Digital Commons Network^™

Comparison Of Α-Glucosyl Hesperidin Of Citrus Fruits And Epigallocatechin Gallate Of Green Tea On The Loss Of Rotavirus Infectivity In Cell Culture, Steven M. Lipson, Fatma S. Ozen, Samantha Louis, Laina Karthikeyan

Publications and Research

A number of secondary plant metabolites (e.g., flavonoids) possess antiviral/antimicrobial activity. Most flavonoids, however, are difficult to study, as they are immiscible in water-based systems. The relatively new semisynthetic α-glucosyl hesperitin (GH), and the natural plant product epigallocatechin gallate (EGCG) are unique among most flavonoids, as these flavonoids are highly soluble. The antiviral activity of these plant metabolites were investigated using the rotavirus as a model enteric virus system. Direct loss of virus structural integrity in cell-free suspension and titration of amplified RTV in host cell cultures was measured by a quantitative enzyme-linked immunosorbent assay (qEIA). After 30 min. 100 …

Blocking Anaplerotic Entry Of Glutamine To Tca Cycle Sensitizes K-Ras Mutant Cancer Cells To Cytotoxic Drugs, Mahesh Saqcena, Suman Mukhopadhyay, Carol Hosny, Arwa Alhamed, Amrita Chatterjee, David A. Foster

Publications and Research

Cancer cells undergo a metabolic transformation that allows for increased anabolic demands wherein glycolytic and TCA cycle intermediates are shunted away for the synthesis of biological molecules required for cell growth and division. One of the key shunts is the exit of citrate from the mitochondria and the TCA cycle for the generation of cytosolic acetyl-CoA that can be used for fatty acid and cholesterol biosynthesis. With the loss of mitochondrial citrate, cancer cells rely on the “conditionally essential” amino acid glutamine (Q) as an anaplerotic carbon source for TCA cycle intermediates. While Q deprivation causes G1 cell cycle arrest …

Death Associated Protein Kinase (Dapk) -Mediated Neurodegenerative Mechanisms In Nematode Excitotoxicity, John S. Del Rosario, Katherine Genevieve Feldmann, Towfiq Ahmed, Uzair Amjad, Bakkeung Ko, Junhyung An, Tauhid Mahmud, Maha Salama, Shirley Mei, Daniel Asemota, Itzhak Mano

Publications and Research

Background: Excitotoxicity (the toxic overstimulation of neurons by the excitatory transmitter Glutamate) is a central process in widespread neurodegenerative conditions such as brain ischemia and chronic neurological diseases. Many mechanisms have been suggested to mediate excitotoxicity, but their significance across diverse excitotoxic scenarios remains unclear. Death Associated Protein Kinase (DAPK), a critical molecular switch that controls a range of key signaling and cell death pathways, has been suggested to have an important role in excitotoxicity. However, the molecular mechanism by which DAPK exerts its effect is controversial. A few distinct mechanisms have been suggested by single (sometimes contradicting) studies, and …

Preliminary Phylogenetic Analysis Of The Andean Clade And The Placement Of New Colombian Blueberries (Ericaceae, Vaccinieae), Paola Pedraza-Peñalosa, Nelson R. Salinas, Anne Lucy S. Virnig, Ward C. Wheeler

Publications and Research

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fi eldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. Th is is particularly important, as the monophyly of many of the studied genera have not been confi rmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive …

The Chromatin Remodeler Chd8 Is Required For Activation Of Progesterone Receptor-Dependent Enhancers, María Ceballos-Chávez, Alicia Subtil-Rodríguez, Eugenia G. Giannopoulou, Daniel Soronellas, Elena Vázquez-Chávez, Guillermo P. Vicent, Olivier Elemento, Miguel Beato, José C. Reyes

Publications and Research

While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progesterone receptor (PR) binds regions that display typical features of gene enhancers. Here, we show by ChIP-seq experiments that the chromatin remodeler CHD8 mostly binds promoters under proliferation conditions. However, upon progestin stimulation, CHD8 re-localizes to PR enhancers also enriched in p300 and H3K4me1. Consistently, CHD8 depletion severely impairs progestin-dependent gene regulation. CHD8 binding is PR-dependent but independent of the pioneering factor FOXA1. The SWI/SNF chromatin-remodelling …

