TReND in Africa https://trendinafrica.org Teaching and Research in Natural Sciences for Development in Africa Wed, 15 Apr 2020 10:20:57 +0000 en-US hourly 1 https://wordpress.org/?v=5.4.1 https://trendinafrica.org/wp-content/uploads/2019/11/cropped-logo2019-32x32.png TReND in Africa https://trendinafrica.org 32 32 A message regarding the COVID-19 pandemic https://trendinafrica.org/2020/04/covid19/ https://trendinafrica.org/2020/04/covid19/#respond Tue, 07 Apr 2020 10:14:33 +0000 https://trendinafrica.org/?p=4466

A message to the TReND community

 

Dear TReND in Africa community!

We hope that you are all well. We have seen with horror how Covid-19 is ravaging European countries with good health infrastructures, such as Spain or Italy, and even in the UK, the situation is difficult. As we see the news of how the virus has by now reached most African countries, we wanted to encourage you as academics to play a central role in the local management of this epidemic. Here are some of the things that you can do. This advice is based on what we have seen work or not in Europe and is not comprehensive, but we thought that if we all get together in our respective countries, we might be able to make a big difference in people’s lives.

1 – Please, now more than ever, it is essential that you engage in outreach. We would like to ask all of you to explain to people how the virus works, and how everyone can do their part to protect themselves and others. Here are some key points that you could explain the general population:

  • The virus enters the body mostly through your mouth, nose, and eyes. This is why it is so important to not touch your face while on the street and to wash your hands
  • The virus is covered in a layer of fat if that layer is destroyed then the virus dies. Soap destroys fat, therefore is the best weapon we have against the spread of the virus. This is why washing hands regularly with soapy water is so important. The virus can stay on surfaces for a very long time (it is not clear how long but could be days!), therefore it is important to wash surfaces, also food like vegetables bought in the market should be washed with soapy water before putting in the home. Because fat is also dissolved with heat, cooking food is another efficient way of destroying the virus. We found that explaining things in these simple terms to the general public was very effective.
  • The virus is transmitted when people cough onto other people or surfaces that are touched by other people. Therefore, if you leave the house, try to not touch many surfaces and always wash your hands afterward. Because when people cough the virus can travel in the air up to 2 meters, it is important to keep a distance of at least 2 meters between you and anyone else when on the street. This is what the authorities here call social distancing.
  • The virus is not killed with antibiotics, in fact, there currently is no treatment (don’t trust things you may have seen in social media/news). If people develop symptoms such as fever and dry cough, the best thing they can do is to stay at home without close contact with anyone to not transmit the virus. If they are feeling seriously ill, they should be taken to the hospital with careful social distancing measures.
  • Most facial masks are effective if worn by the infected person to not transmit it to the rest. However, as a healthy individual, wearing a mask offers only limited protection. In particular, when you wear a mask you tend to touch your face more, increasing the risk of transmitting the virus from your hands to your eyes where it can enter your body. Therefore, masks can be efficient, but only if used correctly. It is important to explain this to people, so people who have access to or can build their own masks wear them but do so in the right way, and importantly don’t get a false sense of protection. You can still catch it even while wearing a mask.
  • In addition to conducting outreach activities, we encourage scientists to engage in dispelling misconceptions on social media platforms, by writing posts and making short videos. Most times, people download such videos and share them with other groups. This will help in debunking the disinformation going around on this new disease. We advise scientists to be guided by science supported by authorized institutions, such as the World Health Organisation, in the content they
    produce.
  • We recently launched the African Science Literacy Network (ASLN) dedicated to promoting science awareness through scientists – journalists collaboration (www.AfricanSciLit.org [1]). ASLN has launched a COVID-19 dedicated page for articles and myth busters in English and different African languages (https://www.africanscilit.org/covid-19-updates). Get in touch with them if you wish to contribute articles in English or your local language to enhance awareness about COVID-19 during this trying time (info@africanscilit.org).
  • Finally, in the coming days, we will try to set up a google drive folder with resources for outreach for Covid.

