DOCSLIB.ORG

Profile of Jay C. Dunlap

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Profile of Jay C. Dunlap PROFILE PROFILE Profile of Jay C. Dunlap Paul Gabrielsen Science Writer On moonless nights, the wakes of oceangoing back to oceanography,” Dunlap says, “but I boats sparkle with the blue bioluminescence just thought clocks were the greatest things of unicellular dinoflagellates. As a graduate I’deverheardabout.” He chose to attend student at Harvard University, Jay C. Dunlap Harvard. pondered the carefully orchestrated biological Dunlap found Hastings’ approach to his rhythms that direct dinoflagellates to produce students’ research to be supportive but hands light only at night. Dunlap, a student of off. “He provided all these resources,” Dunlap oceanography at the time, realized that the says, “but he never told people what to do. He field of biological rhythms was still a wide- would give you great feedback on what you open frontier, with many fundamental ques- were doing, but you needed to find your own tions yet to be answered. “This was a place,” way. And if you were lucky enough to do that, he says, “where I could make a mark.” then you really learned how to do science.” Dunlap, Nathan Smith Professor and Chair In 1977, Dunlap attended a 10-week of Genetics at Dartmouth’s Geisel School of summer course on biological rhythms at Medicine and a member of the National Hopkins Marine Station in Pacific Grove, Academy of Sciences since 2009, has devoted California organized by Colin Pittendrigh, his career to answering those fundamental who, along with Hastings, had made pio- questions. His work has uncovered how cir- neering advances in the field of rhythms. The cadian rhythms work at a genetic level, how course attracted scientists studying rhythms environmental cues, such as light, can set bi- along with their graduate students, who, ological clocks, and how the clock can regu- Dunlap says, composed an entire generation Jay C. Dunlap in the 1990s with strains of late key cellular mechanisms. of rhythms biologists. Pittendrigh himself Neurospora and race tubes for visualizing circadian rhythm in development. Photo cour- Oceanography and Biochemistry taught extensively and brought in other sci- “ tesy of Joseph Mehling (Dartmouth College, Dunlap grew up in York, Pennsylvania as the entists to share what they had learned. It was an incredible smorgasbord of everything Hanover, NH). third of four children. He became an Eagle ” Scoutandwaschosenasoneofadozen that was going on in the field of rhythms, Dunlap says, “and an introduction to every- for Scouting’sNationalExplorationAward, insensitive to ambient temperature or nutri- body who was doing it.” which required applicants to write essays tion. “By sticking to a restricted definition,” Pittendrigh, Hastings, and other chrono- about their career goals. Dunlap had explored says Dunlap, “much of the biological noise biologists had made great strides in rhythms biochemistry at a summer program for high that came from loosely considering non- research beginning in the 1950s but had also school students at Ohio University and imag- circadian developmental or metabolic cycles “ run up against roadblocks. First, although ined a goal of studying biochemical ocean- fell away. With a defined phenotype you can ” therewereempiricalgeneralizationsabout ography. Earning the award, he says, do genetics” (2). circadian rhythms as biological cycles with solidified his interest in oceanography and Second, the research was hampered by a aperiodofaboutaday(1),thefieldlacked led him to attend the University of Wash- lack of molecular biological tools. As Dunlap a rigorous means to exclude extraneous ington beginning in 1970. began his postdoctoral fellowship with Jerry ’ rhythmic but noncircadian processes. “With After earning bachelors degrees in ocean- Feldman at the University of California, that loose definition, you end up pulling in ography and chemistry in 1974, Dunlap was Santa Cruz in 1979, he began laying the all sorts of biology that has no common admitted to two prominent oceanography groundwork for pushing through this molecular basis,” Dunlap says. graduate schools: Scripps Institution for roadblock. Oceanography and Woods Hole Oceano- “The most important thing to my mind,” graphic Institution. On the suggestion of a Dunlap says, “was restricting the phenotype Building and Winding a Clock friend, Dunlap also interviewed at Harvard to what we now consider in the strict sense a Dunlap aimed at elucidating the genetic and met J. Woodland “Woody” Hastings, circadian rhythm. This effort by Hastings, and molecular mechanism of the clock and whose