Mutatis Mutandis

<!DOCTYPE html> Collaborations

Collaborations

We are all part of the lovely iGEM community

Collaborations are a very necessary way of interacting with different groups of people and together achieving a common goal. It brings about the sense of teamwork and collaborative efforts of different teams to do something for the good of the world. We understand this emotion put forth by iGEM and have made an effort at working together with other iGEM teams.

We collaborated with other iGEM 2019 teams in different ways:

Water sample collection :
Collecting water samples from India iGEM teams and analyzing them for lead concentrations
Mentoring IISER Tirupati iGEM 2019 team :
The second collaboration of ours is mentoring the IISER Tirupati iGEM 2019 Team by helping them with experiments and supporting them in their work.
IISER Kolkata iGEM 2019 Team collaboration :
Assisting IISER Kolkata iGEM team 2019 in spreading awareness about Leishmaniases in our institute.
All India iGEM Meetup attendee :
Attended the All India iGEM Meetup 2019 held organised by IISER Bhopal iGEM team 2019 and gained feedback on our project that helped us improve.
Interactions through Social media :
We interacted with multiple Indian iGEM 2019 Teams through Whatsapp and Facebook to seek and provide help regarding various issues and concerns.

The details are available below

To evaluate the performance of our system, we aimed at evolving a Lead (Pb²⁺) bioremediation gene for better efficiency. We decided to do this concerning a local river of Pune which once was a lifeline has now become wastewater. We decided that it’s necessary to focus not just on our polluted local water body but also look at the bigger picture by focusing on the lead pollution of water bodies across India. The current accepted WHO limit to lead concentration in a water body is reported to be 0.01 mg/L.

For this, we requested all the Indian iGEM 2019 teams to bring water samples from any of the local water bodies of their respective cities to the All India iGEM Meetup. A detailed instruction list was provided to all of them as to how they should provide these samples to us. This included the extensive procedure to be followed for handling the water and the container in which it will be stored and other instructions such as noting the weather condition at the time of collection, any algal growth, the biodiversity (at least to the best of the knowledge of the collector) in the water body, etc.

Click to open Instructions sheet

Once we got these samples, we wanted to analyze these for lead concentrations, for which we used the biosensor biobrick designed by Bielefeld 2015 iGEM team (Part number: BBa_K1758333). This way, we also characterize the working and relative accuracy of the part.

Water Bodies	Location	Weather and Temperature	Biodiversity	Additional Information
Kalpakkam lake	Tamil Nadu	Cloudy, 27^oC	Crayfish, Edible shrimp, Sow bug, Barnacles	Has witnessed higher amount of lead contamination
Chembarambakkam lake	Kanchipuram, Tamil Nadu	Cloudy, 30^oC	Edible fish, Zooplanktons, Benthos	-

Kalpakkam lake, as we can see is surrounded by agricultural fields which probably receives a lot of agricultural runoff. Water for these backwaters come from the bay of bengal, which may also receive some of this runoff. But due to circulation with the bay of bengal, the lead/other heavy metal contaminations would be less. Due to the presence of “edible” fishes, we presume that this water body may not be very polluted.

Chembarambakkam lake as we can see can be called what is called a “dying lake” which is surrounded by houses and agricultural fields. There is no inflow for the lake through any river nor is there a common reservoir to it like the Kalpakkam lake. As a result, any domestic waste dumped into the lake will remain in it until it naturally degrades.

Water Bodies	Location	Weather and Temperature	Biodiversity	Additional Information
Bellandur Lake	Bangalore, Karnataka	Cloudy, 25^oC ; It did not rain for at least a week before collection in the area around IISc.	Water Hyacinth , other than that, could not spot any visible living organism, the water was too polluted to make out. Even insects on the surface of the water could not be spotted. No fish or animal whatsoever.	- Sewage and Effluent from Industries flowing into the lake -Water body having metal contamination , plastics, Heavy foaming,etc

Satellite image of the Bellandur Lake. The green depositions are algal blooms over the blue water and the sample was collected in the region marked with the white pin. As we can see, this too is an example of a dying lake which is almost completely covered by algal blooms. The lake is surrounded by factories and aeronautical industries and receives a huge inflow of industrial and domestic waste that the algae feed upon. The lake also experiences frothing due to discharge of detergents and other heavy metals.