Phylogenomic Identification Of Regulatory Sequences In Bacteria: An Analysis Of Statistical Power And An Application To Borrelia Burgdorferi Sensu Lato, Che I. Martin, Tika Y. Sukarna, Saymon Akther, Girish Ramrattan, Pedro Pagan, Lia Di, Emmanuel F. Mongodin, Claire M. Fraser, Steven E. Schutzer, Benjamin J. Luft, Sherwood R. Casjens, Wei-Gang Qiu

Publications and Research

Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical significance of conserved intergenic spacer (IGS) sequences. Simulations show that the binomial model is robust to variations in the value of evolutionary parameters, including base frequencies and the transition-to-transversion ratio. We …

Climate And Changing Winter Distribution Of Alcids In The Northwest Atlantic, Richard R. Veit, Lisa L. Manne

Publications and Research

Population level impacts upon seabirds from changing climate are increasingly evident, and include effects on phenology, migration, dispersal, annual survivorship, and reproduction. Most population data on seabirds derive from nesting colonies; documented climate impacts on winter ecology are scarce. We studied interannual variability in winter abundance of six species of alcids (Charadriiformes, Alcidae) from a 58-year time series of data collected in Massachusetts 1954–2011. We used counts of birds taken during fall and winter from coastal vantage points. Counts were made by amateur birders, but coverage was consistent in timing and location. We found significant association between winter abundance of …

Isolated T Wave Inversion In Lead Avl: An Ecg Survey And A Case Report, Getaw Worku Hassen, Ana Costea, Claire Carrazco, Tsion Frew, Anand, Jason Feliberti, Roger Chirurgi, Tennyson Smith, Alice Chen, Sarah Thompson, Neola Gushway-Henry, Bonnie Simmons, George Fernaine, Hossein Kalantari, Soheila Talebi

Publications and Research

Background. Computerized electrocardiogram (ECG) analysis has been of tremendous help for noncardiologists, but can we rely on it? The importance of ST depression and T wave inversions in lead aVL has not been emphasized and not well recognized across all specialties. Objective. This study's goal was to analyze if there is a discrepancy of interpretation by physicians from different specialties and a computer-generated ECG reading in regard to a TWI in lead aVL. Methods. In this multidisciplinary prospective study, a single ECG with isolated TWI in lead aVL that was interpreted by the computer as normal was given to all …

Structure And Dynamics Of A Fusion Peptide Helical Hairpin On The Membrane Surface: Comparison Of Molecular Simulations And Nmr, Allyn R. Brice, Themis Lazaridis

Publications and Research

The conserved N-terminal residues of the HA2 subunit of influenza hemagglutinin (fusion peptide) are essential for membrane fusion and viral entry. Recent NMR studies showed that the 23-residue fusion peptide forms a helical hairpin that undergoes rocking motion relative to the membrane surface on a nanosecond time scale. To compare with NMR and to obtain a detailed molecular picture of the peptide–membrane interaction, we performed molecular dynamics simulations of the fusion peptide in explicit dimyristoylphosphatidylcholine and with the IMM1 implicit membrane model. To account for low and neutral pH conditions, simulations were performed with acidic groups (E11 and D19) protonated …

Associations Between Host Gene Expression, The Mucosal Microbiome, And Clinical Outcome In The Pelvic Pouch Of Patients With Inflammatory Bowel Disease, Xochitl C. Morgan, Boyko Kabakchiev, Levi Waldron, Andrea D. Tyler, Timothy L. Tickle, Raquel Milgrom, Joanne M. Stempak, Dirk Gevers, Ramnik J. Xavier, Mark S. Silverberg, Curtis Huttenhower

Publications and Research

Background: Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its pathogenesis. We use the IPAA model of IBD to associate mucosal host gene expression with mucosal microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S rRNA gene sequencing data from paired biopsies from IPAA patients with UC and familial adenomatous polyposis. To achieve power for a genome-wide microbiome-transcriptome association study, we use principal component analysis for transcript and clade reduction, and identify significant co-variation between clades and transcripts. …

