Digital Commons Network^™

Disequilibrium, Adaptation, And The Norse Settlement Of Greenland, Rowan Jackson, Jette Arneborg, Andrew Dugmore, Christian Madsen, Tom Mcgovern, Konrad Smiarowski, Richard Streeter

Publications and Research

There is increasing evidence to suggest that arctic cultures and ecosystems have followed non-linear responses to climate change. Norse Scandinavian farmers introduced agriculture to sub-arctic Greenland in the late tenth century, creating synanthropic landscapes and utilising seasonally abundant marine and terrestrial resources. Using a niche-construction framework and data from recent survey work, studies of diet, and regional-scale climate proxies we examine the potential mismatch between this imported agricultural niche and the constraints of the environment from the tenth to the fifteenth centuries. We argue that landscape modification conformed the Norse to a Scandinavian style of agriculture throughout settlement, structuring and …

Rapid, Field-Deployable Method For Collecting And Preserving Plant Metabolome For Biochemical And Functional Characterization, Sarah A. Skubel, Vyacheslav Dushenkov, Brittany L. Graf, Qingwei Niu, Alexander Poulev, Hetalben Kalariya, Llewellyn C. Foxcroft, Ilya Raskin

Publications and Research

Study of plant metabolome is a growing field of science that catalogs vast biochemical and functional diversity of phytochemicals. However, collecting and storing samples of plant metabolome, sharing these samples across the scientific community and making them compatible with bioactivity assays presents significant challenges to the advancement of metabolome research. We have developed a RApid Metabolome Extraction and Storage (RAMES) technology that allows efficient, highly compact, field-deployable collection and storage of libraries of plant metabolome. RAMES technology combines rapid extraction with immobilization of extracts on glass microfiber filter discs. Two grams of plant tissue extracted in ethanol, using a specially …

Preparation And Characterization Of Chemically-Modified Biomaterials And Their Application As Adsorbents Of Penicillin G, Jesie Silva, Lizebel Morante, Tesfamichael Demeke, Jacqueline Baah-Twum, Abel E. Navarro

Publications and Research

The prevalence of antibiotics in water creates microbial resistance and has a negative impact on the ecosystem. Biomaterials such as spent tea leaves are rich in functional groups and are suitable for chemical modification for diverse applications. This research proposes the use of spent tea leaves of chamomile (CM), green tea (GT), and peppermint (PM) as structural scaffolds for the incorporation of carboxyl, sulfonyl, and thiol groups to improve the adsorption of Penicillin G (Pe). Adsorbents characterization reported a higher number of acidic functional groups, mainly in thiolated products. Scanning electron microscopy (SEM) analysis showed changes on the surfaces of …

Genetic Determinants Of Telomere Length In African American Youth, Andrew M. Zeiger, Marquitta J. White, Celeste Eng, Sam S. Oh, Jonathan Witonsky, Pagé C. Goddard, Maria G. Contreras, Jennifer R. Elhawary, Donglei Hu, Angel C. Y. Mak, Eunice Y. Lee, Kevin L. Keys, Lesly-Anne Samedy, Oona Risse Adams, Joaquín Magaña, Scott Huntsman, Sandra Salazar, Adam Davis, Kelley Meade, Emerita Brigino-Buenaventura, Michael A. Lenoir, Harold J. Farber, Kirsten Bibbins-Domingo, Luisa N. Borrell, Esteban G. Burchard

Publications and Research

Telomere length (TL) is associated with numerous disease states and is affected by genetic and environmental factors. However, TL has been mostly studied in adult populations of European or Asian ancestry. These studies have identified 34 TL-associated genetic variants recently used as genetic proxies for TL. The generalizability of these associations to pediatric populations and racially diverse populations, specifically of African ancestry, remains unclear. Furthermore, six novel variants associated with TL in a population of European children have been identified but not validated. We measured TL from whole blood samples of 492 healthy African American youth (children and adolescents between …

