Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization

Soybean aphids (Aphis glycines Matsumura) are specialized insects that feed on soybean (Glycine max) phloem sap. Transcriptome analyses have shown that resistant soybean plants mount a fast response that limits aphid feeding and population growth. Conversely, defense responses in susceptible plants are slower and it is hypothesized that aphids block effective defenses in the compatible interaction. Unlike other pests, aphids can colonize plants for long periods of time; yet the effect on the plant transcriptome after long-term aphid feeding has not been analyzed for any plant–aphid interaction. We analyzed the susceptible and resistant (Rag1) transcriptome response to aphid feeding in soybean plants colonized by aphids (biotype 1) for 21 days. We found a reduced resistant response and a low level of aphid growth on Rag1 plants, while susceptible plants showed a strong response consistent with pattern-triggered immunity. GO-term analyses identified chitin regulation as one of the most overrepresented classes of genes, suggesting that chitin could be one of the hemipteran-associated molecular pattern that triggers this defense response. Transcriptome analyses also indicated the phenylpropanoid pathway, specifically isoflavonoid biosynthesis, was induced in susceptible plants in response to long-term aphid feeding. Metabolite analyses corroborated this finding. Aphid-treated susceptible plants accumulated daidzein, formononetin, and genistein, although glyceollins were present at low levels in these plants. Choice experiments indicated that daidzein may have a deterrent effect on aphid feeding. Mass spectrometry imaging showed these isoflavones accumulate likely in the mesophyll cells or epidermis and are absent from the vasculature, suggesting that isoflavones are part of a non-phloem defense response that can reduce aphid feeding. While it is likely that aphid can initially block defense responses in compatible interactions, it appears that susceptible soybean plants can eventually mount an effective defense in response to long-term soybean aphid colonization

Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization

Soybean aphids (Aphis glycines Matsumura) are specialized insects that feed on soybean (Glycine max) phloem sap. Transcriptome analyses have shown that resistant soybean plants mount a fast response that limits aphid feeding and population growth. Conversely, defense responses in susceptible plants are slower and it is hypothesized that aphids block effective defenses in the compatible interaction. Unlike other pests, aphids can colonize plants for long periods of time; yet the effect on the plant transcriptome after long-term aphid feeding has not been analyzed for any plant–aphid interaction. We analyzed the susceptible and resistant (Rag1) transcriptome response to aphid feeding in soybean plants colonized by aphids (biotype 1) for 21 days. We found a reduced resistant response and a low level of aphid growth on Rag1 plants, while susceptible plants showed a strong response consistent with pattern-triggered immunity. GO-term analyses identified chitin regulation as one of the most overrepresented classes of genes, suggesting that chitin could be one of the hemipteran-associated molecular pattern that triggers this defense response. Transcriptome analyses also indicated the phenylpropanoid pathway, specifically isoflavonoid biosynthesis, was induced in susceptible plants in response to long-term aphid feeding. Metabolite analyses corroborated this finding. Aphid-treated susceptible plants accumulated daidzein, formononetin, and genistein, although glyceollins were present at low levels in these plants. Choice experiments indicated that daidzein may have a deterrent effect on aphid feeding. Mass spectrometry imaging showed these isoflavones accumulate likely in the mesophyll cells or epidermis and are absent from the vasculature, suggesting that isoflavones are part of a non-phloem defense response that can reduce aphid feeding. While it is likely that aphid can initially block defense responses in compatible interactions, it appears that susceptible soybean plants can eventually mount an effective defense in response to long-term soybean aphid colonization

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Abstract: Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Abstract: Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies

Long-term-survival phase Salmonella enterica: Life cycle comparison with a high persister mutant, and tolerance to atmospheric cold plasma

