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Author (up) Alcock, J.; Maley, C.C.; Aktipis, C.A. file  url
openurl 
  Title Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms Type Journal Article
  Year 2014 Publication BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology Abbreviated Journal Bioessays  
  Volume 36 Issue 10 Pages 940-949  
  Keywords Animals; *Biological Evolution; *Feeding Behavior; Gastrointestinal Tract/*microbiology; Humans; *Microbiota; Models, Biological; Obesity/etiology; Cravings; Evolutionary conflict; Host manipulation; Microbiome; Obesity  
  Abstract Microbes in the gastrointestinal tract are under selective pressure to manipulate host eating behavior to increase their fitness, sometimes at the expense of host fitness. Microbes may do this through two potential strategies: (i) generating cravings for foods that they specialize on or foods that suppress their competitors, or (ii) inducing dysphoria until we eat foods that enhance their fitness. We review several potential mechanisms for microbial control over eating behavior including microbial influence on reward and satiety pathways, production of toxins that alter mood, changes to receptors including taste receptors, and hijacking of the vagus nerve, the neural axis between the gut and the brain. We also review the evidence for alternative explanations for cravings and unhealthy eating behavior. Because microbiota are easily manipulatable by prebiotics, probiotics, antibiotics, fecal transplants, and dietary changes, altering our microbiota offers a tractable approach to otherwise intractable problems of obesity and unhealthy eating.  
  Call Number Serial 2002  
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Author (up) Amaku, M.; Coutinho, F.A.B.; Massad, E. file  url
openurl 
  Title Why dengue and yellow fever coexist in some areas of the world and not in others? Type Journal Article
  Year 2011 Publication Bio Systems Abbreviated Journal Biosystems  
  Volume 106 Issue 2-3 Pages 111-120  
  Keywords Adaptive Immunity/*immunology; Aedes/*virology; Africa/epidemiology; Animals; Asia/epidemiology; Computer Simulation; *Demography; Dengue/*epidemiology/immunology/transmission; Humans; Insect Vectors/*virology; *Models, Biological; South America/epidemiology; Species Specificity; Yellow Fever/*epidemiology/immunology/transmission  
  Abstract Urban yellow fever and dengue coexist in Africa but not in Asia and South America. In this paper, we examine four hypotheses (and various combinations thereof) to explain the absence of yellow fever in urban areas of Asia and South America. In addition, we examine an additional hypothesis that offers an explanation of the coexistence of the infections in Africa while at the same time explaining their lack of coexistence in Asia. The hypotheses we tested to explain the nonexistence of yellow fever in Asia are the following: (1) the Asian Aedes aegypti is relatively incompetent to transmit yellow fever; (2) there would exist a competition between dengue and yellow fever viruses within the mosquitoes, as suggested by in vitro studies in which the dengue virus always wins; (3) when an A. aegypti mosquito that is infected by or latent for yellow fever acquires dengue, it becomes latent for dengue due to internal competition within the mosquito between the two viruses; (4) there is an important cross-immunity between yellow fever and other flaviviruses, dengue in particular, such that a person recovered from a bout of dengue exhibits a diminished susceptibility to yellow fever. This latter hypothesis is referred to below as the “Asian hypothesis.” Finally, we hypothesize that: (5) the coexistence of the infections in Africa is due to the low prevalence of the mosquito Aedes albopictus in Africa, as it competes with A. aegypti. We will refer to this latter hypothesis as the “African hypothesis.” We construct a model of transmission that allows all of the above hypotheses to be tested. We conclude that the Asian and the African hypotheses can explain the observed phenomena, whereas other hypotheses fail to do so.  