Optimizing Spacer Length For Positioning Functional Groups In Bio-Waste, Revathi Iyengar, Maria Faure-Betancourt, Saleh Talukdar, Jinting Ye, Abel E. Navarro

Publications and Research

The goal of this study was to determine the optimal chain length needed for tethering functional groups on bio-wastes. The purpose of modifying the surface of bio-waste is to improve their affinity for phenols. To this end, four different aminated green tea leaves, with the amine group located at the end of 6, 8, 10, and 12 carbons were synthesized. Green approaches to functionalization lead to fewer reactive sites. Optimizing spacer length is one way to ameliorate this. The aminated tea leaves were prepared by a tosylation reaction followed by displacement with a diamine used in excess. The tea leaves …

Sex And The Single Feminist Science Fiction Scholar, Marleen S. Barr

Publications and Research

In the AAUP magazine ACADEME, feminist science fiction scholar Marleen S. Barr discusses her past in light of #MeToo.

The Impact Of Perineuronal Net Digestion Using Chondroitinase Abc On The Intrinsic Physiology Of Cortical Neurons, Philip Chu, Reena Abraham, Kumarie Budhu, Usma Khan, Natalie De Marco Garcia, Joshua C. Brumberg

Publications and Research

Perineuronal nets (PNNs) are a form of aggregate Extracellular Matrix (ECM) in the brain. Recent evidence suggests that the postnatal deposition of PNNs may play an active role in regulating neuroplasticity and, potentially, neurological disorders. Observations of high levels of PNNs expression around somas, proximal dendrites, and axon initial segments of a subtype of neurons have also led to proposals that PNNs may modulate the intrinsic properties of the neurons they ensheathe. While high levels of PNNs are postnatally expressed throughout the neocortex, it is still unclear how they impact the neuronal physiology of the many classes and subtypes of …

Nano And Microsensors For Mammalian Cell Studies, Ioana Voiculescu, Masaya Toda, Naoki Inomata, Takahito Ono, Fang Li

Publications and Research

This review presents several sensors with dimensions at the nano- and micro-scale used for biological applications. Two types of cantilever beams employed as highly sensitive temperature sensors with biological applications will be presented. One type of cantilever beam is fabricated from composite materials and is operated in the deflection mode. In order to achieve the high sensitivity required for detection of heat generated by a single mammalian cell, the cantilever beam temperature sensor presented in this review was microprocessed with a length at the microscale and a thickness in the nanoscale dimension. The second type of cantilever beam presented in …

Perspectives On Natural Philosophy, Stanley N. Salthe

Publications and Research

This paper presents a viewpoint on natural philosophy focusing on the organization of substance, as well as its changes as invited by the Second Law of thermodynamics. Modes of change are pointed to as definitive of levels of organization; these include physical, chemical, and biological modes of change. Conceptual uses of the subsumptive hierarchy format are employed throughout this paper. Developmental change in dissipative structures is examined in some detail, generating an argument for the use of final causality in studies of natural systems. Considerations of ‘internalism’ in science are presented along the way.

Let’S Never Forget: Extinction Is Forever, Aldemaro Romero Jr.

Publications and Research

For many, the conservation of nature is seen as an essential component of human wellbeing. Its value is oftentimes referred to in relation to the four “Es”: economic, environmental, esthetic and ethical values.

From an economic viewpoint, we know that the entire pharmaceutical industry is built upon known natural substances we find in plants and animals, as are the varieties of many domesticated animals we use for food. On the environmental front, we know how essential it is for human health to have an abundant availability of clean water and air.

Esthetically speaking, natural areas represent one of the major …

Adviser Nomination Spurs Questions, Aldemaro Romero Jr.

Publications and Research

After a 19-month delay, the Trump Administration has nominated someone to be the director of the Office of Science and Technology Policy, or as is more colloquially known, the science adviser to the president.

