Life Sciences Commons^™

The Human Disease-Associated Ab Amyloid Core Sequence Forms Functional Amyloids In A Fungal Adhesin, Rachele D. Rameau, Desmond N. Jackson, Audrey Beaussary, Yves F. Dufrêne, Peter N. Lipke

Publications and Research

There is increasing evidence that many amyloids in living cells have physiological functions. On the surfaces of fungal cells, amyloid core sequences in adhesins can aggregate into 100- to 1,000-nm-wide patches to form high-avidity adhesion nanodomains on the cell surface. The nanodomains form through interactions that have amyloid-like properties: binding of amyloid dyes, perturbation by antiamyloid agents, and interaction with homologous sequences. To test whether these functional interactions are mediated by typical amyloid interactions, we substituted an amyloid core sequence, LVFFA, from human A protein for the native sequence IVIVA in the 1,419-residue Candida albicans adhesin Als5p. The chimeric protein …

Targeted Curing Of All Lysogenic Bacteriophage From Streptococcus Pyogenes Using A Novel Counter-Selection Technique, Chad W. Euler, Barbara Juncosa, Patricia A. Ryan, Douglas R. Deutsch, W. Michael Mcshan, Vincent A. Fischetti

Publications and Research

Streptococcus pyogenes is a human commensal and a bacterial pathogen responsible for a wide variety of human diseases differing in symptoms, severity, and tissue tropism. The completed genome sequences of >37 strains of S. pyogenes, representing diverse disease- causing serotypes, have been published. The greatest genetic variation among these strains is attributed to numerous integrated prophage and prophage-like elements, encoding several virulence factors. A comparison of isogenic strains, differing in prophage content, would reveal the effects of these elements on streptococcal pathogenesis. However, curing strains of prophage is often difficult and sometimes unattainable. We have applied a novel counter-selection approach …

Site-Specifically Labeled Immunoconjugates For Molecular Imaging—Part 1: Cysteine Residues And Glycans, Pierre Adumeau, Sai Kiran Sharma, Colleen Brent, Brian M. Zeglis

Publications and Research

Due to their remarkable selectivity and specificity for cancer biomarkers, immunoconjugates have emerged as extremely promising vectors for the delivery of diagnostic radioisotopes and fluorophores to malignant tissues. Paradoxically, however, these tools for precision medicine are synthesized in a remarkably imprecise way. Indeed, the vast majority of immunoconjugates are created via the random conjugation of bifunctional probes (e.g., DOTA-NCS) to amino acids within the antibody (e.g., lysines). Yet antibodies have multiple copies of these residues throughout their macromolecular structure, making control over the location of the conjugation reaction impossible. This lack of site specificity can lead to the formation of …

Function Of Male Sexual Signaling In The Brief Squid (Lolliguncula Brevis), Lauren A. Piperno

Theses and Dissertations

This study explores male signaling in the brief squid. Females spend more time close to males during male signal production, but did not change their orientation to enable mating. Females reduced their own signaling during male signals. Male sexual signaling is directed at females, yet the precise function remains elusive.

The Effects Of Changing Attention And Context In An Awake Offline Processing Period On Visual Long-Term Memory, Timothy M. Ellmore, Anna Feng, Kenneth Ng, Luthfunnahar Dewan, James C. Root

Publications and Research

There is accumulating evidence that sleep as well as awake offline processing is important for the transformation of new experiences into long-term memory (LTM). Yet much remains to be understood about how various cognitive factors influence the efficiency of awake offline processing. In the present study we investigated how changes in attention and context in the immediate period after exposure to new visual information influences LTM consolidation. After presentation of multiple naturalistic scenes within a working memory paradigm, recognition was assessed 30 min and 24 h later in three groups of subjects. One group of subjects engaged in a focused …

Impact Of Irrigation Method On Water Use Efficiency And Productivity Of Fodder Crops In Nepal, Ajay K. Jha, Razan Malla, Mohan Sharma, Jeeban Panthi, Tarendra Lakhankar, Nir Y. Krakauer, Soni M. Pradhanang, Piyush Dahal, Madan Lall Shrestha