  Call Number Serial 1532  
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Author (up) Anderson, J.L.; Albergotti, L.; Proulx, S.; Peden, C.; Huey, R.B.; Phillips, P.C. file  url
openurl 
  Title Thermal preference of Caenorhabditis elegans: a null model and empirical tests Type Journal Article
  Year 2007 Publication The Journal of Experimental Biology Abbreviated Journal J Exp Biol  
  Volume 210 Issue Pt 17 Pages 3107-3116  
  Keywords Acclimatization; Animals; Behavior, Animal; Body Temperature Regulation; Caenorhabditis elegans--physiology; Escherichia coli--growth & development; Models, Biological; Temperature  
  Abstract The preferred body temperature of ectotherms is typically inferred from the observed distribution of body temperatures in a laboratory thermal gradient. For very small organisms, however, that observed distribution might misrepresent true thermal preferences. Tiny ectotherms have limited thermal inertia, and so their body temperature and speed of movement will vary with their position along the gradient. In order to separate the direct effects of body temperature on movement from actual preference behaviour on a thermal gradient, we generate a null model (i.e. of non-thermoregulating individuals) of the spatial distribution of ectotherms on a thermal gradient and test the model using parameter values estimated from the movement of nematodes (Caenorhabditis elegans) at fixed temperatures and on a thermal gradient. We show that the standard lab strain N2, which is widely used in thermal gradient studies, avoids high temperature but otherwise does not exhibit a clear thermal preference, whereas the Hawaiian natural isolate CB4856 shows a clear preference for cool temperatures ( approximately 17 degrees C). These differences are not influenced substantially by changes in the starting position of worms in the gradient, the natal temperature of individuals or the presence and physiological state of bacterial food. These results demonstrate the value of an explicit null model of thermal effects and highlight problems in the standard model of C. elegans thermotaxis, showing the value of using natural isolates for tests of complex natural behaviours.  
  Call Number Serial 260  
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Author (up) Arimoto-Kobayashi, S.; Sakata, H.; Mitsu, K.; Tanoue, H. file  url
openurl 
  Title A possible photosensitizer: Tobacco-specific nitrosamine, 4-(N-methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), induced mutations, DNA strand breaks and oxidative and methylative damage with UVA Type Journal Article
  Year 2007 Publication Mutation Research Abbreviated Journal Mutat Res  
  Volume 632 Issue 1-2 Pages 111-120  
  Keywords Base Sequence; DNA Breaks; DNA Methylation--drug effects, radiation effects; Dose-Response Relationship, Drug; Models, Biological; Molecular Sequence Data; Mutation; Nitrosamines--toxicity; Oxidative Stress--drug effects, radiation effects; Photosensitizing Agents--toxicity; Salmonella typhimurium; Tobacco--chemistry; Ultraviolet Rays--adverse effects  
  Abstract We discovered the directly acting mutagenicity of the tobacco-specific nitrosamine, 4-(N-methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), with UVA light (320-400nm) in Ames bacteria and phage M13mp2 in the absence of metabolic activation. We have investigated the spectrum of mutations caused by UVA-activated NNK. The majority (57%) of induced sequence changes were comprised of GC to CG, GC to TA and GC to AT. This suggested that modification of guanine residues was responsible for these mutations. Hence, we explored the formation of 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxodG) and O(6)-methylguanine (O(6)meG) in the DNA. When calf thymus DNA was treated with NNK and UVA, the amount of 8-oxodG/dG and O(6)meG/G in the DNA increased up to 20-fold and 100-fold, respectively, compared with the untreated control. DNA strand breaks were observed following NNK and UVA treatment, and the strand breaks were suppressed in the presence of scavengers for oxygen and NO radical. The formation of NO was also observed in NNK solutions irradiated with UVA. We analyzed the photodynamic spectrum of mutation induction, 8-oxodG formation and NO formation using monochromatic radiation. The patterns of the action spectra were comparable to the absorption spectrum of NNK. We conclude that NNK may act as a photosensitizer in response to UVA to produce NO and other oxidative and alkylative intermediates following the formation of 8-oxodG and O(6)meG in DNA, which may lead to mutations and DNA strand breaks.  
