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Full-Text Articles in Life Sciences

Fys: Ethics And Technology (Phil 07/Cpsc 15) Syllabus, Ameet Soni, Krista Karbowski Thomason Apr 2019

Fys: Ethics And Technology (Phil 07/Cpsc 15) Syllabus, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

There has been an accelerated shift in the influence of computing technology and the use of algorithms in our daily lives. With this technology comes serious ethical questions. Philosophers are often well-equipped to wrestle with ethical questions, but less well-equipped to wrestle with questions of technology itself. Computer scientists are well-equipped to deal with the problems and challenges of technology, but less well-equipped to deal with the ethical problems and challenges that technology can pose. In this co-taught course, we bring together the two fields to address ethical questions involving social media, data mining, self-driving cars, artificial intelligence, and other ...


Lab Practicum For Bias In Algorithms, Ameet Soni, Krista Karbowski Thomason Apr 2019

Lab Practicum For Bias In Algorithms, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

This is a course assignment to demonstrate potential biases encoded in algorithms (this can be linked more specifically to natural language processing, machine learning, or artificial intelligence) using the Word Embedding Association Test. In lab, students will work with programs that demonstrate the usefulness of word embedding algorithms in finding relationships between words. Then, students will use an implementation of the algorithm in "Semantics derived automatically from language corpora contain human-like biases" by Caliskan et al. to detect gender and racial bias encoded in word embeddings. The assignment has students design and run an experiment using the WEAT algorithm to ...


Illumination Pattern Design With Deep Learning For Single-Shot Fourier Ptychographic Microscopy, Yi Fei Cheng , '21, Megan Strachan , '21, Zachary Weiss , '20, Moniher Deb , '19, Dawn M. Carone, Vidya Ganapati Jan 2019

Illumination Pattern Design With Deep Learning For Single-Shot Fourier Ptychographic Microscopy, Yi Fei Cheng , '21, Megan Strachan , '21, Zachary Weiss , '20, Moniher Deb , '19, Dawn M. Carone, Vidya Ganapati

Biology Faculty Works

Fourier ptychographic microscopy allows for the collection of images with a high space-bandwidth product at the cost of temporal resolution. In Fourier ptychographic microscopy, the light source of a conventional widefield microscope is replaced with a light-emitting diode (LED) matrix, and multiple images are collected with different LED illumination patterns. From these images, a higher-resolution image can be computationally reconstructed without sacrificing field-of-view. We use deep learning to achieve single-shot imaging without sacrificing the space-bandwidth product, reducing the acquisition time in Fourier ptychographic microscopy by a factor of 69. In our deep learning approach, a training dataset of high-resolution images ...


Genetic Interactions Between Bob1 And Multiple 26s Proteasome Subunits Suggest A Role For Proteostasis In Regulating Arabidopsis Development, Elan W. Silverblatt-Buser , '12, Melissa A. Frick , '12, C. Rabeler, Nicholas J. Kaplinsky Apr 2018

Genetic Interactions Between Bob1 And Multiple 26s Proteasome Subunits Suggest A Role For Proteostasis In Regulating Arabidopsis Development, Elan W. Silverblatt-Buser , '12, Melissa A. Frick , '12, C. Rabeler, Nicholas J. Kaplinsky

Biology Faculty Works

Protein folding and degradation are both required for protein quality control, an essential cellular activity that underlies normal growth and development. We investigated how BOB1, an Arabidopsis thaliana small heat shock protein, maintains normal plant development. bob1 mutants exhibit organ polarity defects and have expanded domains of KNOX gene expression. Some of these phenotypes are ecotype specific suggesting that other genes function to modify them. Using a genetic approach we identified an interaction between BOB1 and FIL, a gene required for abaxial organ identity. We also performed an EMS enhancer screen using the bob1-3 allele to identify pathways that are ...


Demethylated Hsatii Dna And Hsatii Rna Foci Sequester Prc1 And Mecp2 Into Cancer-Specific Nuclear Bodies, L. L. Hall, M. Byron, Dawn M. Carone, T. W. Whitfield, G. P. Pouliot, A. Fischer, P. Jones, J. B. Lawrence Mar 2017

Demethylated Hsatii Dna And Hsatii Rna Foci Sequester Prc1 And Mecp2 Into Cancer-Specific Nuclear Bodies, L. L. Hall, M. Byron, Dawn M. Carone, T. W. Whitfield, G. P. Pouliot, A. Fischer, P. Jones, J. B. Lawrence

Biology Faculty Works

This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci. Large nuclear foci of HSATII RNA form and sequester copious MeCP2 ...