Publications and Research

Improved irrigation use efficiency is an important tool for intensifying and diversifying agriculture in Nepal, resulting in higher economic yield from irrigated farmlands with a minimum input of water. Research was conducted to evaluate the effect of irrigation method (furrow vs. drip) on the productivity of nutritious fodder species during off-monsoon dry periods in different elevation zones of central Nepal. A split-block factorial design was used. The factors considered were treatment location, fodder crop, and irrigation method. Commonly used local agronomical practices were followed in all respects except irrigation method. Results revealed that location effect was significant (p < 0.01) with highest fodder productivity seen for the middle elevation site, Syangja. Species effects were also significant, with teosinte (Euchlaena mexicana) having higher yield than cowpea (Vigna unguiculata). Irrigation method impacted green biomass yield (higher with furrow irrigation) but both methods yielded similar dry biomass, while water use was 73% less under drip irrigation. Our findings indicated that the controlled application of water through drip irrigation is able to produce acceptable yields of nutritionally dense fodder species during dry seasons, leading to more effective utilization and resource conservation of available land, fertilizer and water. Higher productivity of these nutritional fodders resulted in higher milk productivity for livestock smallholders. The ability to grow fodder crops year-round in lowland and hill regions of Nepal with limited water storages using low-cost, water-efficient drip irrigation may greatly increase livestock productivity and, hence, the economic security of smallholder farmers.

Characterization Of Fluorescent Proteins For Three- And Four-Color Live-Cell Imaging In S. Cerevisiae, Ryo Higuchi-Sanabria, Enrique J. Garcia, Delia Tomoiaga, Emilia L. Munteanu, Paul Feinstein, Liza A. Pon

Publications and Research

Saccharomyces cerevisiae are widely used for imaging fluorescently tagged protein fusions. Fluorescent proteins can easily be inserted into yeast genes at their chromosomal locus, by homologous recombination, for expression of tagged proteins at endogenous levels. This is especially useful for incorporation of multiple fluorescent protein fusions into a single strain, which can be challenging in organisms where genetic manipulation is more complex. However, the availability of optimal fluorescent protein combinations for 3-color imaging is limited. Here, we have characterized a combination of fluorescent proteins, mTFP1/mCitrine/ mCherry for multicolor live cell imaging in S. cerevisiae. This combination can be used with …

Beyond Baby Steps An Empirical Study Of The Impact Of Environmental Justice Executive Order 12898, Elizabeth Ann Glass Geltman, Gunwant Gill, Miriam Jovanovic

Publications and Research

This study evaluated the impact of Executive Order (EO) 12898 to advance environmental justice. We conducted a review evaluating the frequency and effective use of EO 12898 since execution with particular focus following President Obama’s Plan EJ 2014. We found that both EO 12898 and Plan EJ 2104 had little, if any, impact on federal regulatory decision making. To the extent federal agencies discussed EO 12898, most did so in boilerplate rhetoric that satisfied compliance but was devoid of detailed thought or analysis. In the 21st year, with the exception of the Environmental Protection Agency, very little federal regulatory activity …

Drilling For Common Ground: How Public Opinion Tracks Experts In The Debate Over Federal Regulation Of Shale Oil & Gas Extraction, Elizabeth Ann Glass Geltman

Publications and Research

Public interest in environmental and health impacts from shale oil and gas extraction (what the public calls “fracking”) is growing. Industry claims the public outcry against the new technology is not grounded in science. In February 2013, Resources for the Future (“RFF”) published a list of high priority “risk pathways” that experts from NGOs, academia, government, and industry all agreed were real concerns about fracking. This article used the risk matrix to evaluate whether public comments in dockets of federal agencies that proposed regulation concerning hydraulic fracturing tracked expert concern. The article found that the public tracked many of the …

Human Anatomy And Physiology Preparatory Course: Part 2 Of 4 (Interactive), Carlos Liachovitzky

Open Educational Resources

The overall purpose of these preparatory course set of learning objectives is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

These 40+ learning objectives to prepare for Human Anatomy and Physiology can be downloaded and played in a desktop, or laptop (windows exe file).

The entire course has four parts:

• Part 1
• Part 2
• Part 3
• Part 4

Each learning objective is followed by a set of multiple choice question similar to those found later in a Human Anatomy and Physiology course.

Killer-Cell Immunoglobulin-Like Receptor (Kir) Gene Profiles Modify Hiv Disease Course, Not Hiv Acquisition In South African Women, V. Naranbhai, D. De Assis Rosa, L. Werner, R. Moodley, H. Hong, A. Kharsany, K. Mlisana, S. Sibeko, N. Garrett, D. Chopera, William H. Carr, Q. Abdool Karim, A. V. S. Hill, S. S. Abdool Karim, M. Altfeld, C. M. Gray, T. Ndung’U

Publications and Research

Background: Killer-cell Immunoglobulin-like Receptors(KIR) interact with Human Leukocyte Antigen(HLA) to modify natural killer- and T-cell function. KIR are implicated in HIV acquisition by small studies that have not been widely replicated. A role for KIR in HIV disease progression is more widely replicated and supported by functional studies.