Persister cells and long-term survival (LTS) cells are epigenetic variants that demonstrate a tolerance towards stressful environmental conditions. Persisters can survive exposure to antibiotics while LTS cells can tolerate adverse conditions of the natural environment for extended periods. Bacteria in the LTS phase typically exhibit a decreased vulnerability to physical or chemical antimicrobial treatments compared to exponential- and stationary phase cells. To determine if these two phenomena have a common genetic basis, we measured the viability of a high persister mutant of Salmonella Typhimurium (AS13) throughout four phases of its life cycle under the premise that its high persistence would cause it to enter LTS phase at a higher concentration than the isogenic wild-type strain LT2 or Salmonella Typhimurium ATCC 14028 (Sal 3). All strains were grown in Lysogeny Broth (LB) at 35oC and were initially subjected to a persister cell assay. Over the course of 168 days, a standard plate count was performed at various times to obtain viable cell concentrations of the pathogen at exponential, stationary, death and LTS phases of the life cycle. Counts at 14 days and 140 days represented viable cell concentrations of the S. Typhimurium upon entry in the LTS phase and within the LTS phase, respectively. Stationary phase cells of AS13 had a significantly higher (p0.05) compared to LT2 or Sal3. Based on this result we conclude that the genetic change responsible for the high persister phenotype of AS13 does not increase the viable cell concentration in the LTS phase.   We further evaluated the role of naturally occurring persister cells in the STAT and LTS phase cells of Salmonella Enteritidis ATCC 13076 and evaluated the antimicrobial efficacy of high voltage atmospheric cold plasma (HVACP) against LTS phase and stationary phase (STAT) cells of the pathogen in a model system (PBS, pH 7.0 45kV for 1-4 min) and on shell eggs (60kV for 1-5 min). The effect of HVACP treatments on selected quality characteristics of shell eggs was also evaluated. The S. Enteritidis was grown in tryptic soy broth supplemented with 0.6% yeast extract (TSBYE) at 35oC for 20 h (STAT) and 21days (LTS). A significantly higher persister cell concentration (p<0.05) was found in the LTS phase (4.22log CFU/mL) compared to STAT (1.72 log CFU/mL). A significantly lower (p<0.05) inactivation of LTS phase cells of S. Enteritidis occurred in both the PBS and shell eggs compared to STAT cells. In PBS, microbial reductions (log CFU/mL) of STAT cells were 1.0, 0.95, 1.45, and 1.44 after HVACP treatment for 1.0, 2.0, 3.0, and 4.0 min, respectively. In contrast, reductions (log CFU/mL) of LTS cells were significantly lower (p<0.05) at 0.04 (1 min), 0.06 (2 min) 0.01 (3 min), and 0.11 (4 min). A similar pattern was also observed for shell eggs whereby LTS cells exhibited substantially higher tolerance to HVACP than STAT cells (p < 0.05). No differences among eggshell strength and yolk color between HVACP-treated and untreated eggs were observed. Based on these results, we conclude that LTS cells of S. Enteritidis are more tolerant to HVACP than STAT cells and should be considered in the development of Salmonella inactivation protocols involving HVACP treatment of shell eggs. In conclusion, while high persistence does not improve LTS, the state of persistence appears to contribute to the ability of the pathogen survive HVACP treatment. These results suggest that the phenomenon of persistence should be considered in greater depth when considering treatments to improve food safety

Long-term-survival phase Salmonella enterica: Life cycle comparison with a high persister mutant, and tolerance to atmospheric cold plasma

Persister cells and long-term survival (LTS) cells are epigenetic variants that demonstrate a tolerance towards stressful environmental conditions. Persisters can survive exposure to antibiotics while LTS cells can tolerate adverse conditions of the natural environment for extended periods. Bacteria in the LTS phase typically exhibit a decreased vulnerability to physical or chemical antimicrobial treatments compared to exponential- and stationary phase cells. To determine if these two phenomena have a common genetic basis, we measured the viability of a high persister mutant of Salmonella Typhimurium (AS13) throughout four phases of its life cycle under the premise that its high persistence would cause it to enter LTS phase at a higher concentration than the isogenic wild-type strain LT2 or Salmonella Typhimurium ATCC 14028 (Sal 3). All strains were grown in Lysogeny Broth (LB) at 35oC and were initially subjected to a persister cell assay. Over the course of 168 days, a standard plate count was performed at various times to obtain viable cell concentrations of the pathogen at exponential, stationary, death and LTS phases of the life cycle. Counts at 14 days and 140 days represented viable cell concentrations of the S. Typhimurium upon entry in the LTS phase and within the LTS phase, respectively. Stationary phase cells of AS13 had a significantly higher (p0.05) compared to LT2 or Sal3. Based on this result we conclude that the genetic change responsible for the high persister phenotype of AS13 does not increase the viable cell concentration in the LTS phase.   We further evaluated the role of naturally occurring persister cells in the STAT and LTS phase cells of Salmonella Enteritidis ATCC 13076 and evaluated the antimicrobial efficacy of high voltage atmospheric cold plasma (HVACP) against LTS phase and stationary phase (STAT) cells of the pathogen in a model system (PBS, pH 7.0 45kV for 1-4 min) and on shell eggs (60kV for 1-5 min). The effect of HVACP treatments on selected quality characteristics of shell eggs was also evaluated. The S. Enteritidis was grown in tryptic soy broth supplemented with 0.6% yeast extract (TSBYE) at 35oC for 20 h (STAT) and 21days (LTS). A significantly higher persister cell concentration (p<0.05) was found in the LTS phase (4.22log CFU/mL) compared to STAT (1.72 log CFU/mL). A significantly lower (p<0.05) inactivation of LTS phase cells of S. Enteritidis occurred in both the PBS and shell eggs compared to STAT cells. In PBS, microbial reductions (log CFU/mL) of STAT cells were 1.0, 0.95, 1.45, and 1.44 after HVACP treatment for 1.0, 2.0, 3.0, and 4.0 min, respectively. In contrast, reductions (log CFU/mL) of LTS cells were significantly lower (p<0.05) at 0.04 (1 min), 0.06 (2 min) 0.01 (3 min), and 0.11 (4 min). A similar pattern was also observed for shell eggs whereby LTS cells exhibited substantially higher tolerance to HVACP than STAT cells (p < 0.05). No differences among eggshell strength and yolk color between HVACP-treated and untreated eggs were observed. Based on these results, we conclude that LTS cells of S. Enteritidis are more tolerant to HVACP than STAT cells and should be considered in the development of Salmonella inactivation protocols involving HVACP treatment of shell eggs. In conclusion, while high persistence does not improve LTS, the state of persistence appears to contribute to the ability of the pathogen survive HVACP treatment. These results suggest that the phenomenon of persistence should be considered in greater depth when considering treatments to improve food safety