Catecholaminergic Innervation Of Central And Peripheral Auditory Circuitry Varies With Reproductive State In Female Midshipman Fish, Porichthys Notatus, Paul M. Forlano, Zachary N. Ghahramani, Camillia M. Monestime, Philip Kurochkin, Alena Chernenko, Dmitriy Milkis

Publications and Research

In seasonal breeding vertebrates, hormone regulation of catecholamines, which include dopamine and noradrenaline, may function, in part, to modulate behavioral responses to conspecific vocalizations. However, natural seasonal changes in catecholamine innervation of auditory nuclei is largely unexplored, especially in the peripheral auditory system, where encoding of social acoustic stimuli is initiated. The plainfin midshipman fish, Porichthys notatus, has proven to be an excellent model to explore mechanisms underlying seasonal peripheral auditory plasticity related to reproductive social behavior. Recently, we demonstrated robust catecholaminergic (CA) innervation throughout the auditory system in midshipman. Most notably, dopaminergic neurons in the diencephalon have widespread projections …

Multidisciplinary Intensive Rehabilitation Treatment Improves Sleep Quality In Parkinson's Disease, Giuseppe Frazzitta, Roberto Maestri, Davide Ferrazzoli, Giulio Riboldazzi, Rossana Bera, Cecilia Fontanesi, Roger P. Rossi, Gianni Pezzoli, Maria Felice Ghilardi

Publications and Research

Background Sleep disturbances are among the most common non-motor symptoms of Parkinson’s disease (PD), greatly interfering with daily activities and diminishing life quality. Pharmacological treatments have not been satisfactory because of side effects and interactions with anti-parkinsonian drugs. While studies have shown that regular exercise improves sleep quality in normal aging, there is no definitive evidence in PD.

Methods In a retrospective study, we determined whether an intense physical and multidisciplinary exercise program improves sleep quality in a large group of patients with PD.

We analyzed the scores of PD Sleep Scale (PDSS), which was administered twice, 28 days apart, …

Accuracy Of Highly Sexually Active Gay And Bisexual Men’S Predictions Of Their Daily Likelihood Of Anal Sex And Its Relevance For Intermittent Event-Driven Hiv Pre-Exposure Prophylaxis, Jeffrey T. Parsons, H. Jonathon Rendina, Christian Grov, Ana Ventuneac, Brian Mustanski

Publications and Research

Objective: We sought to examine highly sexually active gay and bisexual men’s accuracy in predicting their sexual behavior for the purposes of informing future research on intermittent, event-driven HIV Pre-Exposure Prophylaxis (PrEP).

Design: For 30 days, 92 HIV-negative men completed a daily survey about their sexual behavior (n = 1,688 days of data) and indicated their likelihood of having anal sex with a casual male partner the following day.

Method: We utilized multilevel modeling to analyze the association between self-reported likelihood of and subsequent engagement in anal sex.

Results: We found a linear association between men’s reported likelihood …

Collaborative Curriculum Revision Project: Documentarian's Report, Anastasia Chiu

Publications and Research

The fourth series of Collaborative Curriculum Revision Project workshops, created by the DOE/CUNY Library Collaborative and project managed by Graduate NYC, took place in spring 2015. It comprised five professional development workshop sessions held in March at Graduate NYC’s/CUNY Central Office in Downtown Brooklyn. Faculty and librarians from the New York City College of Technology and Sunset Park High School gathered, developed a shared collection of teaching strategies for preparing students for the college experience, and revised a high school earth science curricular unit. To inform revisions to the high school curricular unit, participants engaged in conversations on common teaching …

Historical And Contemporary Demography Of Leaf-Toed Geckos (Phyllodactylidae: Phyllodactylus) In The Mexican Dry Forest, Christopher Blair, Victor H. Jiménez Arcos, Fausto R. Méndez De La Cruz, Robert W. Murphy

Publications and Research

Disentangling the relative influence of historical versus contemporary processes shaping the spatial distribution of genetic variation is critical if we are to effectively mitigate key biodiversity issues. We utilize a comprehensive approach based on different molecular marker types and analytical methods to understand the demographic consequences of recent habitat fragmentation in a spatially explicit context. We focus our efforts on native leaf-toed geckos (Phyllodactylus tuberculosus saxatilis) throughout fragmented habitat in the tropical dry forest of northern Mexico as recent evidence suggests that geographic ranges for these geckos may be much smaller than currently realized. However, no data are …

