First team meeting was led by Ari Edmonds (2017 and 2018 Macquarie University iGEM team member), introducing synthetic biology and how the competition works. We met our advisors from the Department of Molecular Sciences and met Abigail Sison from iGEM HQ
Professor Robert Willows discussed theoretical aspects of H₂ biosensors and NiFe hydrogenases in E. coli which guided us in researching and reading literature
We set up team accounts for Gmail, Facebook, Instagram and Twitter. We also brainstormed possible team names
Eli and Sam brainstormed ways we can address human practices through a prototype

Wet Lab

Anika, Daniel, Jerresa, Tasneem and Zoe prepared LB CAM and LB AMP plates. We transformed DH5ɑ with Plac, cyclic di-GMP phosphodiesterase, double terminator, RBS (parts from the 2019 iGEM distribution kit) in an attempt to build a component of our biosensor while we waited for synthesised parts to arrive

Dry Lab

As a team, we discussed logo ideas and potential contacts who can help to design and digitise our ideas.
Alice, Carly and Eli drafted emails for human practices stakeholders, industry experts and sponsorship
Anika, Carly, Daniel, Tasneem and Zoe brainstormed activity ideas for Macquarie University Open Day and developed an online survey based on which was shared to our social media pages
Jerresa, Josip, Sam, Tasneem and Zoe researched methods for detecting cyclic-di-GMP.
Each team member drafted their bios for the wiki.

Wet Lab

Transformations of Plac, cyclic di-GMP phosphodiesterase, double terminator, RBS we performed last week was unsuccessful. Anika, Daniel, Jerresa, Tasneem and Zoe reattempted these transformations.
We attempted to make our own competent E. coli cells.

Dry Lab

Everyone researched factors which may affect the functioning of cyclic-di-GMP phosphodiesterase.
Eli and Sam received feedback from A/Prof Louise Brown regarding their prototype design,
Alice and Tasneem received feedback from A/Prof Louise Brown regarding emails for human practices and sponsorship document
Carly, Jerresa, Josip and Sam summarised the literature we read and highlighted important points and protocols we could use for our parts
Ari showed us how to plan part construction using standard assembly and 3A assembly.

Wet Lab

We learned how to prepare an agarose gel, use the NanoDrop and Gel Visualiser
Anika, Daniel, Jerresa, Tasneem and Zoe miniprepped the plasmids containing Plac, cyclic di-GMP phosphodiesterase, double terminator, RBS then determined DNA concentration using the NanoDrop. We digested samples with EcoRI, PstI and XbaI then ran digests on a 1 % agarose gel.
Anika, Daniel, Jerresa, Tasneem and Zoe completed standard assembly for Plac and RBS
Anika, Daniel, Jerresa, Tasneem and Zoe completed 3A assembly for cyclic di-GMP phosphodiesterase, double terminator and TET backbone
After digestion, we ran samples in a 1 % agarose gel and annotated bands

Dry Lab

Alice finalised our sponsorship document and emails for human practices and contacted 35+ companies and organisations
We attended the Department of Molecular Sciences Masters of Research poster session and interacted with postgraduate research students and their supervisors. We noted what layouts and designs made posters stand out, ideas for our Jamboree poster
Jerresa and Tasneem contacted Team Edinburgh UG and Team NU_Kazakhstan for a possible collaboration as we are all working with hydrogen producing microbes
Received our hydrogenase gblock from IDT so we started planning for digestion and ligation reactions
Alice, Carly, Eli, Jerresa, Tasneem and Zoe attended the CSIRO ON Prime Finals at the Sydney Startup Hub to support the Macquarie Biohydrogen group
We started preparing a presentation for our advisors summarising the work completed during our intensive month long iGEM bootcamp
We received replies from Bondi Bioworks and Bioplatforms Australia, organised meetings for next week
Alice and Eli attended a meeting with Andrew Gilbert from Bioplatforms Australia to discuss our project
James Brown from Bondi Bioworks visited the team on campus to discuss entrepreneurship in synthetic biology and his expertise in the field