  Call Number Serial 86  
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Author (up) Changeux, J.-P. file  url
openurl 
  Title The concept of allosteric interaction and its consequences for the chemistry of the brain Type Journal Article
  Year 2013 Publication The Journal of Biological Chemistry Abbreviated Journal J Biol Chem  
  Volume 288 Issue 38 Pages 26969-26986  
  Keywords Allosteric Regulation/physiology; Brain Chemistry/*physiology; History, 20th Century; History, 21st Century; Humans; *Models, Biological; *Molecular Dynamics Simulation; Nerve Tissue Proteins/*metabolism; Portraits as Topic; Prokaryotic Cells/physiology; Allosteric Regulation; Membrane Proteins; Neurons; Nicotinic Acetylcholine Receptors; Synaptic Plasticity  
  Abstract Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions.  
  Call Number Serial 1878  
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Author (up) Changeux, J.-P. file  url
openurl 
  Title The concept of allosteric interaction and its consequences for the chemistry of the brain Type Journal Article
  Year 2013 Publication The Journal of Biological Chemistry Abbreviated Journal J Biol Chem  
  Volume 288 Issue 38 Pages 26969-26986  
  Keywords Allosteric Regulation/physiology; Brain Chemistry/*physiology; History, 20th Century; History, 21st Century; Humans; *Models, Biological; *Molecular Dynamics Simulation; Nerve Tissue Proteins/*metabolism; Portraits as Topic; Prokaryotic Cells/physiology; Allosteric Regulation; Membrane Proteins; Neurons; Nicotinic Acetylcholine Receptors; Synaptic Plasticity  
  Abstract Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions.  
  Call Number Serial 1888  
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Author (up) Farley, C.T.; Gonzalez, O. file  url
openurl 
  Title Leg stiffness and stride frequency in human running Type Journal Article
  Year 1996 Publication Journal of Biomechanics Abbreviated Journal J Biomech  
  Volume 29 Issue 2 Pages 181-186  
  Keywords Adaptation, Physiological; Adult; Biomechanical Phenomena; Elasticity; Gait/*physiology; Humans; Leg/*physiology; Ligaments/physiology; Male; Models, Biological; Muscle, Skeletal/physiology; Running/*physiology; Stress, Mechanical; Tendons/physiology; Weight-Bearing  
  Abstract When humans and other mammals run, the body's complex system of muscle, tendon and ligament springs behaves like a single linear spring ('leg spring'). A simple spring-mass model, consisting of a single linear leg spring and a mass equivalent to the animal's mass, has been shown to describe the mechanics of running remarkably well. Force platform measurements from running animals, including humans, have shown that the stiffness of the leg spring remains nearly the same at all speeds and that the spring-mass system is adjusted for higher speeds by increasing the angle swept by the leg spring. The goal of the present study is to determine the relative importance of changes to the leg spring stiffness and the angle swept by the leg spring when humans alter their stride frequency at a given running speed. Human subjects ran on treadmill-mounted force platform at 2.5ms-1 while using a range of stride frequencies from 26% below to 36% above the preferred stride frequency. Force platform measurements revealed that the stiffness of the leg spring increased by 2.3-fold from 7.0 to 16.3 kNm-1 between the lowest and highest stride frequencies. The angle swept by the leg spring decreased at higher stride frequencies, partially offsetting the effect of the increased leg spring stiffness on the mechanical behavior of the spring-mass system. We conclude that the most important adjustment to the body's spring system to accommodate higher stride frequencies is that leg spring becomes stiffer.  