Methods: To assess the role of KIR and KIR ligands in HIV acquisition and disease course, we studied at-risk women in South Africa between 2004–2010. Logistic regression was used for nested case–control analysis of 154 women who acquired vs. 155 who did not acquire HIV, despite high exposure. Linear mixed-effects models were …

Human Anatomy And Physiology Preparatory Course: Part 3 Of 4 (Interactive), Carlos Liachovitzky

Open Educational Resources

he overall purpose of these preparatory course set of learning objectives is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

These 40+ learning objectives to prepare for Human Anatomy and Physiology can be downloaded and played in a desktop, or laptop (windows exe file).

The entire course has four parts:

• Part 1
• Part 2
• Part 3
• Part 4

Each learning objective is followed by a set of multiple choice question similar to those found later in a Human Anatomy and Physiology course.

Teaching Evolution: Blog As A Liminal Space, Shylaja Akkaraju, Alexander Wolf

Publications and Research

A threshold concept is a challenging concept that acts as a doorway leading to deeper understanding and a dramatic shift in perception. A learner that is in- volved in grasping a threshold concept is said to be undergoing a threshold expe- rience within a liminal space or learning environment. We used the blog as a lim- inal space for our students to engage with the theory of evolution, which is a threshold concept. In order to teach evolution effectively it is necessary to address both understanding and acceptance of evolutionary theory. To explore the latter in an introductory biology course, …

Synthetic Functionalized Scaffolds For Culture And Maintenance Of Primary Human Hepatocytes, Douglas Macpherson

Dissertations and Theses

There is deficit in the number of human livers that are available for transplantation. Additionally, there is no reliable model for the liver environment available for laboratory research. Tissue engineering provides alternatives for organ transplantation. We have created a supramolecular biomaterial out of simple peptide and saccharide building blocks to act as a hydrogel scaffold to support culture of liver cells. Using a self-­‐assembling peptide fiber decorated with functional molecules, we were able to culture primary human hepatocytes demonstrate their viability and maintenance of phenotype. The hydrogel material was formed by co-assembly in aqueous buffer and characterized using transmission electron …

Job Stress, Inflammation, And Atherosclerosis: A Reflection, Renzo Bianchi, Irvin Sam Schonfeld

Publications and Research

Stress in general has been associated with inflammation and atherosclerosis (Sapolsky, 2004; Slavich and Irwin, 2014). The accumulation of inadequately controlled studies has become a concern (Bianchi, 2016; Schonfeld & Bianchi, 2016). Stronger efforts should be made to take into account both empirically identified and theoretically likely confounders in this research field. Assessing the contribution of job-related factors to given outcomes without simultaneously considering the role of relevant non-job factors is unwarranted. Results from inadequately controlled studies can lead to our making ineffective, or even counter-productive, decisions in terms of public health policies.

Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer

Publications and Research

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

Natural Cultch Type Influences Habitat Preference And Predation, But Not Survival, In Reef-Associated Species, Erica A. Levine, Stephen Gosnell J., Emily M. Goetz, Christopher R. Malinowski

Publications and Research

A shared origin with fresh and dredged cultch and availability via mining have made fossil cultch a commonly used reef restoration substrate. However, important differences in shape and size between whole-shell cultch and fossil cultch may impact the complexity of reefs constructed from these materials. To determine if these differences may impact the development of restored reefs, we quantified the interstitial space each cultch type provides and constructed reef mesocosms to measure (1) the immediate effects of exposure to each cultch type on mortality of blue crab (Callinectes sapidus) and pink shrimp (Farfantepenaeus duorarum); (2) the …

Unworking Milton: Steps To A Georgics Of The Mind, Steven Swarbrick

Publications and Research

Traditionally read as a poem about laboring subjects who gain power through abstract and abstracting forms of bodily discipline, John Milton’s Paradise Lost (1667, 1674) more compellingly foregrounds the erotics of the Garden as a space where humans and nonhumans intra-act materially and sexually. Following Christopher Hill, who long ago pointed to not one but two revolutions in the history of seventeenth-century English radicalism—the first, ‘the one which succeeded[,] . . . the protestant ethic’; and the second, ‘the revolution which never happened,’ which sought ‘communal property, a far wider democracy[,] and rejected the protestant ethic’—I show how Milton’s Paradise …

