Chaston Blog
Blog
13 Jan 2021
Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms. Want to read more closely, simulations are a little dense for me now.
The gut microbiota is a transmissible determinant of skeletal maturation
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
The gut microbiota is a transmissible determinant of skeletal maturation
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
8 Jan 2021
The fliK Gene Is Required for the Resistance of Bacillus thuringiensis to Antimicrobial Peptides and Virulence in Drosophila melanogaster Interesting to us because we're looking at flagellar genes as being important for persisting within the host.
Natural history of model organisms: The secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology. Helpful study, good framework for considering larval density, which we normally just control by putting 30-60 larvae in a vial.
Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime. They show this by comparing SNVs in the microbiota between twin pairs, and showing that twin pairs can share strains with unique genetic signatures. I haven't thought carefully about if their method of setting a strain-specific variant threshold is too circular to be useful, but i think it's a clever approach and a useful way to get at a challenging question. Now - start freezing poop from twin pairs!
Merging Fungal and Bacterial Community Profiles via an Internal Control Interesting idea for a control for mixed bacterial and fungal amplifications.
Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Fascinating!
Systemic Regulation of Host Energy and Oogenesis by Microbiome-Derived Mitochondrial Coenzymes
Natural history of model organisms: The secret (group) life of Drosophila melanogaster larvae and why it matters to developmental ecology. Helpful study, good framework for considering larval density, which we normally just control by putting 30-60 larvae in a vial.
Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime. They show this by comparing SNVs in the microbiota between twin pairs, and showing that twin pairs can share strains with unique genetic signatures. I haven't thought carefully about if their method of setting a strain-specific variant threshold is too circular to be useful, but i think it's a clever approach and a useful way to get at a challenging question. Now - start freezing poop from twin pairs!
Merging Fungal and Bacterial Community Profiles via an Internal Control Interesting idea for a control for mixed bacterial and fungal amplifications.
Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. Fascinating!
Systemic Regulation of Host Energy and Oogenesis by Microbiome-Derived Mitochondrial Coenzymes
24 Sep 2020
Experimentally induced intrasexual mating competition and sex-specific evolution in female and male nematodes. Cool exp that manually alters sex ratio and shows changes during experimental evolution.
Host and altitude factors affect rumen bacteria in cattle. Could look for it in our deer dataset.
Seasonal morphotypes of Drosophila suzukii differ in key life-history traits during and after a prolonged period of cold exposure. Looks at overwintering populations of the flies. they live way longer than melanogaster (5-7months!)
Effect of gut microbiota on α-amanitin tolerance in Drosophila tripunctata. The microbiota likely do not contribute to the flies' tolerance for alpha-amanitin, a mushroom toxin in these mushroom-feeding flies consume.
MicrobiomeExplorer: An R package for the analysis and visualization of microbial communities. Been thinking of trying to do something like this, excited to see if this will save the trouble!
A conserved role for sleep in supporting Spatial Learning in Drosophila. Cool to try an MGWA on it.
A test of the Niche Variation Hypothesis in a ruminant herbivore. Something to think about in our dataset.
The Incidence and Outcomes of COVID-19 in IBD Patients: A Rapid Review and Meta-analysis. Small sample size, but are people with IBD protected from COVID? Maybe.
The peculiar structure of Acetobacter pasteurianus CIP103108 LPS core oligosaccharide. Just cataloguing a surface structure on Acetobacter paper.
One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Wow - great work.
Drosophila melanogaster, a new model for exercise research. Would love to do an MGWA on Drosophila and exercise, too!
Host and altitude factors affect rumen bacteria in cattle. Could look for it in our deer dataset.
Seasonal morphotypes of Drosophila suzukii differ in key life-history traits during and after a prolonged period of cold exposure. Looks at overwintering populations of the flies. they live way longer than melanogaster (5-7months!)
Effect of gut microbiota on α-amanitin tolerance in Drosophila tripunctata. The microbiota likely do not contribute to the flies' tolerance for alpha-amanitin, a mushroom toxin in these mushroom-feeding flies consume.
