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Gene environment interactions

A Trey Belew, Caroline Junqueira, Gabriela F Rodrigues-Luiz, Bruna M Valente, Antonio Edson R Oliveira, Rafael B Polidoro, Luciana W Zuccherato, Daniella C Bartholomeu, Sergio Schenkman, Ricardo T Gazzinelli, Barbara A Burleigh, Najib M El-Sayed, Santuza M R Teixeira
Trypanosoma cruzi, the protozoan that causes Chagas disease, has a complex life cycle involving several morphologically and biochemically distinct stages that establish intricate interactions with various insect and mammalian hosts. It has also a heterogeneous population structure comprising strains with distinct properties such as virulence, sensitivity to drugs, antigenic profile and tissue tropism. We present a comparative transcriptome analysis of two cloned T. cruzi strains that display contrasting virulence phenotypes in animal models of infection: CL Brener is a virulent clone and CL-14 is a clone that is neither infective nor pathogenic in in vivo models of infection...
December 14, 2017: PLoS Pathogens
Srimoyee Ghosh, Sylvia A Vetrone, Paul W Sternberg
Cell outgrowth is a hallmark of some non-migratory developing cells during morphogenesis. Understanding the mechanisms that control cell outgrowth not only increases our knowledge of tissue and organ development, but can also shed light on disease pathologies that exhibit outgrowth-like behavior. C. elegans is a highly useful model for the analysis of genes and the function of their respective proteins. In addition, C. elegans also has several cells and tissues that undergo outgrowth during development. Here we discuss the outgrowth mechanisms of nine different C...
2017: Worm
Sarah A Signor, Mohammad Abbasi, Paul Marjoram, Sergey V Nuzhdin
Indirect genetic effects (IGEs) describe the effect of the genes of social partners on the phenotype of a focal individual. Here, we measure indirect genetic effects using the "coefficient of interaction" (Ψ) to test whether Ψ evolved between Drosophila melanogaster and D. simulans. We compare Ψ for locomotion between ethanol and nonethanol environments in both species, but only D. melanogaster utilizes ethanol ecologically. We find that while sexual dimorphism for locomotion has been reversed in D. simulans, there has been no evolution of social effects between these two species...
December 2017: Ecology and Evolution
Abhishek Ghosh, Anirban Ray, Aniruddha Basu
Oppositional defiant disorder (ODD) is diagnosed broadly on the basis of frequent and persistent angry or irritable mood, argumentativeness/defiance, and vindictiveness. Since its inception in the third Diagnostic and Statistical Manual of Mental Disorders, epidemiological and longitudinal studies have strongly suggested a distinct existence of ODD that is different from other closely related externalizing disorders, with different course and outcome and possibly discrete subtypes. However, several issues, such as symptom threshold, dimensional versus categorical conceptualization, and sex-specific symptoms, are yet to be addressed...
2017: Psychology Research and Behavior Management
Michael Francki, Esther Walker, Dora Li, Kerrie Forrest
The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074 and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively...
December 13, 2017: Genome Génome / Conseil National de Recherches Canada
Haoyuan Jing, Siddhartha Das
Lipid-bilayer-encapsulated nanoparticles (LBLENPs) or NP-supported LBL systems, such as protocells (which are lipid bilayer encapsulated mesoporous silica nanoparticles or MSNPs) have received extensive attention for applications like targeted drug and gene deliveries, multimodal diagnostics, characterization of membrane-geometry sensitive molecules, etc. Very often electrostatic-mediated interactions have been hypothesized to play key roles in the functioning of these LBLENPs. Despite that, very little has been done to theoretically quantify the fundamental electric double layer (EDL) electrostatics of such LBLENPs...
December 13, 2017: Electrophoresis
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
Kyle W Wellband, John W Heath, Daniel D Heath
Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute transcriptional responses to stress and it is unclear if these effects are heritable. To address these gaps in knowledge, we assayed levels of messenger RNA for 14 candidate genes at rest and in response to a 24-h confinement stress for 72 half-sib families of Chinook salmon reared in two different environments (hatchery and semi-natural stream channel)...
January 2018: Heredity
Margaret I Steele, Waldan K Kwong, Marvin Whiteley, Nancy A Moran
Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi, a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins...