Experimental Shifts In Intraclutch Egg Color Variation Do Not Affect Egg Rejection In A Host Of A Non-Egg-Mimetic Avian Brood Parasite, Rebecca Croston, Mark E. Hauber

Publications and Research

Avian brood parasites lay their eggs in the nests of other birds, and impose the costs associated with rearing parasitic young onto these hosts. Many hosts of brood parasites defend against parasitism by removing foreign eggs from the nest. In systems where parasitic eggs mimic host eggs in coloration and patterning, extensive intraclutch variation in egg appearances may impair the host’s ability to recognize and reject parasitic eggs, but experimental investigation of this effect has produced conflicting results. The cognitive mechanism by which hosts recognize parasitic eggs may vary across brood parasite hosts, and this may explain variation in experimental …

A Reproducible Approach To High-Throughput Biological Data Acquisition And Integration, Daniela Börnigen, Yo Sup Moon, Gholamali Rahnavard, Levi Waldron, Lauren Mciver, Afrah Shafquat, Eric A. Franzosa, Larissa Miropolsky, Christopher Sweeney, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower

Publications and Research

Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, …

The Role Of Prenatal Care And Social Risk Factors In The Relationship Between Immigrant Status And Neonatal Morbidity: A Retrospective Cohort Study, María Paz-Zulueta, Javier Llorca, Raquel Sarabia-Lavín, Francisco Bolumar, Luis Rioja, Abraham Delgado, Miguel Santibáñez

Publications and Research

Background and Aim Literature evaluating association between neonatal morbidity and immigrant status presents contradictory results. Poorer compliance with prenatal care and greater social risk factors among immigrants could play roles as major confounding variables, thus explaining contradictions. We examined whether prenatal care and social risk factors are confounding variables in the relationship between immigrant status and neonatal morbidity. Methods Retrospective cohort study: 231 pregnant African immigrant women were recruited from 2007–2010 in northern Spain. A Spanish population sample was obtained by simple random sampling at 1:3 ratio. Immigrant status (Spanish, Sub-Saharan and Northern African), prenatal care (Kessner Index adequate, intermediate …

Glycine And Gabaa Receptors Mediate Tonic And Phasic Inhibitory Processes That Contribute To Prepulse Inhibition In The Goldfish Startle Network, Paul C.P. Curtin, Thomas Preuss

Publications and Research

Prepulse inhibition (PPI) is understood as a sensorimotor gating process that attenuates sensory flow to the startle pathway during early stages (20--1000 ms) of information processing. Here, we applied in vivo electrophysiology and pharmacology to determine if PPI is mediated by glycine receptors (GlyRs) and/or GABAA receptors (GABAARs) in the goldfish auditory startle circuit. Specifically, we used selective antagonists to dissect the contributions of target receptors on sound-evoked postsynaptic potentials (PSPs) recorded in the neurons that initiate startle, the Mauthner-cells (M-cell). We found that strychnine, a GlyR antagonist, disrupted a fast-activated (5 ms) and rapidly (<50 >ms) decaying (feed-forward) inhibitory …

From The Field To The Lab: Best Practices For Field Preservation Of Bat Specimens For Molecular Analyses, Angelique Corthals, Alynn Martin, Omar M. Warsi, Megan Woller-Skar, Winston Lancaster, Amy Russell, Liliana M. Dávalos

Publications and Research

Studies in molecular ecology depend on field-collected samples for genetic information, and the tissue sampled and preservation conditions strongly affect the quality of the DNA obtained. DNA yields from different tissue types have seldom been compared, and the relative performance of storage media has never been directly tested, even though these media may influence DNA degradation under field conditions. We analyzed DNA yield from buccal swabs and wing punches harvested from live bats using nucleic acid quantification as well as quantitative PCR for a single-copy nuclear locus. We also compared DNA yields from wing tissue preserved in three media: ethanol, …