research on bioluminescence in sin- Pittendrigh, and others made my work pos- the circadian system. A handful of circadian ” gle-celled dinoflagellates had led to an inves- sible. A circadian rhythm, as it has come to clock-related mutant gene loci had been tigation of the circadian clock elements of be defined, has a period around 24 hours previously identified in Chlamydomonas the dinoflagellates’ light show. Dunlap was under constant conditions. The timing of fascinated. “My rationalization was that I peaks and troughs in the cycle can be moved This is a Profile of a recently elected member of the National could study a marine organism and learn by exposure to real-world time cues, like light Academy of Sciences to accompany the member’s Inaugural biochemistry and physiology, and then go and temperature, but the period is relatively Article on page 16995 in issue 48 of volume 111. www.pnas.org/cgi/doi/10.1073/pnas.1514590112 PNAS Early Edition | 1of3 Downloaded by guest on September 29, 2021 chromosome walk through the Neurospora the genes involved would be organism- genome, examining short DNA sequences specific, they put forth that the organizing and reintroducing them into Neurospora to principles of clock–gene output regulation identify the sequence that altered the fungus’ would be similar in all eukaryotes. circadian behavior. Meanwhile, Loros, work- ing at Dartmouth as a postdoctoral fellow, Clock-Controlled Genes began the first screens for clock-controlled For the Inaugural Article by Dunlap and genes or ccgs, which have products that are coworkers (12), he and his colleagues col- involved in circadian output rather than laborated with the US Department of Energy the core circadian mechanism. The frq gene to perform high-throughput RNA sequenc- was cloned in 1986, and the first ccgs were ing on Neurospora cells over the course of found in 1987, with both results published two days under constant conditions. The in 1989 (4, 5). The cloning of frq was results, he says, indicate multiple overlapping featured on the cover of Nature,thefirst levels of regulation for fine-tuning clock- of seven journal covers featuring the regulated gene expression. “There are genes work by Dunlap and Loros. These genes whose expression is active at one time of day provided the molecular entrée into the but whose RNA products peak much later,” circadian system. he says. “There are genes whose expression is Dunlap notes that the logic underlying cyclical, but whose gene product is steadily circadian clocks in fungi and animals is quite present, and genes that are expressed con- ” Jay C. Dunlap and Jennifer Loros in 2009 similar. Both are driven by a feedback loop, stantly, but whose products are rhythmic. Up to 40% of Neurospora’s genes may be with the genetic and physical map of Neu- in which two proteins constitute a hetero- dimericgeneswitchthatdrivesexpressionof controlled by the circadian clock, he found. rospora. Photo courtesy of Jon Gilbert Fox one or more genes, and those gene products, Daytime-transcribed genes were typically re- (photographer). in turn, act as negative elements to depress lated to metabolism, whereas nighttime genes the activity of the transcription factor (6). were involved in cell growth. The result, he says, is cyclical expression of green algae, fruit flies, and Neurospora crassa, Championing Neurospora the filamentous fungus used by the renowned frq, detectable by levels of the prototypic Dunlap and Loros have remained at Dart- geneticists Beadle and Tatum (3) to develop protein FRQ. After the elements of the mouth’s Geisel School of Medicine while their 1941 “one gene-one enzyme” hypothesis feedback loop began to fall into place, Dunlap andLoroscouldaskhowreal-worldtime raising their two children and mentoring of genetic function (3). At the time, only one more than 40 students and postdoctorate of the three organisms, Neurospora, could be cues, like light, can reset the clock. They found that exposure to light promoted the students, nearly two-thirds of whom have genetically transformed. Therefore, Dunlap “ ’ expression of frq.Furthermore,exposureto entered academia. It snowonderwefound began his study of the fungus that continues ” “ light at different points of the feedback loop out so much, he says, given such terrific today. “It’sawonderfulorganism,” he says, ” could shift the phase of the circadian cycle. people to work with. Dunlap also serves with well-defined genetic tools that make the ’ For example, early light exposure while frq as the first chair of the school s Genetics genome of Neurospora relatively simple to levels were increasing could bring frq mRNA Department, which