Genotype-specific Changes Research Articles

Topography and Ensemble Activity in the Auditory Cortex of a Mouse Model of Fragile X Syndrome.

Autism spectrum disorder (ASD) is often associated with social communication impairments and specific sound processing deficits, for example, problems in following speech in noisy environments. To investigate underlying neuronal processing defects located in the auditory cortex (AC), we performed two-photon Ca2+ imaging in FMR1 (fragile X messenger ribonucleoprotein 1) knock-out (KO) mice, a model for fragile X syndrome (FXS), the most common cause of hereditary ASD in humans. For primary AC (A1) and the anterior auditory field (AAF), topographic frequency representation was less ordered compared with control animals. We additionally analyzed ensemble AC activity in response to various sounds and found subfield-specific differences. In A1, ensemble correlations were lower in general, while in secondary AC (A2), correlations were higher in response to complex sounds, but not to pure tones. Furthermore, sound specificity of ensemble activity was decreased in AAF. Repeating these experiments 1 week later revealed no major differences regarding representational drift. Nevertheless, we found subfield- and genotype-specific changes in ensemble correlation values between the two times points, hinting at alterations in network stability in FMR1 KO mice. These detailed insights into AC network activity and topography in FMR1 KO mice add to the understanding of auditory processing defects in FXS.

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

BackgroundRye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear.ResultsAn RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases.The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response.ConclusionOur work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

Molecular Characterization of BK Polyomavirus Replication in Allogeneic Hematopoietic Cell Transplantation Patients.

High-level BK polyomavirus (BKPyV) replication in allogeneic hematopoietic cell transplantation (HCT) predicts failing immune control and BKPyV-associated hemorrhagic cystitis. To identify molecular markers of BKPyV replication and disease, we scrutinized BKPyV DNA-loads in longitudinal urine and plasma pairs from 20 HCT patients using quantitative nucleic acid testing (QNAT), DNase-I treatment prior to QNAT, next-generation sequencing (NGS), and tested cell-mediated immunity. We found that larger QNAT amplicons led to under-quantification and false-negatives results (P < .001). DNase-I reduced urine and plasma BKPyV-loads by >90% (P < .001), indicating non-encapsidated BKPyV genomes. DNase-resistant urine BKPyV-loads remained infectious in cell culture. BKPyV genome fragmentation of ≤250 bp impaired NGS coverage of genetic variation using 1000-bp and 5000-bp amplicons. Conversely, 250-bp amplicons captured viral minority variants. We identified genotype-specific and genotype-independent changes in capsid Vp1 or T-antigen predicted to escape from antibody neutralization or cytotoxic CD8 T-cells, respectively. Genotype-specific changes in immunodominant 9mers were associated with reduced or absent CD8 T-cell responses. Thus, failure to control BKPyV replication in HCT Patients may involve insufficient genotype-specific cytotoxic CD8 T-cell responses, potentially predictable by low neutralizing antibodies as well as genotype-independent immune escape. Our results provide new insights for patient evaluation and for designing immune protection through neutralizing antibodies, adoptive T-cell therapy, or vaccines.

Genetic diversity as a paramount factor determining wheat adaptation to drought stress

Wheat (Triticum aestivum L.) is a globally important crop for food and nutritional security that requires sufficient water supply for optimal production. All stages of wheat growth and development are adversely affected by reduced water supply, which limit productivity across large areas of Central and Southern Europe. Since drought episodes are expected to occur more frequently and with a greater intensity, the research efforts are devoted to identification of key traits associated with drought resistance that could be used as direct and indirect selection criteria for wheat drought tolerance. We evaluated and quantified several key genetic and molecular features of wheat genotypes with contrasting drought tolerance under severe dehydration triggered by the treatment of wheat with 250 mM sorbitol in hydroponic systems. Plant status was evaluated non-destructively by measuring leaf chlorophyll index, nitrogen content, and leaf relative water content. The drought-tolerant genotype displayed higher chlorophyll and nitrogen content, when grown under drought and benign conditions. Since root architecture appears to be a key trait for breeding against dehydration, we analysed the members of the DEEPER ROOTING (DRO) gene family that allow the root to penetrate deeper into soil, which could increase the yield even upon water shortage. Expression patterns of the DRO members showed genotype-specific changes under drought stress, which correlated well with plant drought tolerance. Our experiments suggest that genes affecting root system architecture could contribute to development of wheat cultivars with higher drought adaptability.

