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Construction, Programming and Testing of Measurement Equipment for Microbe Culturing in Space - Contribution to the MOREBAC Experiment, Part of the MIST-Project

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Construction, Programming and Testing of Measurement Equipment for Microbe Culturing in Space - Contribution to the MOREBAC Experiment, Part of the MIST-Project UPTEC F 16062 Examensarbete 30 hp Februari 2017 Construction, programming and testing of measurement equipment for microbe culturing in space - Contribution to the MOREBAC experiment, part of the MIST-project Oscar Årling Abstract Construction, programming and testing of measurement equipment for microbe culturing in space Oscar Årling Teknisk- naturvetenskaplig fakultet UTH-enheten Many different bacteria have essential roles in the process of recycling organic waste, making them useful tools when it comes to Besöksadress: establishing artificial ecosystems, a key technology to master in Ångströmlaboratoriet Lägerhyddsvägen 1 the expansion of human space travel. Hus 4, Plan 0 In order to further investigate bacteria growth conditions during Postadress: space travel, the MOREBAC experiment was formulated. The objective Box 536 751 21 Uppsala was to design an experimental setup and develop measurement equipment with the capability of confirming successful Telefon: resuscitation of freeze-dried bacteria in space by measuring 018 – 471 30 03 bacteria growth, on-board the student-built MIST-satellite. Telefax: 018 – 471 30 00 The experimental setup prototype consisted of an acrylic chip wherein the bacteria would be placed during experiments and an Hemsida: optical measurements configuration using a photosensor with the http://www.teknat.uu.se/student purpose of detecting bacteria cell growth. For experimental environment monitoring, a temperature sensor and a pressure sensor were calibrated. An Arduino Nano microcontroller was programmed to control all electrical components during measurements. During the optical density measurements blue dyed water and E.coli bacteria in nutrition media were used as test samples. Provided varying blue dye or bacteria cell concentrations, in the form of dilution series and growth-over-time-series, the equipment proved capable of producing measurements that indicate the optical density of the test sample. Furthermore, a prototype experiment protocol simulating events that will occur in the final experiment design, was implemented and was able to produce real-time monitoring graphs of optical, temperature and pressure measurements, as well as documentation of all events and measurement data. Handledare: Håkan Jönsson Ämnesgranskare: Maria Tenje Examinator: Tomas Nyberg ISSN: 1401-5757, UPTEC F 16062 Summary in Swedish Ända sedan den första månlandningen har en av mänsklighetens stora utmaningar och strävanden varit att erövra större delar av universum. Att kolonisera andra himlakroppar är ingen lätt uppgift när dessa inte ens tillåter växter att grönska eller har en atmosfär som tillåter oss att andas. Men det som inte nns kan man alltid försöka skapa. Så, för att vi människor någonsin ska kunna kolonisera andra planeter behöver vi kunna återskapa den omgivning som jorden erbjuder så pass likt att vi faktiskt kan överleva i den. För att skapa en sådan omgivning krävs många olika komponenter för att systemet inte ska fallera. I ett fungerande ekosystem krävs bland annat organismer som kan hantera avfall genom nedbrytning som därigenom tillåter andra organsimer att återanvända avfallet. En mycket viktig komponent i alla ekosystem är bakterier, just på grund av deras delaktighet i nedbrytningen. Bakterier kommer i många olika format och i deras mångfald nner man att de kan uträtta många olika utgifter. Medan vissa bakteriearter orsakar sjukdomar, nns det andra som fullbordar viktiga kretslopp i naturen som exempelvis kväve- cykeln. På KTH pågår projekt kallat MIST (MIniature STudent satellite) där tanken är att konstruera en satellit vari sju olika experiment ska utföras under satellitens omloppsbana kring jorden. Ett av dessa experiment är MOREBAC, som går ut på undersöka odlandet av bakterier i rymden, närmare bestämt frystorkade bakterier och hur väl man kan lyckas återuppliva dessa från deras dvala. I detta examensarbete har målet varit att konstruera mätutrustning för MORE- BAC:s räkning. Mätutrustningen ska tjäna syftet att kunna identiera huruvida koncentrationen bakterier ökar efter återupplivningsförsöket som kommer att ske från frystorkad form. Dessutom ska utrustningen kunna kunna mäta relevanta förhållanden i omgivningen, i detta fall temperatur och tryck. Alla elektriska komponenter, såsom sensorer, resistorer och LED kopplades till en Arduino Nano microcontroller, som programmerades via datorn och sedan kunde 3 man via datorn skicka uppgifter till microcontrollern som i sin tur styrde de elek- triska komponenterna så att de utförde dessa uppgifter. För att kunna odla bakterierna måste vi ha