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Optimization of culture and analysis methods for enhancing long-term Brugia malayi survival, molting and motility in vitro

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Parasitology Open 2018年 4卷 e3-e3页

作者： I. M. Lu T. Kassis A. M. Rogers A. Schudel J. Weil C. C. Evans A. R. Moorhead S. N. Thomas J. B. Dixon Parker H. Petit Institute for Bioengineering & Bioscience Georgia Institute of Technology Atlanta GA 30332 USA George W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta GA 30332 USA School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA 30332 USA School of Materials Science and Engineering Georgia Institute of Technology Atlanta GA 30332 USA School of Chemical & Biomolecular Engineering Georgia Institute of Technology Atlanta GA 30332 USA Department of Infectious Diseases College of Veterinary Medicine University of Georgia Athens GA 30602 USA Winship Cancer Institute Emory University Atlanta GA 30322 USA Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology Atlanta GA 30332 USA

Lymphatic filariasis is a neglected tropical disease caused by roundworm parasites such as Brugia malayi that spread via a mosquito vector. In vitro culture of these parasites provides controlled conditions to understand parasite biology and provides a cheaper way to screen potential micro- and macrofilaricides. Published studies have used a wide array of approaches and metrics regarding in vitro cultures of B. malayi; as a result, drawing comparisons and identifying the reasons why inability to reproduce outcomes are difficult. This study sought to determine conditions that ensure reproducible outcomes and used evaluation metrics that are easily measured and can be automated to ensure objectivity. We found culturing B. malayi third-stage larvae (L3) in endothelial basal media supplemented with 20% fetal bovine serum and 75 µm ascorbic acid in a temperature- and humidity-controlled incubator produced better survival and molting rates as well as longer and more motile parasites than previously reported. The benefit of ascorbic acid seemed to be unique to L3 parasites, as the addition of ascorbic acid to adult parasites had no significant impact on survival or motility. The methods reported in this study will help in designing experiments for both parasite behaviour studies and drug screening applications for disease eradication.

关键词： Ascorbic acid Brugia malayi long-term culture lymphatic filariasis

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

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Nature biotechnology 2020年第4期38卷 504页

作者： Christian Lieven Moritz E Beber Brett G Olivier Frank T Bergmann Meric Ataman Parizad Babaei Jennifer A Bartell Lars M Blank Siddharth Chauhan Kevin Correia Christian Diener Andreas Dräger Birgitta E Ebert Janaka N Edirisinghe José P Faria Adam M Feist Georgios Fengos Ronan M T Fleming Beatriz García-Jiménez Vassily Hatzimanikatis Wout van Helvoirt Christopher S Henry Henning Hermjakob Markus J Herrgård Ali Kaafarani Hyun Uk Kim Zachary King Steffen Klamt Edda Klipp Jasper J Koehorst Matthias König Meiyappan Lakshmanan Dong-Yup Lee Sang Yup Lee Sunjae Lee Nathan E Lewis Filipe Liu Hongwu Ma Daniel Machado Radhakrishnan Mahadevan Paulo Maia Adil Mardinoglu Gregory L Medlock Jonathan M Monk Jens Nielsen Lars Keld Nielsen Juan Nogales Intawat Nookaew Bernhard O Palsson Jason A Papin Kiran R Patil Mark Poolman Nathan D Price Osbaldo Resendis-Antonio Anne Richelle Isabel Rocha Benjamín J Sánchez Peter J Schaap Rahuman S Malik Sheriff Saeed Shoaie Nikolaus Sonnenschein Bas Teusink Paulo Vilaça Jon Olav Vik Judith A H Wodke Joana C Xavier Qianqian Yuan Maksim Zakhartsev Cheng Zhang Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark. Systems Biology Lab Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit Amsterdam Amsterdam the Netherlands. BioQUANT/COS Heidelberg University Heidelberg Germany. Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Systems Biotechnology Lausanne Switzerland. iAMB-Institute of Applied Microbiology ABBt-Aachen Biology and Biotechnology RWTH Aachen University Aachen Germany. Department of Bioengineering University of California La Jolla CA USA. Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada. Human Systems Biology Laboratory Instituto Nacional de Medicina Genomica & Coordinación de la Investigación Científica-Red de Apoyo a la Investigación UNAM Mexico City Mexico. Institute for Systems Biology Seattle WA USA. Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens Institute for Biomedical Informatics (IBMI) Tübingen Germany. Department of Computer Science University of Tübingen Tübingen Germany. German Center for Infection Research (DZIF) partner site Tübingen Tübingen Germany. Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane Queensland Australia. Argonne National Laboratory Lemont IL USA. Analytical Biosciences Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research Leiden University Leiden the Netherlands. Department of Systems Biology Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid Spain. Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain. Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Oslo Norway