High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines

BackgroundHigh temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues for plant performance under various environmental stimuli is the crown. However, the molecular characterization of this region remains poorly investigated. Gibberellins play a fundamental role in whole-plant stature formation. This study identified plant stature modifications and crown-specific transcriptome re-modeling in gibberellin-deficient barley sdw1.a (BW827) and sdw1.d (BW828) mutants exposed to increased temperature.ResultsThe deletion around the sdw1 gene in BW827 was found to encompass at least 13 genes with primarily regulatory functions. A bigger genetic polymorphism of BW828 than of BW827 in relation to wild type was revealed. Transcriptome-wide sequencing (RNA-seq) revealed several differentially expressed genes involved in gibberellin metabolism and heat response located outside of introgression regions. It was found that HvGA20ox4, a paralogue of the HvGA20ox2 gene, was upregulated in BW828 relative to other genotypes, which manifested as basal internode elongation. The transcriptome response to elevated temperature differed in the crown of sdw1.a and sdw1.d mutants; it was most contrasting for HvHsf genes upregulated under elevated temperature in BW828, whereas those specific to BW827 were downregulated. In-depth examination of sdw1 mutants revealed also some differences in their phenotypes and physiology.ConclusionsWe concluded that despite the studied sdw1 mutants being genetically related, their heat response seemed to be genotype-specific and observed differences resulted from genetic background diversity rather than single gene mutation, multiple gene deletion, or allele-specific expression of the HvGA20ox2 gene. Differences in the expressional reaction of genes to heat in different sdw1 mutants, found to be independent of the polymorphism, could be further explained by in-depth studies of the regulatory factors acting in the studied system. Our findings are particularly important in genetic research area since molecular response of crown tissue has been marginally investigated, and can be useful for wide genetic research of crops since barley has become a model plant for them.

Genetic mapping and identification of a QTL determining tolerance to freezing stress in Fragaria vesca L.

Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. vesca accessions have been shown to have adapted to low-temperature stresses. To study the genetics of freezing tolerance, a F. vesca mapping population of 143 seedlings segregating for differential responses to freezing stress was raised. The progeny was mapped using ‘Genotyping-by-Sequencing’ and a linkage map of 2,918 markers at 851 loci was resolved. The mapping population was phenotyped for freezing tolerance response under controlled and replicated laboratory conditions and subsequent quantitative trait loci analysis using interval mapping revealed a single significant quantitative trait locus on Fvb2 in the physical interval 10.6 Mb and 15.73 Mb on the F. vesca v4.0 genome sequence. This physical interval contained 896 predicted genes, several of which had putative roles associated with tolerance to abiotic stresses including freezing. Differential expression analysis of the 896 QTL-associated gene predictions in the leaves and crowns from ‘Alta’ and ‘NCGR1363’ parental genotypes revealed genotype-specific changes in transcript accumulation in response to low temperature treatment as well as expression differences between genotypes prior to treatment for many of the genes. The putative roles, and significant interparental differential expression levels of several of the genes reported here identified them as good candidates for the control of the effects of freezing tolerance at the QTL identified in this investigation and the possible role of these candidate genes in response to freezing stress is discussed.

Metabolite Profiling and Network Analysis Reveal Coordinated Changes in Low-N Tolerant and Low-N Sensitive Maize Genotypes under Nitrogen Deficiency and Restoration Conditions.

