A transcriptome-wide association study (TWAS) integrates data from genome-wide association studies and gene expression mapping studies for investigating the gene regulatory mechanisms underlying diseases. Existing TWAS methods are primarily univariate in nature, focusing on analyzing one outcome trait at a time. However, many complex traits are correlated with each other and share a common genetic basis. Consequently, analyzing multiple traits jointly through multivariate analysis can potentially improve the power of TWASs. Here, we develop a method, moPMR-Egger (multiple outcome probabilistic Mendelian randomization with Egger assumption), for analyzing multiple outcome traits in TWAS applications. moPMR-Egger examines one gene at a time, relies on its cis-SNPs that are in potential linkage disequilibrium with each other to serve as instrumental variables, and tests its causal effects on multiple traits jointly. A key feature of moPMR-Egger is its ability to test and control for potential horizontal pleiotropic effects from instruments, thus maximizing power while minimizing false associations for TWASs. In simulations, moPMR-Egger provides calibrated type I error control for both causal effects testing and horizontal pleiotropic effects testing and is more powerful than existing univariate TWAS approaches in detecting causal associations. We apply moPMR-Egger to analyze 11 traits from 5 trait categories in the UK Biobank. In the analysis, moPMR-Egger identified 13.15% more gene associations than univariate approaches across trait categories and revealed distinct regulatory mechanisms underlying systolic and diastolic blood pressures.Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is associated with congenital absence of the uterus, cervix, and the upper part of the vagina; it is a sex-limited trait. Disrupted development of the Müllerian ducts (MD)/Wölffian ducts (WD) through multifactorial mechanisms has been proposed to underlie MRKHS. In this study, exome sequencing (ES) was performed on a Chinese discovery cohort (442 affected subjects and 941 female control subjects) and a replication MRKHS cohort (150 affected subjects of mixed ethnicity from North America, South America, and Europe). Phenotypic follow-up of the female reproductive system was performed on an additional cohort of PAX8-associated congenital hypothyroidism (CH) (n = 5, Chinese). By analyzing 19 candidate genes essential for MD/WD development, we identified 12 likely gene-disrupting (LGD) variants in 7 genes PAX8 (n = 4), BMP4 (n = 2), BMP7 (n = 2), TBX6 (n = 1), HOXA10 (n = 1), EMX2 (n = 1), and WNT9B (n = 1), while LGD variants in these genes were not detected in control samples (p = 1.27E-06). Interestingly, a sex-limited penetrance with paternal inheritance was observed in multiple families. One additional PAX8 LGD variant from the replication cohort and two missense variants from both cohorts were revealed to cause loss-of-function of the protein. From the PAX8-associated CH cohort, we identified one individual presenting a syndromic condition characterized by CH and MRKHS (CH-MRKHS). Our study demonstrates the comprehensive utilization of knowledge from developmental biology toward elucidating genetic perturbations, i.e., rare pathogenic alleles involving the same loci, contributing to human birth defects.A new study of the macaque visual cortex has revealed that visual area V4 performs substantial analysis of solid shape structure. The findings draw new attention to the embedding of local three-dimensional shape analysis into the early cortical stages of visual processing.The diverse ways and environments in which animals move are correlated with morphology1, but morphology is not sufficient to predict how animals move because behavioral innovations can create new capacities. We document a new mode of snake locomotion - 'lasso locomotion' - that allows the brown treesnake (Boiga irregularis) to ascend **** larger smooth cylinders than any previously known behavior. This lasso locomotion may facilitate exploiting resources that might otherwise be unobtainable and contribute to the success and impact of this highly invasive species. VIDEO ABSTRACT.Tracy Ainsworth and Barbara Brown introduce the causes and consequences of coral bleaching.Sleep is critical for diverse aspects of brain function in animals ranging from invertebrates to humans. Powerful genetic tools in the fruit fly Drosophila melanogaster have identified - at an unprecedented level of detail - genes and neural circuits that regulate sleep. This research has revealed that the functions and neural principles of sleep regulation are largely conserved from flies to mammals. Further, genetic approaches to studying sleep have uncovered mechanisms underlying the integration of sleep and many different biological processes, including circadian timekeeping, metabolism, social interactions, and aging. These findings show that in flies, as in mammals, sleep is not a single state, but instead consists of multiple physiological and behavioral states that change in response to the environment, and is shaped by life history. Here, we review advances in the study of sleep in Drosophila, discuss their implications for understanding the fundamental functions of sleep that are likely to be conserved among animal species, and identify important unanswered questions in the field.Centromeres, the chromosomal loci that ensure chromosome segregation by directing kinetochore assembly, are typically marked by the histone CENP-A. A study in CENP-A-deficient insects finds that virtually any chromosomal region with low nucleosome turnover can assemble kinetochores, highlighting the extraordinary plasticity of holocentromeres.Norepinephrine and acetylcholine regulate brain activity during changes in arousal and attention that are also reflected in fluctuations of the pupil. New research suggests that during goal-directed behavior, serotonin is also associated with pupil dilation.Animals display a diversity of life cycles, including larvae in some lineages but not in others. https://www.selleckchem.com/products/ap-3-a4-enoblock.html A new study reveals a shared genetic toolkit in many animals that regulates the transition to the juvenile form, from an embryo or a larva.