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Smart Bandages: Smart Bandage for Monitoring and Treatment of Chronic Wounds (Small 33/2018)

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Small 2018年第33期14卷

作者： Pooria Mostafalu Ali Tamayol Rahim Rahimi Manuel Ochoa Akbar Khalilpour Gita Kiaee Iman K. Yazdi Sara Bagherifard Mehmet R. Dokmeci Babak Ziaie Sameer R. Sonkusale Ali Khademhosseini Biomaterials Innovation Research Center Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02139 USA Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA 02139 USA Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA Department of Mechanical and Materials Engineering University of Nebraska Lincoln Lincoln NE 68588 USA Birck Nanotechnology Center School of Electrical and Computer Engineering Purdue University West Lafayette IN 47907 USA Nano Lab Department of Electrical and Computer Engineering Tufts University Medford MA 02155 USA Center of Nanotechnology King Abdulaziz University Jeddah 21569 Saudi Arabia KU Convergence Science and Technology Institute Department of Stem Cell and Regenerative Biotechnology Konkuk University Hwayang-dong Kwangjin-gu Seoul 05029 Republic of Korea Department of Chemical and Biomolecular Engineering Department of Bioengineering Department of Radiology California NanoSystems Institute (CNSI) University of California Los Angeles CA 90095 USA

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Kinetic Transition Networks for the Thomson Problem and Smale’s Seventh Problem

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Physical Review Letters 2016年第2期117卷 028301-028301页

作者： Dhagash Mehta Jianxu Chen Danny Z. Chen Halim Kusumaatmaja David J. Wales Department of Applied and Computational Mathematics and Statistics University of Notre Dame Notre Dame Indiana 46556 USA Centre for the Subatomic Structure of Matter Department of Physics School of Physical Sciences University of Adelaide Adelaide South Australia 5005 Australia Department of Chemical and Biomolecular Engineering University of Notre Dame Notre Dame Indiana 46556 USA Department of Computer Science and Engineering University of Notre Dame Notre Dame Indiana 46556 USA Department of Physics Durham University South Road Durham DH1 3LE United Kingdom University Chemical Laboratories Lensfield Road Cambridge CB2 1EW United Kingdom

The Thomson problem, arrangement of identical charges on the surface of a sphere, has found many applications in physics, chemistry and biology. Here, we show that the energy landscape of the Thomson problem for N particles with N=132, 135, 138, 141, 144, 147, and 150 is single funneled, characteristic of a structure-seeking organization where the global minimum is easily accessible. Algorithmically, constructing starting points close to the global minimum of such a potential with spherical constraints is one of Smale’s 18 unsolved problems in mathematics for the 21st century because it is important in the solution of univariate and bivariate random polynomial equations. By analyzing the kinetic transition networks, we show that a randomly chosen minimum is, in fact, always “close” to the global minimum in terms of the number of transition states that separate them, a characteristic of small world networks.

关键词： Kinetic theory Mathematical physics Random graphs

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Stability for Receding-horizon Stochastic Model Predictive Control

Stability for Receding-horizon Stochastic Model Predictive C...

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American Control Conference

作者： Joel A. Paulson Stefan Streif Ali Mesbah Department of Chemical and Biomolecular Engineering University of California Berkeley CA 94720 USA Department of Computer Science and Automation Technische Universitat Ilmenau 98684 Ilmenau Germany

ISBN: (纸本)9781479917730

A stochastic model predictive control (SMPC) approach is presented for discrete-time linear systems with arbitrary time-invariant probabilistic uncertainties and additive Gaussian process noise. Closed-loop stability of the SMPC approach is established by appropriate selection of the cost function. Polynomial chaos is used for uncertainty propagation through system dynamics. The performance of the SMPC approach is demonstrated using the Van de Vusse reactions.