någonting att odla dem i, något förslutet som inte tillåter bakterierna att yga omkring hursomhelst, vilket de gärna gör när gravitationen är liten. Vi använde ett genomskinligt chip med en in- loppskanal där näringsämnen till bakterierna kunde pumpas in och en utloppskanal för att kunna pumpa ut gas och vätska. Eftersom vi vill kunna bestämma bakteriekoncentration utnyttjade vi det faktum att bakterier absorberar mer ljus ju högre koncentrationen är. På så sätt kunde vi använda en ljuskänslig sensor till att bedömma hur stor andel ljus bakterierna absorberade när de belystes med en riktad ljusstråle från en LED. Exempelvis, om en liten mängd ljus skulle släppas igenom bakterierna betyder det att de ab- sorberar en stor andel av ljuset, vilket tyder på en hög koncentration av dem. Mätningar på olika bakteriekoncentrationer gav oss därmed en bra referens till vilka mätvärden som motsvaras av en viss koncentration. Inledningsvis, för att testa den principen och för att undvika tidskrävande bakterieodlingsförberedelser, testades mätutrustningen på olika spädningar av färgat vatten. Temperatursensorn och trycksensorn testades för olika temperaturer respektive trycknivåer och påvisade båda två att de var linjärt beroende av mätvärdena utan märkbara avvikelser, vilket innebar att de kunde anses som tillförlitliga för refer- ensmätningar av dessa storheter på intervallen 25 ◦C till 70 ◦C, respektive -80 kPa till 30 kPa. När alla komponenter hade testats separat testades de alla samtidigt enligt exper- imentprotokollet, vilket innefattar alla händelser som kommer ske när satelliten är satt i bruk och det är dags för experimentet att utföras. Under testutförandet av experimentprotokollet skapades, samtidigt som mätningarna pågick, en visualiser- ing med tre grafer föreställande mätningar på absorbans, temperatur och tryck. Dessutom dokumenterades alla händelser i en l på datorn. Från resultatet av utförandet av experimentprotokollet kunde det konstateras att händelserna dokumenterades som de skulle och att mätutrustningen kunde följa temperatur-, tryck- och absorbansförändringarna som skedde. Dock antydde ab- sorbansmätningarna ett temperaturberoende, vilket innebär att den valda ljussen- sorn omkalibreras eller bytas ut mot en ljussensor utan temperaturberoende. I fortsättningsarbetet kommer det behövas försök till återupplivning av frystorkade bakterier, utredning och åtgärd för ljussensorns temperaturberoende samt paral- lella experimentutföranden, med varierande parametrar så som tidsperiod, djup på chippets bakteriebrunn. 4 Contents 1 Introduction 7 1.1 Aim of Project . .7 1.2 Bacteria in Space . .7 1.3 Life Support Systems and Pocket Earth Ecosystems . .8 1.4 Detecting Bacteria Growth . .9 1.5 Studies of Previous Work . 11 2 Background 13 2.1 The MIST satellite project . 13 2.2 MOREBAC . 14 2.3 The Employer . 14 3 Theory 15 3.1 Experiment Limitations . 15 3.2 Serial Communication . 16 3.3 Experimental Preparations and Procedure . 16 3.4 Experiment Protocol . 17 4 Design, Construction and Testing 20 4.1 Electrical Components . 20 4.1.1 Microcontroller and Computer Softwares . 22 4.1.2 Optical Measurement Components . 23 4.1.3 Temperature and Pressure Sensor Calibration . 24 4.1.4 Choosing Resistances . 25 4.2 Chip design . 26 4.3 Optical Measurement Conguration . 28 4.4 Arduino and Processing programming . 29 4.5 Dye and Bacteria Measurements . 30 4.6 Experiment Protocol Testing . 31 5 Results 32 5 5.1 Resistance tests . 33 5.1.1 Analytical Resistances . 33 5.1.2 Typical Photoresistance Measurements . 35 5.2 Dye and Bacteria measurements . 36 5.3 Temperature and Pressure Calibration . 39 5.4 Experiment Protocol . 40 5.4.1 Logged Events . 41 5.4.2 Real Time Monitoring Graph . 42 6 Discussion 44 6.1 Conclusion . 46 6.2 Future work . 47 References . 48 6 Chapter 1 Introduction In this section, the underlying circumstances that motivate the MOREBAC-experiment are presented, such as the usefulness of bacteria in life support systems and arti- cial ecosystems. Also, the aim of the project, what approaches were taken to get there, and design limitations are all discussed. 1.1 Aim of Project The aim of this master thesis was to develop measuring equipment for the detection of growth of resuscitated freeze-dried bacteria, on-board a student built satellite orbiting Earth. Initiating the MOREBAC project, this rst phase of the project served to establish a basis for other students to continue working on to reach a nal product that will be able to be incorporated into the MIST-satellite. 1.2 Bacteria in Space Bacteria can be useful in many appliances related to the recycling of biological waste, which would be particularly crucial on space missions where the resources that are brought along must last throughout the duration of the mission. Bringing bacteria out into space requires rigorous connement to avoid any con- tamination on-board the vessel. Furthermore, the bacteria are living cells that require nutrition
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