Collaborative project for merAB database development

[Mersor cium]

Dear Mersorcium community,

I hope this email finds you well. Following our recent seminar on "Identification and verification of merAB genes", we wanted to reach out regarding the idea that emerged about developing a curated merAB genes database. Given our shared interest in improving the identification of these genes, we believe that a collaborative effort could be highly beneficial to the research community.

If you are open to discussing this further, we would love to schedule a meeting to explore how we could organize this initiative. Please reply to this email if you would be interested in participating at any level in this project, or feel free to share any thoughts you might have.  

Additionally, we encourage you to share this information with whomever you may think is also interested. 

We look forward to hearing from you.

Best wishes,

MERSORCIUM consortium board

[Nicola Gambardella]

Hello,

I would be very interested in participating in this initiative.

I have developed a simple software for MerAB identification and I think that a merAB gene database would be very beneficial to the scientific community and beyond.

Best regard,

Nicola

Nicola Gambardella, M.Sc.

Investigador | Researcher

https://becarios.fundacionlacaixa.org/nicola-gambardella--B006487

 

CIIMAR | Interdisciplinary Centre of Marine and Environmental Research

of the University of Porto

Terminal de Cruzeiros do Porto de Leixões

Avenida General Norton de Matos, S/N

4450-208 Matosinhos | Portugal

E-mail: ngambardella@ciimar.up.pt

Tel. (+351) 223 401 8xx

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From: merso...@googlegroups.com <merso...@googlegroups.com> on behalf of Mersor cium <merso...@gmail.com>
Sent: Tuesday, March 11, 2025 2:25:19 PM
To: merso...@googlegroups.com; Mersor cium
Subject: [Mersorcium] Collaborative project for merAB database development

 

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[Carla Pereira-Garcia]

Hello, 

I already said during the session that I think is a great idea and that I would be interested in participating! 

I hope more people answer soon and we can make it happen!! 

Cheers, 

Carla. 

El 11 mar 2025, a las 16:09, 'Nicola Gambardella' via Mersorcium <merso...@googlegroups.com> escribió:

Hello,

I would be very interested in participating in this initiative.

I have developed a simple software for MerAB identification and I think that a merAB gene database would be very beneficial to the scientific community and beyond.

Best regard,

Nicola

Nicola Gambardella, M.Sc.

Investigador | Researcher

https://becarios.fundacionlacaixa.org/nicola-gambardella--B006487

 

CIIMAR | Interdisciplinary Centre of Marine and Environmental Research

of the University of Porto

Terminal de Cruzeiros do Porto de Leixões

Avenida General Norton de Matos, S/N

4450-208 Matosinhos | Portugal

E-mail: ngambardella@ciimar.up.pt

Tel. (+351) 223 401 8xx

<OutlookEmoji-1717578994089c6cda800-3fda-454f-97a0-fd007a2ccb54.png>

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From: merso...@googlegroups.com <merso...@googlegroups.com> on behalf of Mersor cium <merso...@gmail.com>
Sent: Tuesday, March 11, 2025 2:25:19 PM
To: merso...@googlegroups.com; Mersor cium
Subject: [Mersorcium] Collaborative project for merAB database development

 

⚠️EXTERNAL E-MAIL⚠️
--

Dear Mersorcium community,

I hope this email finds you well. Following our recent seminar on "Identification and verification of merAB genes", we wanted to reach out regarding the idea that emerged about developing a curated merAB genes database. Given our shared interest in improving the identification of these genes, we believe that a collaborative effort could be highly beneficial to the research community.

If you are open to discussing this further, we would love to schedule a meeting to explore how we could organize this initiative. Please reply to this email if you would be interested in participating at any level in this project, or feel free to share any thoughts you might have.  

Additionally, we encourage you to share this information with whomever you may think is also interested. 

We look forward to hearing from you.