关键词： SMPC Uncertainty Propagation Predictive control Stochastic models System dynamics discrete time systems

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Designing a self-regulating biomolecular comparator

Designing a self-regulating biomolecular comparator

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American Control Conference

作者： Deepak K Agrawal Elisa Franco Rebecca Schulman Department of Chemical and Biomolecular Engineering Johns Hopkins University Baltimore Maryland 21218 United States Department of Mechanical Engineering 900 University Avenue University of California at Riverside Riverside CA 92521 USA Department of Chemical and Biomolecular Engineering and Computer Science Johns Hopkins University Baltimore Maryland 21218 United States

ISBN: (纸本)9781479917730

A major goal of biomolecular engineering is to build large systems of reactions with controlled input-output behavior. One challenge is that some reactions within such a system can be unreliable, so that rectification of these signals will be needed. biomolecular oscillators, for example, typically have fluctuations in the amplitude response that can limit its ability to control downstream processes. In this paper, we describe a simple reaction module, or biomolecular comparator, that can take such signals as input and produces a square wave-like output. The comparator produces an output at a constant high level whenever the source input is above some predefined threshold concentration and a constant low signal otherwise. This functionality is verified though simulations and theoretical analysis. We also discuss important constraints on the comparator's design. This work could make it possible to develop precise oscillatory molecular signals that allow for the dynamic control of synthetic biomolecular systems.

关键词： COMPARATORS Biological techniques signals Self-Control dynamic control rectification distilling Theoretical analysis

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Correction to: Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques

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Malaria journal 2017年第1期16卷 486页

作者： Yan Tang Chester J Joyner Monica Cabrera-Mora Celia L Saney Stacey A Lapp Mustafa V Nural Suman B Pakala Jeremy D DeBarry Stephanie Soderberg Jessica C Kissinger Tracey J Lamb Mary R Galinski Mark P Styczynski School of Chemical & Biomolecular Engineering Georgia Institute of Technology Atlanta GA USA. Malaria Host-Pathogen Interaction Center Emory Vaccine Center Yerkes National Primate Research Center Emory University Atlanta GA USA. Institute of Bioinformatics University of Georgia Athens GA USA. Department of Computer Science University of Georgia Athens GA USA. Department of Genetics University of Georgia Athens GA USA. Center for Tropical and Emerging Global Diseases University of Georgia Athens GA USA. Department of Pathology University of Utah Salt Lake City UT USA. Division of Infectious Diseases Department of Medicine Emory University Atlanta GA USA. School of Chemical & Biomolecular Engineering Georgia Institute of Technology Atlanta GA USA. mark.styczynski@chbe.gatech.edu. Malaria Host-Pathogen Interaction Center Emory Vaccine Center Yerkes National Primate Research Center Emory University Atlanta GA USA. mark.styczynski@chbe.gatech.edu.

After publication of the article [1], it was brought to our attention that several symbols were missing from Fig. 1, including some cited in the figure's key. The correct version of the figure is shown below ...

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Global, regional, and national sex-specific burden and control of the HIV epidemic, 1990–2019, for 204 countries and territories: the Global Burden of Diseases Study 2019

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The Lancet HIV 2021年第10期8卷 e633-e651页