MicrobiomeExplorer: An R package for the analysis and visualization of microbial communities. Been thinking of trying to do something like this, excited to see if this will save the trouble!
A conserved role for sleep in supporting Spatial Learning in Drosophila. Cool to try an MGWA on it.
A test of the Niche Variation Hypothesis in a ruminant herbivore. Something to think about in our dataset.
The Incidence and Outcomes of COVID-19 in IBD Patients: A Rapid Review and Meta-analysis. Small sample size, but are people with IBD protected from COVID? Maybe.
The peculiar structure of Acetobacter pasteurianus CIP103108 LPS core oligosaccharide. Just cataloguing a surface structure on Acetobacter paper.
One fly-one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster. Wow - great work.
Drosophila melanogaster, a new model for exercise research. Would love to do an MGWA on Drosophila and exercise, too!
17 Sep 2020
Sleep-length differences are associated with altered longevity in the fruit fly Drosophila melanogaster. As it says - short sleep flies have longer lifespan; long-sleep flies have shorter lifespan.
Inside the supergene of the bird with four sexes. Never heard of this before, but "
The species mates disassortatively with respect to the supergene [ESR1]; that is, each breeding pair consists of one individual with it and one without it. This species has therefore been called the "bird with four sexes"." Apparently there are more than 1000 genes in this supergene. can't access the article yet.
Diabolical dilemmas of COVID-19: An empirical study into Dutch society's trade-offs between health impacts and other effects of the lockdown. Fascinating results, including that the elderly and educated were the most willing to sacrifice the economy and education for health.
Temperature transcends partner specificity in the symbiosis establishment of a cnidarian. Really cool finding, although just reading the abstract can't tell if this is mostly because at high temperatures the bacteria that don't survive at high temperatures aren't there (i.e. more about environmental filtering than G x E interactions).
Influence of host genetics in shaping the rumen bacterial community in beef cattle. Really well done paper identifying genetic links between cattle and specific members of their microbial communities.
Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease. As it says. Lachnospiraceae are important.
Inside the supergene of the bird with four sexes. Never heard of this before, but "
The species mates disassortatively with respect to the supergene [ESR1]; that is, each breeding pair consists of one individual with it and one without it. This species has therefore been called the "bird with four sexes"." Apparently there are more than 1000 genes in this supergene. can't access the article yet.
Diabolical dilemmas of COVID-19: An empirical study into Dutch society's trade-offs between health impacts and other effects of the lockdown. Fascinating results, including that the elderly and educated were the most willing to sacrifice the economy and education for health.
Temperature transcends partner specificity in the symbiosis establishment of a cnidarian. Really cool finding, although just reading the abstract can't tell if this is mostly because at high temperatures the bacteria that don't survive at high temperatures aren't there (i.e. more about environmental filtering than G x E interactions).
Influence of host genetics in shaping the rumen bacterial community in beef cattle. Really well done paper identifying genetic links between cattle and specific members of their microbial communities.
Gut Microbiota and Metabolome Alterations Associated with Parkinson's Disease. As it says. Lachnospiraceae are important.
15 Sep 2020
Gut Bacterial Species Distinctively Impact Host Purine Metabolites during Aging in Drosophila. In aged flies, A. persici increases allantoin by activating IMD. L. plantarum can decrease allantoin by scavenging dietary purines.
Identification of multidimensional Boolean patterns in microbial communities. I'd like to see if this pulls out different results on datasets using simpler fruit fly microbiomes.
Endurance and sprint training affect immune function differently in green anole lizards ( Anolis carolinensis). Animals invest different resources in immunity based on their exercise training (endurance trained lost cell-mediated, sprint-trained lost wound healing, neither affected acquired immunity).
Stagewise resolution of temperature-dependent embryonic and postembryonic development in the cowpea seed beetle Callosobruchus maculatus (F.). Defines the effect of temperature on timing of development in a seed beetle. Might want to look at papers that define the same for Drosophila.
Peroxisome-associated Sgroppino links fat metabolism with survival after RNA virus infection in Drosophila
"Together, our results establish a genetic link between the peroxisomal protein Sgroppino, fat metabolism, and resistance to virus infection."