2 – Early detection of cases followed by isolation is very important, in fact, it was deemed by the WHO as the best strategy to control the virus.
However, to detect positive cases, one needs to test. Now, testing is being a limiting factor everywhere. Here in the UK universities are trying to help the health system with this, but it is not easy. So we would like to ask you to be pro-active, please engage with your government and other institutions, every country needs to make use of all of its facilities and workforce to get enough testing going, but this needs to be prepared in advance. You possibly still have a few weeks before locally it gets as bad as it already is over here, but now is the time to engage in these conversations. There are some internationally approved tests, but these are expensive to run, there are not enough machines or reagents even in the UK to take on the required demand, and therefore people have started trying alternative
testing methods in research laboratories. When these are shown to work, we will try to convince our governments that several testing strategies need to be approved. Once they are approved, we gain capacity. This is the kind of discussion you need to engage in. Check the existing facilities and knowledge at your institution, inform yourselves, and engage with the government. Read up on and if you can try different diagnostic tests and evaluate which one is the best, then communicate this clearly to the government to get these officially approved for testing. Tens of thousands of the world’s top scientists in relevant fields are currently working together to find solutions, so the state of knowledge in this field changes daily. So keep up with the relevant literature, if you have the right expertise to digest them. You can find attached here a summary of the diagnostic tests that are out there with some explanation. Please read through these papers, forward this email to your colleagues. And again, by tomorrow we might already know more. Keep up to date.

Lastly, there is also a big effort from the open hardware community to help out, you can find a summary of these efforts in a paper we have recently written: https://www.preprints.org/manuscript/202003.0362/v1

It might seem that a single researcher cannot do anything, but together we can make a big difference. Ask yourselves, if not you, then who in your region can help?

 

Best wishes,

Lucia

In name of the TReND team.

 

 

A collection of useful links and information

This is a place to share protocols and information on Covid diagnostic methods and efforts at our institutions. 

To join the OpenCOVID discussion:

https://join.slack.com/t/open-covid19/shared_invite/zt-cbji2hte-8jdoHpJDKg80ZliPVCIjqw (Slack Invitation)

https://app.slack.com/client/TUU48M0T1/C0103J8NF46/thread/C0102E5J2S3-1584911869.324700 (link to chlg-detect channel)

Overview

Tests basically fall into nucleic acid tests that detect viral RNA and reveal active infection and serological (antibody) tests that reveal well-established or prior infection. In general viral RNA tests will be more sensitive in the early stages of infection before antibodies have been generated. At present, viral RNA tests roughly divide into PCR tests which are typically the most sensitive and quantitative and other test strategies which are likely to be qualitative / less sensitive but may be simpler to run outside a laboratory setting.

PCR Tests

To do RT-qPCR but without RNA extraction

https://www.biorxiv.org/content/10.1101/2020.03.20.001008v1.full.pdf

To extract RNA without kit

http://www.en-journal.org/journal/view.html?uid=513&vmd=Full

Digital Droplet PCR for simpler quantification.

Alternative methods that do not use qPCR

These mostly come under the heading of isothermal amplification. NEB has pretty good coverage at their isothermal amplification page. In general these are likely to be qualitative rather than quantitative, less sensitive but simpler and faster to run and more compatible with point of care use. Some integrated procedures with one tube lysis/reaction look particularly interesting. The widely touted Abbott ID NOW test is of this class.

RT-LAMP

This protocol was recommended by Guy Aidelberg:https://pubs.acs.org/doi/10.1021/acs.analchem.5b04054

This is the one from NEB (this is the one being tried at the crick):https://www.medrxiv.org/content/10.1101/2020.02.26.20028373v1.full.pdf

Another one: https://www.medrxiv.org/content/10.1101/2020.02.20.20025874v1.full.pdf

NEAR (Nicking and extension amplification reaction)

Patent: https://patents.google.com/patent/US20090081670A1/en

Test for flu based on NEAR by Alere/Abbott: https://www.sciencedirect.com/science/article/pii/S1386653214002145

RPA (Recombinase Polymerase Amplification)

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040204

https://www.twistdx.co.uk/en/rpa

SENSR

https://www.medrxiv.org/content/10.1101/2020.03.05.20031971v2.full.pdf

CRISPR based

https://www.broadinstitute.org/files/publications/special/COVID-19%20detection%20(updated).pdf SHERLOCK (Broad)

https://www.medrxiv.org/content/10.1101/2020.03.06.20032334v1.full.pdf DETECTR (UCSF/Mammoth)