作者： Jahagirdar, Deepa Walters, Magdalene K. Novotney, Amanda Brewer, Edmond D. Frank, Tahvi D. Carter, Austin Biehl, Molly H. Abbastabar, Hedayat Abhilash, E.S. Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Adekanmbi, Victor Adeyinka, Daniel Adedayo Adnani, Qorinah Estiningtyas Sakilah Afzal, Saira Aghababaei, Soodabeh Ahinkorah, Bright Opoku Ahmad, Sajjad Ahmadi, Keivan Ahmadi, Sepideh Ahmadpour, Ehsan Ahmed, Muktar Beshir Rashid, Tarik Ahmed Salih, Yusra Ahmed Aklilu, Addis Akram, Tayyaba Akunna, Chisom Joyqueenet Al Hamad, Hanadi Alahdab, Fares Alanezi, Fahad Mashhour Aleksandrova, Ekaterina A. Alene, Kefyalew Addis Ali, Liaqat Alipour, Vahid Almustanyir, Sami Alvis-Guzman, Nelson Ameyaw, Edward Kwabena Amu, Hubert Andrei, Catalina Liliana Andrei, Tudorel Anvari, Davood Arabloo, Jalal Aremu, Olatunde Arulappan, Judie Atnafu, Desta Debalkie Quintanilla, Beatriz Paulina Ayala Ayza, Muluken Altaye Azari, Samad Darshan, B.B. Banach, Maciej Bärnighausen, Till Winfried Barra, Fabio Barrow, Amadou Basu, Sanjay Bazargan-Hejazi, Shahrzad Belay, Habtamu Gebrehana Berheto, Tezera Moshago Bezabhe, Woldesellassie Mequanint Bezabih, Yihienew Mequanint Bhagavathula, Akshaya Srikanth Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bibi, Sadia Bijani, Ali Bisignano, Catherine Bolarinwa, Obasanjo Afolabi Boloor, Archith Boltaev, Azizbek A. Briko, Nikolay Ivanovich Buonsenso, Danilo Burkart, Katrin Butt, Zahid A. Cao, Chao Charan, Jaykaran Chatterjee, Souranshu Chattu, Soosanna Kumary Chattu, Vijay Kumar Choudhari, Sonali Gajanan Chu, Dinh-Toi Couto, Rosa A.S. Cowden, Richard G. Dachew, Berihun Assefa Dadras, Omid Dagnew, Amare Belachew Dahlawi, Saad M.A. Dai, Xiaochen Dandona, Lalit Dandona, Rakhi das Neves, José Degenhardt, Louisa Demeke, Feleke Mekonnen Desta, Abebaw Alemayehu Deuba, Keshab Dhamnetiya, Deepak Dhungana, Govinda Prasad Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Doan, Linh Phuong Dorostkar, Fariba Edinur, Hisham Atan Effiong, Andem Eftekharzadeh, Sahar El Sayed Zaki, Maysaa Elayedath, Rajesh Elhadi, Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Division of Allergy and Infectious Diseases University of Washington Seattle WA United States Department of Global Health University of Washington Seattle WA United States School of Social Work University of Washington Seattle WA United States Department of Medicine University of Washington Seattle WA United States Vagelos College of Physicians and Surgeones Columbia University Medical Center New York NY United States Division of Data Analytics and Delivery for Impact WHO Geneva Switzerland Advanced Diagnostic and Interventional Radiology Research Centre Tehran University of Medical Sciences Tehran Iran Multiple Sclerosis Research Centre Tehran University of Medical Sciences Tehran Iran School of Public Health Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Paediatric Chronic Kidney Disease Research Centre Tehran University of Medical Sciences Tehran Iran Department of Psychiatry Tehran University of Medical Sciences Tehran Iran Metabolomics and Genomics Research Centre Tehran University of Medical Sciences Tehran Iran Sina Trauma and Surgery Research Centre Tehran University of Medical Sciences Tehran Iran Research Centre for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Non-Communicable Diseases Research Centre Tehran University of Medical Sciences Tehran Iran Department of Botany Sree Narayana Guru College Chelannur Kozhikode India Clinical Sciences Department University of Sharjah Sharjah United Arab Emirates Mass Communication Department University of Sharjah Sharjah United Arab Emirates Department of Health-Care Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Department of Population Medicine Ca

Background: The sustainable development goals (SDGs) aim to end HIV/AIDS as a public health threat by 2030. Understanding the current state of the HIV epidemic and its change over time is essential to this effort. This study assesses the current sex-specific HIV burden in 204 countries and territories and measures progress in the control of the epidemic. Methods: To estimate age-specific and sex-specific trends in 48 of 204 countries, we extended the Estimation and Projection Package Age-Sex Model to also implement the spectrum paediatric model. We used this model in cases where age and sex specific HIV-seroprevalence surveys and antenatal care-clinic sentinel surveillance data were available. For the remaining 156 of 204 locations, we developed a cohort-incidence bias adjustment to derive incidence as a function of cause-of-death data from vital registration systems. The incidence was input to a custom Spectrum model. To assess progress, we measured the percentage change in incident cases and deaths between 2010 and 2019 (threshold >75% decline), the ratio of incident cases to number of people living with HIV (incidence-to-prevalence ratio threshold <0·03), and the ratio of incident cases to deaths (incidence-to-mortality ratio threshold <1·0). Findings: In 2019, there were 36·8 million (95% uncertainty interval [UI] 35·1–38·9) people living with HIV worldwide. There were 0·84 males (95% UI 0·78–0·91) per female living with HIV in 2019, 0·99 male infections (0·91–1·10) for every female infection, and 1·02 male deaths (0·95–1·10) per female death. Global progress in incident cases and deaths between 2010 and 2019 was driven by sub-Saharan Africa (with a 28·52% decrease in incident cases, 95% UI 19·58–35·43, and a 39·66% decrease in deaths, 36·49–42·36). Elsewhere, the incidence remained stable or increased, whereas deaths generally decreased. In 2019, the global incidence-to-prevalence ratio was 0·05 (95% UI 0·05–0·06) and the global incidence-to-mortality ratio was