Nitrogen (N), applied in the form of a nitrogenous fertilizer, is one of the main inputs for agricultural production. Food production is closely associated with the application of N. However, the application of nitrogenous fertilizers to agricultural fields is associated with heavy production of nitrous oxide because agricultural crops can only utilize 30–40% of applied N, leaving behind unused 60–70% N in the environment. The global warming effect of this greenhouse gas is approximately 300 times more than of carbon dioxide. Under the present scenario of climate change, it is critical to maintain the natural balance between food production and environmental sustainability by targeting traits responsible for improving nitrogen-use-efficiency (NUE). Understanding of the molecular mechanisms behind the metabolic alterations due to nitrogen status needs to be addressed. Additionally, mineral nutrient deficiencies and their associated metabolic networks have not yet been studied well. Given this, the alterations in core metabolic pathways of low-N tolerant (LNT) and low-N sensitive (LNS) genotypes of maize under N-deficiency and their efficiency of recovering the changes upon resupplying N were investigated by us, using the GC–MS and LC–MS based metabolomic approach. Significant genotype-specific changes were noted in response to low-N. The N limitation affected the whole plant metabolism, most significantly the precursors of primary metabolic pathways. These precursors may act as important targets for improving the NUE. Limited availability of N reduced the levels of N-containing metabolites, organic acids and amino acids, but soluble sugars increased. Major variations were encountered in LNS, as compared to LNT. This study has revealed potential metabolic targets in response to the N status, which are indeed the prospective targets for crop improvement.

Characterization of indoleamine-2,3-dioxygenase 1, tryptophan-2,3-dioxygenase, and Ido1/Tdo2 knockout mice

Indoleamine-2,3-dioxygenase 1 (IDO1) and tryptophan-2,3-dioxygenase 2 (TDO2) degrade tryptophan (Trp) to kynurenine (Kyn), and these enzymes have promise as therapeutic targets. A comprehensive characterization of potential safety liabilities of IDO1 and TDO2 inhibitors using knockout (KO) mice has not been assessed, nor has the dual Ido1/Tdo2 KO been reported. Here we characterized male and female mice with KOs for Ido1, Tdo2, and Ido1/Tdo2 and compared findings to the wild type (WT) mouse strain, evaluated for 14 days, using metabolomics, transcriptional profiling, behavioral analysis, spleen immunophenotyping, comprehensive histopathological analysis, and serum clinical chemistry.Multiple metabolomic changes were seen in KO mice. For catabolism of Trp to Kyn and anthranilic acid, both substrates were decreased in liver of Tdo2 and dual KO mice. Metabolism of Trp to serotonin and its metabolites resulted in an increase in 5-Hydroxyindole-3-acetic acid in the Tdo2 and dual KO mice. Ido1 and dual KO mice displayed a Kyn reduction in plasma but not in liver. Nicotinamide synthesis and conversion of glucose to lactic acid were not impacted. A slight decrease in serum alkaline phosphatase was seen in all KOs, and small changes in liver gene expression of genes unrelated to tryptophan metabolism were observed. Regarding other parameters, no genotype-specific changes were observed.In summary, this work shows metabolomic pathway changes for metabolites downstream of tryptophan in these KO mice, and suggests that inhibition of the IDO1 and TDO2 enzymes would be well tolerated whether inhibited individually or in combination since no safety liabilities were uncovered.

Abstract 2470: Comprehensive functional modeling of pan-cancer risk SNP rs6983267 in human CRC cells via scarless CRISPR/Cas9 genome editing