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Service and Excellence: Collaborative Science Symposium 2020 at the University of Zambia https://trendinafrica.org/2020/03/service-and-excellence-collaborative-science-symposium-2020-at-the-university-of-zambia/ Wed, 04 Mar 2020 15:03:46 +0000 https://trendinafrica.org/?p=4420

Researchers from Germany and the U.S. set off to train African junior scientists in their careers at Collaborative Science Symposium 2020

By Franziska Bröker, Miriam Rateike, and Renée Hartig

It is early January, rainy season, and research questions are looming in the air: How has mining the Central African Copper Belt impacted soil bacterial populations? How do fungi influence one of Zambia’s most important agricultural products – peanuts? From preparing a proposal to pitching a poster, students at the University of Zambia researched such questions during the Collaborative Science Symposium 2020. This week-long training program introduced natural science undergraduates and graduates to accessible research methods, scientific soft skills, and a network of international mentors, empowering young scientists to move their careers forward.

Teaming up for the unexpected

For this purpose, six researchers from the Max Planck Society (Germany) and Temple University (PA, USA) teamed up to travel to Lusaka, Zambia’s buzzing capital. Prepared for the expected, and excited for the unexpected, the Symposium team expressed the shared motivation to educate and learn. The University of Zambia was the first in the country to open its doors in 1966, and today welcomes you with its motto in big print: Service and Excellence. A mission not only reflected on the campus gates but also in the symposium.

“It was already the second year that the Collaborative Science Symposium materialized in Zambia after its launch in early 2019, together with the non-profit organization TReND in Africa,” says Dr. Renée Hartig, a neurobiologist and TReND program coordinator. “TReND aims to address the lack of human, material and financial resources hindering research proficiency on the African continent.”

Hands-on training from coding to scientific writing

Overlooking palm trees, a group of 30 students took hold of a journey through the layers of the scientific method. Teams conceived of research projects, building on material from morning lectures which touched on topics including literature review, experimental design, statistics and machine learning. The symposium participants demonstrated a profound ability to absorb the information presented in the lectures as they assembled it into coherent research proposals, posters, and elevator pitches. During afternoon sessions, the leading team from Germany and the U.S. offered hands-on training in computer programming, public speaking, and scientific writing. These one-on-one practical sessions also laid the foundations for cultural exchange and future mentoring.

Symposium workshop topics, such as research ethics and fairness in machine learning, sparked discussions on the impact and responsibilities of scientists. It also had the six teaming researchers think about questions like how to promote online resources at universities with limited internet access. In short, the symposium proved to be a truly bidirectional learning experience that opened new intellectual territory to all. “We encouraged participants to pursue their scientific ambitions, and returned home with a much broader horizon ourselves”, states PhD student Franziska Bröker.

True service and excellence in higher education

Service and Excellence in higher education was reflected at the Collaborative Science Symposium. High agility revealed a scientific maturity and commitment to knowledge. We met brilliant young scientists that brought tremendous hard work and motivation to the classroom. Friendships and mentorships that were developed are maintained remotely – a symposium that doesn’t end with the last talk.

This programme should continue each and every year. It’s been great. It’s an excellent way of starting any year by learning skills that will be applied during the course of the year,” says Namakando Mebelo, a fourth year undergraduate studying microbiology.

During this year’s symposium two African graduate students spoke via video recordings in the classroom about their experiences with going abroad for graduate studies. Kandamali Deus Francis from Tanzania, a PhD student at Beijing Jiaotong University (Beijing, China), encouraged students to get out of their comfort zone and join research, highlighting the importance of multidisciplinary research and international cooperation. Elie Ngomseu Mambou from Cameroon, a PhD student at McGill University (Montreal, Canada), fortified: “I believe in a new generation of African leaders that will lead by education.”

Within two years, the Collaborative Science Symposium has gained support from the Max Planck Society, Tübingen University, University of California Los Angeles, University of Central Florida and Temple University. We explicitly thank our supporters and the Max Planck Society for their financial support and trust in us to effectively turn resources into useful knowledge, sustainable relationships, and lasting impressions. Additionally, we thank Dr. Daniel Fleiter, Head of Communications at the Max Planck Institute for Biological Cybernetics, for his helpful comments on this article for press release.