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Polymerized ionic liquid films in strong electric fields: Ion transport and nanopatterning 10

Polymerized ionic liquid films in strong electric fields: Io...

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10th Annual TechConnect World Innovation Conference and Expo, Held Jointly with the 18th Annual Nanotech Conference and Expo, and the 2015 National SBIR/STTR Conference

作者： Kumar, Rajeev Bocharova, Vera Strelcov, Evgheni Tselev, Alexander Collins, Liam Kravchenko, Ivan I. Berdzinski, Stefan Strehmel, Veronika Ovchinnikova, Olga S. Minutolo, Joseph A. Sangoro, Joshua R. Agapov, Alexander L. Kisliuk, Alexander Sokolov, Alexei P. Kalinin, Sergei V. Sumpter, Bobby G. Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak RidgeTN United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN United States Chemical Sciences Division Oak Ridge National Laboratory Oak RidgeTN United States School of Physics University College Dublin Belfield Dublin 4 Ireland Department of Chemistry Institute for Coatings and Surface Chemistry Krefeld Germany Department of Chemical and Biomolecular Engineering University of Tennessee KnoxvilleTN United States Department of Chemistry University of Tennessee KnoxvilleTN United States

ISBN: (纸本)9781498747271

We have recently studied local ion transport and structural changes in thin films of an imidazoliimi based polymerized ionic liquid (PIL) using an integrated experiment-theory approach. We find that experimental data for the kinetics of charging and steady state current-voltage relations could be explained by taking into account the dissociation of ion-pairs xmder an applied electric field (known as the Wien effect). Onsager's theory of the Wien effect coupled with the Poisson-Nemst-Planck (PNP) formalism for the ion transport is found to be in excellent agreement with the experimental results. We also demonstrated that by means of atomic force microscopy (AFM) one can form topographical features on the surface of PIL-based thin films with a significantly lower electric potential and power consumption as compared to non-conductive polymer materials. Furthermore, by tuning the applied voltage and ambient air humidity, reproducible control over the dimensions of the structures formed is achieved.

关键词： Liquid films

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Emulating cellular automata in chemical reaction-diffusion networks

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20th International Conference on DNA computing and Molecular Programming, DNA 2014

作者： Scalise, Dominic Schulman, Rebecca Chemical and Biomolecular Engineering Johns Hopkins University United States Computer Science Johns Hopkins University United States

ISBN: (纸本)9783319112947

chemical reactions and diffusion can produce a wide variety of static or transient spatial patterns in the concentrations of chemical species. Little is known, however, about what dynamical patterns of concentrations can be reliably programmed into such reaction-diffusion systems. Here we show that given simple, periodic inputs, chemical reactions and diffusion can reliably emulate the dynamics of a deterministic cellular automaton, and can therefore be programmed to produce a wide range of complex, discrete dynamics. We describe a modular reaction-diffusion program that orchestrates each of the fundamental operations of a cellular automaton: storage of cell state, communication between neighboring cells, and calculation of cells’ subsequent states. Starting from a pattern that encodes an automaton’s initial state, the concentration of a "state" species evolves in space and time according to the automaton’s specified rules. To show that the reaction-diffusion program we describe produces the target dynamics, we simulate the reaction-diffusion network for two simple 1-dimensional cellular automata using coupled partial differential equations. Reaction-diffusion based cellular automata could potentially be built in vitro using networks of DNA molecules that interact via branch migration processes and could in principle perform universal computation, storing their state as a pattern of molecular concentrations, or deliver spatiotemporal instructions encoded in concentrations to direct the behavior of intelligent materials. © Springer International Publishing Switzerland 2014.

关键词： Cellular automata

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