Wet Lab

No colonies from our standard assembly and 3A assembly plates
Digested hydrogenase gblock and KAN backbone with EcoRI and PstI, ligated then transformed. Colonies on transformed plates were inoculated to prepare liquid cultures
Anika, Daniel, Eli, Jerresa, Tasneem, Sam and Zoe carried out miniprep of the phosphodiesterase, followed by digestion and ran samples on an agarose gel and SDS-PAGE

Dry Lab

First week of semester!
Sam consulted our advisor, Russel, for planning our biofilm formation assay with the phosphodiesterase. Daniel, Jerresa and Sam also worked with our advisor, Dr Edward Moh to compare protocols for biofilm formation assays found in literature. We considered
parameters such as culture duration, dilution, media, incubation periods, wash steps and stains
We received a reply from Fire + Rescue NSW. Alice arranged a meeting with Paul Beylerian (Fire + Rescue NSW Scientific Officer) who will visit us on campus for an interview. We started preparing questions to ask and researched background information on Fire + Rescue NSW
We had our first weekly meeting with our advisors. Alice, Anika, Carly, Daniel, Eli, Josip, Sam and Tasneem presented a slideshow with our accomplishments throughout the iGEM bootcamp
We received our riboswitch with and without the terminator stem loop (R_ON and R_OFF)
Alice and Eli met with Andrew Gilbert from Bioplatforms Australia to discuss our project

Wet Lab

Jerresa and Sam ran an SDS-PAGE of YHJH in Lac and YHJH in KAN
Sam prepared 5 liquid cultures of yhjh for the preliminary biofilm assay
Started assembly of our riboswitch

Dry Lab

Our advisor, Dr Paul Jaschke, ordered the hydrogenase component of our biosensor from Twist
Alice contacted various high schools who may be interested in hearing about our project
Alice, Zoe, A/Prof Louise Brown and Sam King attended an interview with Paul Beylerian from Fire + Rescue NSW. We developed a better understanding of the limitations of current gas detectors used by firefighters
We received our first silver sponsorship from Labcyte!
Jerresa presented the weekly update presentation to our advisors
Hannah joined our iGEM team! She is completing a Masters of Research and plans to help us with laboratory work and writing literature reviews for the wiki.

Wet Lab

Sam checked the preliminary biofilm assay for the yhjh part and performed the wash step with acetic acid and OD readings.
Anika transformed the ligated R_ON and R_OFF plasmids in DH5α though plates had no colonies.
Carly, Daniel, Eli, Josip, Sam, Tasneem and Zoe reattempted the transformation of R_ON and R_OFF
Two biofilm assays were prepared. One plate will be incubated at 28 °C, the other incubated at room temperature (kept in the drawer).
Jerresa prepared overnight cultures of R_ON and R_OFF transformations. Anika, Jerresa, Daniel, Tasneem and Zoe miniprepped these transformations which was followed by digestion. Jerresa and Tasneem ran an agarose gel of the digested R_ON and R_OFF samples.

Dry Lab

Alice, Carly, Daniel, Jerresa, Tasneem and Zoe have volunteered to represent our team at the Macquarie University Open Day. We started discussing ideas about engaging ways to interact with visitors and prospective students relating to our project.
With the help of our advisor, Dr Roy Walker, we contacted Team Edinburgh for a possible collaboration as they are using the 2017 Macquarie iGEM team’s construct.
Carly, Josip and Tasneem participated in a Skype call with Team NTU Singapore to discuss a possible collaboration. For the past 3 years, Macquarie Australia and NTU Singapore have collaborated by performing qPCR and SDS-PAGE for parts. We decided it would be great to continue this collaborative relationship.
Alice started preparing presentations for high school visits
Carly finalised our iGEM poster for the Macquarie University Open Day
The team presented the weekly update presentation to our advisors
Alice and Jerresa attended an interview with Macquarie University PhD recipient, Dr Vanessa Pirotta. Dr Vanessa is experienced in science communication and has a strong passion for sharing science with non-scientific audiences. She discussed how we can engage with our social media followers, gave advice on creating presentations and taught us ways to communicate complex information in inspiring and relatable terms
Alice drafted a second round of emails for human practices and sponsorships based on the feedback given by Dr Vanessa Pirotta
Alice, Ari, Carly, Daniel, Jerresa, Tasneem and Zoe represented the team at the Macquarie University Open Day. Our stall was located next to the teaching laboratories where the tours ended. This gave us the opportunity to educate tour groups about iGEM and how we plan to utilise synthetic biology to address issues. Ari demonstrated a hydrogen fuel cell toy car and we encouraged visitors to complete our short survey