Water Bodies

Location

Weather and Temperature

Biodiversity

Additional Information

IISER Kolkata Gate 7 water pump

Kolkata, West Bengal

The weather was sunny and humid. In the middle of monsoon, i.e. Rain is very frequent. Average temp is near 30°C

Types of living organisms found inside: Algae, soil microbes, nematodes(probabilistic). E.coli, Salmonella, S. aureus, P. aeruginosa

-The source of this water pump is from groundwater reserves that get replenished by local water bodies, (i.e. lakes, ponds, rivers etc). It is very unsafe for drinking.

-These water bodies may be used as dumping grounds for sewage and other wastes. The water pump is located in a rural setting with many villages and fields nearby.

- Arsenic contamination is also very viable

The water source as we can see is from a water pump in the middle of the city which presumably receives a lot of domestic waste and since the main source of this is the groundwater which can sometimes easily get contaminated with heavy metals due to inappropriate waste disposal from the surrounding household and shops. This risk of contamination makes the water not very suitable for consumption thereby affecting lives of nearby people.

Water Bodies	Location	Weather and Temperature	Biodiversity	Additional Information
Small permanent lake in Chithera village	Tehsil Dadri, Uttar Pradesh	The water sample they collected was in mid-july, it was hot, humid, and it would rain occasionally. It was a sunny, humid afternoon with average temperatures around 35^oC(max.)-27^oC(min) at the time we collected our sample. It had rained that week.	They could observe water hyacinth and green water with some filamentous growth indicating algal growth; The area is frequented by rural animals like cattle (cows, buffaloes), dogs and cats. However, we would like to mention that Dadri is a part of the vast Surajpur wetland ecosystem which has a unique biodiversity, and is visited by migratory birds, is well-documented and is currently threatened due to anthropogenic factors like agriculture, urbanization etc.	There were a few small artificial canals flowing into the pond that could have been dumping domestic, cattle and agricultural waste. Since Dadri is a wetland area, the other inlet/source of water for this pond would be groundwater and rainwater.

Some additional information provided by the team was the biodiversity of the Surajpur wetland Ecosystem which is as follows:
Flora: 220 species of Plants were recorded including 155 Herbs, 11 Shrubs, 36 Tree and 18 species of Hebasius Climbers.

Fauna: Total 180 birds species (Water birds - 82, Woodland birds - 99, Grassland birds - 49) with 48 families were recorded. * 13 species of fish were recorded. * Total 58 invertebrates (Butterflies - 44, Dragonflies - 6, Annelids - 3, Arthropods - 3, Mollecus - 2) were recorded. * 8 species of reptiles were recorded. * 6 species of mammals were recorded.
Looking at all this information, we interpret that this reservoir is a lifeline to many species of birds and insects. The algal blooms and vegetation on this lake may be fed upon by birds and fishes and may be a part of an extensive food chain. Being a part of a national restricted ecosystem, there may be appropriate drainage and sewage treatment systems before discharging them into the lake. Nevertheless, we will know upon looking at the lead concentration of this lake.

Water Bodies	Location	Weather and Temperature	Biodiversity	Additional Information
Lake/reservoir near IISER Tirupati	Tirupati, Andhra Pradesh	-	- There are several trees and vegetation around the lake (No specific species of vegetation provided by the collector). -Some fish are seen in the lake and there have also been washed up dead fish.	-There are no industries around the water body but there is some amount of garbage thrown nearby and into the lake. - There are several trees and vegetation around the lake, some fish are seen in the lake and we have also seen washed up dead fish.

As we can see from this lake, it is drying up resulting in the exposure of the sand and dirt depositions that have occured due to constant run-off from agricultural fields. The lake does not have any natural sources or sink for circulation indicating that the only sources of water for this lake would be rainwater and groundwater. Due to poor enrichment and circulation of water, it leads to the lake becoming inhabitable for many aquatic organisms explaining the washed up dead fish.

Water Bodies

Location

Weather and Temperature

Biodiversity

Additional Information

Khadakwasla dam backwaters through with the Mutha river flows

Pune, Maharashtra

Temperature was about 15-20^oC and it was monsoon. It was raining heavily around the time of water sample collection.

