Digital Commons Network^™

Amino Acids And Mtor Mediate Distinct Metabolic Checkpoints In Mammalian G1 Cell Cycle, Mahesh Saqcena, Deepak Menon, Deven Patel, Suman Mukhopadhyay, Victor Chow, David A. Foster

Publications and Research

Objective In multicellular organisms, cell division is regulated by growth factors (GFs). In the absence of GFs, cells exit the cell cycle at a site in G1 referred to as the restriction point (R) and enter a state of quiescence known as G0. Additionally, nutrient availability impacts on G1 cell cycle progression. While there is a vast literature on G1 cell cycle progression, confusion remains – especially with regard to the temporal location of R relative to nutrient-mediated checkpoints. In this report, we have investigated the relationship between R and a series of metabolic cell cycle checkpoints that regulate passage …

Pkc Activation In Niemann Pick C1 Cells Restores Subcellular Cholesterol Transport, Farshad Tamari, Fannie W. Chen, Chunlei Li, Jagrutiben Chaudhari, Yiannis A. Ioannou

Publications and Research

Activation of protein kinase C (PKC) has previously been shown to ameliorate the cholesterol transport defect in Niemann Pick Type C1 (NPC1) cells, presumably by increasing the soluble levels of one of its substrates, vimentin. This activity would then restore the vimentin cycle in these cells and allow vimentin-dependent retrograde transport to proceed. Here, we further investigate the effects of PKC activation in NPC1 cells by evaluating different isoforms for their ability to solubilize vimentin and correct the NPC1 cholesterol storage phenotype. We also examine the effects of PKC activators, including free fatty acids and the PKC-specific activator diazoxide, on …

Β-Catenin-Independent Activation Of Tcf1/Lef1 In Human Hematopoietic Tumor Cells Through Interaction With Atf2 Transcription Factors, Luca Grumolato, Guizhong Liu, Tomomi Haremaki, Sathish Kumar Mungamuri, Phyllus Mong, Gal Akiri, Pablo Lopez-Bergami, Adriana Arita, Youssef Anouar, Marek Mlodzik, Ze'ev A. Ronai, Joshua Brody, Daniel C. Weinstein, Stuart A. Aaronson

Publications and Research

The role of Wnt signaling in embryonic development and stem cell maintenance is well established and aberrations leading to the constitutive up-regulation of this pathway are frequent in several types of human cancers. Upon ligand-mediated activation, Wnt receptors promote the stabilization of β-catenin, which translocates to the nucleus and binds to the T-cell factor/lymphoid enhancer factor (TCF/LEF) family of transcription factors to regulate the expression of Wnt target genes. When not bound to β-catenin, the TCF/LEF proteins are believed to act as transcriptional repressors. Using a specific lentiviral reporter, we identified hematopoietic tumor cells displaying constitutive TCF/LEF transcriptional activation in …

Taxonomic Revision Of The Olingos (Bassaricyon), With Description Of A New Species, The Olinguito, Kristofer M. Helgen, C. Miguel Pinto, Roland Kays, Laura E. Helgen, Mirian T. N. Tsuchiya, Aleta Quinn, Don E. Wilson, Jesús E. Maldonado

Publications and Research

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (B. gabbii), lowland species with eastern, cis-Andean (B. alleni) and western, trans- Andean (B. medius) distributions, and a species endemic to cloud forests in …

Candidatus Syngnamydia Venezia, A Novel Member Of The Phylum Chlamydiae From The Broad Nosed Pipefish, Syngnathustyphle Typhle, Alexander Fehr, Elisabeth Walther, Heike Schmidt-Posthaus, Lisbeth Nufer, Anthony B. Wilson, Miroslav Svercel, Denis Richter, Helmut Segner, Andreas Pospischil, Lloyd Vaughan

Publications and Research

Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to …

Transcriptome Deep-Sequencing And Clustering Of Expressed Isoforms From Favia Corals, Shaadi F. Pooyaei Mehr, Rob Desalle, Hung-Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea.