The Collaborative Science Symposium 2020 was held by Dr. Renée Hartig and Franziska Bröker, Max Planck Institute for Biological Cybernetics, Anastasia Lado and Miriam Rateike, Max Planck Institute for Intelligent Systems, both in Tübingen, Germany and Professors Kevin Arceneaux and Valentina Parma, from Temple University, Philadelphia, USA.

If anyone is interested in this program and feels that they would like to take part at some point, please do reach out! Just send an email to science.symposium19@gmail.com expressing your interest and an effort will be made to incorporate your ambitions for the next journey.

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Applications open now! https://trendinafrica.org/2019/08/applications-open-now/ https://trendinafrica.org/2019/08/applications-open-now/#respond Fri, 23 Aug 2019 12:28:36 +0000 http://trendinafrica.org/?p=3979 Invertebrate Neuroscience 2019. Only 3 days left to apply!

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Applications open now: Science Communication and Journalism https://trendinafrica.org/2019/07/applications-open-now-science-communication-and-journalism/ https://trendinafrica.org/2019/07/applications-open-now-science-communication-and-journalism/#respond Mon, 29 Jul 2019 14:27:44 +0000 http://trendinafrica.org/?p=3973 Apply here

 

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Applications open now – TReND pre-SONA workshop https://trendinafrica.org/2018/11/applications-open-now-trend-pre-sona-workshop/ https://trendinafrica.org/2018/11/applications-open-now-trend-pre-sona-workshop/#respond Mon, 26 Nov 2018 15:29:33 +0000 http://trendinafrica.org/?p=3969

Apply now at bit.ly/2QkZyP5

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Applications open: 1st Advanced Open Labware Course, Cape Town https://trendinafrica.org/2018/01/applications-open-1st-advanced-open-labware-course-cape-town/ https://trendinafrica.org/2018/01/applications-open-1st-advanced-open-labware-course-cape-town/#respond Tue, 16 Jan 2018 10:45:55 +0000 http://trendinafrica.org/?p=3917 We are pleased to announce the 1st Advanced Open Labware Course, to be held in Cape Town, South Africa this April. Applications open now!

Apply here!

Also, please help us spread the word! For example, why not print the poster.pdf and hang it on your Departmental notice board? Thanks!

 

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2nd TReND Science festival-Nigeria https://trendinafrica.org/2017/10/2nd-trend-science-festival-nigeria/ https://trendinafrica.org/2017/10/2nd-trend-science-festival-nigeria/#respond Tue, 10 Oct 2017 20:50:01 +0000 http://trendinafrica.org/?p=3899 We are excited to announce our 2nd Science Festival, happening on

20th – 21st November 2017

Yobe State University, Nigeria

 

If you would like to attend, please lasix order online send expression of interest to participate by 31st October to

M.Bukar-Maina@sussex.ac.uk

 

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TReND’s Volunteering Program is waiting for you! https://trendinafrica.org/2017/08/trends-volunteering-program-is-waiting-for-you/ https://trendinafrica.org/2017/08/trends-volunteering-program-is-waiting-for-you/#respond Tue, 29 Aug 2017 12:15:34 +0000 http://trendinafrica.org/?p=3864 During the first half of 2017 things were quite busy for TReND’s Volunteering ProgramSeven European researchers visited Universities in Sudan, Tanzania, Sierra Leone and Ethiopia, and more projects are one the making! Below you can read what some of our volunteers thought about their experiences.

If you get inspired and would also like to spend some time teaching in Africa, apply to our Volunteering Program now!

Anna Bennis

PhD candidate Dept Clinical Genetics, VU University, Amsterdam, Netherlands
Volunteered  at the University of Freetown, Sierra Leone, between mid-February and mid-April 2017

“Creativity is such an important part of science. I am very happy with the effort of the students and so proud of them! And also I had a really good time teaching and talking with them”

“I really enjoyed discussing research with the students. I remember the amazement and enthusiasm about sheep Dolly and the possibility to clone, and all the questions that came up. We talked about what makes a cell a cell: what does it consist of, what makes a neuron a neuron and a skin cell a skin cell when the DNA is the same in every cell”

Dr. Luisa Vigevani and Dr. Domenica Marchese

Post docs at the Centre of genomic Regulation, Barcelona, Spain
Volunteers at the University of Khartoum, Sudan, in April 2017

“What mainly rewarded us from this volunteering experience was to see that students were very curious and excited to learn, but also very eager to show and discuss with us their projects and results. This, in fact, was an interesting occasion of professional growth also for us!”