Best wishes,

MERSORCIUM consortium board

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You received this message because you are subscribed to the Google Groups "Mersorcium" group.
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<OutlookEmoji-17175789940895743c01f-7e37-4fac-81ae-e9e4ac09f964.png><OutlookEmoji-1717578994089a82c5fe5-8689-489e-820d-79890689d6f4.png><OutlookEmoji-1717578994089758fc31a-2afd-406b-9fef-eef82f7c0eb2.png><OutlookEmoji-171757899408946ba4009-ebe7-42e9-9838-66f0ee956267.png>

[ch.chr...@yahoo.gr]

Hello all,

I am the author of the paperwork "Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea" that published in 2021 in Frontiers.

I had produced and published (and shared here some time ago) the database I had created with merAB genes.

Though my time is really limited, I would be happy to share any data I have, and help in any way.

Let me know how I can be of help

With best regards,

Christos 

https://groups.google.com/d/msgid/mersorcium/B09FCE0D-A52F-4C4C-9FEA-642185FD143A%40gmail.com

.

[Eric Capo]

Hi all,

Happy to give a hand as well. That is a great news that we also have Christos onboard for this! The merA and merB HMM profiles I built for marky-coco are based on his database (Christakis et al 2021). In my point of view, it would be great to get a curated database AND mer gene reference trees, as the one done for hgcAB genes by Caitlin Gionfriddo in Hg-MATE. That would allow us to do phylogenetic identification of each new merA and merB genes without having to redo trees for each new project. We did some with Isa few weeks ago and it tooks >2 weeks for a merA tree while pplacer in a ref tree take 5 seconds per gene.

Enough words for tonight, I am super keen to provide help but even more excited to see the new generation working on this 🙂

Cheers

Eric

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From: 'ch.chr...@yahoo.gr' via Mersorcium <merso...@googlegroups.com>
Sent: Tuesday, March 11, 2025 20:25
To: cperei...@gmail.com <cperei...@gmail.com>; Nicola Gambardella <ngamba...@ciimar.up.pt>
Cc: Mersor cium <merso...@gmail.com>; merso...@googlegroups.com <merso...@googlegroups.com>
Subject: Re: [Mersorcium] Collaborative project for merAB database development

 

To view this discussion visit https://groups.google.com/d/msgid/mersorcium/969179695.4665557.1741721113452%40mail.yahoo.com.

[Alyssa Azaroff]

Hello

I am eager to be involved in this initiative!

Cheers,

Alyssa

To view this discussion visit https://groups.google.com/d/msgid/mersorcium/GVYP280MB0890663DECE061536C962EBA81D12%40GVYP280MB0890.SWEP280.PROD.OUTLOOK.COM.

[Carla Pereira-Garcia]

Hello!! 

But the way Eric, didn’t you start this process to add the mer genes into the second version of the Hg-MATE. How far did you get? Could you share with us what was done or if you had any course of action already in motion. Maybe we can revisit your original thoughts and built on that. 

Also, I haven’t worked on anything similar and I think it’s the case for most people. So I think I speak for everyone when I say that those involved on the creation of the Hg-MATE or Christos with your merAB db, please share your process. Where did you start? What’s the first step on a massive project like this one?? 

I think that we need to make a smaller thread of mails with those of us who are interested in participating so the rest of the mersorcium members dont get spammed with it. I’ll create a subgroup just for this and we can start discussing. 

Cheers, 

Carla. 

[Eric Capo]

Hi Carla and all,

Indeed, we have been working on having a merAB db for marky-coco sometimes ago (in 2022). I share attached the draft of the mer catalogue. Feel free to use this as a basis.

To create an up-to-date catalogue of merAB amino acid sequences, here is the strategy one could use. Collect data

• from isolates (literature)
• from single-cell assembled genomes (searching for merAB homologs and manual verification from SAGs database and literature)
• from MAGs (downloading GTDB DB of MAGs ,searching for merAB amino acid sequences)
• from environmental contigs (digging into literature, maybe only the Hg-cycling datasets).

Of course, Christakis et al 2021 is a good starting point but there is likely a need to re-analyze new DNA dataset online for better detection.

Hope this helps.