Congress established the White House Office of Science and Technology Policy (OSTP) in 1976. President Gerald Ford, a Republican, signed the act creating the agency into law. That took place after President Nixon disbanded the then-called “President Advisory Committee” in 1973.

The mandate for the agency is to provide the president and others within the Executive Office of the President with advice on the scientific, engineering, …

Immobilization Nematodes For Live Imaging Using An Agarose Pad Produced With A Vinyl Record, Katherine A. Rivera Gomez, Mara Schvarzstein

Publications and Research

Numerous microfluidic systems have been developed and used for live imaging of Caenorhabditis nematodes (Allen et al., 2008; Zhang et al., 2008; Krajniak and Lu, 2010; Krajniak et al., 2013; Cornaglia et al., 2015). These systems can be costly, complex to set up, or require high-maintenance between uses. In addition, microfluidic rigs can be thick, preventing live imaging of worms from strains expressing low fluorescence fusion proteins. In the absence of elaborate microfluidic rigs, most live imaging protocols utilize flat agarose pads along with anesthetics and/or microbeads to immobilize the nematodes (Kim et al., 2013). Since this method does not …

Disparities In Pulmonary Fibrosis Care In The United States: An Analysis From The Nationwide Inpatient Sample, Adam W. Gaffney, Steffie Woolhander, David Himmelstein, Danny Mccormick

Publications and Research

Background: Idiopathic pulmonary fibrosis is a disease with high morbidity and mortality. Care for these patients, including lung transplantation, may provide significant benefits, but is resource-intensive and expensive. Disadvantaged patients with IPF may hence be at risk for receiving inferior care.

Methods: We analyzed data from the Nationwide Inpatient Sample, a database consisting of all hospitalizations from a 20% sample of US hospitals. We identified adults hospitalized with IPF between 1998 and 2011 using ICD-9 codes. We assessed the effect of insurance coverage and socioeconomic status (SES) on lung transplantation, a treatment that may improve survival. We also examined the …

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …

Shipboard Design And Fabrication Of Custom 3d-Printed Soft Robotic Manipulators For The Investigation Of Delicate Deep-Sea Organisms, Daniel M. Vogt, Kaitlyn P. Becker, Brennan T. Phillips, Moritz A. Graule, Randi D. Rotjan, Timothy M. Shank, Erik E. Cordes, Robert J. Wood, David F. Gruber

Publications and Research

Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine biological applications. It is particularly useful in facilitating delicate interactions with fragile marine organisms. This study describes the shipboard design, 3D printing and integration of custom soft robotic manipulators for investigating and interacting with deep-sea organisms. Soft robotics manipulators were tested down to 2224m via a Remotely-Operated Vehicle (ROV) in the Phoenix Islands Protected Area (PIPA) and facilitated the study of a diverse suite of soft-bodied and fragile marine life. Instantaneous feedback from the ROV pilots and biologists allowed for rapid re-design, such as adding ªfingernailsº, …

African Trypanosomes Evade Immune Clearance By Oglycosylation Of The Vsg Surface Coat, Jason Pinger, Dragana Nešić, Liaqat Ali, Francisco Aresta-Branco, Mirjana Lilic, Shanin Chowdhury, Hee-Sook Kim, Joseph Verdi, Jayne Raper, Michael A. J. Ferguson, F. Nina Papavasiliou, C. Erec Stebbins

Publications and Research

The African trypanosome, Trypanosoma brucei spp., is a paradigm for antigenic variation, the orchestrated alteration of cell surface molecules to evade host immunity. The parasite elicits robust antibody-mediated immune responses to its Variant Surface Glycoprotein (VSG) coat, but evades immune clearance by repeatedly accessing a large genetic VSG repertoire and “switching” to antigenically distinct VSGs. This persistent immune evasion has been ascribed exclusively to amino acid variance on the VSG surface presented by a conserved underlying protein architecture. We establish here that this model does not account for the scope of VSG structural and biochemical diversity. The 1.4Å resolution crystal …

