000
km/s) compared to the general population of SNe Ia. While these characteristics are consistent with some Ca-rich SNe Ia, particularly SN 2016hnk, SN 2023adsy is intrinsically brighter than the low-
�
Ca-rich population. Although such an object is too red for any low-
�
cosmological sample, we apply a fiducial standardization approach to SN 2023adsy and find that the SN 2023adsy luminosity distance measurement is in excellent agreement (
≲
1
�
) with
Λ
CDM. Therefore unlike low-
�
Ca-rich SNe Ia, SN 2023adsy is standardizable and gives no indication that SN Ia standardized luminosities change significantly with redshift. A larger sample of distant SNe Ia is required to determine if SN Ia population characteristics at high-
�
truly diverge from their low-
�
counterparts, and to confirm that standardized luminosities nevertheless remain constant with redshift.
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...Sérgio Sacani
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted Brγ emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual H−K and K−L colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (≈15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 ± 20◦, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holes– stars: formation– Galaxy: center– galaxies: star formation
Mechanisms and Applications of Antiviral Neutralizing Antibodies - Creative B...Creative-Biolabs
Neutralizing antibodies, pivotal in immune defense, specifically bind and inhibit viral pathogens, thereby playing a crucial role in protecting against and mitigating infectious diseases. In this slide, we will introduce what antibodies and neutralizing antibodies are, the production and regulation of neutralizing antibodies, their mechanisms of action, classification and applications, as well as the challenges they face.
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...PsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
Embracing Deep Variability For Reproducibility and Replicability
Abstract: Reproducibility (aka determinism in some cases) constitutes a fundamental aspect in various fields of computer science, such as floating-point computations in numerical analysis and simulation, concurrency models in parallelism, reproducible builds for third parties integration and packaging, and containerization for execution environments. These concepts, while pervasive across diverse concerns, often exhibit intricate inter-dependencies, making it challenging to achieve a comprehensive understanding. In this short and vision paper we delve into the application of software engineering techniques, specifically variability management, to systematically identify and explicit points of variability that may give rise to reproducibility issues (eg language, libraries, compiler, virtual machine, OS, environment variables, etc). The primary objectives are: i) gaining insights into the variability layers and their possible interactions, ii) capturing and documenting configurations for the sake of reproducibility, and iii) exploring diverse configurations to replicate, and hence validate and ensure the robustness of results. By adopting these methodologies, we aim to address the complexities associated with reproducibility and replicability in modern software systems and environments, facilitating a more comprehensive and nuanced perspective on these critical aspects.
https://hal.science/hal-04582287
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxgoluk9330
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptx
ISSY33 - 2017 06 26
1. Mining Saccharomyces diversity and experimental
evolution for cellulosic biofuel and beer applications
David Peris, Postdoctoral Research Associate
Department of Genetics, University of Wisconsin-Madison
27th June 2017
@djperis
2. Domesticated Saccharomyces cerevisiae for alcoholic beverage production
Carbon sources
Glucose
Fructose
Glu Glu
Maltose
Glu Glu Glu
Maltotriose
glycolysis
Carbon products
Ethanol
Other
compounds
fermentation
3. Most S. cerevisiae can not consume xylose
Proteins,
Oils, Ash (0-2%)
Hemicellulose
(19-34%)
Lignin
(21-32%)
Cellulose
(33-51%)
Glucose
Xylose
Sugars (C6/C5)
Piotrowski et al 2014 Front Microbiol
4. Toxins inhibits the ethanol production
Proteins,
Oils, Ash (0-2%)
Hemicellulose
(19-34%)
Lignin
(21-32%)
Cellulose
(33-51%)
Glucose
Xylose
HMF
Ferulic
acid
p-coumaric
acid
Feruloyl amide
Sodium
acetate
Acetamide
Sugars (C6/C5) Hydrolysate Toxins
Piotrowski et al 2014 Front Microbiol
Ethanol
5. Engineering chassis S. cerevisiae for xylose consumption
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
Wohlbach et al. 2009 PNAS
Sato et al. 2013 AEM
Y732n
CHASSIS
Xylose
6. S. cerevisiae is still not happy with the toxins
Wohlbach et al. 2009 PNAS
Sato et al. 2013 AEM
Y732n
CHASSIS
Xylose Hydrolysate toxins
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
7. The diversity in S. cerevisiae is low
Liti et al 2009 Nature
S. cerevisiae
0.8% nucleotide diversity
8. America C