  Call Number Serial 148  
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Author (up) Frols, S.; White, M.F.; Schleper, C. file  url
openurl 
  Title Reactions to UV damage in the model archaeon Sulfolobus solfataricus Type Journal Article
  Year 2009 Publication Biochemical Society Transactions Abbreviated Journal Biochem Soc Trans  
  Volume 37 Issue Pt 1 Pages 36-41  
  Keywords DNA Damage; DNA Repair--genetics; Gene Expression Profiling; Models, Biological; Sulfolobus solfataricus--cytology, genetics, radiation effects; Ultraviolet Rays  
  Abstract Mechanisms involved in DNA repair and genome maintenance are essential for all organisms on Earth and have been studied intensively in bacteria and eukaryotes. Their analysis in extremely thermophilic archaea offers the opportunity to discover strategies for maintaining genome integrity of the relatively little explored third domain of life, thereby shedding light on the diversity and evolution of these central and important systems. These studies might also reveal special adaptations that are essential for life at high temperature. A number of investigations of the hyperthermophilic and acidophilic crenarchaeote Sulfolobus solfataricus have been performed in recent years. Mostly, the reactions to DNA damage caused by UV light have been analysed. Whole-genome transcriptomics have demonstrated that a UV-specific response in S. solfataricus does not involve the transcriptional induction of DNA-repair genes and it is therefore different from the well-known SOS response in bacteria. Nevertheless, the UV response in S. solfataricus is impressively complex and involves many different levels of action, some of which have been elucidated and shed light on novel strategies for DNA repair, while others involve proteins of unknown function whose actions in the cell remain to be elucidated. The present review summarizes and discusses recent investigations on the UV response of S. solfataricus on both the molecular biological and the cellular levels.  
  Call Number Serial 15  
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Author (up) Gajer, P.; Brotman, R.M.; Bai, G.; Sakamoto, J.; Schutte, U.M.E.; Zhong, X.; Koenig, S.S.K.; Fu, L.; Ma, Z.S.; Zhou, X.; Abdo, Z.; Forney, L.J.; Ravel, J. file  url
openurl 
  Title Temporal dynamics of the human vaginal microbiota Type Journal Article
  Year 2012 Publication Science Translational Medicine Abbreviated Journal Sci Transl Med  
  Volume 4 Issue 132 Pages 132ra52  
  Keywords Bacteria/classification/genetics; Female; Humans; Magnetic Resonance Spectroscopy; Metabolome; Metabolomics; Metagenome/genetics/*physiology; Models, Biological; Phylogeny; Time Factors; Vagina/*microbiology; Microbiome  
  Abstract Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk of diseases that affect women's health. Here, we describe the temporal dynamics of the composition of vaginal bacterial communities in 32 reproductive-age women over a 16-week period. The analysis revealed the dynamics of five major classes of bacterial communities and showed that some communities change markedly over short time periods, whereas others are relatively stable. Modeling community stability using new quantitative measures indicates that deviation from stability correlates with time in the menstrual cycle, bacterial community composition, and sexual activity. The women studied are healthy; thus, it appears that neither variation in community composition per se nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis.  
  Call Number Serial 2175  
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Author (up) Gray, R.D.; Atkinson, Q.D. file  url
doi  openurl
  Title Language-tree divergence times support the Anatolian theory of Indo-European origin Type Journal Article
  Year 2003 Publication Nature Abbreviated Journal Nature  
  Volume 426 Issue 6965 Pages 435-439  
  Keywords Agriculture/history; Algorithms; Archaeology/methods; Bayes Theorem; *Emigration and Immigration; Europe/ethnology; History, Ancient; Humans; India/ethnology; *Language; Linguistics; Markov Chains; Middle East/ethnology; Models, Biological; Monte Carlo Method; *Phylogeny; Time Factors  
  Abstract Languages, like genes, provide vital clues about human history. The origin of the Indo-European language family is “the most intensively studied, yet still most recalcitrant, problem of historical linguistics”. Numerous genetic studies of Indo-European origins have also produced inconclusive results. Here we analyse linguistic data using computational methods derived from evolutionary biology. We test two theories of Indo-European origin: the 'Kurgan expansion' and the 'Anatolian farming' hypotheses. The Kurgan theory centres on possible archaeological evidence for an expansion into Europe and the Near East by Kurgan horsemen beginning in the sixth millennium BP. In contrast, the Anatolian theory claims that Indo-European languages expanded with the spread of agriculture from Anatolia around 8,000-9,500 years bp. In striking agreement with the Anatolian hypothesis, our analysis of a matrix of 87 languages with 2,449 lexical items produced an estimated age range for the initial Indo-European divergence of between 7,800 and 9,800 years bp. These results were robust to changes in coding procedures, calibration points, rooting of the trees and priors in the bayesian analysis.  
  Call Number Serial 500  
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