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Articles 1 - 6 of 6
Full-Text Articles in Life Sciences
Gain-Of-Function Experiments With Bacteriophage Lambda Uncover Residues Under Diversifying Selection In Nature, Rohan Maddamsetti, Daniel T. Johnson, Stephanie J. Spielman, Katherine L. Petrie, Debora S. Marks, Justin R. Meyer
Gain-Of-Function Experiments With Bacteriophage Lambda Uncover Residues Under Diversifying Selection In Nature, Rohan Maddamsetti, Daniel T. Johnson, Stephanie J. Spielman, Katherine L. Petrie, Debora S. Marks, Justin R. Meyer
Biological Sciences Faculty Publications
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here, we demonstrate that two residues of λ’s J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative …
A Robust Deep Model For Improved Classification Of Ad/Mci Patients, Feng Li, Loc Tran, Kim-Han Thung, Shuiwang Ji, Dinggang Shen, Jiang Li
A Robust Deep Model For Improved Classification Of Ad/Mci Patients, Feng Li, Loc Tran, Kim-Han Thung, Shuiwang Ji, Dinggang Shen, Jiang Li
Electrical & Computer Engineering Faculty Publications
Accurate classification of Alzheimer's disease (AD) and its prodromal stage, mild cognitive impairment (MCI), plays a critical role in possibly preventing progression of memory impairment and improving quality of life for AD patients. Among many research tasks, it is of a particular interest to identify noninvasive imaging biomarkers for AD diagnosis. In this paper, we present a robust deep learning system to identify different progression stages of AD patients based on MRI and PET scans. We utilized the dropout technique to improve classical deep learning by preventing its weight coadaptation, which is a typical cause of overfitting in deep learning. …
Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji
Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji
Computer Science Faculty Publications
Background: Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are expressed only in specific cell-types. Analysis of cell-type-specific gene expression patterns can provide insights into the relationship between genes, connectivity, brain regions, and cell-types. However, automated methods for identifying cell-type-specific genes are lacking to date.
Results: Here, we describe a set of computational methods for identifying cell-type-specific genes in the mouse brain by automated image computing of in situ hybridization (ISH) expression patterns. We applied invariant image feature …
Testing The Role Of Male-Male Competition In The Evolution Of Sexual Dimorphism: A Comparison Between Two Species Of Porcelain Crabs, J. Antonio Baeza, Cynthia M. Asorey
Testing The Role Of Male-Male Competition In The Evolution Of Sexual Dimorphism: A Comparison Between Two Species Of Porcelain Crabs, J. Antonio Baeza, Cynthia M. Asorey
Biological Sciences Faculty Publications
Theory predicts marked sexual dimorphism in terms of body size and body structures used as weapons (e.g. chelipeds) in gonochoric species with intense male sexual competition for receptive females and reduced or no sexual dimorphism in species where competition among males is trivial. We tested this hypothesis using a pair of closely-related species of symbiotic porcelain crabs as a model. In one species that inhabits sea anemones solitarily, competition among males for receptive females is unimportant. In a second species that dwells as dense aggregations on sea urchins, malemale competition for sexual partners is recurrent. We expected considerable sexual dimorphism …
Computational Network Analysis Of The Anatomical And Genetic Organizations In The Mouse Brain, Shuiwang Ji
Computational Network Analysis Of The Anatomical And Genetic Organizations In The Mouse Brain, Shuiwang Ji
Computer Science Faculty Publications
Motivation: The mammalian central nervous system (CNS) generates high-level behavior and cognitive functions. Elucidating the anatomical and genetic organizations in the CNS is a key step toward understanding the functional brain circuitry. The CNS contains an enormous number of cell types, each with unique gene expression patterns. Therefore, it is of central importance to capture the spatial expression patterns in the brain. Currently, genome-wide atlas of spatial expression patterns in the mouse brain has been made available, and the data are in the form of aligned 3D data arrays. The sheer volume and complexity of these data pose significant challenges …
Sensory Genes And Mate Choice: Evidence That Duplications, Mutations, And Adaptive Evolution Alter Variation In Mating Cue Genes And Their Receptors, Lisa Horth
Biological Sciences Faculty Publications
Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’ products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and …