A transcriptome-wide association study (TWAS) integrates data from genome-wide association studies and gene expression mapping studies for investigating the gene regulatory mechanisms underlying diseases. Existing TWAS methods are primarily univariate in nature, focusing on analyzing one outcome trait at a time. However, many complex traits are correlated with each other and share a common genetic basis. Consequently, analyzing multiple traits jointly through multivariate analysis can potentially improve the power of TWASs. Here, we develop a method, moPMR-Egger (multiple outcome probabilistic Mendelian randomization with Egger assumption), for analyzing multiple outcome traits in TWAS applications. moPMR-Egger examines one gene at a time, relies on its cis-SNPs that are in potential linkage disequilibrium with each other to serve as instrumental variables, and tests its causal effects on multiple traits jointly. A key feature of moPMR-Egger is its ability to test and control for potential horizontal pleiotropic effects from instruments, thus maximizing power while minimizing false associations for TWASs. In simulations, moPMR-Egger provides calibrated type I error control for both causal effects testing and horizontal pleiotropic effects testing and is more powerful than existing univariate TWAS approaches in detecting causal associations. We apply moPMR-Egger to analyze 11 traits from 5 trait categories in the UK Biobank. In the analysis, moPMR-Egger identified 13.15% more gene associations than univariate approaches across trait categories and revealed distinct regulatory mechanisms underlying systolic and diastolic blood pressures.Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is associated with congenital absence of the uterus, cervix, and the upper part of the vagina; it is a sex-limited trait. Disrupted development of the Müllerian ducts (MD)/Wölffian ducts (WD) through multifactorial mechanisms has been proposed to underlie MRKHS. In this study, exome sequencing (ES) was performed on a Chinese discovery cohort (442 affected subjects and 941 female control subjects) and a replication MRKHS cohort (150 affected subjects of mixed ethnicity from North America, South America, and Europe). Phenotypic follow-up of the female reproductive system was performed on an additional cohort of PAX8-associated congenital hypothyroidism (CH) (n = 5, Chinese). By analyzing 19 candidate genes essential for MD/WD development, we identified 12 likely gene-disrupting (LGD) variants in 7 genes PAX8 (n = 4), BMP4 (n = 2), BMP7 (n = 2), TBX6 (n = 1), HOXA10 (n = 1), EMX2 (n = 1), and WNT9B (n = 1), while LGD variants in these genes were not detected in control samples (p = 1.27E-06). Interestingly, a sex-limited penetrance with paternal inheritance was observed in multiple families. One additional PAX8 LGD variant from the replication cohort and two missense variants from both cohorts were revealed to cause loss-of-function of the protein. From the PAX8-associated CH cohort, we identified one individual presenting a syndromic condition characterized by CH and MRKHS (CH-MRKHS). Our study demonstrates the comprehensive utilization of knowledge from developmental biology toward elucidating genetic perturbations, i.e., rare pathogenic alleles involving the same loci, contributing to human birth defects.A new study of the macaque visual cortex has revealed that visual area V4 performs substantial analysis of solid shape structure. The findings draw new attention to the embedding of local three-dimensional shape analysis into the early cortical stages of visual processing.The diverse ways and environments in which animals move are correlated with morphology1, but morphology is not sufficient to predict how animals move because behavioral innovations can create new capacities. We document a new mode of snake locomotion - 'lasso locomotion' - that allows the brown treesnake (Boiga irregularis) to ascend much larger smooth cylinders than any previously known behavior. This lasso locomotion may facilitate exploiting resources that might otherwise be unobtainable and contribute to the success and impact of this highly invasive species. VIDEO ABSTRACT.Tracy Ainsworth and Barbara Brown introduce the causes and consequences of coral bleaching.Sleep is critical for diverse aspects of brain function in animals ranging from invertebrates to humans. Powerful genetic tools in the fruit fly Drosophila melanogaster have identified - at an unprecedented level of detail - genes and neural circuits that regulate sleep. This research has revealed that the functions and neural principles of sleep regulation are largely conserved from flies to mammals. Further, genetic approaches to studying sleep have uncovered mechanisms underlying the integration of sleep and many different biological processes, including circadian timekeeping, metabolism, social interactions, and aging. These findings show that in flies, as in mammals, sleep is not a single state, but instead consists of multiple physiological and behavioral states that change in response to the environment, and is shaped by life history. Here, we review advances in the study of sleep in Drosophila, discuss their implications for understanding the fundamental functions of sleep that are likely to be conserved among animal species, and identify important unanswered questions in the field.Centromeres, the chromosomal loci that ensure chromosome segregation by directing kinetochore assembly, are typically marked by the histone CENP-A. A study in CENP-A-deficient insects finds that virtually any chromosomal region with low nucleosome turnover can assemble kinetochores, highlighting the extraordinary plasticity of holocentromeres.Norepinephrine and acetylcholine regulate brain activity during changes in arousal and attention that are also reflected in fluctuations of the pupil. New research suggests that during goal-directed behavior, serotonin is also associated with pupil dilation.Animals display a diversity of life cycles, including larvae in some lineages but not in others. https://www.selleckchem.com/products/ap-3-a4-enoblock.html A new study reveals a shared genetic toolkit in many animals that regulates the transition to the juvenile form, from an embryo or a larva.
0 Kommentare
0 Geteilt
90 Ansichten
0 Bewertungen