Cheers

Eric

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From: Carla Pereira-Garcia <cperei...@gmail.com>
Sent: Wednesday, March 12, 2025 16:19
To: Alyssa Azaroff <Alyssa....@aces.su.se>
Cc: Eric Capo <eric...@umu.se>; Nicola Gambardella <ngamba...@ciimar.up.pt>; ch.chr...@yahoo.gr <ch.chr...@yahoo.gr>; Mersor cium <merso...@gmail.com>; merso...@googlegroups.com <merso...@googlegroups.com>

E-mail: ngamba...@ciimar.up.pt

[Céline Lavergne]

Dear all, 

As I also mentioned during the last Mersorcium seminar, I think this dataset/tool is needed and would be very useful for further research!

Would be happy to contribute!  

Best,

Céline Lavergne, PhD

Associate Researcher

Microbial Ecology // Ecotoxicology
~~~~
HUB AMBIENTAL UPLA 
Facultad de Ciencias Naturales y Exactas

University of Playa Ancha, Chile
Tel: +569 4298-2246

https://twitter.com/celine_lavergne

To view this discussion visit https://groups.google.com/d/msgid/mersorcium/GVYP280MB0890F28E4BCAEBF3F250F14881D32%40GVYP280MB0890.SWEP280.PROD.OUTLOOK.COM.

[Ester María López García]

Hello everyone!

I'm also interested in contributing to implement the DB! Thanks Eric for sharing that information.

Maybe we could stard gathering in a shared Google Sheet the info of the sequences we could use to create the DB, as for the Hg-MATE-DB.v1. It's an idea, let's see how many of us are interested in that and we could do that if you agree.

Best,

Ester-Maria López-García, PhD candidate

Bioinformatics and Microbiology

Institut de Ciències del Mar (ICM-CSIC)

CNRS-ANR | Université de Pau et des Pays de l'Adour | Universitat Autònoma de Barcelona

To view this discussion visit https://groups.google.com/d/msgid/mersorcium/CAOTht7Vcb0dunapMyqNgm%3D7seyk4wzVRQGY_E4NbTspJJjjyKA%40mail.gmail.com.

[Carla Pereira-Garcia]

Hi, 

I’ve created the smaller group but some people haven’t accepted. I think it might be because it’s been spamed. Please check your spam folder and join in. 

Thank you, 

Carla. 

El 13 mar 2025, a las 12:36, Ester María López García <estermlo...@gmail.com> escribió:

Hello everyone!

I'm also interested in contributing to implement the DB! Thanks Eric for sharing that information.

Maybe we could stard gathering in a shared Google Sheet the info of the sequences we could use to create the DB, as for the Hg-MATE-DB.v1. It's an idea, let's see how many of us are interested in that and we could do that if you agree.

Best,

Ester-Maria López-García, PhD candidate

Bioinformatics and Microbiology

Institut de Ciències del Mar (ICM-CSIC)

CNRS-ANR | Université de Pau et des Pays de l'Adour | Universitat Autònoma de Barcelona

<IBfK00nNOceCaFHd.png><KgjJGEhzKvrLs3bo.png><wYvkhFGRf9Rf7vIZ.png>

To view this discussion visit https://groups.google.com/d/msgid/mersorcium/0bcb2229-79f9-4d2e-b09a-d6387104990c%40gmail.com.

[Allwin Mabesraj]

Hello, 

I want to express my interest in joining the initiative to prepare the database. 

I have not done any bioinformatics recently, but I have been working Mer A and B for the past 4 years, and I have developed a nanobiosensor for detection of MeHg in water. 

I am an early-stage researcher from the ITN PROJECT GMOS Train. I can give some input from a wet lab perspective. 

My recent review on MeHg detection- https://doi.org/10.1016/j.trac.2025.118157 

My recent policy brief- https://www.gmos-train.eu/wp-content/uploads/2025/01/Policy-brief-3.pdf 

Best 

Allwin Mabes Raj

Jozef Stefan Institute

Slovenia

IOS. d. o. o

Slovenia

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[isasanz.92]

Dear Mersorcium community,

I hope this email finds you well :)

We have started to plan the creation of a curated merAB genes database. Given our shared interest in improving the identification of these genes, we believe that a collaborative effort could be highly beneficial to the research community.

We know that some researchers, had already raised interest in collaborating with this initiative. If you haven't contacted us before and you are open to discuss this further, we would love to add you to a specific group we have for the development of this initiative. Please, reply to this email if you would like to be part of this initiative and/or have any questions.