This document summarizes research on the effect of the DSK gastro-peptide on feeding behaviors in Drosophila Melanogaster. The researcher conducted three experiments: a proboscis extension reflex assay to determine feeding behaviors, an ingestion assay to measure food intake, and a food availability assay to examine ingestion initiation. The results found that flies with increased levels of DSK tended not to eat in the food availability assay, while flies with decreased DSK levels ate more in the ingestion assay. The PER assay also showed increased proboscis extension when DSK neurons were silenced. Overall, the preliminary data provides promise that manipulating DSK could prevent eating disorders, which may help address long-term health issues in mammalian models like
Patch Size Dependent Grazing on a Caribbean Coral Reefstoyleg
This study assessed how the size of cleared algal patches on a Caribbean coral reef affected grazing by herbivorous fish and algal succession. Larger patch sizes of 200cm2 saw significantly higher numbers of fish bites compared to smaller 25cm2 patches. A logistic regression model showed that the likelihood of a fish biting increased with larger patch size. While initial clearing reduced algal cover from 76.76% to 12.5%, algal cover recovered to 56.03% within 12 weeks, indicating the current herbivore regime was insufficient to fully maintain the reef in a low algal state without optimal sized cleared patches.
An augmented review_about_lighting_programs_for_broiler_productionghulam abbas
This document reviews research on lighting programs for broiler chicken production. It discusses how light affects broiler physiology and behavior, and the impact of different light sources, intensities, durations and colors on broiler performance measures like feed consumption and weight gain. Specifically, it finds that low light intensities generally improve feed consumption and weight gain compared to high intensities. Intermittent lighting schedules also tend to improve feed intake over continuous lighting. Additionally, certain light colors like blue-green can stimulate growth while red-orange stimulates reproduction. Overall, the review aims to help optimize lighting programs to improve broiler welfare and farm profitability.
Kittens typically gain weight once neutered, leading to a potential risk of early obesity. Early neutering reduced rapid weight gain and could be considered as an intervention to promote to healthy weight regulation. Presented at the Waltham InternationaI Nutrition Science Symposium, October 2016, Chicago
Exploring the Dynamics of The Microbiome in Health and DiseaseLarry Smarr
Remote Invited Provocateur Lecture
2017 Innovation Lab on Quantitative Approaches to Biomedical Data Science:
Challenges in our Understanding of the Microbiome
San Diego, CA
June 19, 2017
Traditional energy requirement calculations may not be accurate for small dog breeds, with implications for recommended food intake and early obesity. Presented at the Waltham International Nutrition Science Symposium, Chicago, October 2016.
This study characterized the muscle buffering capacity of three mysticete whale species - gray whales, humpback whales, and minke whales - across different developmental stages. The results showed:
1) Humpback and minke whale calves had lower buffering capacity than adults, suggesting it increases with maturity.
2) Juvenile humpback and gray whales exhibited higher buffering capacity than adults, which may allow them to utilize anaerobic respiration and extend dive durations.
3) Gray whale adults had lower buffering capacity than juveniles, indicating they rely on alternative respiration pathways.
4) Water content analysis validated the buffering capacity results, with no significant differences between species or age classes
The study examined the effects of dietary selenium level (0.3 ppm vs 3.0 ppm) and source (organic vs inorganic) on selenium retention in red blood cells and plasma in pigs over three time periods. The results showed that higher selenium levels led to greater selenium concentrations in red blood cells than plasma. Organic selenium was retained more in red blood cells than inorganic selenium. Selenium concentrations in both blood components increased over time from the nursery to finisher stages. The conclusions were supported by existing research showing the source and level of selenium supplementation affects blood selenium concentrations.
This document summarizes research on the effect of the DSK gastro-peptide on feeding behaviors in Drosophila Melanogaster. The researcher conducted three experiments: a proboscis extension reflex assay to determine feeding behaviors, an ingestion assay to measure food intake, and a food availability assay to examine ingestion initiation. The results found that flies with increased levels of DSK tended not to eat in the food availability assay, while flies with decreased DSK levels ate more in the ingestion assay. The PER assay also showed increased proboscis extension when DSK neurons were silenced. Overall, the preliminary data provides promise that manipulating DSK could prevent eating disorders, which may help address long-term health issues in mammalian models like
Patch Size Dependent Grazing on a Caribbean Coral Reefstoyleg
This study assessed how the size of cleared algal patches on a Caribbean coral reef affected grazing by herbivorous fish and algal succession. Larger patch sizes of 200cm2 saw significantly higher numbers of fish bites compared to smaller 25cm2 patches. A logistic regression model showed that the likelihood of a fish biting increased with larger patch size. While initial clearing reduced algal cover from 76.76% to 12.5%, algal cover recovered to 56.03% within 12 weeks, indicating the current herbivore regime was insufficient to fully maintain the reef in a low algal state without optimal sized cleared patches.