Comparison Of The Acute Effects Of Traditional Versus High Velocity Resistance Training On Metabolic, Cardiovascular, And Psychophysiological Responses In Elderly Hypertensive Women, Vânia Silva Macedo Orsano, Wilson Max Almeida Monteiro De Moraes, Nuno Manuel Frade De Sousa, Felipe Carmo De Moura, Ramires Alsamir Tibana, Alessandro De Oliveira Silva, Silvana Schwerz Funghetto, Brad J. Schoenfeld, Jonato Prestes

Publications and Research

Objectives: The aim of the present study was to compare the acute effects of traditional resistance training (RT) versus high velocity RT (HVRT) on metabolic, cardiovascular, and psychophysiological responses in elderly hypertensive women.

Methods: Fifteen elderly women (mean age ± standard deviation, 67.1±6.9 years) classified as having hypertension stage 1 or 2 were randomly allocated to complete traditional RT or HVRT; 1 week later, subjects allocated to RT completed the HVRT session and vice-versa. Heart rate, blood pressure, affective response, perceived effort, and blood samples analyzing lactate, nitrate, nitrite, oxidative damage (thiobarbituric acid reactive substances [TBARS]), and 6-hydroxy-2,5,7,8- tetramethylchroman-2-carboxylic acid …

Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow

Publications and Research

We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …

Climate-Informed Environmental Inflows To Revive A Drying Lake Facing Meteorological And Anthropogenic Droughts, Aneseh Alborzi, Ali Mirchi, Hamed Moftakhari, Iman Mallakpour, Sara Alian, Ali Nazemi, Elmira Hassanzadeh, Omid Mazdiyasni, Samaneh Ashraf, Kaveh Madani, Hamid Norouzi, Marzi Azarderakhsh, Ali Mehran, Mojtaba Sadegh, Andrea Castelletti, Amir Aghakouchak

Publications and Research

The rapid shrinkage of Lake Urmia, one of the world's largest saline lakes located in northwestern Iran, is a tragic wake-up call to revisit the principles of water resources management based on the socio-economic and environmental dimensions of sustainable development. The overarching goal of this paper is to set a framework for deriving dynamic, climate-informed environmental inflows for drying lakes considering both meteorological/climatic and anthropogenic conditions. We report on the compounding effects of meteorological drought and unsustainable water resource management that contributed to Lake Urmia's contemporary environmental catastrophe. Using rich datasets of hydrologic attributes, water demands and withdrawals, as well …

Dual Graph Partitioning Highlights A Small Group Of Pseudoknot-Containing Rna Submotifs, Swati Jain, Cigdem S. Bayrak, Louis Petingi, Tamar Schlick

Publications and Research

RNA molecules are composed of modular architectural units that define their unique structural and functional properties. Characterization of these building blocks can help interpret RNA structure/function relationships. We present an RNA secondary structure motif and submotif library using dual graph representation and partitioning. Dual graphs represent RNA helices as vertices and loops as edges. Unlike tree graphs, dual graphs can represent RNA pseudoknots (intertwined base pairs). For a representative set of RNA structures, we construct dual graphs from their secondary structures, and apply our partitioning algorithm to identify non-separable subgraphs (or blocks) without breaking pseudoknots. We report 56 subgraph blocks …

An Interview With Cesare Montecucco, Mandë Holford, Andreas Rummel

Publications and Research

Cesare Montecucco is a member of the board of various leading scientific journals. His research focus is on the regeneration of the peripheral nervous system and on the mechanisms of action of toxins and related diseases, including tetanus, botulism, anthrax and Helicobacter pylori-associated diseases. In this interview, we talked to Cesare Montecucco about his career, learning and culture.