was organized in the manipulate. However, Dunlap says, “It’sbi- levels to their peak immediately instead of late-1990s. ologically complex enough to be interesting.” at a later time, thereby advancing clock In the mid-1990s, Dunlap and Loros began During his postdoctoral fellowship, Dun- phase. Similarly, late exposure to light could work on a textbook with the goal of codifying lap learned basic molecular techniques and restimulate frq mRNA production and effect the field of rhythms biology, and the final worked closely with biology graduate stu- a phase delay. The result had broad signifi- effort drew significant help from chronobi- dents, including Jennifer Loros. Loros and cance, because clocks in both Neurospora and ology pioneer Patricia DeCoursey. Published Dunlap later forged a permanent partnership, mammals are reset through light induction in 2004 as Chronobiology: Biological Time- marrying in 1984. Loros has since established of negative elements.
Load more

Recommended publications
  • Casein Kinase 1 Isoforms in Degenerative Disorders
    CASEIN KINASE 1 ISOFORMS IN DEGENERATIVE DISORDERS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Theresa Joseph Kannanayakal, M.Sc., M.S. * * * * * The Ohio State University 2004 Dissertation Committee: Approved by Professor Jeff A. Kuret, Adviser Professor John D. Oberdick Professor Dale D. Vandre Adviser Professor Mike X. Zhu Biophysics Graduate Program ABSTRACT Casein Kinase 1 (CK1) enzyme is one of the largest family of Serine/Threonine protein kinases. CK1 has a wide distribution spanning many eukaryotic families. In cells, its kinase activity has been found in various sub-cellular compartments enabling it to phosphorylate many proteins involved in cellular maintenance and disease pathogenesis. Tau is one such substrate whose hyperphosphorylation results in degeneration of neurons in Alzheimer’s disease (AD). AD is a slow neuroprogessive disorder histopathologically characterized by Granulovacuolar degeneration bodies (GVBs) and intraneuronal accumulation of tau in Neurofibrillary Tangles (NFTs). The level of CK1 isoforms, CK1α, CK1δ and CK1ε has been shown to be elevated in AD. Previous studies of the correlation of CK1δ with lesions had demonstrated its importance in tau hyperphosphorylation. Hence we investigated distribution of CK1α and CK1ε with the lesions to understand if they would play role in tau hyperphosphorylation similar to CK1δ. The kinase results were also compared with lesion correlation studies of peptidyl cis/trans prolyl isomerase (Pin1) and caspase-3. Our results showed that among the enzymes investigated, CK1 isoforms have the greatest extent of colocalization with the lesions. We have also investigated the distribution of CK1α with different stages of NFTs that follow AD progression.
    [Show full text]
  • 406 | Tutto Arabi - Veterinary Biorhythm
    406 | TUTTO ARABI - www.tuttoarabi.com VETERINARY BIORHYTHM by Domenico Bergero, Cynthia Préfontaine Rhythm! • infradian rhythms, which are long-term cycles, such as the To horses, as for men, the passing of time has an impact on annual migration or reproduction cycles found in certain many conscious or automatic activities. When it comes to animals or the human menstrual cycle. men, in particular athletes, we talk about “biorhythm”, i.e. the • ultradian rhythms, which are short cycles, such as the 90-minute effect that longer or shorter cycles can have on performance. REM cycle, the 4-hour nasal cycle, or the 3-hour cycle of But what about our adventure buddy? growth hormone production. They have periods of less than 24 hours. Chronobiology • tidal rhythms, commonly observed in marine life, which follow Chronobiology, from the Greek “chronos” (time) and the (roughly) 12-hour transition from high to low tide “biologia” (study of life), is a field of science that examines and back. periodic (cyclic) phenomena in living organisms and their adaptation to solar and lunar related rhythms. Hormones and physical performance Chronobiological studies include but are not limited to As everyone knows, physical performance is, among other comparative anatomy, physiology, genetics, molecular things, under the control of hormones that determine higher biology and behavior of organisms within biological rhythms or lesser fitness. These hormones can be produced continually mechanics. or, more often than not, can be mero present at certain The variations of the timing and duration of biological times (peak or acrophase) and then decrease. Let’s see which activity in living organisms occur for many essential hormones are involved and what are the best moments for biological processes.