Abstract With the continued emergence of Genome-Wide Association study-identified risk loci for complex diseases as well as a sharp increase in the number of variants of uncertain significance (VUS) identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Our lab has previously published a novel variant modeling pipeline which combines CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) technology to create scarless isogenic cell models of cancer variants in ~1 month. In this study, we utilize our pipeline to model risk Single Nucleotide Polymorphism (SNP) rs6983267 in human colorectal cancer (CRC) cells and present the first functional characterization for this risk SNP at the most precise level possible with current technology, isogenic clones of the same cell lines that only differ by a single base. Rs6983267 is located within a known Mycenhancer and has been shown to exert risk-allele specific increase in enhancer activity. However, we do not observe risk-allele specific upregulation of Mycexpression in our isogenic models. Instead, we find that presence of the risk allele confers significant effects within the cell locally, modulating activity of adjacent binding site for WNT transcription factor, TCF7L2, and a subset of genes associated with enhancer function. Through 3D interaction analysis, we identify difference in interactions incisacross the three genotypes including the loss of interaction with Mycin the heterozygous and homozygous reference lines, indicating genotype-specific changes of enhancer gene targets in CRC cells. Together, these variations lead to global effects, affecting transcriptional expression of genes involved in WNT signaling, cell-to-cell adhesion and PI3K-Akt signaling pathways. These results suggest the loss of a single risk allele in CRC cells confers a transcriptional change associated with overall decreased cancer activity despite expression of the putative target gene of the enhancer, Myc, not being significantly affected. Interestingly, engineered loss of both risk alleles in CRC cells does not further the overall effect, indicating the activation of a compensatory mechanism, possibly due to redundancy of regulatory pathways affected. Activation of such compensatory mechanisms could demonstrate an important limitation to the use of established cancer cell lines in the functional modeling of risk-associated variants, which are the current standard models in the field. Our study provides an important contribution to the current efforts of functional characterization of novel VUSs and non-coding SNPs associated with cancer risk. It will become important to consider validation standards and functional thresholds for inclusion of lower penetrance susceptibility alleles in clinical decision-making as the field continues to advance towards the ultimate goal of precision medicine in cancer. Citation Format: Nicole B. Coggins, Henriette O'Geen, David J. Segal, Luis G. Carvajal-Carmona. Comprehensive functional modeling of pan-cancer risk SNP rs6983267 in human CRC cells via scarless CRISPR/Cas9 genome editing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2470.

Abstract B05: Comprehensive functional modeling of pan-cancer risk SNP rs6983267 in human CRC cells via scarless CRISPR/Cas9 genome editing

Abstract With the continued emergence of genome-wide association study-identified risk loci for complex diseases as well as a sharp increase in the number of variants of uncertain significance (VUS) identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Our lab has previously published a novel variant modeling pipeline that combines CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) technology to create scarless isogenic cell models of cancer variants in ~1 month. In this study, we utilize our pipeline to model risk single-nucleotide polymorphism (SNP) rs6983267 in human colorectal cancer (CRC) cells and present the first functional characterization for this risk SNP at the most precise level possible with current technology, isogenic clones of the same cell lines that only differ by a single base. Rs6983267 is located within a known Myc enhancer and has been shown to exert risk-allele specific increase in enhancer activity. However, we do not observe risk-allele specific upregulation of Myc expression in our isogenic models. Instead, we find that presence of the risk allele confers significant effects within the cell locally, modulating activity of adjacent binding site for WNT transcription factor, TCF7L2, and a subset of genes associated with enhancer function. Through 3D interaction analysis, we identify difference in interactions in cis across the three genotypes including the loss of interaction with Myc in the heterozygous and homozygous reference lines, indicating genotype-specific changes of enhancer gene targets in CRC cells. Together, these variations lead to global effects, affecting transcriptional expression of genes involved in WNT signaling, cell-to-cell adhesion, and PI3K-Akt signaling pathways. These results suggest the loss of a single risk allele in CRC cells confers a transcriptional change associated with overall decreased cancer activity despite expression of the putative target gene of the enhancer, Myc, not being significantly affected. Interestingly, engineered loss of both risk alleles in CRC cells does not further the overall effect, indicating the activation of a compensatory mechanism, possibly due to redundancy of regulatory pathways affected. Activation of such compensatory mechanisms could demonstrate an important limitation to the use of established cancer cell lines in the functional modeling of risk-associated variants, which are the current standard models in the field. Our study provides an important contribution to the current efforts of functional characterization of novel VUSs and noncoding SNPs associated with cancer risk. It will become important to consider validation standards and functional thresholds for inclusion of lower penetrance susceptibility alleles in clinical decision-making as the field continues to advance towards the ultimate goal of precision medicine in cancer. Citation Format: Nicole B. Coggins, Henriette O'Geen, David J. Segal, Luis G. Carvajal-Carmona. Comprehensive functional modeling of pan-cancer risk SNP rs6983267 in human CRC cells via scarless CRISPR/Cas9 genome editing [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr B05.

Proteomic profiling of a large cohort of HCM patients: Genotype-specific protein changes

Proteomic profiling of a large cohort of HCM patients: Genotype-specific protein changes

Genome structure predicts modular transcriptome responses to genetic and environmental conditions.

