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Full-Text Articles in Life Sciences
Optimizing Read Mapping To Reference Genomes To Determine Composition And Species Prevalence In Microbial Communities, John Martin, Sean Sykes, Sarah Young, Karthik Kota, Riva Sanka, Nihar U. Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva
Optimizing Read Mapping To Reference Genomes To Determine Composition And Species Prevalence In Microbial Communities, John Martin, Sean Sykes, Sarah Young, Karthik Kota, Riva Sanka, Nihar U. Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva
Study of Biological Complexity Publications
The Human Microbiome Project (HMP) aims to characterize the microbial communities of 18 body sites from healthy individuals. To accomplish this, the HMP generated two types of shotgun data: reference shotgun sequences isolated from different anatomical sites on the human body and shotgun metagenomic sequences from the microbial communities of each site. The alignment strategy for characterizing these metagenomic communities using available reference sequence is important to the success of HMP data analysis. Six next-generation aligners were used to align a community of known composition against a database comprising reference organisms known to be present in that community. All aligners …
Genome-Wide Association Study Heterogeneous Cohort Homogenization Via Subject Weight Knock-Down, Andre X. C. N. Valente, Joseph Zischkau, Joo H. Shin, Yuan Gao, Abhijit Sarkar
Genome-Wide Association Study Heterogeneous Cohort Homogenization Via Subject Weight Knock-Down, Andre X. C. N. Valente, Joseph Zischkau, Joo H. Shin, Yuan Gao, Abhijit Sarkar
Study of Biological Complexity Publications
Population structure can be a source of both false-positive and false-negative findings in a genome-wide association study. This article proposes an approach that helps to reduce the false-positives. It consists of homogenizing the diseased/healthy phenotype ratio across the cohort, by decreasing the statistical weight of selected individuals. After homogenization, the cohort is statistically handled as if originating from a single well-mixed population. The method was applied to homogenize a Parkinson's disease genome-wide association study cohort.
Shared Resistance To Aging And Als In Neuromuscular Junctions Of Specific Muscles, Gregorio Valdez, Juan C. Tapia, Jeff W. Lichtman, Michael A. Fox, Joshua R. Sanes
Shared Resistance To Aging And Als In Neuromuscular Junctions Of Specific Muscles, Gregorio Valdez, Juan C. Tapia, Jeff W. Lichtman, Michael A. Fox, Joshua R. Sanes
Anatomy and Neurobiology Publications
Normal aging and neurodegenerative diseases both lead to structural and functional alterations in synapses. Comparison of synapses that are generally similar but respond differently to insults could provide the basis for discovering mechanisms that underlie susceptibility or resistance to damage. Here, we analyzed skeletal neuromuscular junctions (NMJs) in 16 mouse muscles to seek such differences. We find that muscles respond in one of three ways to aging. In some, including most limb and trunk muscles, age-related alterations to NMJs are progressive and extensive during the second postnatal year. NMJs in other muscles, such as extraocular muscles, are strikingly resistant to …
Prey Responses To Predator Chemical Cues: Disentangling The Importance Of The Number And Biomass Of Prey Consumed, Michael W. Mccoy, Justin C. Touchon, Tobias Landberg, Karen M. Warkentin, James R. Vonesh
Prey Responses To Predator Chemical Cues: Disentangling The Importance Of The Number And Biomass Of Prey Consumed, Michael W. Mccoy, Justin C. Touchon, Tobias Landberg, Karen M. Warkentin, James R. Vonesh
Biology Publications
To effectively balance investment in predator defenses versus other traits, organisms must accurately assess predation risk. Chemical cues caused by predation events are indicators of risk for prey in a wide variety of systems, but the relationship between how prey perceive risk in relation to the amount of prey consumed by predators is poorly understood. While per capita predation rate is often used as the metric of relative risk, studies aimed at quantifying predator-induced defenses commonly control biomass of prey consumed as the metric of risk. However, biomass consumed can change by altering either the number or size of prey …
Optogenetic Stimulation Of The Corticothalamic Pathway Affects Relay Cells And Gabaergic Neurons Differently In The Mouse Visual Thalamus, Chris W. D. Jurgens, Karen A. Bell, A. Rory Mcquiston, William Guido
Optogenetic Stimulation Of The Corticothalamic Pathway Affects Relay Cells And Gabaergic Neurons Differently In The Mouse Visual Thalamus, Chris W. D. Jurgens, Karen A. Bell, A. Rory Mcquiston, William Guido
Anatomy and Neurobiology Publications
The dorsal lateral geniculate nucleus (dLGN) serves as the primary conduit of retinal information to visual cortex. In addition to retinal input, dLGN receives a large feedback projection from layer VI of visual cortex. Such input modulates thalamic signal transmission in different ways that range from gain control to synchronizing network activity in a stimulus-specific manner. However, the mechanisms underlying such modulation have been difficult to study, in part because of the complex circuitry and diverse cell types this pathway innervates. To address this and overcome some of the technical limitations inherent in studying the corticothalamic (CT) pathway, we adopted …