Long-term-survival phase Salmonella enterica: Life cycle comparison with a high persister mutant, and tolerance to atmospheric cold plasma

Persister cells and long-term survival (LTS) cells are epigenetic variants that demonstrate a tolerance towards stressful environmental conditions. Persisters can survive exposure to antibiotics while LTS cells can tolerate adverse conditions of the natural environment for extended periods. Bacteria in the LTS phase typically exhibit a decreased vulnerability to physical or chemical antimicrobial treatments compared to exponential- and stationary phase cells. To determine if these two phenomena have a common genetic basis, we measured the viability of a high persister mutant of Salmonella Typhimurium (AS13) throughout four phases of its life cycle under the premise that its high persistence would cause it to enter LTS phase at a higher concentration than the isogenic wild-type strain LT2 or Salmonella Typhimurium ATCC 14028 (Sal 3). All strains were grown in Lysogeny Broth (LB) at 35oC and were initially subjected to a persister cell assay. Over the course of 168 days, a standard plate count was performed at various times to obtain viable cell concentrations of the pathogen at exponential, stationary, death and LTS phases of the life cycle. Counts at 14 days and 140 days represented viable cell concentrations of the S. Typhimurium upon entry in the LTS phase and within the LTS phase, respectively. Stationary phase cells of AS13 had a significantly higher (p0.05) compared to LT2 or Sal3. Based on this result we conclude that the genetic change responsible for the high persister phenotype of AS13 does not increase the viable cell concentration in the LTS phase.   We further evaluated the role of naturally occurring persister cells in the STAT and LTS phase cells of Salmonella Enteritidis ATCC 13076 and evaluated the antimicrobial efficacy of high voltage atmospheric cold plasma (HVACP) against LTS phase and stationary phase (STAT) cells of the pathogen in a model system (PBS, pH 7.0 45kV for 1-4 min) and on shell eggs (60kV for 1-5 min). The effect of HVACP treatments on selected quality characteristics of shell eggs was also evaluated. The S. Enteritidis was grown in tryptic soy broth supplemented with 0.6% yeast extract (TSBYE) at 35oC for 20 h (STAT) and 21days (LTS). A significantly higher persister cell concentration (p<0.05) was found in the LTS phase (4.22log CFU/mL) compared to STAT (1.72 log CFU/mL). A significantly lower (p<0.05) inactivation of LTS phase cells of S. Enteritidis occurred in both the PBS and shell eggs compared to STAT cells. In PBS, microbial reductions (log CFU/mL) of STAT cells were 1.0, 0.95, 1.45, and 1.44 after HVACP treatment for 1.0, 2.0, 3.0, and 4.0 min, respectively. In contrast, reductions (log CFU/mL) of LTS cells were significantly lower (p<0.05) at 0.04 (1 min), 0.06 (2 min) 0.01 (3 min), and 0.11 (4 min). A similar pattern was also observed for shell eggs whereby LTS cells exhibited substantially higher tolerance to HVACP than STAT cells (p < 0.05). No differences among eggshell strength and yolk color between HVACP-treated and untreated eggs were observed. Based on these results, we conclude that LTS cells of S. Enteritidis are more tolerant to HVACP than STAT cells and should be considered in the development of Salmonella inactivation protocols involving HVACP treatment of shell eggs. In conclusion, while high persistence does not improve LTS, the state of persistence appears to contribute to the ability of the pathogen survive HVACP treatment. These results suggest that the phenomenon of persistence should be considered in greater depth when considering treatments to improve food safety