Gut microbiota changes in patients with autism spectrum disorders. "At the genus level, there was a significant increase in the relative abundance of unidentified Lachnospiraceae, Clostridiales, Erysipelotrichaceae, Dorea, Collinsella, and Lachnoclostridium, whereas Bacteroides, Faecalibacterium, Parasutterella, and Paraprevotella were significantly lower in the ASD group than in the control group"
Warmth Prevents Bone Loss Through the Gut Microbiota. Wow - exposure to 34°C temperatures or a 'warm-adapted' microbiota protects from bone loss. At higher temps microbes produce more polyamines, spermine and spermidine supplementation increase bone strength, and limiting polyamine biosynthesis reduces the warmth benefit to bone strength. Surprising to me, and cool!
Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. "By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential."
Early Life Stress and the Development of the Infant Gut Microbiota: Implications for Mental Health and Neurocognitive Development.
Infants exposed to antibiotics after birth have altered recognition memory responses at one month of age. "Infants exposed to antibiotics exhibited smaller P2 amplitudes for both voice conditions (p = 0.001), with greatest reductions observed for mother's voice in frontal and central scalp regions (p < 0.04). Infants exposed to antibiotics showed larger P2 amplitudes to stranger's as compared to mother's voice, a reversal of the typical response exhibited by unexposed infants. Abnormal ERP responses did not consistently correlate with increased inflammatory cytokines within the antibiotic-exposed group."
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Cool, big dataset.
A survey of entomopathogenic nematodes and their symbiotic bacteria in agricultural areas of northern Thailand. Collection and characterization of more EPNs.
Identification of multidimensional Boolean patterns in microbial communities. I'd like to see if this pulls out different results on datasets using simpler fruit fly microbiomes.
Endurance and sprint training affect immune function differently in green anole lizards ( Anolis carolinensis). Animals invest different resources in immunity based on their exercise training (endurance trained lost cell-mediated, sprint-trained lost wound healing, neither affected acquired immunity).
Stagewise resolution of temperature-dependent embryonic and postembryonic development in the cowpea seed beetle Callosobruchus maculatus (F.). Defines the effect of temperature on timing of development in a seed beetle. Might want to look at papers that define the same for Drosophila.
Peroxisome-associated Sgroppino links fat metabolism with survival after RNA virus infection in Drosophila
"Together, our results establish a genetic link between the peroxisomal protein Sgroppino, fat metabolism, and resistance to virus infection."
Gut microbiota changes in patients with autism spectrum disorders. "At the genus level, there was a significant increase in the relative abundance of unidentified Lachnospiraceae, Clostridiales, Erysipelotrichaceae, Dorea, Collinsella, and Lachnoclostridium, whereas Bacteroides, Faecalibacterium, Parasutterella, and Paraprevotella were significantly lower in the ASD group than in the control group"
Warmth Prevents Bone Loss Through the Gut Microbiota. Wow - exposure to 34°C temperatures or a 'warm-adapted' microbiota protects from bone loss. At higher temps microbes produce more polyamines, spermine and spermidine supplementation increase bone strength, and limiting polyamine biosynthesis reduces the warmth benefit to bone strength. Surprising to me, and cool!
Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. "By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential."
Early Life Stress and the Development of the Infant Gut Microbiota: Implications for Mental Health and Neurocognitive Development.
Infants exposed to antibiotics after birth have altered recognition memory responses at one month of age. "Infants exposed to antibiotics exhibited smaller P2 amplitudes for both voice conditions (p = 0.001), with greatest reductions observed for mother's voice in frontal and central scalp regions (p < 0.04). Infants exposed to antibiotics showed larger P2 amplitudes to stranger's as compared to mother's voice, a reversal of the typical response exhibited by unexposed infants. Abnormal ERP responses did not consistently correlate with increased inflammatory cytokines within the antibiotic-exposed group."
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. Cool, big dataset.
A survey of entomopathogenic nematodes and their symbiotic bacteria in agricultural areas of northern Thailand. Collection and characterization of more EPNs.