Overlapping Signatures Of Chronic Pain In The Dna Methylation Landscape Of Prefrontal Cortex And Peripheral T Cells, Renaud Massart, Sergiy Dymov, Magali Millecamps, Matthew Suderman, Stephanie Gregoire, Kevin Koenigs, Sebastian Alvarado, Maral Tajerian, Laura S. Stone, Moshe Szyf

Publications and Research

We tested the hypothesis that epigenetic mechanisms in the brain and the immune system are associated with chronic pain. Genome-wide DNA methylation assessed in 9 months post nerve-injury (SNI) and Sham rats, in the prefrontal cortex (PFC) as well as in T cells revealed a vast difference in the DNA methylation landscape in the brain between the groups and a remarkable overlap (72%) between differentially methylated probes in T cells and prefrontal cortex. DNA methylation states in the PFC showed robust correlation with pain score of animals in several genes involved in pain. Finally, only 11 differentially methylated probes in …

Human Anatomy And Physiology Preparatory Course: Part 1 Of 4 (Interactive), Carlos Liachovitzky

Open Educational Resources

The overall purpose of these preparatory course set of learning objectives is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

These 40+ learning objectives to prepare for Human Anatomy and Physiology can be downloaded and played in a desktop, or laptop (windows exe file).

The entire course has four parts:

• Part 1
• Part 2
• Part 3
• Part 4

Each learning objective is followed by a set of multiple choice question similar to those found later in a Human Anatomy and Physiology course.

The organization and …

Human Anatomy And Physiology Preparatory Course: Part 4 Of 4 (Interactive), Carlos Liachovitzky

Open Educational Resources

The overall purpose of these preparatory course set of learning objectives is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

These 40+ learning objectives to prepare for Human Anatomy and Physiology can be downloaded and played in a desktop, or laptop (windows exe file).

The entire course has four parts:

• Part 1
• Part 2
• Part 3
• Part 4

Each learning objective is followed by a set of multiple choice question similar to those found later in a Human Anatomy and Physiology course.

A Review On Locomotor Training After Spinal Cord Injury: Reorganization Of Spinal Neuronal Circuits And Recovery Of Motor Function, Andrew C. Smith, Maria Knikou

Publications and Research

Locomotor training is a classic rehabilitation approach utilized with the aim of improving sensorimotor function and walking ability in people with spinal cord injury (SCI). Recent studies have provided strong evidence that locomotor training of persons with clinically complete, motor complete, or motor incomplete SCI induces functional reorganization of spinal neuronal networks at multisegmental levels at rest and during assisted stepping. This neuronal reorganization coincides with improvements in motor function and decreased muscle cocontractions. In this review, we will discuss the manner in which spinal neuronal circuits are impaired and the evidence surrounding plasticity of neuronal activity after locomotor training …

Expression And Function Of A Putative Cox-Like Gene In D. Melanogaster, Michelle S. Batchu

Dissertations and Theses

Cyclooxygenases (COX) are the enzymes that catalyze the conversion of arachidonic acid into prostaglandins. In mammals, isoform COX-1 is constitutively expressed, whereas the isoform COX-2 gene expression is induced, primarily at sites of inflammation. While eicosanoids play a major role in inflammation in insects, their existence in fruit flies has not been reported. Recent computational analyses by Qi and Singh (2014) have identified putative COX-like enzymes in the fruit fly Drosophila melanogaster. Here we compare the expression patterns of these enzymes and the effects of their knockdown in immune cells of D. melanogaster third instar larvae. Because of high genetic …

"Molecular Analysis Of Virulence Factors Unique To Leptopilina Heterotoma-A Parasitic Wasp Of Drosophila Spp.", Noelle Dziedzic

Dissertations and Theses

Endoparasitioid wasps of Drosophila spp. frequently avoid or overcome the immune defense mechanisms of their fly hosts. Leptopilina heterotoma (Lh) is a generalist wasp species, successful on many Drosophila spp. world-wide. During oviposition, the female wasp introduces venom proteins and virus-like particles (VLPs) into developing fly larvae. VLPs are endocytosed by plasmatocytes, a macrophage-like blood cell that is the most abundant hemocyte present in the circulating hemolymph. Once internalized, VLPs destroy plasmatocytes by programmed cell death. To understand the contributions of VLP proteins in VLP trafficking within host cells, we took advantage of proteomic data from purified Lh VLPs. Two …