The river has a lot of fish and birds who collect those fishes. Might have to swim 200-300ms from the shore to have a look at those fish.

-The backwaters has no industry effluents thrown in it since the water is used for irrigation.

-People are seen swimming in the water and it is relatively clean.

-No agricultural fields or industries around the area.

Since water sample collection point is a dam, there won’t be much/any lead contamination. This is indicated by the hush greenery and the vast number of fish seen in the water. Since there are no industrial or agricultural effluents flowing into the reservoir, the amount of pollution caused would be less.

Water Bodies	Location	Weather and Temperature	Biodiversity	Additional Information
Water reservoir inside IISER Bhopal	Bhopal, Madhya Pradesh	Temperature was around 28^oC with a humidity of 90%.The sample was taken during the summer season as a result it was sunny with no traces of rain.	-	The reservoir is constructed for rain water harvesting and usually sees low contamination and low biodiversity. The sample was taken from the upper layer of the reservoir.

The location of this reservoir is inside the institute which raises questions about it being used as a source as well as sink. Being a rainwater harvesting point, it clearly is only replenished by rain water and no rain would mean no circulation which during the summers can mean stagnation. This reservoir is used for most of the institute’s needs and may/may not be a sink to used-up water. Nothing else can be said as we do not have the data of the biodiversity in/or around the reservoir.

Our team has mentored and collaborated with the IISER Tirupati iGEM team 2019 and have helped in trouble shooting their experiments initially during the course of iGEM 2019.

Aarti Kejriwal was mainly involved in helping them out. She helped them out with:

1) Detailed protocol for Competent cells preparation

2) Poster and presentation making for the All India iGEM Meetup

3) Measurement assay

4) General queries regarding troubleshooting of experiments and human practices

Pranav, Utkarsh and Supratim also did a Skype session with them in which we gave them a few tips about human practices and how they should approach teaching school children about synthetic biology, DNA, proteins and the very nature of the central dogma of molecular biology. We also helped them structure their project in the sense that we discussed with them what all medal criterias they had currently filled and what they should focus on next so as to tick off most criterias in the shortest amount of time possible. We hope our support has helped them achieve their goal.

The IISER Kolkata iGEM team 2019 are working on developing a synthetic biology tool for detection of Leishmaniasis before the onset of the protozoan disease. This tool is highly required in today’s world where people don’t have much knowledge and awareness about this disease. Due to this, the disease is checked for only once the symptoms show which, most of the time, is too late. For this concern, the IISER Kolkata iGEM team sent us and the other Indian iGEM 2019 teams a survey form to fill out so that they could assess how much knowledge and awareness do people have about Leishmaniasis around the country. We understand their cause and motivation for doing this survey and forwarded this message to all students of IISER Pune including undergraduate, overgraduate students.

The form has also been made accessible here

IISER-Kolkata 2019 iGEM Survey Form

Because of iGEM 2019, and the All India iGEM Meetup, not only were we able to interact with the IISER Kolkata team and know about Leishmaniasis ourselves, but we were also able to help them by spreading awareness about the disease in our institute.

This year’s All India iGEM Meet-up was held in IISER Bhopal organised by the 2019 IISER Bhopal iGEM team. 12 Indian teams attended the meet-up and every team presented some slides and a poster regarding their projects. Teams helped each other by posing potential problems with the projects and then brainstorming solutions for the same. We talked about safety, viability, usefulness of each project. This helped us a lot in improving our work. This meetup also gave us the opportunity to learn a lot about the delivery of a good scientific presentation and poster.

Professors from IISER Bhopal, Dr. Apurba Lal Kaner and Dr. Ankur Gupta who had been the witness and judges to our project ideas, also had a lot of comments on our project that made us realize many things that we hadn’t been able to think of before. We also met the Asian ambassador Nurul Izzati who had a few tips about presentations in general and how human practices is a very important and necessary way of reaching the common man.

We got to talk to many teams via social media like Whatsapp and Facebook. We filled survey forms of many teams and also forwarded them to the others through whatsapp. We had a very active iGEM India WhatsApp group which was extremely helpful throughout the course of the project, be it the Visa application or DNA ordering or troubleshoot of some experiment, this group always been of incalculable help.

We are people of culture too!

Team:IISER-Pune-India/Collaborations