A Rna-Seq Approach To Identify Putative Toxins From Acrorhagi In Aggressive And Non-Aggressive Anthopleura Elegantissima Polyps, Jason Macrander, Mercer R. Brugler, Marymegan Daly

Publications and Research

Background The use of venom in intraspecific aggression is uncommon and venom-transmitting structures specifically used for intraspecific competition are found in few lineages of venomous taxa. Next-generation transcriptome sequencing allows robust characterization of venom diversity and exploration of functionally unique tissues. Using a tissue-specific RNA-seq approach, we investigate the venom composition and gene ontology diversity of acrorhagi, specialized structures used in intraspecific competition, in aggressive and non-aggressive polyps of the aggregating sea anemone Anthopleura elegantissima (Cnidaria: Anthozoa: Hexacorallia: Actiniaria: Actiniidae). Results Collectively, we generated approximately 450,000 transcripts from acrorhagi of aggressive and non-aggressive polyps. For both transcriptomes we identified 65 …

Estimating Vertex Measures In Social Networks By Sampling Completions Of Rds Trees, Bilal Khan, Kirk Dombrowski, Ric Curtis, Travis Wendel

Publications and Research

This paper presents a new method for obtaining network properties from incomplete data sets. Problems associated with missing data represent well-known stumbling blocks in Social Network Analysis. The method of “estimating connectivity from spanning tree completions” (ECSTC) is specifically designed to address situations where only spanning tree(s) of a network are known, such as those obtained through respondent driven sampling (RDS). Using repeated random completions derived from degree information, this method forgoes the usual step of trying to obtain final edge or vertex rosters, and instead aims to estimate network-centric properties of vertices probabilistically from the spanning trees themselves. In …

National Livestock Policy Of Nepal: Needs And Opportunities, Upendra B. Pradhanang, Soni M. Pradhanang, Arhan Sthapit, Nir Y. Krakauer, Ajay K. Jha, Tarendra Lakhankar

Publications and Research

This paper describes Nepal’s national livestock policies and considers how they can be improved to help meet the pressing national challenges of economic development, equity, poverty alleviation, gender mainstreaming, inclusion of marginalized and underprivileged communities, and climate vulnerability. Nepal is in the process of transforming its government from a unitary system to a federal democratic structure through the new constitution expected by 2015, offering the opportunity to bring a new set of priorities and stakeholders to policymaking. Nepal’s livestock subsector comes most directly within the purview of the National Agricultural Policy 2004, Agro-Business Policy, 2006 and Agricultural Sectoral Operating Policies …

A Global Database Of Lake Surface Temperatures Collected By In Situ And Satellite Methods From 1985–2009, Sapna Sharma, Derek K. Gray, Jordan S. Read, Catherine M. O’Reilly, Philipp Schneider, Anam Qudrat, Corinna Gries, Samantha Stefanoff, Stephanie E. Hampton, Simon Hook, John D. Lenters, David M. Livingstone, Peter B. Mcintyre, Rita Adrian, Mathew G. Allan, Orlane Anneville, Lauri Arvola, Jay Austin, John Bailey, Jill S. Baron, Nihar R. Samal

Publications and Research

Global environmental change has influenced lake surface temperatures, a key driver of ecosystem structure and function. Recent studies have suggested significant warming of water temperatures in individual lakes across many different regions around the world. However, the spatial and temporal coherence associated with the magnitude of these trends remains unclear. Thus, a global data set of water temperature is required to understand and synthesize global, long-term trends in surface water temperatures of inland bodies of water. We assembled a database of summer lake surface temperatures for 291 lakes collected in situ and/or by satellites for the period 1985–2009. In addition, …

Now You See It, Now You Don’T: Flushing Hosts Prior To Experimentation Can Predict Their Responses To Brood Parasitism, Daniel Hanley, Peter Samas, Josef Heryán, Mark E. Hauber, Tomáš Grim

Publications and Research

Brood parasitic birds lay their eggs in other birds’ nests, leaving hosts to raise their offspring. To understand parasite-host coevolutionary arms races, many studies have examined host responses to experimentally introduced eggs. However, attending parents often need to be flushed from their nests to add experimental eggs. If these birds witness parasitism events, they may recognize and reject foreign eggs more readily than parents who did not. We found that, after being flushed, female blackbirds, Turdus merula, remained close to their nests. Flushed females were more likely to eject foreign eggs and did so more quickly than females that …

