scholarly journals Quantitative Genetic Analysis of the Maize Leaf Microbiome

2018 ◽  
Author(s):  
Jason G. Wallace ◽  
Karl A. Kremling ◽  
Edward S. Buckler
Keyword(s):  
Community Diversity ◽  
Exact Nature ◽  
Common Environment ◽  
Operational Taxonomic Units ◽  
Metabolic Functions ◽  
Genome Wide ◽  
Significant Enrichment ◽  
Heritability Analysis ◽  
Founder Events ◽  
Diversity Metrics

AbstractThe degree to which an organism can affect its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We address this question by analyzing the metabolically active bacteria of the maize phyllosphere across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades (individual operational taxonomic units and higher-level groupings), and 9042 predicted metagenomic functions. We find that only a few few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the amount of Methylobacteria present in each sample, and we find significant enrichment for traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identifies a small number of associated loci for these heritable traits, including two loci (on maize chromosomes 7 and 10) that affect a large number of traits even after correcting for correlations among traits. This work is among the most comprehensive analyses of the maize phyllosphere to date. Our results indicate that while most of the maize phyllosphere composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host plant genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on the phenotype of host plants.

scholarly journals Quantitative Genetics of the Maize Leaf Microbiome

2018 ◽  
Vol 2 (4) ◽  
pp. 208-224 ◽  
Author(s):  
Jason G. Wallace ◽  
Karl A. Kremling ◽  
Lynsey L. Kovar ◽  
Edward S. Buckler
Keyword(s):  
Community Diversity ◽  
Exact Nature ◽  
Multiple Traits ◽  
Exact Test ◽  
Maize Leaf ◽  
Microbiome Composition ◽  
Metabolic Functions ◽  
Genome Wide ◽  
Founder Events ◽  
Diversity Metrics

The degree to which the genotype of an organism can affect the composition of its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We analyzed the metabolically active bacteria of maize leaves across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades, and 9,042 predicted metagenomic functions. We find that only a few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the Methylobacteria in each sample. Among these heritable metabolic traits, Fisher’s exact test identifies significant overrepresentation of traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identified a small number of associated loci for these heritable traits, including two that affect multiple traits. Our results indicate that while most of the maize leaf microbiome composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on their host. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

scholarly journals Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

2019 ◽  
Vol 20 (13) ◽  
pp. 3315 ◽  
Author(s):  
Simona Cantarella ◽  
Davide Carnevali ◽  
Marco Morselli ◽  
Anastasia Conti ◽  
Matteo Pellegrini ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Human Fibroblasts ◽  
Rna Polymerase Iii ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Hela Cell Lines ◽  
Significant Enrichment ◽  
Alu Rna

Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.

scholarly journals Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations

Blood ◽  
2012 ◽  
Vol 120 (10) ◽  
pp. 2076-2086 ◽  
Author(s):  
Britta Will ◽  
Li Zhou ◽  
Thomas O. Vogler ◽  
Susanna Ben-Neriah ◽  
Carolina Schinke ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Genetic Alterations ◽  
Fish Analysis ◽  
Exact Nature ◽  
Clinical Relapse ◽  
Hematopoietic Stem ◽  
Molecular Alterations ◽  
Genome Wide ◽  
Stem And Progenitor Cells ◽  
Specific Expansion

Abstract Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage−/CD34+/CD38−/CD90+) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS is characterized by expansion of phenotypic common myeloid progenitors, whereas higher-risk cases revealed expansion of granulocyte-monocyte progenitors. Genome-wide analysis of sorted MDS HSCs revealed widespread methylomic and transcriptomic alterations. STAT3 was an aberrantly hypomethylated and overexpressed target that was validated in an independent cohort and found to be functionally relevant in MDS HSCs. FISH analysis demonstrated that a very high percentage of MDS HSC (92% ± 4%) carry cytogenetic abnormalities. Longitudinal analysis in a patient treated with 5-azacytidine revealed that karyotypically abnormal HSCs persist even during complete morphologic remission and that expansion of clonotypic HSCs precedes clinical relapse. This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations.

scholarly journals Epigenome-Wide DNA Methylation Analysis of Monozygotic Twins Discordant for Diurnal Preference