Understanding the plasticity, robustness and modularity of transcriptome expression to genetic and environmental conditions is crucial to deciphering how organisms adapt in nature. To test how genome architecture influences transcriptome profiles, we quantified expression responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stresses throughout development. We found that 56% of the 8,795 differentially expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold vs. heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic vs. environmental vs. interaction effects, as well as their genomic spatial distributions, functional attributes and rates of molecular evolution at the sequence level. Genes in modules enriched for simple effects of either genotype or temperature alone tend to evolve especially rapidly, consistent with disproportionate influence of adaptation or weaker constraint on these subsets of loci. Chromosome-scale heterogeneity in nucleotide polymorphism, however, rather than the scale of individual genes predominates as the source of genetic differences among expression profiles, and natural selection regimes are largely decoupled between coding sequences and noncoding flanking sequences that contain cis-regulatory elements. These results illustrate how the form of transcriptome modularity and genome structure contribute to predictable profiles of evolutionary change.

Female Life-History Trade-Offs and the Maintenance of Genetic Variation in Drosophila melanogaster.

Why do we observe substantial variation in fitness-related traits under strong natural or sexual selection? While there is support for several selective and neutral mechanisms acting in select systems, we lack a comprehensive analysis of the relative importance of various mechanisms within a single system. Furthermore, while sexually selected male traits have been a central focus of this paradox, female sexual traits have rarely been considered. In this study, I evaluate the contribution of various selective mechanisms to the maintenance of substantial variation in female attractiveness and offspring production observed among Drosophila melanogaster genotypes. I tested for contributions from antagonistic pleiotropy, frequency-dependent selection, changing environments, and sexual conflict. I found negative genetic correlations between some traits (male attractiveness vs. female resistance to male harm, early-life offspring production vs. reproductive senescence) and genotype-specific changes in fitness between environments. However, no measurement found strong trade-offs among the fitness components of these genotypes. Overall, I find little evidence that any one mechanism is strong enough to maintain genetic variation on its own. Instead, I suggest that many mechanisms may weaken the selection among genotypes, which would collectively allow neutral processes such as mutation-selection balance to maintain genetic variation within populations.

Rs10732516 polymorphism at the IGF2/H19 locus associates with a genotype-specific trend in placental DNA methylation and head circumference of prenatally alcohol-exposed newborns.

Study QuestionDoes prenatal alcohol exposure (PAE) affect regulation of the insulin-like growth factor 2 (IGF2)/H19 locus in placenta and the growth-restricted phenotype of newborns?Summary AnswerPAE results in genotype-specific trends in both placental DNA methylation at the IGF2/H19 locus and head circumference (HC) of newborns.What is Known AlreadyPAE can disturb development of the nervous system and lead to restricted growth of the head, even microcephaly. To clarify the etiology of alcohol-induced growth restriction, we focused on the imprinted IGF2/H19 locus known to be important for normal placental and embryonic growth. The expression of IGF2 and a negative growth controller H19 are regulated by the H19 imprinting control region (H19 ICR) with seven-binding sites for the methylation-sensitive zinc-finger regulatory protein CTCF. A single nucleotide polymorphism rs10732516 G/A in the sixth-binding site has shown to associate with genotype-specific DNA methylation profiles at the H19 ICR.Study Design, Size, DurationBy grouping 39 alcohol-exposed and 100 control samples according to rs10732516 polymorphism we explored alcohol-induced, genotype-specific changes in DNA methylation at the H19 ICR and the promoter region of H19 (H19 differentially methylated region). Also, IGF2 and H19 mRNA expression level in placenta as well as the phenotypes of newborns were examined.Participants/Materials, Setting, MethodsWe explored alcohol-induced, genotype-specific changes in placental DNA methylation by MassARRAY EpiTYPER and allele-specific changes by bisulphite sequencing. IGF2 and H19 expression in placenta were analyzed by quantitative PCR and the HC, birthweight and birth length of newborns were examined using national growth charts.Main Results and the Role of ChanceWe observed a consistent trend in genotype-specific changes in DNA methylation at H19 ICR in alcohol-exposed placentas. DNA methylation level in the normally highly methylated paternal allele of rs10732516 paternal A/maternal G genotype was decreased in alcohol-exposed placentas. In addition to decreased IGF2 mRNA expression in alcohol-exposed placentas of this specific genotype (P = 0.03), we observed significantly increased expression of H19 in relation to IGF2 when comparing all alcohol-exposed placentas to unexposed controls (P = 0.006). Furthermore, phenotypic examination showed a significant genotype-specific association between the alcohol exposure and HC of newborns (P = 0.001).Limitations Reasons for CautionOwing to the exceptional character of the alcohol-exposed human samples collected in this study, the sample size is restricted. An increased sample size and functional studies are needed to confirm these data and clarify the biological significance or causality of the observed associations.Wider Implications of the FindingsOur results suggest that the rs10732516 polymorphism associates with the alcohol-induced alterations in DNA methylation profiles and head growth in a parent-of-origin manner. We also introduce a novel genotype-specific approach for exploring environmental effects on the IGF2/H19 locus and ultimately on embryonic growth.Study Funding/Competing Interest(s)This work was supported by the Academy of Finland (258304), The Finnish Foundation for Alcohol Studies, Finnish Cultural Foundation, Juho Vainio Foundation, Yrjö Jahnsson Foundation and Arvo and Lea Ylppö Foundation. No competing interests are declared.