Results: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs …

Associations Between The Legal Context Of Hiv, Perceived Social Capital, And Hiv Antiretroviral Adherence In North America, J Craig Phillips, Allison Webel, Carol Dawson Rose, Inge B. Corless, Kathleen M. Sullivan, Joachim Voss, Dean Wantland, Kathleen Nokes, John Brion, Wei-Ti Chen, Scholastika Iipinge, Lucille Sanzero Eller, Lynda Tyer-Viola, Marta Rivero-Méndez, Patrice K. Nicholas, Mallory O. Johnson, Mary Maryland, Jeanne Kemppainen, Carmen J. Portillo, Puangtip Chaiphibalsarisdi

Publications and Research

Background Human rights approaches to manage HIV and efforts to decriminalize HIV exposure/transmission globally offer hope to persons living with HIV (PLWH). However, among vulnerable populations of PLWH, substantial human rights and structural challenges (disadvantage and injustice that results from everyday practices of a well-intentioned liberal society) must be addressed. These challenges span all ecosocial context levels and in North America (Canada and the United States) can include prosecution for HIV nondisclosure and HIV exposure/transmission. Our aims were to: 1) Determine if there were associations between the social structural factor of criminalization of HIV exposure/transmission, the individual factor of perceived …

Habitual Chocolate Consumption May Increase Body Weight In A Dose-Response Manner, James A. Greenberg, Brian Buijsse

Publications and Research

Objective Habitual chocolate intake was recently found to be associated with lower body weight in three cross-sectional epidemiological studies. Our objective was to assess whether these cross-sectional results hold up in a more rigorous prospective analysis. Methods We used data from the Atherosclerosis Risk in Communities cohort. Usual dietary intake was assessed by questionnaire at baseline (1987–98), and after six years. Participants reported usual chocolate intake as the frequency of eating a 1-oz (∼28 g) serving. Body weight and height were measured at the two visits. Missing data were replaced by multiple imputation. Linear mixed-effects models were used to evaluate …

Functional Connectivity In The First Year Of Life In Infants At-Risk For Autism: A Preliminary Near-Infrared Spectroscopy Study, Brandon Keehn, Jennifer B. Wagner, Helen Tager-Flusberg, Charles A. Nelson

Publications and Research

Background: Autism spectrum disorder (ASD) has been called a “developmental disconnection syndrome,” however the majority of the research examining connectivity in ASD has been conducted exclusively with older children and adults. Yet, prior ASD research suggests that perturbations in neurodevelopmental trajectories begin as early as the first year of life. Prospective longitudinal studies of infants at risk for ASD may provide a window into the emergence of these aberrant patterns of connectivity. The current study employed functional connectivity near-infrared spectroscopy (NIRS) in order to examine the development of intra- and inter-hemispheric functional connectivity in high- and low-risk infants across the …

Exposure To Advertisement Calls Of Reproductive Competitors Activates Vocal-Acoustic And Catecholaminergic Neurons In The Plainfin Midshipman Fish, Porichthys Notatus, Christopher L. Petersen, Miky Timothy, D. Spencer Kim, Ashwin A. Bhandiwad, Robert A. Mohr, Joseph A. Sisneros, Paul M. Forlano

Publications and Research

While the neural circuitry and physiology of the auditory system is well studied among vertebrates, far less is known about how the auditory system interacts with other neural substrates to mediate behavioral responses to social acoustic signals. One species that has been the subject of intensive neuroethological investigation with regard to the production and perception of social acoustic signals is the plainfin midshipman fish, Porichthys notatus, in part because acoustic communication is essential to their reproductive behavior. Nesting male midshipman vocally court females by producing a long duration advertisement call. Females localize males by their advertisement call, spawn and deposit …

Reflections On The 2013 Gsc-Gsa ‘Roof Of The World’ China Meeting And Chengdu, Nazrul I. Khandaker

Publications and Research

The recently concluded First Joint Scientific Meeting of Geological Society of China (GSC) and Geological Society of America (GSA) proceeded efficiently in the modern setting of the Jinjiang Hotel, Chengdu, Sichuan Province, China. GSA’s International Section played a key role bringing this meeting to the overseas communities. The meeting, titled ‘Roof of the World’, ended on 19^th June, 2013, followed by several field trips that lasted from three to six days. The meeting was designed to promote and bolster the academic communication between the GSC and GSA, and covered a wide range of topics presented through 15 technical sessions …

The Discrimination Power Of Structural Superindices, Matthias Dehmer, Abbe Mowshowitz

Publications and Research

In this paper, we evaluate the discrimination power of structural superindices. Superindices for graphs represent measures composed of other structural indices. In particular, we compare the discrimination power of the superindices with those of individual graph descriptors. In addition, we perform a statistical analysis to generalize our findings to large graphs.

What Should Science Reference Librarians Do With Books Classified As Science That Aren't Science: Revisiting The Well-Known Worlds In Collision By Immanuel Velikovsky As A Case Study., Philip Barnett Ph.D.