Prmt5-Mediated Regulation Of Developmental Myelination, Antonella Scaglione, Julia Patzig, Jialiang Liang, Rebecca Frawley, Jabez Bok, Angeliki Mela, Camila Yattah, Jingxian Zhang, Shun Xie Teo, Ting Zhou, Shuibing Chen, Emily Bernstein, Peter Canoll, Ernesto Guccione, Patricia Casaccia

Publications and Research

Oligodendrocytes (OLs) are the myelin-forming cells of the central nervous system. They are derived from differentiation of oligodendrocyte progenitors through a process requiring cell cycle exit and histone modifications. Here we identify the histone arginine methyl-transferase PRMT5, a molecule catalyzing symmetric methylation of histone H4R3, as critical for developmental myelination. PRMT5 pharmacological inhibition, CRISPR/cas9 targeting, or genetic ablation decrease p53-dependent survival and impair differentiation without affecting proliferation. Conditional ablation of Prmt5 in progenitors results in hypomyelination, reduced survival and differentiation. Decreased histone H4R3 symmetric methylation is followed by increased nuclear acetylation of H4K5, and is rescued by pharmacological inhibition of …

Nanostructured Fibers As A Versatile Photonic Platform: Radiative Cooling And Waveguiding Through Transverse Anderson Localization, Norman Nan Shi, Cheng-Chia Tsai, Michael J. Carter, Jyotirmoy Mandal, Adam C. Overvig, Matthew Y. Sfeir, Ming Lu, Catherine L. Craig, Gary D. Bernard, Yuan Yang, Nanfang Yu

Publications and Research

Broadband high reflectance in nature is often the result of randomly, three-dimensionally structured materials. This study explores unique optical properties associated with one-dimensional nanostructures discovered in silk cocoon fibers of the comet moth, Argema mittrei. The fibers are populated with a high density of air voids randomly distributed across the fiber cross-section but are invariant along the fiber. These filamentary air voids strongly scatter light in the solar spectrum. A single silk fiber measuring ~50 μm thick can reflect 66% of incoming solar radiation, and this, together with the fibers' high emissivity of 0.88 in the mid-infrared range, allows …

Anthropometrics, Metabolic Syndrome, And Mortality Hazard, Nir Krakauer, Jesse C. Krakauer

Publications and Research

Independent indices (height, body mass index, a body shape index, and hip index) derived from basic anthropometrics have been found to be powerful predictors of mortality hazard, especially when the attributable risks are summed over these indices to give an anthropometric risk index (ARI). The metabolic syndrome (MS) is defined based on the co-occurrence of anthropometric, clinical, and laboratory criteria and is also widely employed for evaluating disease risk. Here, we investigate correlations between ARI and MS in a general population sample, the United States Third National Health and Nutrition Examination Survey. Baseline values of ARI and MS were also …

Water Pharmacophore: Designing Ligands Using Molecular Dynamics Simulations With Water, Sang Won Jung, Minsup Kim, Steven Ramsey, Tom Kurtzman, Art E. Cho

Publications and Research

In this study, we demonstrate a method to construct a water-based pharmacophore model which can be utilized in the absence of known ligands. This method utilizes waters found in the binding pocket, sampled through molecular dynamics. Screening of compound databases against this water-based pharmacophore model reveals that this approach can successfully identify known binders to a target protein. The method was tested by enrichment studies of 7 therapeutically important targets and compared favourably to screening-by-docking with Glide. Our results suggest that even without experimentally known binders, pharmacophore models can be generated using molecular dynamics with waters and used for virtual …

Discriminating Radiation Injury From Recurrent Tumor With [18f]Parpi And Amino Acid Pet In Mouse Models, Patrick L. Donabedian, Susanne Kossatz, John A. Engelbach, Stephen A. Jannetti, Brandon Carney, Robert J. Young, Wolfgang A. Weber, Joel R. Garbow, Thomas Reiner

Publications and Research

Background

Radiation injury can be indistinguishable from recurrent tumor on standard imaging. Current protocols for this differential diagnosis require one or more follow-up imaging studies, long dynamic acquisitions, or complex image post-processing; despite much research, the inability to confidently distinguish between these two entities continues to pose a significant dilemma for the treating clinician. Using mouse models of both glioblastoma and radiation necrosis, we tested the potential of poly(ADP-ribose) polymerase (PARP)-targeted PET imaging with [¹⁸F]PARPi to better discriminate radiation injury from tumor.