Surveying the diversity of Saccharomyces genus
Phylogenomic tree
Strains from 23 available lineages
0.05
n = 980 strains
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Holarctic &
Patagonia B
Peris et al 2017 BFB
9. America C
The Saccharomyces diversity is huge
0.05
n = 980 strains
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Holarctic &
Patagonia B
Phylogenomic tree
Strains from 23 available lineages
Dujon 2006 TIG
10. America C
S. mikatae & S. paradoxus are more tolerant to ACSH conditions
0.05
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
EU & America A
Far East
America B
Peris et al 2017 BFB
11. S. uvarum can consume xylose
0.05
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. arboricola
S. uvarum
S. eubayanus
Peris et al 2017 BFB
12. Improvement of S. cerevisiae chassis strain
The most tolerant of a panel of S. cerevisiae
Engineered with xylose utilization genes
Engineered with Hydrolysate tolerance traits
Y732n
CHASSIS v2.0
Xylose Hydrolysate toxins
13. Industrial Saccharomyces hybrids
Gonzalez et al. 2008
Dunn et al. 2008
Peris et al. 2012a,b,c,2014,2016,2017b
Libkind et al. 2011
Almeida et al 2014
S. pastorianus
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
S. eubayanus
S. bayanus
14. Generation of hybrids to combine genetic traits and generate diversity
S.mikatae
XHaploid (n)
S. cerevisiae
CHASSIS
Peris et al 2017 BFB
Haploid (n)
MATa MAT
MATa/MAT
15. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
0
1
2
3
4
5
0
1
2
3
4
5
RC/MRC
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI
sppIDer (species IDentifier) 1:1 chromosome of each parent
Chromosome
Peris et al 2017 BFB
Quinn et al In preparation
Chromosome
Sequencing
coverage S. cerevisiae
S. mikatae
16. Adaptive evolution of the unstable hybrid: new mutations
Peris et al 2017 BFB
R1
30ºC
14days
17. Bottlenecks and new passages in fresh media
R1 …
30ºC
14days
Peris et al 2017 BFB
18. The best variants will survive
R1 R9…
50 Generation
30ºC
14days
ACSH
Peris et al 2017 BFB
19. One of the evolved hybrids retain the genetic traits of the parents
Peris et al 2017 BFB
The evolved hybrids consume similar levels of xylose
The growth rate of the evolved hybrid is similar to the parents
More generation might generate a better strain than the
parents.
20. One of the evolved hybrids retain the genetic traits of the parents
Peris et al 2017 BFB
The evolved hybrids consume similar levels of xylose
The growth rate of the evolved hybrid is similar to the parents
More generation might generate a better strain than the
parents.
Chromosome
Chromosome
Sequencing
coverage S. cerevisiae
S. mikatae
22. HyPr promotes gene conversion in the MAT locus
a/ a/
a/a /
NATMX HYGMX
NATMX HYGMX
HO
expression
Alexander et al 2016 FGB
23. Convert the rare-mating to frequent-mating with HyPr
a/ a/
a/a /
X
NATMX HYGMX
NATMX HYGMX
NATMX HYGMX
HO
expression
a/a//
Alexander et al 2016 FGB
24. Marker-free hybrids
a/ a/
a/a /
X
NATMX HYGMX
NATMX HYGMX
NATMX HYGMX
HO
expression
a/a//
a/a//
Remove selection
pressure
Alexander et al 2016 FGB
25. Ryan Moriarty
X X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
Proof of concept: higher order hybrids using HyPr?
26. Double hybrids were done!
X X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
27. A four species hybrid was done!
X
X
X X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
30. We have evidence for a six species hybrid!
X
X
X X
X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
31. Restriction fragment Length Polymorphism give some clues
M349-Sc
M456–Sc
M495–ScxSpxSaxSu
M359-Sa
M356-Su
M461–Sax
Su
BRE5
S.cerevisiae
S.paradoxus
S.mikatae
S.kudriavzevii
S.uvarum
S.arboricola
Hybrid(6x->12n)
X
X
32. Complex hybrids generate diversity for industrial applications
X
X
X X
X
S. paradoxus
S. mikatae
S. arboricola
S. kudriavzevii
S. uvarum
S. cerevisiae
33. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
34. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
Hybridization is a short-term solution to combine interesting strain with interesting
industrial traits and a method for characterizing those traits
35. Conclusions
There is a huge diversity in yeasts in general, and Saccharomyces in particular
waiting to be discovered and exploited
Hybridization is a short-term solution to combine interesting strain with interesting
industrial traits and a method for characterizing those traits
With HyPr we are able to generate higher order hybrids and diversity to address
important genetic questions and fix industrial problems
36. Thank you
Chris T. Hittinger
Ryan V. Moriarty
Quinn Langdon
William Alexander
Meihua Kuang
Kayla Sylvester
Emily Baker
Hittinger Lab Members
Wild YEAST program
Trey Sato
Li Hinchman
Lucas Parreiras
Jeff Piotrowski
Diego Libkind
Jose Paulo Sampaio
Paula Gonçalves
Christian Landry
Jean-Baptiste Leducq
Guillaume Charron
Justin Fay
Katie Hyma
Fengyan Bai
Qi Ming Wang
Yaoping Zhang
Alex Reau
Haibo Li
David Benton
Yury Bukhman
HPLC Service
Mick McGee
Audrey Gasch
Maria Sardi
UW & GLBRC Collaboration