Publications and Research

Students browsing the science sections in their library may naturally assume that all of the books are scientifically valid and accurate. Science collections may also contain books that may not now be accurate, either because they are out-of-date, or never belonged there. While out-of-date knowledge can sometimes be beneficial, invalid books can only mislead. The well-known book Worlds in Collision by Immanuel Velikovsky is a case study on how librarians can handle such books. For these books, an explanatory note can be placed on the book's online catalog entry or even in the book. The book can also be weeded …

Secondary Organic Aerosols Over Oceans Via Oxidation Of Isoprene And Monoterpenes From Arctic To Antarctic, Qi-Hou Hu, Zhou-Qing Xie, Xin-Ming Wang, Hui Kang, Quan-Fu He, Pengfei Zhang

Publications and Research

Isoprene and monoterpenes are important precursors of secondary organic aerosols (SOA) in continents. However, their contributions to aerosols over oceans are still inconclusive. Here we analyzed SOA tracers from isoprene and monoterpenes in aerosol samples collected over oceans during the Chinese Arctic and Antarctic Research Expeditions. Combined with literature reports elsewhere, we found that the dominant tracers are the oxidation products of isoprene. The concentrations of tracers varied considerably. The mean average values were approximately one order of magnitude higher in the Northern Hemisphere than in the Southern Hemisphere. High values were generally observed in coastal regions. This phenomenon was …

30 Days In The Life: Daily Nutrient Balancing In A Wild Chacma Baboon, Caley A. Johnson, David Raubenheimer, Jessica M. Rothman, David Clarke, Larissa Swedell

Publications and Research

For most animals, the ability to regulate intake of specific nutrients is vital to fitness. Recent studies have demonstrated nutrient regulation in nonhuman primates over periods of one observation day, though studies of humans indicate that such regulation extends to longer time frames. Little is known about longer-term regulation in nonhuman primates, however, due to the challenges of multiple-day focal follows. Here we present the first detailed study of nutrient intake across multiple days in a wild nonhuman primate. We conducted 30 consecutive all day follows on one female chacma baboon (Papio hamadryas ursinus) in the Cape Peninsula of South …

Tethered Domains And Flexible Regions In Trnase Zl, The Long Form Of Trnase Z, Christopher Wilson, Daryl Ramai, Dmitri Serjanov, Neema Lama, Louis Levinger, Emmanuel J. Chang

Publications and Research

tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site …

Technique And Considerations In The Use Of 4x1 Ring High-Definition Transcranial Direct Current Stimulation (Hd-Tdcs), Mauricio F. Villamar, Magdalena Sarah Volz, Marom Bikson, Abhishek Datta, Alexandre F. Dasilva, Felipe Fregni

Publications and Research

High-definition transcranial direct current stimulation (HD-tDCS) has recently been developed as a noninvasive brain stimulation approach that increases the accuracy of current delivery to the brain by using arrays of smaller "high-definition" electrodes, instead of the larger pad-electrodes of conventional tDCS. Targeting is achieved by energizing electrodes placed in predetermined configurations. One of these is the 4x1-ring configuration. In this approach, a center ring electrode (anode or cathode) overlying the target cortical region is surrounded by four return electrodes, which help circumscribe the area of stimulation. Delivery of 4x1-ring HD-tDCS is capable of inducing significant neurophysiological and clinical effects in …

Targeting The Endocannabinoid System For Neuroprotection: A 19f-Nmr Study Of A Selective Faah Inhibitor Binding With An Anandamide Carrier Protein, Hsa, Jianqin Zhuang, De-Ping Yang, Xiaoyu Tian, Spyros P. Nikas, Rishi Sharma, Jason Jianxin Guo, Alexandros Makriyannis

Publications and Research

Fatty acid amide hydrolase (FAAH), the enzyme involved in the inactivation of the endocannabinoid anandamide (AEA), is being considered as a therapeutic target for analgesia and neuroprotection. We have developed a brain permeable FAAH inhibitor, AM5206, which has served as a valuable pharmacological tool to explore neuroprotective effects of this class of compounds. In the present work, we characterized the interactions of AM5206 with a representative AEA carrier protein, human serum albumin (HSA), using 19F nuclear magnetic resonance (NMR) spectroscopy. Our data showed that as a drug carrier, albumin can significantly enhance the solubility of AM5206 in aqueous environment. Through …