Revised Distributional Estimates For The Recently Discovered Olinguito (Bassaricyon Neblina), Using Museum And Science Records, Beth E. Gerstner

Dissertations and Theses

In the context of global change, a necessary first step for the conservation of species is gaining a good understanding of their distributional limits. This is especially important for biodiversity hotspots with high endemism such as the Northern Andes. The olinguito (Procyonidae: Bassaricyon neblina) is a recently described, medium-sized carnivoran found in Northern Andean cloud forests. A preliminary distributional model was published along with the original description, and I here provide revised distributional estimates using updated locality records and more current ENM methods. I build ecological niche models in Maxent using occurrence data (georeferenced museum records and citizen science-derived photo-vouchers) …

Insights Into The Molecular Antiviral Mechanism Of Pokeweed Protein From Phytolacca Americana, Valentina R. Aitbakieva, Artem V. Domashevskiy

Publications and Research

Agriculture is an indispensable part of every person’s life, ensuring that nutritious and inexpensive food is readily available. As any other organisms, plants are subject to numerous parasitic infections. Biological evolution has allowed plants to produce a variety of toxic compounds to deal with their pathogens. American pokeweed plant (Phytolacca americana) manufactures pokeweed antiviral protein, a ribosome inactivating protein that disrupts protein synthesis and lowers infectivity of many plant and animal viruses. The intricate mechanism of PAP antiviral activity entails a delicate coordination and interplay of several factors, allowing the plant to battle its invaders. Here, we examine the molecular …

The Mitogenome Of The Bed Bug Cimex Lectularius (Hemiptera: Cimicidae), Sergios-Orestis Kolokotronis, Jonathan Foox, Jeffrey A. Rosenfeld, Mercer R. Brugler, Darryl Reeves, Joshua B. Benoit, Warren Booth, Grant Robison, Michael Steffen, Zoe Sakas, Subba R. Palli, Coby Schal, Stephen Richards, Apurva Narechania, Richard H. Baker, Louis N. Sorkin, George Amato, Christopher E. Mason, Mark E. Siddall, Rob Desalle

Publications and Research

We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.

Comparative Phylogeography Of Ethiopian Anurans: Impact Of The Great Rift Valley And Pleistocene Climate Change, Xenia Freilich, Jose D. Anadon, Jolanta Bukala, Ordaliza Calderon, Ronveer Chakraborty, Stephanie Boissinot

Publications and Research

Background: The Ethiopian highlands are a biodiversity hotspot, split by the Great Rift Valley into two distinct systems of plateaus and mountains. The Rift Valley is currently hot and dry and acts as a barrier to gene flow for highland-adapted species. It is however unlikely that the conditions in the Rift were inhospitable to highland species during the entire Pleistocene. To assess the significance of the Ethiopian Rift as a biogeographic barrier as well as the impact Pleistocene climatic changes have had on the evolution of Ethiopian organisms, we performed phylogeographic analyses and developed present and past niche models on …

Living With Coyotes, Owen H. Agnew

Capstones

Coyotes have been slowly moving into New York State from Canada since the 1930s. They reached Westchester County and the Bronx decades ago, and their numbers have been slowly rising. Sighting in Manhattan reached an all-time high last spring, and pet attacks in Westchester County have increased slightly in the last several years. But the slight increase in sightings and pet attacks in recent years has been amplified on social media in towns like Chappaqua, New York, where anxiety and fear about coyotes has pitted neighbors against neighbors.

Main character Frank Vincenti is a Long Island barber and a self-proclaimed …

Special Muscles, Annamaria C. Scaccia

Capstones

Special Muscles is a documentary that explores living with Duchenne muscular dystrophy, a fatal degenerative disease that weakens the muscles at an aggressive rate. The film will give an uncensored look at how one family copes with inevitability of the disease and their journey chasing a promising experimental cure.

Special Muscles follows 7-year-old Pietro Scarso and his family as they face the challenges, complications and promise of treating Pietro’s progressive muscle disorder. The film travels from New York to Los Angeles to Philadelphia to document the Scarso family’s race against time as Pietro undergoes a 96-week clinical trial for Eteplirsen, …