Wet Lab

Daniel, Tasneem and Zoe repeated the agarose gel due to diffusion of the samples and distorted bands
Josip and Sam prepared digestion of the enzymes, PstI, SpeI, XbaI and EcoRI to check if they were still usable. Jerresa and Zoe ran a 1 % agarose gel of the digests
Sam prepared the next biofilm formation assay.

Dry Lab

We took headshots for team introductions on our social media pages
The team presented the weekly update presentation to our advisors
We were getting inconsistent results from our agarose gels. After consultation with Professor Robert Willows, we concluded that it may be due to the activity of our enzymes. Thi decided to order new enzymes (EcoRI, PstI, XbaI, SpeI, NdeI)

Wet Lab

Carly, Eli and Hannah digested the riboswitch with EcoRI (single) and PstI (double). Eli and Zoe ran an agarose gel of the digests. The gel did not appear to run properly (agarose didn’t melt, samples were not loaded properly) so it was repeated
Sam took the OD readings of last week’s biofilm formation assay and followed suggestions from our advisor, Dominic, regarding the wash step and measurement

Dry Lab

We received replies from Hazer Group and Maximator, organised phone call interviews for next week
Carly continued planning a collaboration with Team NTU Singapore
Carly, Jerresa and Ari participated in a Skype call with Team NU_Kazahkstan to discuss our projects and possible ways we could collaborate
We received a platinum sponsorship from Bioplatforms Australia and a bronze sponsorship the Macquarie University Student Representative Committee!
Our advisor, Samuel King, organised a human practices meeting with Alice, Anika, Carly and Daniel to discuss ways to address the medal criteria
Alice, Daniel, Jerresa and Zoe presented our project to high school students at Brigidine College, St Ives
Alice and Jerresa volunteered to represent the team at the Synthetic Biology Australasia Conference in Brisbane in October. They started planning flights, accommodation and registration with the guidance of A/Prof Louise Brown, Anwar Sunna and Louise Burton (CSIRO)
Josip ordered riboswitches with inducible promoters (lac and tac)
The team presented the weekly update presentation to our advisors

Wet Lab

We made observations for R_ON and R_OFF plates
According to a paper found by Sam, E. coli Nissle 1917 is more efficient in producing biofilms compared to DH5α. We obtained these cells from our advisors, Dr Paul Jaschke and Dominic Logel, which were used to make competent cells
We decided to rebuild the cyclic-di-GMP phosphodiesterase plasmid

Dry Lab

Selected photos from the Brigidine school presentation to upload to our social media pages
Jerresa, Sam and Zoe presented the weekly update presentation to our advisors
Daniel started designing our team shirts and received feedback from our advisors
Ari, Daniel, Jerresa, Sam and Zoe participated in a photoshoot for the Faculty of Science and Engineering
We were approached by Team UAAAN to collaborate and planned a video call for next week
Alice started drafting the abstract for the wiki and Synthetic Biology Australasia Conference

Wet Lab

Hannah retransformed the PDE in Nissle 1917 with the following changes to our protocol
We sent sent R_ON and R_OFF samples for sequencing
Hannah performed miniprep of PDE and miniprep of yhjh KAN and CAM
Hannah also helped prepare overnight liquid culture for cyclic-di-GMP and R_ON CAM and R_OFF CAM
With the guidance of Professor Robert Willows, we prepared a preliminary GFP fluorescence assay using our riboswitch. Unfortunately, when we tested variables (growth media, temperature), the plate dried out and results were highly variable.