Rapid Staining Method To Detect And Identify Downy Mildew (Peronospora Belbahrii) In Basil1, Adolfina R. Koroch, Thomas S. Villani, Robert M. Pyne, James E. Simon

Publications and Research

• Premise of the study: Demand for fresh-market sweet basil continues to increase, but in 2009 a new pathogen emerged, threatening commercial field/greenhouse production and leading to high crop losses. This study describes a simple and effective staining method for rapid microscopic detection of basil downy mildew (Peronospora belbahrii) from leaves of basil (Ocimum basilicum). • Methods and Results: Fresh leaf sections infected with P. belbahrii were placed on a microscope slide, cleared with Visikol™, and stained with iodine solution followed by one drop of 70% sulfuric acid. Cell walls of the pathogen were stained with a distinct coloration, providing …

An Integrative Framework For Bayesian Variable Selection With Informative Priors For Identifying Genes And Pathways, Bin Peng, Dianwen Zhu, Bradley P. Ander, Xiaoshuai Zhang, Fuzhong Xue, Frank R. Sharp, Xiaowei Yang

Publications and Research

The discovery of genetic or genomic markers plays a central role in the development of personalized medicine. A notable challenge exists when dealing with the high dimensionality of the data sets, as thousands of genes or millions of genetic variants are collected on a relatively small number of subjects. Traditional gene-wise selection methods using univariate analyses face difficulty to incorporate correlational, structural, or functional structures amongst the molecular measures. For microarray gene expression data, we first summarize solutions in dealing with ‘large p, small n’ problems, and then propose an integrative Bayesian variable selection (iBVS) framework for simultaneously identifying causal …

Evolution And Allometry Of Calcaneal Elongation In Living And Extinct Primates, Doug M. Boyer, Erik R. Seiffert, Justin T. Gladman, Jonathan I. Bloch

Publications and Research

Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by …

Neurophysiological Processing Of Emotion And Parenting Interact To Predict Inhibited Behavior: An Affective-Motivational Framework, Ellen M. Kessel, Rebecca F. Huselid, Jennifer M. Decicco, Tracy A. Dennis

Publications and Research

Although inhibited behavior problems are prevalent in childhood, relatively little is known about the intrinsic and extrinsic factors that predict a child's ability to regulate inhibited behavior during fear- and anxiety-provoking tasks. Inhibited behavior may be linked to both disruptions in avoidance-related processing of aversive stimuli and in approach-related processing of appetitive stimuli, but previous findings are contradictory and rarely integrate consideration of the socialization context. The current exploratory study used a novel combination of neurophysiological and observation-based methods to examine whether a neurophysiological measure sensitive to approach- and avoidance-oriented emotional processing, the late positive potential (LPP), interacted with observed …

The Association Between A Medical History Of Depression And Gestational Diabetes In A Large Multi-Ethnic Cohort In The United States, Katherine Bowers, S. Katherine Laughon, Sungduk Kim, Sunni L. Mumford, Jennifer Brite, Michele Kiely, Cuilin Zhang

Publications and Research

Background: Both major depression and gestational diabetes mellitus (GDM) are prevalent among women of reproductive age. Our objective was to determine whether a medical history of depression is related to subsequent development of GDM.

Methods: The Consortium on Safe Labor was a US retrospective cohort study of 228 562 births between 2002 and 2008. Exclusion criteria for the present analysis included multiple gestation pregnancies (n = 5059), pre-existing diabetes (n = 12 771), deliveries(n = 395), site GDM prevalence (

Results: The final analytic population included 121 260 women contributing 128 295 pregnancies, of which 5606 were affected by GDM. …

A Randomized Clinical Trial Of Trans-Dermal Nicotine Replacement In Pregnant African-American Smokers, Ayman El-Mohandes, Richard Windsor, Sylvia Tan, David C. Perry, Marie G. Gantz, Michele Kiely

Publications and Research

We compared acceptability, adherence and efficacy of trans-dermal nicotine patches and cognitive behavioral therapy (Group 1) to cognitive behavioral therapy alone (Group 2) in minority pregnant smokers. This is a randomized controlled trial. 52 women were recruited during pregnancy with a mean gestational age 18.5 ± 5.0 weeks and followed through delivery. Randomization was by site and initial cotinine levels. Interventionists and interviewers were blinded to group assignment. Two different nicotine replacement therapy dosing regiments were administered according to the baseline salivary cotinine level. A process evaluation model summarized patient adherence. The main outcome measure was self-report of cessation since …