An augmented review_about_lighting_programs_for_broiler_productionghulam abbas
This document reviews research on lighting programs for broiler chicken production. It discusses how light affects broiler physiology and behavior, and the impact of different light sources, intensities, durations and colors on broiler performance measures like feed consumption and weight gain. Specifically, it finds that low light intensities generally improve feed consumption and weight gain compared to high intensities. Intermittent lighting schedules also tend to improve feed intake over continuous lighting. Additionally, certain light colors like blue-green can stimulate growth while red-orange stimulates reproduction. Overall, the review aims to help optimize lighting programs to improve broiler welfare and farm profitability.
Kittens typically gain weight once neutered, leading to a potential risk of early obesity. Early neutering reduced rapid weight gain and could be considered as an intervention to promote to healthy weight regulation. Presented at the Waltham InternationaI Nutrition Science Symposium, October 2016, Chicago
Exploring the Dynamics of The Microbiome in Health and DiseaseLarry Smarr
Remote Invited Provocateur Lecture
2017 Innovation Lab on Quantitative Approaches to Biomedical Data Science:
Challenges in our Understanding of the Microbiome
San Diego, CA
June 19, 2017
Traditional energy requirement calculations may not be accurate for small dog breeds, with implications for recommended food intake and early obesity. Presented at the Waltham International Nutrition Science Symposium, Chicago, October 2016.
This study characterized the muscle buffering capacity of three mysticete whale species - gray whales, humpback whales, and minke whales - across different developmental stages. The results showed:
1) Humpback and minke whale calves had lower buffering capacity than adults, suggesting it increases with maturity.
2) Juvenile humpback and gray whales exhibited higher buffering capacity than adults, which may allow them to utilize anaerobic respiration and extend dive durations.
3) Gray whale adults had lower buffering capacity than juveniles, indicating they rely on alternative respiration pathways.
4) Water content analysis validated the buffering capacity results, with no significant differences between species or age classes
The study examined the effects of dietary selenium level (0.3 ppm vs 3.0 ppm) and source (organic vs inorganic) on selenium retention in red blood cells and plasma in pigs over three time periods. The results showed that higher selenium levels led to greater selenium concentrations in red blood cells than plasma. Organic selenium was retained more in red blood cells than inorganic selenium. Selenium concentrations in both blood components increased over time from the nursery to finisher stages. The conclusions were supported by existing research showing the source and level of selenium supplementation affects blood selenium concentrations.
Ocean acidification decreases pH in surface waters due to absorbed CO2, threatening marine life. A study tested the effects of elevated CO2 and single versus multiple male spawnings on fertilization success in sea urchins. Results showed elevated CO2 did not significantly impact fertilization success. While male identity marginally affected success, multiple male spawnings unexpectedly reduced female success compared to individual males. This implies different evolutionary pressures on males and females and that optimal aggregation densities may exist for reproduction under ocean acidification.
Machine Learning in Healthcare by Mehrdad YazdaniData Con LA
Abstract:- Using Machine Learning to Identify Major Shifts in Human Gut MicrobiomeProtein Family Abundance in Disease Inflammatory Bowel Disease (IBD) is an autoimmune condition that is observed to be associated with major alterations in the gut microbiome taxonomic composition. Here we classify major changes in microbiome protein family abundances between healthy subjects and IBD patients. We use machine learning to analyze results obtained previously from computing relative abundance of ~10,000 KEGG orthologous protein families in the gut microbiome of a set of healthy individuals and IBD patients. We develop a machine learning pipeline, involving the Kolomogorv-Smirnov test, to identify the 100 most statistically significant entries in the KEGG database. Then we use these 100 as a training set for a Random Forest classifier to determine ~5% the KEGGs which are best at separating disease and healthy states. Lastly, we developed a Natural Language Processing classifier of the KEGG description files to predict KEGG relative over- or under- abundance. As we expand our analysis from 10,000 KEGG protein families to one million proteins identified in the gut microbiome, scalable methods for quickly identifying such anomalies between health and disease states will be increasingly valuable for biological interpretation of sequence data.
2015 Sujkowski, Bazzell, et al endurance exercise and selective breeding exte...Brian Bazzell, PharmD
The document describes a study comparing the effects of endurance exercise training and selective breeding for longevity on healthspan and gene expression in Drosophila melanogaster. The study found that both endurance training and selective breeding for longevity increased endurance, cardiac performance, mobility, autophagy, and stress defense pathways, while decreasing carbohydrate metabolism and odorant receptor expression. Microarray analysis revealed that 65% of gene expression changes from selective breeding were also seen with endurance training. Both interventions downregulated several members of the methuselah-like gene family, and knockdown of one such gene extended healthspan measures. The results suggest endurance exercise training and selective breeding act through overlapping genetic pathways to extend healthspan.