Carolina Thieleke Matos

Former postdoc at Postdoctoral Researcher at Imperial College London and University College of London, London, UK
Volunteered at the IMTU University, Tanzania, in January 2017

“When IMTU University asked me to join them for a couple of months I could not believe it. Luckily I was able to take that opportunity and in six months I was flying on my way to Dar es Salam to teach parasitology.  I can tell you that I ended up learning more than teaching.  Thanks to Trend in Africa organization, this kind of exchange is now possible and everyone that has the chance should do it!”

 

One of Carolina’s students said:

“It was really a great honour and privilege meeting Madame Carolina and spending a few months with her, apart from her friendly nature it was very eye opening and encouraging for me to learn more about what is really out there and she has only just increased my curiosity to keep on striving to attain new knowledge and information only to apply them in my home town and try making it a better place…”

 

Click here to learn more about TReND’s Volunteering Program now

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Applications open now: 7th Neuroscience school, Gombe, Nigeria https://trendinafrica.org/2017/08/applications-open-now-7th-neuroscience-school-gombe-nigeria/ https://trendinafrica.org/2017/08/applications-open-now-7th-neuroscience-school-gombe-nigeria/#respond Tue, 01 Aug 2017 13:20:37 +0000 http://trendinafrica.org/?p=3846 We are excited to announce the 7th installment of our annual Drosophila Neurogenetics course, this time to be held at Gombe State University, Nigeria.

13th November – 2nd December 2017.

Deadline Sept 1st 2017. Applications are now closed!

For an impression of previous schools, see here:

Past neuroscience schools

– 4th IBRO school on insect neuroscience and Drosophila neurogenetics, KIU Dar es Salaam campus, Tanzania. 24th October 13th November 2016 . Course Booklet, Picture Gallery

–  5th TReND/ISN school on insect neuroscience and Drosophila neurogenetics, KIU Dar es Salaam campus, Tanzania. 17th August 05th September 2015 . Course Booklet, Picture Gallery

– 3rd IBRO school on insect neuroscience and Drosophila neurogenetics, Department of Zoology, University of Dar es Salaam, Tanzania. 11th-30th August 2014 . Applications will likely open in April 2014. Course Booklet, Picture Gallery

– 2nd IBRO school on insect neuroscience and Drosophila neurogenetics, School of Health Sciences, Kampala International University, Uganda. 19th August – 8th September 2013. Full report. programme. Course Booklet. Picture Gallery

– 1st IBRO school on insect neuroscience and Drosophila neurogenetics, School of Health Sciences, Kampala International University, Uganda. 20th August – 7th September 2012. report. programme. Course Booklet . Picture Gallery

– Drosophila neurogenetics course. School of Health Sciences, Kampala International University, Uganda. 10th – 29th October 2011. Blog of the course. Picture Gallery

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Outreach in Entebbe, Uganda https://trendinafrica.org/2017/07/outreach-in-entebbe-uganda/ https://trendinafrica.org/2017/07/outreach-in-entebbe-uganda/#respond Fri, 21 Jul 2017 09:20:33 +0000 http://trendinafrica.org/?p=3837 Our outreach team used their spare time before the SONA Conference in Entebbe last month to inspire students from six secondary schools about science. They got the students to learn first hand, through experiments, about fractionating and estimating protein concentration in house flies; learned how to investigate learning and memory in fruit fly larvae; couple the DNA and some students even got to simulate brain signal speed and how it goes aberrant in cases of dementia. At the end, students made a presentation on their experiments, for which many won prizes and reagent leftovers were donated to all the schools that participated. Many thanks to Mahmoud, Yunusa and Sadiq for organising the outreach. We thank the Serpell lab, University of Sussex UK and the Galizia lab, University of Konstanz, Germany,  for donating some reagents used for the outreach.  See some pictures for impression.

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