Exploring Epigenetic Regulation Of Fear Memory And Biomarkers Associated With Post-Traumatic Stress Disorder, Stephanie A. Maddox, Glenn E. Schafe, Kerry J. Ressler

Publications and Research

This review examines recent work on epigenetic mechanisms underlying animal models of fear learning as well as its translational implications in disorders of fear regulation, such as Post-traumatic Stress Disorder (PTSD). Specifically, we will examine work outlining roles of differential histone acetylation and DNA-methylation associated with consolidation, reconsolidation, and extinction in Pavlovian fear paradigms. We then focus on the numerous studies examining the epigenetic modifications of the Brain-derived neurotrophin factor (BDNF) pathway and the extension of these findings from animal models to recent work in human clinical populations. We will also review recently published data on FKBP5 regulation of …

Moderate Alcohol Use And Cardiovascular Disease From Mendelian Randomization, Shiu Lun Au Yeung, Chaoqiang Jiang, Kar Keung Cheng, Benjamin J. Cowling, Bin Liu, Weisen Zhang, Tai Hing Lam, Gabriel M. Leung, Mary Schooling

Publications and Research

Background
Observational studies show moderate alcohol use negatively associated with ischemic heart disease (IHD) and cardiovascular disease (CVD). However, healthier attributes among moderate users compared to never users may confound the apparent association. A potentially less biased way to examine the association is Mendelian randomization, using alcohol metabolizing genes which influence alcohol use.

Methods
We used instrumental variable analysis with aldehyde dehydrogenase 2 (ALDH2) genotypes (AA/GA/GG) as instrumental variables for alcohol use to examine the association of alcohol use (10 g ethanol/day) with CVD risk factors (blood pressure, lipids and glucose) and morbidity (self-reported IHD and CVD) among men in …

Scientific Communication Before And After Networked Science, John Carey

Publications and Research

Recent decades have seen extensive changes in how researchers in the sciences work. Online platforms enabled by Web 2.0 technologies (collectively known as “open” or “networked” science) have created multiple new channels for informal communications, revolutionizing the ways in which scientists collaborate and share results. Meanwhile, digitization and open access publishing have brought fundamental change to modes of publication and distribution for scientific journals. Yet the primary vehicle for the formal publication of results, the scientific article, has been much slower to alter in format. This paper will examine the functions that peer-reviewed journals have served within the scientific community …

Environmental Protection Agency Consultations With Indian Tribes: An Intercultural Struggle Over Process Of 'Consent', Denise Scannell Guida

Publications and Research

On November 6, 2000, President Bill Clinton signed his final executive order on

Consultation and Coordination with Tribal Governments. It was his last attempt to establish meaningful consultation processes with American Indians in the development of federal environmental policies. Based on ongoing environmental issues between the two cultures and the rising concern for environmental justice, the United States government wanted to identify the necessary improvements in communication and coordination among tribal and federal environmental programs, specifically regarding issues of information exchange, and creating partnerships among stakeholders. An analysis of the executive order, and a case study of the U.S. …

Imdb Network Revisited: Unveiling Fractal And Modular Properties From A Typical Small-World Network, Lazaros K. Gallos, Fabricio Q. Potiguar, José S. Andrade, Hernan A. Makse

Publications and Research

We study a subset of the movie collaboration network, http://www.imdb.com, where only adult movies are included. We show that there are many benefits in using such a network, which can serve as a prototype for studying social interactions. We find that the strength of links, i.e., how many times two actors have collaborated with each other, is an important factor that can significantly influence the network topology. We see that when we link all actors in the same movie with each other, the network becomes small-world, lacking a proper modular structure. On the other hand, by imposing a threshold on …

Neuromolecular Imaging Shows Temporal Synchrony Patterns Between Serotonin And Movement Within Neuronal Motor Circuits In The Brain, Patricia A. Broderick

Publications and Research

The present discourse links the electrical and chemical properties of the brain with neurotransmitters and movement behaviors to further elucidate strategies to diagnose and treat brain disease. Neuromolecular imaging (NMI), based on electrochemical principles, is used to detect serotonin in nerve terminals (dorsal and ventral striata) and somatodendrites (ventral tegmentum) of reward/motor mesocorticolimbic and nigrostriatal brain circuits. Neuronal release of serotonin is detected at the same time and in the same animal, freely moving and unrestrained, while open-field behaviors are monitored via infrared photobeams. The purpose is to emphasize the unique ability of NMI and the BRODERICK PROBE® biosensors to …