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
The document summarizes a study examining how three E. coli strains (E455, E1140, E455L) utilize gluconate differently and how this affects their fitness in seawater. Key findings:
- Genes involved in gluconate metabolism were upregulated in E455L and environmental strain E1140 compared to wild-type E455.
- In gluconate-supplemented medium, E455L grew slower than E455 but survived longer, showing higher fitness. E1140 grew slowest but reached highest density.
- All strains decayed slower in gluconate-supplemented seawater than seawater alone. E455L showed highest
This study assessed the use of an engineered periosteum consisting of chitosan nanofibers, luciferase-expressing adipose-derived stem cells (Luc-ASCs), FGF-2, and TGF-β1 coated on mouse femur bone allografts implanted into a critical bone defect. The engineered periosteum delivered Luc-ASCs and growth factors to the defect site. While statistical analysis found no difference in new bone formation between groups, treatments including Luc-ASCs showed 24% more new bone formation than uncoated controls. This suggests a polysaccharide-based engineered periosteum may be a feasible approach to improve bone allograft healing.
Generalizing phylogenetics to infer patterns of shared evolutionary eventsJamie Oaks
This document discusses generalizing phylogenetics to infer patterns of shared evolutionary events. It begins by outlining how shared ancestry is a fundamental property of life and how phylogenetics is progressing as the statistical foundation of comparative biology. It then discusses how violating the assumption of independent divergences can provide insights into processes like biogeography, gene family evolution, and endosymbiont evolution. The document considers challenges in accounting for shared divergences, like the complexity of gene trees and sampling over all possible models, and proposes two approaches: using existing methods or approximate Bayesian computation with a diffuse Dirichlet process prior.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
Biological evolution occurs through four main mechanisms: natural selection, genetic drift, biased mutation, and gene flow. Natural selection involves variation in traits, inheritance of traits, a high population growth rate, and differential survival and reproduction based on traits suited for the environment. Genetic drift is the random changes in genetic makeup between generations due to chance rather than adaptation. Biased mutation refers to certain types of mutations occurring more frequently in certain locations in DNA. Gene flow is the exchange of alleles between populations through migration and reproduction.
metabolic acceleration and the evolution of human brainJoão Soares
Humans have larger brains, higher reproductive output, and longer lifespans than other great apes, presenting an "energetic paradox" that requires more energy expenditure. This study found that:
1) Humans have higher total daily energy expenditure (TEE) than chimpanzees, bonobos, gorillas and orangutans, even after controlling for factors like body size and physical activity.
2) Much of the increased human TEE is due to a higher basal metabolic rate (BMR), indicating increased metabolic activity of organs.
3) Humans also have a greater percentage of body fat than other great apes.
The findings suggest humans evolved an "accelerated
Recognizing the Patterns Within: How Biomedical Data Can Reveal Health vs. Di...Larry Smarr
Keynote
Session on Challenges of Pattern Recognition in Biomedical Data
The Pacific Symposium on Biocomputing (PSB) 2018
Big Island, HI
January 6, 2018
This document discusses the large-scale production and purification of synthetic spider silk proteins using E. coli. Researchers cloned and expressed spider silk genes from the golden orb-weaving spider Nephila clavipes in E. coli. They tested different genetic vectors (SX and 19K) and protein constructs (MaSP1, FlAS3, FlYS3) and found that the SX vector produced more consistent growth and higher optical densities during fermentation. SDS-PAGE and western blot analysis confirmed production of the target proteins. Optical density curves showed the 19K vector grew faster with the FlYS3 construct. The goal is to quantify and test the mechanical properties of the synthesized spider silk proteins for commercial applications.
This document reviews the debate around whether adaptation occurs through the accumulation of many alleles of small effect or through large mutations. It discusses early theories of micro-mutationism proposed by Darwin and macro-mutationism proposed by Huxley. Later, Fisher argued adaptation requires "conformity of parts" best achieved through small mutations. However, the document finds little evidence supporting the claim that adaptation always involves small effect genes. Some adaptations involve major genes, and more genetic studies of adaptation are needed.
1. The study investigated whether caloric restriction (CR) or resveratrol supplementation could maintain anti-tumor immune responses mediated by an OX40 agonist immunotherapy during aging.
2. Mice were placed on a CR diet or resveratrol-supplemented diet starting at 4-6 months of age and remained on the diet until 12 months of age.
3. CR maintained OX40-mediated anti-tumor immunity in 12-month-old mice, but resveratrol supplementation did not. CR also fully sustained antigen-specific CD4 T cell priming, whereas CD8 T cell priming was only partially maintained compared to young mice.
Generalizing phylogenetics to infer shared evolutionary eventsJamie Oaks
This document discusses generalizing phylogenetics to infer shared evolutionary events. It begins by noting that current phylogenetics assumes independent divergences, which is often violated in reality through shared processes like biogeography, gene family evolution, and disease transmission. The author proposes a framework to account for shared divergences, which would improve phylogenetic inference and provide insights into codiversification processes. Key challenges include approximating high-dimensional integrals and sampling over all possible divergence models.