    [Show full text]
  • CKI and CKII Mediate the FREQUENCY-Dependent Phosphorylation of the WHITE COLLAR Complex to Close the Neurospora Circadian Negative Feedback Loop
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop Qun He,1,2 Joonseok Cha,1 Qiyang He,1,3 Heng-Chi Lee,1 Yuhong Yang,1,4 and Yi Liu1,5 1Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 2State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100094, China The eukaryotic circadian oscillators consist of circadian negative feedback loops. In Neurospora,itwas proposed that the FREQUENCY (FRQ) protein promotes the phosphorylation of the WHITE COLLAR (WC) complex, thus inhibiting its activity. The kinase(s) involved in this process is not known. In this study, we show that the disruption of the interaction between FRQ and CK-1a (a casein kinase I homolog) results in the hypophosphorylation of FRQ, WC-1, and WC-2. In the ck-1aL strain, a knock-in mutant that carries a mutation equivalent to that of the Drosophila dbtL mutation, FRQ, WC-1, and WC-2 are hypophosphorylated. The mutant also exhibits ∼32 h circadian rhythms due to the increase of FRQ stability and the significant delay of FRQ progressive phosphorylation. In addition, the levels of WC-1 and WC-2 are low in the ck-1aL strain, indicating that CK-1a is also important for the circadian positive feedback loops. In spite of its low accumulation in the ck-1aL strain, the hypophosphorylated WCC efficiently binds to the C-box within the frq promoter, presumably because it cannot be inactivated through FRQ-mediated phosphorylation.
    [Show full text]
  • Profile of Jay C. Dunlap
    PROFILE PROFILE Profile of Jay C. Dunlap Paul Gabrielsen Science Writer On moonless nights, the wakes of oceangoing back to oceanography,” Dunlap says, “but I boats sparkle with the blue bioluminescence just thought clocks were the greatest things of unicellular dinoflagellates. As a graduate I’deverheardabout.” He chose to attend student at Harvard University, Jay C. Dunlap Harvard. pondered the carefully orchestrated biological Dunlap found Hastings’ approach to his rhythms that direct dinoflagellates to produce students’ research to be supportive but hands light only at night. Dunlap, a student of off. “He provided all these resources,” Dunlap oceanography at the time, realized that the says, “but he never told people what to do. He field of biological rhythms was still a wide- would give you great feedback on what you open frontier, with many fundamental ques- were doing, but you needed to find your own tions yet to be answered. “This was a place,” way. And if you were lucky enough to do that, he says, “where I could make a mark.” then you really learned how to do science.” Dunlap, Nathan Smith Professor and Chair In 1977, Dunlap attended a 10-week of Genetics at Dartmouth’s Geisel School of summer course on biological rhythms at Medicine and a member of the National Hopkins Marine Station in Pacific Grove, Academy of Sciences since 2009, has devoted California organized by Colin Pittendrigh, his career to answering those fundamental who, along with Hastings, had made pio- questions. His work has uncovered how cir- neering advances in the field of rhythms. The cadian rhythms work at a genetic level, how course attracted scientists studying rhythms environmental cues, such as light, can set bi- along with their graduate students, who, ological clocks, and how the clock can regu- Dunlap says, composed an entire generation Jay C.