A Wider Pelvis Does Not Increase Locomotor Cost In Humans, With Implications For The Evolution Of Childbirth, Anna G. Warrener, Kristi L. Lewton, Herman Pontzer, Daniel E. Lieberman

Publications and Research

The shape of the human female pelvis is thought to reflect an evolutionary trade-off between two competing demands: a pelvis wide enough to permit the birth of large-brained infants, and narrow enough for efficient bipedal locomotion. This trade-off, known as the obstetrical dilemma, is invoked to explain the relative difficulty of human childbirth and differences in locomotor performance between men and women. The basis for the obstetrical dilemma is a standard static biomechanical model that predicts wider pelves in females increase the metabolic cost of locomotion by decreasing the effective mechanical advantage of the hip abductor muscles for pelvic stabilization …

Improved Evidence-Based Genome-Scale Metabolic Models For Maize Leaf, Embryo, And Endosperm, Samuel M. D. Seaver, Louis M. T. Bradbury, Océane Frelin, Raphy Zarecki, Eytan Ruppin, Andrew D. Hanson, Christopher S. Henry

Publications and Research

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …

Comparative Genomics Of Cluster O Mycobacteriophages, Steven G. Cresawn, Welkin H. Pope, Deborah Jacobs-Sera, Charles A. Bowman, Daniel A. Russell, Rebekah M. Dedrick, Tamarah Adair, Kirk R. Anders, Sarah Ball, David Bollivar, Caroline Breitenberger, Sandra H. Burnett, Kristen Butela, Deanna Byrnes, Sarah Carzo, Kathleen A. Cornely, Trevor Cross, Richard L. Daniels, David Dunbar, Ann M. Findley, Urszula P. Golebiewska

Publications and Research

Mycobacteriophages – viruses of mycobacterial hosts – are genetically diverse but morphologically are all classified in the Caudovirales with double-stranded DNA and tails. We describe here a group of five closely related mycobacteriophages – Corndog, Catdawg, Dylan, Firecracker, and YungJamal – designated as Cluster O with long flexible tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles, Catdawg particles, and Corndog-infected cells confirms expression of half of the predicted gene products and indicates a non-canonical mechanism for translation of the Corndog tape measure protein. Bioinformatic analysis identifies 8–9 strongly predicted SigA promoters and all five Cluster O …

The Hosoya Entropy Of A Graph, Abbe Mowshowitz, Matthias Dehmer

Publications and Research

This paper demonstrates properties of Hosoya entropy, a quantitative measure of graph complexity based on a decomposition of the vertices linked to partial Hosoya polynomials. Connections between the information content of a graph and Hosoya entropy are established, and the special case of Hosoya entropy of trees is investigated.

Drosophila Muller F Elements Maintain A Distinct Set Of Genomic Properties Over 40 Million Years Of Evolution, Wilson Leung, Christopher D. Shaffer, Laura K. Reed, Sheryl T. Smith, William Barshop, William Dirkes, Matthew Dothager, Paul Lee, Jeannette Wong, David Xiong, Han Yuan, James E. J. Bedard, Joshua F. Machone, Seantay D. Patterson, Amber L. Price, Bryce A. Turner, Srebrenka Robic, Erin K. Luippold, Shannon R. Mccartha, Tezin A. Walji, Karim A. Sharif, Tenzin Choeying, Jason S. Macias, Fareed Sanusi, Karvyn Torchon, Yuying Gosser, Shubha Govind, Nicole Clarke-Medley, Leslie Guadron, Dawn Lau, Alvin Lu, Cheryl Mazzeo, Mariam Meghdari, Simon Ng, Brad Pamnani, Olivia Plante, Yuki Kwan Wa Shum, Roy Song, Gerard P. Mcneil, Adeola Adebayo, Kate Bagaeva, Justina Chinwong, Chrystel Dol, Eunice George, Kirk Haltaufderhyde, Joanna Haye, Manpreet Kaur, Max Semon, Dmitri Serjanov, Anika Toorie, Christopher Wilson

Publications and Research

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have …