2015 ◽  
Vol 18 (6) ◽  
pp. 662-669 ◽  
Author(s):  
Chloe C. Y. Wong ◽  
Michael J. Parsons ◽  
Kathryn J. Lester ◽  
Joe Burrage ◽  
Thalia C. Eley ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Circadian Clock ◽  
Monozygotic Twins ◽  
Enrichment Analysis ◽  
Genome Wide ◽  
Analysis Strategy ◽  
Diurnal Preference ◽  
Significant Enrichment ◽  
Longitudinal Twin Study ◽  
Mz Twins

Diurnal preference is an individual's preference for daily activities and sleep timing and is strongly correlated with the underlying circadian clock and the sleep-wake cycle validating its use as an indirect circadian measure in humans. Recent research has implicated DNA methylation as a mechanism involved in the regulation of the circadian clock system in humans and other mammals. In order to evaluate the extent of epigenetic differences associated with diurnal preference, we examined genome-wide patterns of DNA methylation in DNA from monozygotic (MZ) twin-pairs discordant for diurnal preference. MZ twins were selected from a longitudinal twin study designed to investigate the interplay of genetic and environmental factors in the development of emotional and behavioral difficulties. Fifteen pairs of MZ twins were identified in which one member scored considerably higher on the Horne–Ostberg Morningness–Eveningness Questionnaire (MEQ) than the other. Genome-wide DNA methylation patterns were assessed in twins’ buccal cell DNA using the Illumina Infinium HumanMethylation450 BeadChips. Quality control and data pre-processing was undertaken using the wateRmelon package. Differentially methylated probes (DMPs) were identified using an analysis strategy taking into account both the significance and the magnitude of DNA methylation differences. Our data indicate that DNA methylation differences are detectable in MZ twins discordant for diurnal preference. Moreover, downstream gene ontology (GO) enrichment analysis on the top-ranked diurnal preference associated DMPs revealed significant enrichment of pathways that have been previously associated with circadian rhythm regulation, including cell adhesion processes and calcium ion binding.

scholarly journals Eating behavior in the Old Order Amish: heritability analysis and a genome-wide linkage analysis

2002 ◽  
Vol 75 (6) ◽  
pp. 1098-1106 ◽  
Author(s):  
Nanette I Steinle ◽  
Wen-Chi Hsueh ◽  
Soren Snitker ◽  
Toni I Pollin ◽  
Hakan Sakul ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Eating Behavior ◽  
Old Order Amish ◽  
Old Order ◽  
Genome Wide ◽  
A Genome ◽  
Heritability Analysis

scholarly journals Fine-scale resolution and analysis of runs of homozygosity in domestic dogs

2018 ◽  
Author(s):  
Aaron J. Sams ◽  
Adam R. Boyko
Keyword(s):  
Inbreeding Depression ◽  
Genetic Architecture ◽  
Domestic Dogs ◽  
Selective Sweeps ◽  
Runs Of Homozygosity ◽  
Identical By Descent ◽  
Density Maps ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Significant Enrichment

Abstract/SummaryInbreeding and consanguinity leave distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase (Mb)) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long versus short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied.In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 500 homozygous deleterious recessive genotypes in the panel, 90% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14% were contained in short (0.5 - 2.5 Mb) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH).In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short versus long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.

scholarly journals Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3889 ◽  
Author(s):  
Robert C. Edgar
Keyword(s):  
Ribosomal Rna ◽  
De Novo ◽  
Community Diversity ◽  
Reference Database ◽  
Mock Community ◽  
Variable Regions ◽  
Operational Taxonomic Units ◽  
Sequencing Technologies ◽  
Generation Sequencing ◽  
Mock Communities

Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs). Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed), then clusters unmatched reads using a de novo method (open). Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs) was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.

scholarly journals Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones

2020 ◽  
Vol 17 (2) ◽  
pp. 436 ◽  
Author(s):  
Yongkui Yang ◽  
Longfei Wang ◽  
Feng Xiang ◽  
Lin Zhao ◽  
Zhi Qiao
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
Activated Sludge ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Wastewater Sludge ◽  
Community Diversity ◽  
Nitrogen And Phosphorus ◽  
Metabolic Functions

Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs.

Sign in / Sign up

Export Citation Format

Share Document