Spectral Patterns Reveal Early Resistance Reactions of Barley Against Blumeria graminis f. sp. hordei.

Differences in early plant-pathogen interactions are mainly characterized by using destructive methods. Optical sensors are advanced techniques for phenotyping host-pathogen interactions on different scales and for detecting subtle plant resistance responses against pathogens. A microscope with a hyperspectral camera was used to study interactions between Blumeria graminis f. sp. hordei and barley (Hordeum vulgare) genotypes with high susceptibility or resistance due to hypersensitive response (HR) and papilla formation. Qualitative and quantitative assessment of pathogen development was used to explain changes in hyperspectral signatures. Within 48 h after inoculation, genotype-specific changes in the green and red range (500 to 690 nm) and a blue shift of the red-edge inflection point were observed. Manual analysis indicated resistance-specific reflectance patterns from 1 to 3 days after inoculation. These changes could be linked to host plant modifications depending on individual host-pathogen interactions. Retrospective analysis of hyperspectral images revealed spectral characteristics of HR against B. graminis f. sp. hordei. For early HR detection, an advanced data mining approach localized HR spots before they became visible on the RGB images derived from hyperspectral imaging. The link among processes during pathogenesis and host resistance to changes in hyperspectral signatures provide evidence that sensor-based phenotyping is suitable to advance time-consuming and cost-expensive visual rating of plant disease resistances.

Charting Frontotemporal Dementia: From Genes to Networks.

Frontotemporal dementia (FTD) is a genetically and clinically heterogeneous syndrome that is characterized by overlapping clinical symptoms involving behavior, personality, language and/or motor functions and degeneration of the frontal and temporal lobes. The term frontotemporal lobar degeneration (FTLD) is used to describe the proteinopathies associated with clinical FTD. Emerging evidence from network-based neuroimaging studies, such as resting state functional MRI and diffusion tensor MRI studies, have implicated specific large-scale brain networks in the pathogenesis of FTD syndromes, suggesting a new paradigm for explaining the distributed and heterogeneous spreading patterns of pathological proteins in FTLD. In this review, we overview recent research on the study of FTD syndromes as connectivity disorders in symptomatic patients as well as genotype-specific changes in asymptomatic FTD-related gene mutation carriers. Characterizing brain network breakdown in these subjects using neuroimaging may help anticipate the diagnosis and perhaps prevent the devastating impact of FTD.

Circulating microRNA signature of genotype-by-age interactions in the long-lived Ames dwarf mouse.