Identifying Parkinson’S Patients: A Functional Gradient Boosting Approach, D. S. Dhami, Ameet Soni, D. Page, S. Natarajan Jan 2017

Identifying Parkinson’S Patients: A Functional Gradient Boosting Approach, D. S. Dhami, Ameet Soni, D. Page, S. Natarajan

Computer Science Faculty Works

Parkinson’s, a progressive neural disorder, is difficult to identify due to the hidden nature of the symptoms associated. We present a machine learning approach that uses a definite set of features obtained from the Parkinson’s Progression Markers Initiative (PPMI) study as input and classifies them into one of two classes: PD (Parkinson’s disease) and HC (Healthy Control). As far as we know this is the first work in applying machine learning algorithms for classifying patients with Parkinson’s disease with the involvement of domain expert during the feature selection process. We evaluate our approach on 1194 patients ...


Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins Sep 2016

Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "The Least Likely Man: Marshall Nirenberg And The Discovery Of The Genetic Code" By F. H. Portugal, John B. Jenkins Jun 2016

Review Of "The Least Likely Man: Marshall Nirenberg And The Discovery Of The Genetic Code" By F. H. Portugal, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "Race Unmasked: Biology And Race In The Twentieth Century" By M. Yudell, John B. Jenkins Dec 2015

Review Of "Race Unmasked: Biology And Race In The Twentieth Century" By M. Yudell, John B. Jenkins

Biology Faculty Works

No abstract provided.


An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky May 2015

An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky

Biology Faculty Works

We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to determine whether uncharacterized short mutant lines are GA responsive. These data allow students to place the mutation in the GA signal transduction pathway. During weeks 2 and 3, plants are genotyped for Mendel's "le" mutation using a derived cleaved polymorphic sequences (dCAPS) PCR assay. This laboratory allows students to make a direct ...


Review Of "The Pku Paradox: A Short History Of A Genetic Disease" By D. B. Paul And J. P. Brosco, John B. Jenkins Dec 2014

Review Of "The Pku Paradox: A Short History Of A Genetic Disease" By D. B. Paul And J. P. Brosco, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "Translational Stem Cell Research: Issues Beyond The Debate On The Moral Status Of The Human Embryo" Edited By K. Hug And G. Hermerén, John B. Jenkins Jun 2013

Review Of "Translational Stem Cell Research: Issues Beyond The Debate On The Moral Status Of The Human Embryo" Edited By K. Hug And G. Hermerén, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins Dec 2012

Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins

Biology Faculty Works

No abstract provided.


Some Like It Hot, Some Like It Warm: Phenotyping To Explore Thermotolerance Diversity, C. H. Yeh, Nicholas J. Kaplinsky, C. Hu, Y. Y. Charng Oct 2012

Some Like It Hot, Some Like It Warm: Phenotyping To Explore Thermotolerance Diversity, C. H. Yeh, Nicholas J. Kaplinsky, C. Hu, Y. Y. Charng

Biology Faculty Works

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This ‘thermotolerance diversity’ means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables ...


Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik Feb 2012

Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik

Computer Science Faculty Works

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. While previous ...


Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr. Feb 2012

Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr.

Computer Science Faculty Works

Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's ...


Temperature Compensation Of Auxin Dependent Developmental Patterning, Nicholas J. Kaplinsky Dec 2009

Temperature Compensation Of Auxin Dependent Developmental Patterning, Nicholas J. Kaplinsky

Biology Faculty Works

The establishment of localized auxin gradients plays a central role in developmental patterning in plants. Auxin levels and responses have been shown to increase with temperature although developmental patterning is not affected. This suggests the existence of a homeostatic mechanism that ensures that patterning occurs normally over a range of temperatures. We recently described the cloning and characterization of BOBBER1 (BOB1), an Arabidopsis gene which encodes a small heat shock protein. BOB1 is required for the establishment of auxin gradients and for normal developmental patterning. BOB1 is also required for organismal thermotolerance and localizes to heat shock granules at elevated ...