    [Show full text]
  • Crystal Structure of the Avirulence Gene Avrlm4-7 of Leptosphaeria Maculans. Illuminates Its Evolutionary and Functional Charact
    Crystal structure of the Avirulence Gene AvrLm4-7 of Leptosphaeria maculans. Illuminates its evolutionary and functional characteristics Isabelle Fudal, Francoise Blaise, K Blondeau, M. Graille, A. Labarde, A. Doisy, Bm Tyler, S.D. Kale, Guillaume Daverdin, Marie-Helene Balesdent, et al. To cite this version: Isabelle Fudal, Francoise Blaise, K Blondeau, M. Graille, A. Labarde, et al.. Crystal structure of the Avirulence Gene AvrLm4-7 of Leptosphaeria maculans. Illuminates its evolutionary and functional characteristics. 26. Fungal Genetics Conference at Asilomar, Mar 2011, Asilomar, United States. pp.234. hal-01000740 HAL Id: hal-01000740 https://hal.archives-ouvertes.fr/hal-01000740 Submitted on 6 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 26th Fungal Genetics Conference at Asilomar March 15-20 2011 Principle Financial Sponsors Genetics Society of America Burroughs Wellcome Fund US National Institutes of Health Novozymes Great Lakes Bioenergy Research Center Konkuk University Bio Molecular Informatics Center Genencor, A Danisco Division
    [Show full text]
  • Abstracts from the Neurospora 2002 Conference
    Fungal Genetics Reports Volume 49 Article 13 Abstracts from the Neurospora 2002 conference Neurospora 2002 conference Follow this and additional works at: https://newprairiepress.org/fgr This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. Recommended Citation Neurospora 2002 conference. (2002) "Abstracts from the Neurospora 2002 conference," Fungal Genetics Reports: Vol. 49, Article 13. https://doi.org/10.4148/1941-4765.1195 This Supplementary Material is brought to you for free and open access by New Prairie Press. It has been accepted for inclusion in Fungal Genetics Reports by an authorized administrator of New Prairie Press. For more information, please contact [email protected]. Abstracts from the Neurospora 2002 conference Abstract Abstracts and Poster abstracts from the Neurospora 2002 conference This supplementary material is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol49/iss1/13 : Abstracts from the Neurospora 2002 conference Neurospora 2002 Schedule March 14-17, 2002 Invited Abstracts Asilomar Conference Center Pacific Grove, CA. Poster Abstracts SCIENTIFIC PROGRAM Index Barry Bowman Gloria Turner Schedule of Activities Thursday, March 14 3:00 - 6:00 pm, Registration: Administration 6:00 - 7:00 pm, Dinner: Crocker 7:00 - 10:00 pm, Mixer: Kiln Friday, March 15 7:30 - 8:30 am, Breakfast, Crocker 8:30 - 12:00 Noon, Session I, Chapel Genomic Analysis : Mary Anne Nelson, Chair 8:35 - Bruce Birren, MIT, Whitehead Institute. "Genome sequencing for Neurospora crassa." 9:05 - Gertrud Mannhaupt, Heinrich-Heine-University. "The MIPS Neurospora crassa database- MNCDB." 9:30 - Chuck Staben, U. of Kentucky. "Gene finding and annotation for fungal genomes." 9:55 - Alan Radford, University of Leeds.