Does Energy Availability Predict Gastropod Reproductive Strategies? Craig McClain
Energy availability predicts some gastropod reproductive strategies. The study analyzed data on 189 gastropod families to examine relationships between energy availability, larval development strategies, and hermaphroditism. Results showed that planktotrophic larvae were more common at lower productivity, supporting Thorson's hypothesis. However, hermaphroditism decreased rather than increased with lower energy availability, contrary to predictions. Accounting for taxonomy, the relationship with hermaphroditism disappeared. Overall, energy constraints seem to select for adaptations conserving energy or bet-hedging in patchy environments.
This study examined the effects of lifelong weight cycling on lifespan in male mice. Mice were placed on either a low-fat diet, high-fat diet, or cycled diet that alternated between low-fat and high-fat every 4 weeks, causing weight fluctuations. The weight cycled mice experienced large fluctuations in body weight and fat mass over time. Surprisingly, the lifespan of weight cycled mice was not significantly different than mice on a low-fat diet, despite cycling between overweight and normal weight periods. In contrast, mice that remained on a high-fat diet had a significantly shorter lifespan than the other groups. This is the first controlled animal study to demonstrate that weight cycling itself did not decrease lifespan
This document summarizes an article that appeared in a journal published by Elsevier. The attached copy is provided to the author for non-commercial research and education purposes only. Other uses such as reproduction, distribution, selling, or posting to third party websites are prohibited without permission. Authors are allowed to post their version of the article to their personal or institutional websites for archiving purposes, and the document provides a link for authors to view Elsevier's full author rights and manuscript policies.
Ocean acidification decreases pH in surface waters due to absorbed CO2, threatening marine life. A study tested the effects of elevated CO2 and single versus multiple male spawnings on fertilization success in sea urchins. Results showed elevated CO2 did not significantly impact fertilization success. While male identity marginally affected success, multiple male spawnings unexpectedly reduced female success compared to individual males. This implies different evolutionary pressures on males and females and that optimal aggregation densities may exist for reproduction under ocean acidification.
Machine Learning in Healthcare by Mehrdad YazdaniData Con LA
Abstract:- Using Machine Learning to Identify Major Shifts in Human Gut MicrobiomeProtein Family Abundance in Disease Inflammatory Bowel Disease (IBD) is an autoimmune condition that is observed to be associated with major alterations in the gut microbiome taxonomic composition. Here we classify major changes in microbiome protein family abundances between healthy subjects and IBD patients. We use machine learning to analyze results obtained previously from computing relative abundance of ~10,000 KEGG orthologous protein families in the gut microbiome of a set of healthy individuals and IBD patients. We develop a machine learning pipeline, involving the Kolomogorv-Smirnov test, to identify the 100 most statistically significant entries in the KEGG database. Then we use these 100 as a training set for a Random Forest classifier to determine ~5% the KEGGs which are best at separating disease and healthy states. Lastly, we developed a Natural Language Processing classifier of the KEGG description files to predict KEGG relative over- or under- abundance. As we expand our analysis from 10,000 KEGG protein families to one million proteins identified in the gut microbiome, scalable methods for quickly identifying such anomalies between health and disease states will be increasingly valuable for biological interpretation of sequence data.
2015 Sujkowski, Bazzell, et al endurance exercise and selective breeding exte...Brian Bazzell, PharmD
The document describes a study comparing the effects of endurance exercise training and selective breeding for longevity on healthspan and gene expression in Drosophila melanogaster. The study found that both endurance training and selective breeding for longevity increased endurance, cardiac performance, mobility, autophagy, and stress defense pathways, while decreasing carbohydrate metabolism and odorant receptor expression. Microarray analysis revealed that 65% of gene expression changes from selective breeding were also seen with endurance training. Both interventions downregulated several members of the methuselah-like gene family, and knockdown of one such gene extended healthspan measures. The results suggest endurance exercise training and selective breeding act through overlapping genetic pathways to extend healthspan.
Dynamics of Your Gut Microbiome in Health and DiseaseLarry Smarr
This document summarizes a presentation by Dr. Larry Smarr on the dynamics of the gut microbiome in health and disease. It discusses how the gut microbiome contains hundreds of microbial species that vary significantly between healthy and diseased states. Dr. Smarr has tracked his own gut microbiome and biomarkers over time, discovering an autoimmune disease. He is now collaborating on a project combining deep metagenomic sequencing and supercomputing to map differences in the gut microbiome between healthy and inflammatory bowel disease patients.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
The document summarizes a study examining how three E. coli strains (E455, E1140, E455L) utilize gluconate differently and how this affects their fitness in seawater. Key findings:
- Genes involved in gluconate metabolism were upregulated in E455L and environmental strain E1140 compared to wild-type E455.
- In gluconate-supplemented medium, E455L grew slower than E455 but survived longer, showing higher fitness. E1140 grew slowest but reached highest density.