Dry Lab

Received our hydrogenase (Hyd 1A and 1B) and riboswitches with promoters. Josip started planning assembly of these parts
Carly, Tasneem and Sam presented the weekly update presentation to our advisors. During our meeting, we finalised the SBA and wiki abstract with feedback from advisors
Alice, Carly, Sam, Eli, Tasneem, Zoe, Hannah, Jerresa and Josip discussed gel image from 09/09 with Thi and Ed. When overnight cultures were made, two colonies may have been selected or incomplete digestion. Alternatively, colonies were not transformants and possible contamination from the miniprep kit.
Ed, Thi, Carly and Jerresa participated in a video call with NTU Singapore. We hope to send our riboswitch after sequencing confirmation so they can perform qPCR. They will send us a cell lysate and nuclear pellets for protein expression and SDS-PAGE
Carly and Jerresa participated in a Skype call with Team UAAAN to discuss possible ways we could collaborate
Carly, Jerresa, A/Prof Louise Brown, Prof Robert Willows and Macquarie biohydrogen group participated in a phone call interview with Mark Edwards (Hazer Group)
Jerresa and A/Prof Louise Brown submitted the team roster, abstract and title, safety form and track selection
Received a reply from USYD for collaboration, arranging a Skype call for next Monday
Alice prepared questions for the BOC interview which Carly sent and confirmed our meeting next Monday

Wet Lab

Josip and Tasneem used the NanoDrop to find DNA concentration of yhjh, R_ON CAM, R_OFF CAM, cyclic-di-GMP minipreps from 06/09
Daniel performed an agarose gel to check the hydrogenase and cyclic-di-GMP
Hannah, Josip and Zoe prepared an assay for our riboswitch with different salt concentrations
Josip prepared liquid culture from transformant colonies from TAC_ON, TAC_OFF, LAC_ON, LAC _OFF plates

Dry Lab

Alice, Carly, Jerresa, Sam, Zoe, Professor Robert Willows, Samuel King, Dr Tony Jerkovic attended a meeting with Chris Dolman from BOC, Australia's leading gas & safety equipment specialist
Eli, Josip, Jerresa, Thi and Dr Paul Jaschke planned for Gibson Assembly of hydrogenase (Twist)
Alice, Carly, Eli and Jerresa worked on prototype design and feedback from interviews
Carly and Jerresa participated in video call with Team Sydney Australia. We decided the best way to collaborate would be performing an SDS-PAGE for one of their proteins, and in return, replicate one of our GFP assays. We organised a time to exchange samples
Carly and Jerresa also arranged a video call with Team UAAAN for next week
Anika worked on the UNSW Symposium slideshow
Alice, Carly and Jerresa worked on content for the wiki
Carly and Tasneem presented the weekly update presentation to our advisors. We also did a team selection process for Boston where members pitched their contributions, team achievements and what they hope to achieve from attending the Jamboree. Carly, Eli, Jerresa, Sam, Tasneem and Zoe applied.

Wet Lab

Josip and Hannah performed digestion of Hyd 1A and 1B, cyclic-di-GMP using enzyme E for single digestion and a combination of E and N for the double digestion
Hannah prepared competent cells of Nissle and DH5α
Daniel and Anika performed digestion of Hyd and cyclic-di-GMP PDE
Eli conducted a Gibson Assembly with the hydrogenase fragments and KAN backbone, which was transformed by Tasneem in DH5α
Anika, Daniel, Sam and Tasneem restreaked colonies from Hydrogenase and CDG plates plus positive and negative controls
Anika, Daniel, Hannah and Zoe made 2 agarose gels for Tac _ON/OFF; Lac _ON/OFF, Hydrogenase digests and CDG PCR, W and W/O digests and annotated both gels
Jerresa prepared samples prepared for sequencing (CDG W KAN 3, CDG W/O CAM 2, Lac R_OFF 1, Lac R_OFF 2, Lac R_ON 1, Lac R_ON 2, Lac R_ON 4
Jerresa and Sam transformed PDE with DH5α (commercial and homemade)
Sam performed a Polymerase Chain Reaction (PCR) for the CAM backbone, KAN backbone and colony.
Carly, Jerresa and Zoe made LB media and plates (LB CAM and LB KAN)
Eli and Tasneem performed retransformation of Hyd 1A and Hyd 1B
Sam made Congo Red plates for the spot assay
Sam prepared a Congo red spot plate
Hannah prepared glycerol stocks of Lac R_OFF red colonies CAM, Lac R_OFF green colonies CAM, R_ON CAM 1 DH5α, R_OFF CAM 1 DH5α
Hannah, Jerresa, Sam GFP Assay of Constitutive and Inducible Riboswitches with LB