Bobber1 Is A Noncanonical Arabidopsis Small Heat Shock Protein Required For Both Development And Thermotolerance, Dahlia Erin Perez , '08, J. S. Hoyer, Ayanna Iman Johnson , '09, Zachary Ray Moody , '07, J. Lopez, Nicholas J. Kaplinsky Sep 2009

Bobber1 Is A Noncanonical Arabidopsis Small Heat Shock Protein Required For Both Development And Thermotolerance, Dahlia Erin Perez , '08, J. S. Hoyer, Ayanna Iman Johnson , '09, Zachary Ray Moody , '07, J. Lopez, Nicholas J. Kaplinsky

Biology Faculty Works

Plants have evolved a range of cellular responses to maintain developmental homeostasis and to survive over a range of temperatures. Here, we describe the in vivo and in vitro functions of BOBBER1 (BOB1), a NudC domain containing Arabidopsis (Arabidopsis thaliana) small heat shock protein. BOB1 is an essential gene required for the normal partitioning and patterning of the apical domain of the Arabidopsis embryo. Because BOB1 loss-of-function mutants are embryo lethal, we used a partial loss-of-function allele (bob1-3) to demonstrate that BOB1 is required for organismal thermotolerance and postembryonic development. Recombinant BOB1 protein functions as a molecular chaperone and prevents ...


Partitioning The Apical Domain Of The Arabidopsis Embryo Requires The Bobber1 Nudc Domain Protein, R. J. Jurkuta, Nicholas J. Kaplinsky, Jennifer Elizabeth Spindel , '10, M. K. Barton Jul 2009

Partitioning The Apical Domain Of The Arabidopsis Embryo Requires The Bobber1 Nudc Domain Protein, R. J. Jurkuta, Nicholas J. Kaplinsky, Jennifer Elizabeth Spindel , '10, M. K. Barton

Biology Faculty Works

The apical domain of the embryo is partitioned into distinct regions that will give rise to the cotyledons and the shoot apical meristem. In this article, we describe a novel screen to identify Arabidopsis thaliana embryo arrest mutants that are defective in this partitioning, and we describe the phenotype of one such mutant, bobber1. bobber1 mutants arrest at the globular stage of development, they express the meristem-specific SHOOTMERISTEMLESS gene throughout the top half of the embryo, and they fail to express the AINTEGUMENTA transcript normally found in cotyledons. Thus, BOBBER1 is required to limit the extent of the meristem domain ...


Review Of "Plant Exploration For Longwood Gardens" By T. Aniśko, Nicholas J. Kaplinsky Dec 2006

Review Of "Plant Exploration For Longwood Gardens" By T. Aniśko, Nicholas J. Kaplinsky

Biology Faculty Works

No abstract provided.


Review Of "Illuminating Life: Selected Papers From Cold Spring Harbor (1903-1969). Volume 1" By J. Witkowski, John B. Jenkins Mar 2001

Review Of "Illuminating Life: Selected Papers From Cold Spring Harbor (1903-1969). Volume 1" By J. Witkowski, John B. Jenkins

Biology Faculty Works

No abstract provided.


The Paradigm Of Huntington Disease, John B. Jenkins, P. M. Conneally Jul 1989

The Paradigm Of Huntington Disease, John B. Jenkins, P. M. Conneally

Biology Faculty Works

No abstract provided.


Review Of "The Nature And Origin Of The Biological World" By E. J. Ambrose, John B. Jenkins Sep 1983

Review Of "The Nature And Origin Of The Biological World" By E. J. Ambrose, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "Case Studies In Genetics" By M. A. Tribe, I. Tallan, And M. R. Eraut, John B. Jenkins Dec 1979

Review Of "Case Studies In Genetics" By M. A. Tribe, I. Tallan, And M. R. Eraut, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "Introduction To Biometrical Genetics" By K. Mather And J. L. Jinks, John B. Jenkins Mar 1979

Review Of "Introduction To Biometrical Genetics" By K. Mather And J. L. Jinks, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "The Problem Of Life" By C. U. M. Smith, John B. Jenkins Dec 1977

Review Of "The Problem Of Life" By C. U. M. Smith, John B. Jenkins

Biology Faculty Works

No abstract provided.


Review Of "History Of The Life Sciences. An Annotated Bibliography" By P. Smit, John B. Jenkins Sep 1977

Review Of "History Of The Life Sciences. An Annotated Bibliography" By P. Smit, John B. Jenkins

Biology Faculty Works

No abstract provided.


Attitudes On Population Crisis At A Small Liberal-Arts College, John B. Jenkins, R. C. Mitchell Apr 1973

Attitudes On Population Crisis At A Small Liberal-Arts College, John B. Jenkins, R. C. Mitchell

Biology Faculty Works

No abstract provided.


Spontaneous Mutation Rate In The Dumpy Region Of Drosophila, John B. Jenkins Oct 1972

Spontaneous Mutation Rate In The Dumpy Region Of Drosophila, John B. Jenkins

Biology Faculty Works

No abstract provided.