December 12, 2017: MBio
Ci Fu, Nicholas Donadio, Maria E Cardenas, Joseph Heitman
The Ca2+/calmodulin-dependent protein phosphatase calcineurin orchestrates sexual reproduction, stress responses, and virulence via branched downstream pathways in the opportunistic human fungal pathogen, Cryptococcus neoformans The calcineurin binding protein Cbp1, the calcineurin temperature suppressor Cts1, the calcineurin responsive zinc finger transcription factor Crz1, and the calcineurin targets Pbp1, Tif3, and Puf4 all function downstream of calcineurin to orchestrate distinct cellular processes. To elucidate how the calcineurin pathway regulatory network governs unisexual reproduction, stress responses, and virulence, we have analyzed the self-filamentous C...
December 12, 2017: Genetics
Harihar Jaishree Subrahmaniam, Cyril Libourel, Etienne-Pascal Journet, Jean-Benoît Morel, Stéphane Muños, Andreas Niebel, Sylvain Raffaele, Fabrice Roux
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison to other types of biotic interactions. By listing 63 QTL mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition vs commensalism vs reciprocal helping vs asymmetry)...
December 12, 2017: Plant Journal: for Cell and Molecular Biology
Abid Hussain, Ming-Yi Tian, Shuo-Yang Wen
The survival and foraging of Coptotermesformosanus Shiraki in a microbe-rich environment reflect the adaptation of an extraordinary, sophisticated defense mechanism by the nest-mates. We aimed to explore the host pathogen interaction by studying caste-specific volatile chemistry and genes encoding the antioxidant defense of winged imagoes, nymphs, soldiers and workers of Formosan subterranean termites. Qualitative analyses of C.formosanus Shiraki performed by HS-SPME/GC-MS showed considerable variations in the chemical composition of volatile organic compounds (VOCs) and their proportions among all the castes...
December 12, 2017: International Journal of Molecular Sciences
Remy Colin, Christelle Rosazza, Ady Vaknin, Victor Sourjik
Cellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway...
December 12, 2017: ELife
Kevin D Kohl, Denise M Dearing, Seth R Bordenstein
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates it has only been investigated using samples from feces or the distal colon...
December 11, 2017: Molecular Ecology
Xiaoqing He, Yi Jin, Meixia Ye, Nan Chen, Jing Zhu, Jingqi Wang, Libo Jiang, Rongling Wu
How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively...
2017: Frontiers in Microbiology
Jan-Ulrich Kreft, Caroline M Plugge, Clara Prats, Johan H J Leveau, Weiwen Zhang, Ferdi L Hellweger
Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level...
2017: Frontiers in Microbiology
Davorka Gulisija, Joshua B Plotkin
While theory offers clear predictions for when recombination will evolve in changing environments, it is unclear what natural scenarios can generate the necessary conditions. The Red Queen hypothesis provides one such scenario, but it requires antagonistic host-parasite interactions. Here we present a novel scenario for the evolution of recombination in finite populations: the genomic storage effect due to phenotypic plasticity. Using analytic approximations and Monte-Carlo simulations, we demonstrate that balanced polymorphism and recombination evolve between a target locus that codes for a seasonally selected trait and a plasticity modifier locus that modulates the effects of target-locus alleles...
December 11, 2017: Nature Communications
Qiong Cheng, Yong-Kun Li, Feng Lu, Lianhua Yin, Yin-Zhou Wang, Wen Wei, Qian Lin
Aims: To investigate the association of several single nucleotide polymorphisms (SNPs) within ACYP2 gene and additional gene- environment interaction with ischemic stroke (IS) risk in a Chinese population. Results: IS risk was significantly higher in carriers with the G allele of rs11896604 than those with CC genotype (CG or GG versus CC), adjusted OR (95%CI) =1.60 (1.18-2.20), and higher in carriers with the A allele of rs12615793 than those with GG genotype (GA or AA versus GG), adjusted OR (95%CI) = 1...
November 17, 2017: Oncotarget
Ying Zhang, Nan Jia, Feng Hu, Naijun Fan, Xiaohua Guo, Han Du, Changlin Mei, Chunfang Gao
Aims: To investigate the association of several single nucleotide polymorphisms (SNPs) within RAGE gene and additional gene- smoking interaction with diabetic nephropathy (DN) risk in Chinese patients with type 2 diabetes mellitus (T2DM). Methods: A total of 865 participants (570 males, 295 females) were selected, including 430 T2DM complicated DN patients and 435 controls (T2DM patients without DN). Generalized multifactor dimensionality reduction (GMDR) was used to screen the best interaction combination among SNPs and smoking...
November 14, 2017: Oncotarget
Anastasia Kottara, James P J Hall, Ellie Harrison, Michael A Brockhurst
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid...
December 4, 2017: FEMS Microbiology Ecology
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