- All strains decayed slower in gluconate-supplemented seawater than seawater alone. E455L showed highest
This study assessed the use of an engineered periosteum consisting of chitosan nanofibers, luciferase-expressing adipose-derived stem cells (Luc-ASCs), FGF-2, and TGF-β1 coated on mouse femur bone allografts implanted into a critical bone defect. The engineered periosteum delivered Luc-ASCs and growth factors to the defect site. While statistical analysis found no difference in new bone formation between groups, treatments including Luc-ASCs showed 24% more new bone formation than uncoated controls. This suggests a polysaccharide-based engineered periosteum may be a feasible approach to improve bone allograft healing.
Generalizing phylogenetics to infer patterns of shared evolutionary eventsJamie Oaks
This document discusses generalizing phylogenetics to infer patterns of shared evolutionary events. It begins by outlining how shared ancestry is a fundamental property of life and how phylogenetics is progressing as the statistical foundation of comparative biology. It then discusses how violating the assumption of independent divergences can provide insights into processes like biogeography, gene family evolution, and endosymbiont evolution. The document considers challenges in accounting for shared divergences, like the complexity of gene trees and sampling over all possible models, and proposes two approaches: using existing methods or approximate Bayesian computation with a diffuse Dirichlet process prior.
Large Memory High Performance ComputingEnables Comparison Across Human Gut M...Larry Smarr
This document summarizes a talk about research analyzing gut microbiome data from patients with autoimmune diseases and healthy subjects. The research used large memory high performance computing on the Gordon supercomputer to analyze over 1.2 trillion DNA bases of metagenomic sequencing data from the gut microbiomes. Analysis found major shifts in microbial ecology between healthy subjects and those with Crohn's disease or ulcerative colitis. Therapies for one subject's Crohn's disease reduced certain phyla but others remained at high levels. The research aims to develop noninvasive microbial diagnostics and new therapeutic tools for managing the microbiome.
Biological evolution occurs through four main mechanisms: natural selection, genetic drift, biased mutation, and gene flow. Natural selection involves variation in traits, inheritance of traits, a high population growth rate, and differential survival and reproduction based on traits suited for the environment. Genetic drift is the random changes in genetic makeup between generations due to chance rather than adaptation. Biased mutation refers to certain types of mutations occurring more frequently in certain locations in DNA. Gene flow is the exchange of alleles between populations through migration and reproduction.
metabolic acceleration and the evolution of human brainJoão Soares
Humans have larger brains, higher reproductive output, and longer lifespans than other great apes, presenting an "energetic paradox" that requires more energy expenditure. This study found that:
1) Humans have higher total daily energy expenditure (TEE) than chimpanzees, bonobos, gorillas and orangutans, even after controlling for factors like body size and physical activity.
2) Much of the increased human TEE is due to a higher basal metabolic rate (BMR), indicating increased metabolic activity of organs.
3) Humans also have a greater percentage of body fat than other great apes.
The findings suggest humans evolved an "accelerated
Recognizing the Patterns Within: How Biomedical Data Can Reveal Health vs. Di...Larry Smarr
Keynote
Session on Challenges of Pattern Recognition in Biomedical Data
The Pacific Symposium on Biocomputing (PSB) 2018
Big Island, HI
January 6, 2018
This document discusses the large-scale production and purification of synthetic spider silk proteins using E. coli. Researchers cloned and expressed spider silk genes from the golden orb-weaving spider Nephila clavipes in E. coli. They tested different genetic vectors (SX and 19K) and protein constructs (MaSP1, FlAS3, FlYS3) and found that the SX vector produced more consistent growth and higher optical densities during fermentation. SDS-PAGE and western blot analysis confirmed production of the target proteins. Optical density curves showed the 19K vector grew faster with the FlYS3 construct. The goal is to quantify and test the mechanical properties of the synthesized spider silk proteins for commercial applications.
This document reviews the debate around whether adaptation occurs through the accumulation of many alleles of small effect or through large mutations. It discusses early theories of micro-mutationism proposed by Darwin and macro-mutationism proposed by Huxley. Later, Fisher argued adaptation requires "conformity of parts" best achieved through small mutations. However, the document finds little evidence supporting the claim that adaptation always involves small effect genes. Some adaptations involve major genes, and more genetic studies of adaptation are needed.
1. The study investigated whether caloric restriction (CR) or resveratrol supplementation could maintain anti-tumor immune responses mediated by an OX40 agonist immunotherapy during aging.
2. Mice were placed on a CR diet or resveratrol-supplemented diet starting at 4-6 months of age and remained on the diet until 12 months of age.
3. CR maintained OX40-mediated anti-tumor immunity in 12-month-old mice, but resveratrol supplementation did not. CR also fully sustained antigen-specific CD4 T cell priming, whereas CD8 T cell priming was only partially maintained compared to young mice.