Results

In mice with experimental radiation necrosis, lesion uptake on [¹⁸F]PARPi-PET was similar to …

Consensus On Molecular Subtypes Of High-Grade Serous Ovarian Carcinoma, Gregory M. Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Zhaleh Safikhani, Deena Ma Gendoo, Giovanni Parmigiani, Michael Birrar, Benjamin Haibe-Kains, Levi Waldron

Publications and Research

Purpose: The majority of ovarian carcinomas are of high-grade serous histology, which is associated with poor prognosis. Surgery and chemotherapy are the mainstay of treatment, and molecular characterization is necessary to lead the way to targeted therapeutic options. To this end, various computational methods for gene expression-based subtyping of high-grade serous ovarian carcinoma (HGSOC) have been proposed, but their overlap and robustness remain unknown.

Experimental Design: We assess three major subtype classifiers by meta-analysis of publicly available expression data, and assess statistical criteria of subtype robustness and classifier concordance. We develop a consensus classifier that represents the subtype classifications of …

Future Ozone-Related Acute Excess Mortality Under Climate And Population Change Scenarios In China: A Modeling Study, Kai Chen, Arlene M. Fiore, Renjie Chen, Leiwen Jiang, Bryan Jones, Alexandra Schneider, Annette Peters, Jun Bi, Haidong Kan, Patrick L. Kinney

Publications and Research

Background Climate change is likely to further worsen ozone pollution in already heavily polluted areas, leading to increased ozone-related health burdens. However, little evidence exists in China, the world's largest greenhouse gas emitter and most populated country. As China is embracing an aging population with changing population size and falling age-standardized mortality rates, the potential impact of population change on ozone-related health burdens is unclear. Moreover, little is known about the seasonal variation of ozone-related health burdens under climate change. We aimed to assess near-term (mid-21st century) future annual and seasonal excess mortality from short-term exposure to ambient ozone in …

Post-Traumatic Stress Disorder And Cardiovascular Diseases: A Cohort Study Of Men And Women Involved In Cleaning The Debris Of The World Trade Center Complex, Molly Remsch, Zoey Laskaris, Janine D. Flory, Consuelo Mora-Mclaughlin, Alfredo Morabia

Publications and Research

BACKGROUND: To determine whether post-traumatic stress disorder (PTSD) is a risk factor for myocardial infarction (MI) and stroke, beyond the expected effects from recognized cardiovascular risk factors and depression.

METHODS AND RESULTS: World Trade Center-Heart is an observational prospective cohort study of 6481 blue-collar first responders nested within the World Trade Center Health Program in New York City. Baseline measures in 2012 and 2013 included blood pressure, weight and height, and blood lipids. PTSD, depression, smoking, and dust exposure during the 2001 cleanup were self-reported. During the 4-year follow-up, outcomes were assessed through (1) interview-based incident, nonfatal MI, and stroke, …

Forest Drought Resistance Distinguished By Canopy Height, Wei Fang, Peipei Xu, Tao Zhou, George Hendrey, Xiang Zhao

Publications and Research

How are the survival and growth of trees under severe drought affected by their size? While some studies have shown that large trees are more vulnerable to drought than smaller trees, others found that small trees are the more vulnerable. We explored the potential relationships between canopy height and forest responses to drought indicated by tree mortality, tree ring width index (RWI), and normalized difference vegetation index (NDVI) in the southwestern United States (SWUS) in 2002. In that year many trees had zero tree ring growth due to mortality and dieback, presumably related to drought-stress. With RWI data from a …