    [Show full text]
  • Latitudinal Cline of Chronotype
    www.nature.com/scientificreports OPEN Latitudinal cline of chronotype Mario André Leocadio-Miguel 1, Fernando Mazzili Louzada2, Leandro Lourenção Duarte3, Roberta Peixoto Areas4, Marilene Alam5, Marcelo Ventura Freire4, John Fontenele-Araujo1, Luiz Menna-Barreto4 & Mario Pedrazzoli4 The rotation of the Earth around its own axis and around the sun determines the characteristics of Received: 15 February 2017 the light/dark cycle, the most stable and ancient 24 h temporal cue for all organisms. Due to the tilt in the earth’s axis in relation to the plane of the earth’s orbit around the sun, sunlight reaches the Earth Accepted: 2 June 2017 differentially depending on the latitude. The timing of circadian rhythms varies among individuals of Published: xx xx xxxx a given population and biological and environmental factors underlie this variability. In the present study, we tested the hypothesis that latitude is associated to the regulation of circadian rhythm in humans. We have studied chronotype profiles across latitudinal cline from around 0° to 32° South in Brazil in a sample of 12,884 volunteers living in the same time zone. The analysis of the results revealed that humans are sensitive to the different sunlight signals tied to differences in latitude, resulting in a morning to evening latitudinal cline of chronotypes towards higher latitudes. The concept of chronotype, which is the expression of diurnal preferences or circadian phenotype, including rise and bedtime preferences, has received a strong consideration from studies in human chronobiology1. It is generally accepted that the chronotype distribution in populations is the same, no matter where the population is geographically localized.
    [Show full text]
  • Robust Normalization of Luciferase Reporter Data
    Technical Note Robust Normalization of Luciferase Reporter Data Andrea Repele † and Manu * Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA * Correspondence: [email protected] † Current address: JMB—Center for Immunity and Immunotherapies, Seattle Children’s Hospital, Seattle, WA 98105, USA. Received: 17 June 2019; Accepted: 22 July 2019; Published: 25 July 2019 Abstract: Transient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub. Keywords: luciferase reporter; transfection efficiency; normalization; gene regulation; promoter; enhancer 1. Introduction Transient reporter assays are an important and widely used tool in the study of gene regulation [1–4], intracellular cell signaling [5–7], and other areas of molecular, cellular, and developmental biology [8–10].
    [Show full text]
  • Pressure Accelerates the Circadian Clock of Cyanobacteria
    www.nature.com/scientificreports OPEN Pressure accelerates the circadian clock of cyanobacteria Ryo Kitahara 1,2, Katsuaki Oyama2, Takahiro Kawamura2, Keita Mitsuhashi2, Soichiro Kitazawa1, Kazuhiro Yasunaga1, Natsuno Sagara1, Megumi Fujimoto2 & Kazuki Terauchi2,3 Received: 12 April 2019 Although organisms are exposed to various pressure and temperature conditions, information remains Accepted: 7 August 2019 limited on how pressure afects biological rhythms. This study investigated how hydrostatic pressure Published: xx xx xxxx afects the circadian clock (KaiA, KaiB, and KaiC) of cyanobacteria. While the circadian rhythm is inherently robust to temperature change, KaiC phosphorylation cycles that were accelerated from 22 h at 1 bar to 14 h at 200 bars caused the circadian-period length to decline. This decline was caused by the pressure-induced enhancement of KaiC ATPase activity and allosteric efects. Because ATPase activity was elevated in the CI and CII domains of KaiC, while ATP hydrolysis had negative activation volumes (ΔV≠), both domains played key roles in determining the period length of the KaiC phosphorylation cycle. The thermodynamic contraction of the structure of the active site during the transition state might have positioned catalytic residues and lytic water molecules favourably to facilitate ATP hydrolysis. Internal cavities might represent sources of compaction and structural rearrangement in the active site. Overall, the data indicate that pressure diferences could alter the circadian rhythms of diverse organisms with evolved thermotolerance, as long as enzymatic reactions defning period length have a specifc activation volume. Circadian rhythms are endogenous timing systems that induce the circadian clock, resulting in numerous organisms, from cyanobacteria to higher animals, being adapted to the day-night cycle1,2.