Generalizing phylogenetics to infer shared evolutionary eventsJamie Oaks
This document discusses generalizing phylogenetics to infer shared evolutionary events. It begins by noting that current phylogenetics assumes independent divergences, which is often violated in reality through shared processes like biogeography, gene family evolution, and disease transmission. The author proposes a framework to account for shared divergences, which would improve phylogenetic inference and provide insights into codiversification processes. Key challenges include approximating high-dimensional integrals and sampling over all possible divergence models.
Does Energy Availability Predict Gastropod Reproductive Strategies? Craig McClain
Energy availability predicts some gastropod reproductive strategies. The study analyzed data on 189 gastropod families to examine relationships between energy availability, larval development strategies, and hermaphroditism. Results showed that planktotrophic larvae were more common at lower productivity, supporting Thorson's hypothesis. However, hermaphroditism decreased rather than increased with lower energy availability, contrary to predictions. Accounting for taxonomy, the relationship with hermaphroditism disappeared. Overall, energy constraints seem to select for adaptations conserving energy or bet-hedging in patchy environments.
This study examined the effects of lifelong weight cycling on lifespan in male mice. Mice were placed on either a low-fat diet, high-fat diet, or cycled diet that alternated between low-fat and high-fat every 4 weeks, causing weight fluctuations. The weight cycled mice experienced large fluctuations in body weight and fat mass over time. Surprisingly, the lifespan of weight cycled mice was not significantly different than mice on a low-fat diet, despite cycling between overweight and normal weight periods. In contrast, mice that remained on a high-fat diet had a significantly shorter lifespan than the other groups. This is the first controlled animal study to demonstrate that weight cycling itself did not decrease lifespan
This document summarizes an article that appeared in a journal published by Elsevier. The attached copy is provided to the author for non-commercial research and education purposes only. Other uses such as reproduction, distribution, selling, or posting to third party websites are prohibited without permission. Authors are allowed to post their version of the article to their personal or institutional websites for archiving purposes, and the document provides a link for authors to view Elsevier's full author rights and manuscript policies.
RESVERATROL DERIVATIVES WITH INCREASED BIOAVAILABILITYGanesan Venkatesan
This document describes an in silico screening project to identify resveratrol derivatives with increased bioavailability and binding affinity to the SIRT-1 protein. The objectives are to screen derivatives of resveratrol, a natural compound found in grapes and red wine, using molecular docking simulations to find derivatives with stronger binding to SIRT-1, a protein involved in longevity pathways, and improved absorption and bioavailability compared to resveratrol. The methodology involves using online databases and molecular modeling software to identify potential derivatives, evaluate their drug-like properties, and model their binding to SIRT-1.
We Are More Than What We Eat Dietary Interventions Depend on Sex and Genetic ...InsideScientific
To learn more visit: https://insidescientific.com/webinar/we-are-more-than-what-we-eat-dietary-interventions-depend-on-sex-and-genetic-background/
Despite evidence that sex and genetic background are key factors in the response to diet, most studies of how diet regulates metabolic health and even longevity in mice examine only a single strain and sex.
Using multiple strains and both male and female mice, Dr Lamming's team has found that improvements in metabolic health and in longevity in response to reduced levels of protein or specific amino acids strongly depend on sex and strain. While some phenotypes were conserved across strains and sexes, including increased glucose tolerance and energy expenditure, they observed high variability in adiposity, insulin sensitivity, and circulating hormones. Using a multi-omics approach, they identified mega-clusters of differentially expressed hepatic genes, metabolites, and lipids associated with each phenotype, gaining new insight into role of the energy balance hormone FG21 in the response to protein restriction.
2013 Bazzell, et al dietary composition regulates Drosophila mobility and car...Brian Bazzell, PharmD
The document examines the impact of varying dietary composition on physiological indices related to endurance exercise capacity in Drosophila melanogaster flies. Two genetic backgrounds of flies were fed one of 10 experimental diets that manipulated the ratios and amounts of sucrose and yeast provided. Flies fed balanced low-calorie diets generally showed improved endurance, climbing speed, and cardiac performance compared to those fed high-calorie diets. Within unbalanced diets, flies consuming diets higher in sugar relative to yeast demonstrated greater endurance but impaired cardiac function. The effects of diet composition were found to be reversible within 48 hours if flies switched diets.
From Nutrigenomics to Systems Nutrition - The role of nutrition in metabolic...Norwich Research Park
1) The document discusses moving beyond traditional nutrition science to a systems approach to understand the complex interactions between diet, genes, microbiome, and health.
2) A healthy gut microbiome is essential for overall health, and nutrition plays a key role in shaping the microbiome.
3) While no single "superfood" exists, eating a variety of plants foods along with minimizing highly processed foods can help maintain a flexible system and optimal health.