Dry Lab

The team presented the weekly update presentation to our advisors
Carly and Jerresa visited Team Sydney Australia at their campus to exchange samples for our collaborations
Daniel worked on our shirt design
Jerresa drafted content for the wiki

Wet Lab

We started using our new Qiaprep spin miniprep kit (250). Miniprep and digestion of PDE + R_ON/OFF
Anika performed a digestion of the hydrogenase and Tasneem ran an agarose gel of the digests SDS-PAGE of hydrogenase
Hannah and Zoe prepared glycerol stocks for Lac_ON KAN 2, Lac_OFF KAN 2, R_ON CAM, Tac_OFF KAN 3, Tac_ON KAN 1, Lac_OFF KAN 1, Lac_ON KAN 1, Tac_OFF KAN 2
Josip prepared sequencing reactions for CDG W, CDG W/O, Hyd 1A, PDE, R_ON, R_OFF, LAC_ON, PDE + R_ON CAM 2, PDE + R_ON CAM 4, PDE + R_OFF CAM 1
Hannah prepared overnight cultures for competent cells
Jerresa, Hannah, Russel prepared a GFP assay for the inducible and constitutive riboswitches with salt concentrations

Dry Lab

Alice and Jerresa presented the weekly update presentation to our advisors and practiced their presentation for the Synthetic Biology Australasia Conference
Alice and Jerresa continued working on the SBA presentation with feedback from Associate Professor Louise Brown
Alice worked on content for the wiki
Eli, Josip, Sam, Tasneem, Thi, Dr Edward Moh and Professor Robert Willows discussed the spot assay results

Wet Lab

Josip transformed Hyd A + B colonies 4 and 7, CDG W and CDG W/O, Nissle CDG W KAN, Nissle CDG W/O CAM, DH5α A+B CAM 4, DH5α A+B CAM 7. BL21 (DE3) cells were used for transformation of Team Sydney Australia’s PsiD gene.
Anika, Daniel, Eli, Tasneem and Zoe performed an SDS-PAGE of the transformed PsiD (whole cell lysate, soluble fraction and pellet). Gel was repeated by Hannah
Sam prepared a biofilm formation assay to test the yhjh (with and without the promoter and terminator) in DH5α and Nissle 1917, yhjh + R_ON/R_OFF in DH5α and Nissle 1917
Anika and Zoe performed agarose gel of digests and 3xGibson assembly
Jerresa prepared a GFP assay for the yhjh + R_ON/R_OFF samples
Hannah and Josip miniprepped the CDG and yhjh
Jerresa transformed PDE + R_ON/R_OFF CAM with Nissle 1917

Dry Lab

We assigned team members to each wiki page and descriptions for the special prizes on the judging form
Everyone worked on content for the wiki and descriptions for the judging form
The team presented the weekly update presentation to our advisors

Wet Lab

Jerresa prepared a GFP assay for yhjh + R_ON/R_OFF with sucrose

Dry Lab

Alice and Jerresa travelled to Brisbane to attend the Synthetic Biology Australasia Conference and present our project to the synthetic biology community
Eli, Sam, Tasneem and Zoe worked on the wiki and judging form
Hannah wrote a report for the hydrogenase part
Jerresa presented the weekly advisors meeting. We received feedback on how to write our results and content for the wiki
All team members worked hard to finalise and upload content to the wiki and registry pages

Wet Lab

Sam and Tasneem redid the Congo red plates and Biofilm assay
Daniel performed SDS-PAGE for the Team NTU Singapore collaboration
We assembled the small subunit, large subunit, protease and phosphodiesterase via 3A assembly.

Dry Lab

All team members continued to work hard to finalise and upload content to the wiki and registry pages. Go Team HyDRA!

Wet Lab

Hannah and Jerresa performed an agarose gel for sequence confirmed parts. The last gel for iGEM 2019!

Team:Macquarie Australia/Notebook

NOTEBOOK