    [Show full text]
  • Analysis of Codon Usage Patterns in Giardia Duodenalis Based on Transcriptome Data from Giardiadb
    G C A T T A C G G C A T genes Article Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB Xin Li, Xiaocen Wang, Pengtao Gong, Nan Zhang, Xichen Zhang and Jianhua Li * Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China; [email protected] (X.L.); [email protected] (X.W.); [email protected] (P.G.); [email protected] (N.Z.); [email protected] (X.Z.) * Correspondence: [email protected]; Tel.: +86-431-8783-6172; Fax: +86-431-8798-1351 Abstract: Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite- induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duo- denalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G.
    [Show full text]
  • Circadian Rhythms Controlling the Timing of Behaviour by Anticipating the Environment
    Circadian Rhythms Controlling the timing of behaviour by anticipating the environment • Circadian = circa + dium • Exists in most if not all unicellular and multicellular organisms The Circadian Circuit Environmental Output Inputs Rhythms Light Hormonal Cycles Temperature Rest/Wake Social Activity Feeding Central Pacemaker Health consequences of circadian misalignment Social Jet Lag Shift Work Increased risk of: - Obesity - Diabetes - Cancer - Mental Illness Light at Night Roenneberg et al. (2012) Current Biology Historical Perspective Jean-Jacques d’Ortous de Mairan (1678 – 1771) Hist de l’Acad Royal Sci (Paris), 1729 “…Il est seulement un peu moins marqué lorsqu’on la tient toujours enfermée dans un lieu obscur…” “The sensitive plant hence perceives the sun without seeing it” Rhythms in leaf-opening persist even in the absence of sunlight Historical Perspective Rat Comp Psychol Monographs, 1922 Nathaniel Kleitman (1895 – 1999) Figure 18.4 Sleep and Wakefulness, 1963 Historical Perspective ’Founders of Chronobiology’ 1960 • Conceptual framework of circadian rhythms • Long before any genes or neural circuits were identified Colin Pittendrigh Jürgen Aschoff (1918 – 1996) (1913 – 1998) Cold Spring Harbor Symposium on Quantitative Biology, Vol. XXV Biological Clocks The Circadian Circuit Environmental Output Inputs Rhythms Light Hormonal Cycles Temperature Rest/Wake Social Activity Feeding Central Pacemaker What would a circadian pacemaker look like? The Circadian Circuit Environmental Output Inputs Rhythms Light Hormonal Cycles Temperature
    [Show full text]
  • Neurospora 2018 OCTOBER 18-21 ASILOMAR CONFERENCE CENTER
    PROGRAM and ABSTRACTS Neurospora 2018 OCTOBER 18-21 ASILOMAR CONFERENCE CENTER PACIFIC GROVE CALIFORNIA Cover design by Stephanie Herzog, Technische Universität Braunschweig Neurospora 2018 October 18-21 Asilomar Conference Center Pacific Grove California Scientific Organizers André Fleißner Thomas M. Hammond Technische Universität Braunschweig Illinois State University Neurospora Policy Committee Barry Bowman Jason E. Stajich Molecular Cell & Developmental Biology Dept. Plant Pathology & Microbiology University of California - Santa Cruz University of California - Riverside André Fleißner Thomas M. Hammond Institut für Genetik School of Biological Sciences Technische Universität Braunschweig Illinois State University Brief Schedule Morning Afternoon Evening Thursday Arrival Dinner October 18 Registration Mixer (Heather) Breakfast Lunch Friday Plenary Session I Plenary Session II Dinner October 19 Cell Biology and Metabolism, Signaling and Poster Session Morphogenesis Development Breakfast Lunch Banquet Saturday Plenary Session III Plenary Session IV Speaker October 20 Gene Expression and Genomics, Evolution, and Poster Session Epigenetics Tools Breakfast Sunday Plenary Session V Lunch October 21 Circadian Clocks and Departure Environmental Sensing All Plenary Sessions will be held in Heather. Posters will be displayed in Heather and Toyon throughout the meeting. They should be set up Friday and displayed until the end of the poster session/reception on Saturday evening. Schedule of Activities Thursday, October 18 15:00 - 18:00 p.m. Registration:
    [Show full text]