This study examined the effects of 6 consecutive days of breakfast skipping on energy metabolism and blood glucose levels in 10 healthy young Japanese males. The results showed that repeated breakfast skipping slightly increased blood glucose levels and fluctuations when subjects engaged in sedentary behavior. However, 6 days of breakfast skipping did not significantly affect 24-hour energy expenditure or substrate oxidation. Sedentary lifestyle combined with repeated breakfast skipping may cause abnormal glucose fluctuations.
Activation of AMPK Improves Cognitive Function in C. elegans
This study found that activating AMPK through a constitutively active mutation improved cognitive function in C. elegans as measured by learning assays. Worms with constant AMPK activation showed nearly double the learning ability compared to wild type worms in a salt chemotaxis test, indicating better maintenance of neurological function. Forgetting assays over time also provided insight and suggested reduced memory loss. The results demonstrate that AMPK activation can extend healthspan by preserving cognitive ability in aging.
Dr. Tom Burkey - Host-Microbe Interactions: Effects on nutrition and physiologyJohn Blue
Host-Microbe Interactions: Effects on nutrition and physiology - Dr. Tom Burkey, University of Nebraska-Lincoln, from the 2014 Allen D. Leman Swine Conference, September 15-16, 2014, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2014-leman-swine-conference-material
This study evaluated the effects of adequate protein intake through dietary counseling or protein supplementation on sarcopenic older adults. 56 sarcopenic participants were provided either dietary counseling to encourage protein intake of 1.2-1.5 g/kg body weight per day or an isocaloric protein supplement containing whey protein, leucine and vitamin D. Both groups experienced increases in muscle mass and strength after 12 weeks. However, the supplement group achieved higher protein intake and saw greater improvements in walking speed for those under age 75. The study suggests protein supplementation is a convenient way for sarcopenic older adults to meet protein requirements and may provide additional benefits for physical performance in younger older groups.
This document discusses how the length of the Roux limb in gastric bypass surgery may impact outcomes. It notes that while longer Roux limbs between 150-200 cm do not significantly impact weight loss, even more distal bypass with Roux limbs of only 50-75 cm from the ileocecal valve can cause greater weight loss but also increases risks of nutritional deficiencies. The document reviews evidence from studies comparing standard to longer or more distal Roux limb lengths and their effects on weight loss and complications.
The document discusses the difficulty in equating changes in mass and energy in humans based on net calorie balance alone. It reviews several studies that demonstrate humans do not always lose or gain exact amounts of fat based on calculations of net calorie intake. The studies showed on average only about 70% of an excess or deficit in calories was reflected as changes in body weight or fat mass. The studies implicate genetic and other individual factors that can influence fat balance beyond simply net calories. The document concludes that more factors beyond just calorie balance must affect human fat storage and loss.
This study aims to examine the extent to which important individuals like parents, teachers and coaches from a student's childhood and teenage years influence their self-assessment of skills at the University of Maastricht. The researcher hypothesizes that students who experienced encouraging relationships will show realistic or overestimating self-assessments, while those experiencing unencouraging relationships will lack self-confidence. A sample of 90 3rd year UCM students will complete a questionnaire on self-assessed memory, physical and motor skills, and then perform tasks to detect over or underestimation. Follow-up questions will explore how important individuals evaluated the student's performance to understand influence on self-concept and self-efficacy. The study
The document discusses nutrigenomics and nutrigenetics. It begins with important terms related to omics fields like genomics, nutrigenomics, and epigenetics. It then provides a basic understanding of nutrigenomics and nutrigenetics, including how genetic diversity and environmental factors affect nutrient metabolism and health outcomes. The goals of nutrigenomics are discussed, including customizing nutrition based on an individual's genetics. Experimental approaches like genomics, transcriptomics and metabolomics are used to study these fields. Examples are provided on how nutrigenomics has clarified roles of specific dietary factors and potential applications in disease prevention.
04 May 2015Page 1 of 28ProQuestIntegrating Fundamental Conce.docxmercysuttle
04 May 2015
Page 1 of 28
ProQuest
Integrating Fundamental Concepts of Obesity and Eating Disorders: Implications for the Obesity Epidemic
Author: Macpherson-Sánchez, Ann E, EdD, MNS
ProQuest document link
Abstract: Physiological mechanisms promote weight gain after famine. Because eating disorders, obesity, and dieting limit food intake, they are famine-like experiences. The development of the concept of meeting an ideal weight was the beginning of increasing obesity. Weight stigma, the perception of being fat, lack of understanding of normal growth and development, and increased concern about obesity on the part of health providers, parents, and caregivers have reinforced each other to promote dieting. Because weight suppression and disinhibition provoke long-term weight increase, dieting is a major factor producing the obesity epidemic. The integrated eating disorder-obesity theory included in this article emphasizes that, contrary to dieters, lifetime weight maintainers depend on physiological processes to control weight and experience minimal weight change.