Recent evidence demonstrates that serum levels of specific miRNAs significantly change with age. The ability of circulating sncRNAs to act as signaling molecules and regulate a broad spectrum of cellular functions implicates them as key players in the aging process. To discover circulating sncRNAs that impact aging in the long-lived Ames dwarf mice, we conducted deep sequencing of small RNAs extracted from serum of young and old mice. Our analysis showed genotype-specific changes in the circulating levels of 21 miRNAs during aging [genotype-by-age interaction (GbA)]. Genotype-by-age miRNAs showed four distinct expression patterns and significant overtargeting of transcripts involved in age-related processes. Functional enrichment analysis of putative and validated miRNA targets highlighted cellular processes such as tumor suppression, anti-inflammatory response, and modulation of Wnt, insulin, mTOR, and MAPK signaling pathways, among others. The comparative analysis of circulating GbA miRNAs in Ames mice with circulating miRNAs modulated by calorie restriction (CR) in another long-lived mouse suggests CR-like and CR-independent mechanisms contributing to longevity in the Ames mouse. In conclusion, we showed for the first time a signature of circulating miRNAs modulated by age in the long-lived Ames mouse.

Genotype-specific changes associated to early synthesis of autotetraploids in wild potato species

Polyploidy is an important factor in plant evolution that may trigger drastic genome reorganization and phenotypic differentiation. In the last decade, extensive studies have been carried to understand the consequences of allopolyploidization, where the effects of ploidy change may be confounded by interspecific hybridization. By contrast, less is known on autopolyploidization, which only involves doubling of homologous chromosomes. This study was undertaken to assess leaf anatomical modifications and gene expression changes occurring after doubling the somatic chromosome complement of diploid (2n = 2x = 24) potato species Solanum commersonii Dunal and S. bulbocastanum Dunal. Polyploidization did not induce qualitative changes in leaf structure and, for several leaf traits, anatomic modifications were stochastic. In addition, in both species a diploid superiority was generally observed, suggesting the occurrence of a high-ploidy syndrome. Expression change study was carried out on eight important cell cycle-regulatory genes in plant. It revealed a strong alteration of the expression patterns in the 4x genotypes with respect to the 2x parents. Changes often exceed the twofold, with no consistent trend towards up- or down regulation when comparing 2x vis-a-vis 4x. We discuss the possible relevance of epigenetic changes in controlling the expression of duplicated genes.

α+Thalassemia Antagonizes the Malaria-protective Effects of Sickle-Cell Trait

α+Thalassemia Antagonizes the Malaria-protective Effects of Sickle-Cell Trait

Mechanistic Studies of the Negative Epistatic Malaria-protective Interaction Between Sickle Cell Trait and α+thalassemia

BackgroundIndividually, the red blood cell (RBC) polymorphisms sickle cell trait (HbAS) and α+thalassemia protect against severe Plasmodium falciparum malaria. It has been shown through epidemiological studies that the co-inheritance of both conditions results in a loss of the protection afforded by each, but the biological mechanisms remain unknown. MethodsWe used RBCs from >300 donors of various HbAS and α+thalassemia genotype combinations to study the individual and combinatorial effects of these polymorphisms on a range of putative P. falciparum virulence phenotypes in-vitro, using four well-characterized P. falciparum laboratory strains. We studied cytoadhesion of parasitized RBCs (pRBCs) to the endothelial receptors CD36 and ICAM1, rosetting of pRBCs with uninfected RBCs, and pRBC surface expression of the parasite-derived adhesion molecule P. falciparum erythrocyte membrane protein-1 (PfEMP1). FindingsWe confirmed previous reports that HbAS pRBCs show reduced cytoadhesion, rosetting and PfEMP1 expression levels compared to normal pRBC controls. Furthermore, we found that co-inheritance of HbAS with α+thalassemia consistently reversed these effects, such that pRBCs of mixed genotype showed levels of cytoadhesion, rosetting and PfEMP1 expression that were indistinguishable from those seen in normal pRBCs. However, pRBCs with α+thalassemia alone showed parasite strain-specific effects on adhesion, and no consistent reduction in PfEMP1 expression. InterpretationOur data support the hypothesis that the negative epistasis between HbAS and α+thalassemia observed in epidemiological studies might be explained by host genotype-specific changes in the pRBC-adhesion properties that contribute to parasite sequestration and disease pathogenesis in vivo. The mechanism by which α+thalassemia on its own protects against severe malaria remains unresolved.