Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

Abstract Background Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. This organization of transcriptomes suggests that coordinated evolution of gene expression for clustered genes may also be common. Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution. Results We used a common microarray platform to measure gene expression in seven closely related species in the Drosophila melanogaster subgroup, accounting for confounding effects of sequence divergence. To summarize the correlation structure among genes in a chromosomal region, we analyzed the fraction of variation along the first principal component of the correlation matrix. We analyzed the correlation for blocks of consecutive genes to assess patterns of correlation that may be manifest at different scales of coordinated expression. We find that expression of physically clustered genes does evolve in a coordinated manner in many locations throughout the genome. Our analysis shows that relatively few of these clusters are near heterochromatin regions and that these clusters tend to be over-dispersed relative to the rest of the genome. This suggests that these clusters are not the byproduct of local gene clustering. We also analyzed the pattern of co-expression among neighboring genes within a single Drosophila species: D. simulans. For the co-expression clusters identified within this species, we find an under-representation of genes displaying a signature of recurrent adaptive amino acid evolution consistent with previous findings. However, clusters displaying co-evolution of expression among species are enriched for adaptively evolving genes. This finding points to a tie between adaptive sequence evolution and evolution of the transcriptome. Conclusion Our results demonstrate that co-evolution of expression in gene clusters is relatively common among species in the D. melanogaster subgroup. We consider the possibility that local regulation of expression in gene clusters may drive the connection between adaptive sequence and coordinated gene expression evolution

Algae: Causes and Complications

This panel will explore the causes of algal blooms, the threats they present to Virginia’s waters, and steps being taken to address them

Banner News

https://openspace.dmacc.edu/banner_news/1138/thumbnail.jp

Adaptive Gene Expression Divergence Inferred from Population Genomics

Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. Here, we combined genomic expression data—analyzed in a phylogenetic context—with whole genome light-shotgun sequence data from six Drosophila simulans lines and reference sequences from D. melanogaster and D. yakuba. These data allowed us to use molecular population genetics to test for neutral versus adaptive gene expression divergence on a genomic scale. We identified recent and recurrent adaptive evolution along the D. simulans lineage by contrasting sequence polymorphism within D. simulans to divergence from D. melanogaster and D. yakuba. Genes that evolved higher levels of expression in D. simulans have experienced adaptive evolution of the associated 3′ flanking and amino acid sequence. Concomitantly, these genes are also decelerating in their rates of protein evolution, which is in agreement with the finding that highly expressed genes evolve slowly. Interestingly, adaptive evolution in 5′ cis-regulatory regions did not correspond strongly with expression evolution. Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution

frystreet + friends

A performance of the Fry Street Quartet and others at the Performance Hall at Utah State University, performed on November 8, 2012.https://digitalcommons.usu.edu/music_programs/1174/thumbnail.jp

Age-related changes in concentric and eccentric isokinetic peak torque of the trunk muscles in healthy older versus younger men

Accepted author manuscript version reprinted, by permission, from Journal of Aging and Physical Activity, 2021, volume 29, issue 6, pp. 941–951, https://doi.org/10.1123/japa.2020-0421 © Human Kinetics, Inc. The accepted manuscript may differ from the final published version.This study investigated age-related changes in trunk muscle function in healthy men and the moderating effect of physical activity. Twelve older (67.3 ± 6.0 years) and 12 younger (24.7 ± 3.1 years) men performed isokinetic trunk flexion and extension tests across a range of angular velocities (15°/s–180°/s) and contractile modes (concentric and eccentric). For concentric trunk extension, mixed-effects analysis of covariance revealed a significant interaction between Angular velocity × Age group (p = .026) controlling for physical activity. Follow-up univariate analysis of covariance revealed that the younger group produced significantly greater peak torque for all concentric extension conditions. Eccentric trunk strength was somewhat preserved in the older group. Age-related changes in trunk strength were independent of physical activity. The normal loss of trunk muscle strength in older age is muscle- and contractile-mode specific. These findings provide guidance for effective intervention strategies to offset adverse health outcomes related to trunk strength loss in older adults.Published versio

Platelets kill intraerythrocytic malarial parasites and mediate survival to infection

Platelets play a critical role in the pathogenesis of malarial infections by encouraging the sequestration of infected red blood cells within the cerebral vasculature. But platelets also have well-established roles in innate protection against microbial infections. We found that purified human platelets killed Plasmodium falciparum parasites cultured in red blood cells. Inhibition of platelet function by aspirin and other platelet inhibitors abrogated the lethal effect human platelets exert on P. falciparum parasites. Likewise, platelet-deficient and aspirin-treated mice were more susceptible to death during erythrocytic infection with Plasmodium chabaudi. Both mouse and human platelets bind malarial-infected red cells and kill the parasite within. These results indicate a protective function for platelets in the early stages of erythrocytic infection distinct from their role in cerebral malaria

Maternal nutritional status as a contributing factor for the risk of fetal alcohol spectrum disorders

Compare nutritional status of 57 South African mothers of children with fetal alcohol spectrum disorders (FASD) with 148 mothers of controls