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Full text: Headnote
Physiological mechanisms promote weight gain after famine. Because eating disorders, obesity, and dieting limit food intake, they are famine-like experiences. The development of the concept of meeting an ideal weight was the beginning of increasing obesity. Weight stigma, the perception of being fat, lack of understanding of normal growth and development, and increased concern about obesity on the part of health providers, parents, and caregivers have reinforced each other to promote dieting. Because weight suppression and disinhibition provoke long-term weight increase, dieting is a major factor producing the obesity epidemic. The integrated eating disorder-obesity theory included in this article emphasizes that, contrary to dieters, lifetime weight maintainers depend on physiological processes to control weight and experience minimal weight change. (Am J Public Health. 2015;105:e71-e85. doi:10. 2105/AJPH.2014.302507)
Since 1960, the Centers for Disease Control and Prevention has done periodic surveys of representative samples of the US population, which include measured heights and weights.1 From the 1960 to 1962 to the 1976 to 1980 measurement periods, there was little change in population weight. However, the next survey (1988-1994) showed increases in body mass index (BMI; defined as weight in kilograms divided by the square of height in meters [kg/m2]) that were unanticipated and inexplicable.2 Most of the increase occurred in those with BMI of 30 or greater.3 In 2006, a prominent Centers for Disease Control and Prevention researcher expressed frustration with her incapacity to explain why this happened.2
Losing weight and recuperating from that weight loss is part of the biological heritage of every human being.4-6 However, in the past 70 years, self-induced famine (dieting to achieve and maintain a lower weight)7 became the socie ...
- The document discusses an integrated approach to cancer prevention and treatment through lifestyle changes.
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- Evidence from studies on nutrition, exercise, stress management, and social support suggest that adopting a healthy lifestyle may reduce cancer risk and slow cancer progression. The Prostate Cancer Lifestyle Trial found significant benefits of lifestyle changes for men with early-stage prostate cancer.
Nutritional assessment in chronic liver diseaseShaimaa Elkholy
Protein Energy Malnutrition (PEM) is highly prevalent among patients with chronic liver disease. One of the problems is how to assess these patients nutritionally. yet no standard golden rule for their nutritional assessment.
Similar to Life extension by dietary restriction is not adaptive reallocation (20)
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
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.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
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and the revised UWWTD (Urban Waste Water Treatment Directive)”
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
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Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
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on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
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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
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The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
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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).
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Life extension by dietary restriction is not adaptive reallocation
1. • Dietary restriction (DR) extends longevity
• Adaptive reallocation hypothesis inter-
prets DR effect as an adaptation enabling
later reproduction in favorable conditions
• We evolved Saccharomyces cerevisiae on
DR for 1800 generations
• Multi-generational DR should select for
increased allocation to reproduction and
decreased allocation to longevity
• Reproductive fitness should increase more
during long-term adaptation to DR than to
control conditions
Life extension by dietary restriction is not adaptive reallocation
Roy Z Moger-Reischer, Elizabeth V Snider, Kelsey L McKenzie, Jay T Lennon
Department of Biology, Evolution, Ecology, & Behavior Program
Indiana University
ACKNOWLEDGMENTS
ABSTRACT RESULTS & DISCUSSION
Figure 1: The adaptive reallocation hypothesis.
Figure 3: We assayed relative fitness using
flow cytometry. YPD-evolved lines evolved
higher relative fitness compared to DR-
evolved lines, when measured on either
the respective focal diet or alternate diet.
Survivorship
Time (days)
A B C
Figure 4: DR-evolved lines achieved
higher asymptote OD 600 than YPD-
evolved lines. This suggests natural
selection acted to increase metabolic
efficiency during evolution on long-term
DR.
We owe a debt of gratitude to the
Lacefield lab for assistance with yeast
methods. We thank Danni Boylan and
Derek Hocker for assistance in the
laboratory. Advice on experimental de-
sign from Jake McKinlay and Farrah
Bashey-Visser was sincerely appreciated.
None of our findings support the
adaptive reallocation hypothesis.
However, they are consistent with
the cellular efficiency hypothesis,
which interprets the effect of DR
on longevity as a side effect of
selection for increased cellular
efficiency during famines.
Aging, or senescence, is one of the biggest puzzles in
evolutionary biology. Traditional life history-based
theories for the evolution of senescence predicts that
fecundity-longevity tradeoffs constrain the evolution
of longevity. We tested whether long-term evolution
under dietary restriction, a condition that slows
senescence, selects for increased allocation to repro-
duction and decreased allocation to longevity, as
predicted by life-history theory. Evolved patterns
contradicted the expectations of life-history theory.
Our findings were more consistent with a model in
which the life-extending effect of dietary restriction is
a byproduct of selection for cellular efficiency.
Figure 2: We measured survivorship of evolved lines in synthetic complete medium. Neither evolution treatment caused
changes to survivorship assayed on DR (A,C). Life expectancy was shorter for YPD-evolved lines on assayed control media (B,C).
BACKGROUND