The Molecular Microbiology group began its journey on April 11, 1995, led by a board of directors chaired by Josep Casadesús Pursals and with the aim of bringing together the activity of Spanish microbiologists who were using emerging molecular tools at that time. Since then, the work of the chairmen of the boards of directors (Table), whom we thank for their dedication, has been a constant stimulus for the operation of the group.

The group enjoys excellent health and a constant growth in the number of members, which today exceeds 460. We are also honored to have among our members several of the winners of the Jaime Ferrán award: Enrique Herrero Perpiñán ( 1987), Ernesto García López (1989), Antonio Ventosa Ucero (1991), Íñigo Lasa Uzcudun (2005), Luis Ángel Fernández Herrero (2007), Alejandro Mira Obrador (2009), Bruno González Zorn (2011), David Rodríguez Lázaro ( 2013), Felipe Cava Valenciano (2017) and Álvaro San Millán Cruz (2021). Most of the partners work in Universities (63%) and Public Research Organizations (23%). The rest is divided between hospitals (5%), companies (4%), foreign centers (3%) or foundations (2%). The activity of many of the researchers that make up our group can be consulted in the monographic sections that appeared in the issues of the SEM@foro magazine of December 2014 (number 58) and December 2019 (number 68), the latter coinciding with the 25 years since the group's creation.

Our specialized group promotes interaction between microbiologists from different fields with an interest in molecular processes. This objective is fundamentally developed through the holding of biannual meetings (Figure). These meetings, spread throughout Spain, have been held in Pamplona (1996), Valencia (1998), Madrid (2000), Santander (2002), Jaca (2004), Lleida (2006), Cádiz (2008), Barcelona ( 2010), Palma de Mallorca (2012), Segovia (2014), Seville (2016), Zaragoza (2018) and Granada (2022). From these lines we want to thank the excellent disposition and the work carried out by the organizers of all these meetings, whose philosophy has always been to facilitate the participation of our youngest members, establishing reduced fees for them. In this way, many students have found in these meetings of the group of Micro Molecular a forum where you can publicly present your research and exchange your experiences in a friendly and relaxed atmosphere.

The group has been calling for twelve years an award to distinguish a research work carried out by one of its partners totally or partially in a Spanish laboratory and whose delivery takes place within the framework of the biannual meetings, where the winners give the closing conference . In their first five editions, these awards were sponsored by the company Biomedal and were awarded to the following works:

• Barcelona 2010. Selva L, Viana D, Regev-Yochay G, Trzcinski K, Corpa JM, Lasa I, Novick RP, Penadés JR. (2009). Killing niche competitors by remote-control bacteriophage induction. Proc Natl Acad Sci U S A. 106: 1234-1238.
• Palma de Mallorca 2012. Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simón-Soro A, Pignatelli M, Mira A. (2012). The oral metagenome in health and disease . ISME J. 2012 6: 46-56.
• Segovia 2014. Sánchez-Romero MA, Casadesús J (2014). Contribution of phenotypic heterogeneity to adaptive antibiotic resistance. Proc Natl Acad Sci U S A. 111:355-360.
• Sevilla 2016. Cota I, Sánchez-Romero MA, Hernández SB, Pucciarelli MG, García-del Portillo F, Casadesús J. (2015) Epigenetic control of Salmonella enterica O-antigen chain length: a tradeoff between virulence and bacteriophage resistance. PLos Genet 11: e1005667.
• Zaragoza 2018. Castañeda-García A, Prieto AI, Rodríguez-Beltrán J, Alonso N, Cantillon D, Costas C, Pérez-Lago L, Zegeye ED, Herranz M, Plociński P, Tonjum T, García de Viedma D, Paget M, Waddell SJ, Rojas AM, Doherty AJ, Blázquez J. (2017) A non-canonical mismatch repair pathway in prokaryotes. Nature Comm 8: 14246.

Although the exceptional situation generated by the SARS-CoV-2 pandemic prevented us from holding the meeting scheduled for September 2020 in Granada, the following works, awarded in 2020, were presented in an online session held on October 21, 2020:

• FIRST PRIZE:

Alejandro González-Delgado A, Rodríguez Mestre M, Martínez-Abarca F, Toro N. (2019) Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR–Cas system in Vibrio vulnificus. Nucleic Acids Res. 47:10202-10211.

• SECOND PRIZE

Gonzalo-Asensio J, Pérez I, Aguiló N, Uranga S, Picó A, Lampreave C, Cebollada A, Otal I, Samper S, Martín C. (2018) New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages. PLoS Genet. 14: e1007282.

In 2022, the XIII Meeting of the group was held and the following prizes were awarded for research work:

• Granada 2022. First honorable mention: Catalán-Moreno, A., Cela, M., Menéndez-Gil, P., Irurzun, N., Caballero, C.J., Caldelari, I., Toledo-Arana, A. (2021) RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures. Nucleic Acids Res. 49:3409-3426. Second honorable mention: http://dx.doi.org/10.1037/0033-295X.101.2.203 Rodriguez-Beltran, J., Sørum, V., Toll-Riera, M., de la Vega, C., Peña-Miller, R., San Millan, A. (2020) Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria. Proc. Natl. Acad. Sci. DEER. 117:15755–15762.

One of the hallmarks that characterizes our meetings is the participation of microbiologists who are at different points in their professional careers, which, together with the almost familiar atmosphere that we like to promote, facilitates the exchange of experiences between our younger and other partners with more extensive experience always willing to put their knowledge at the service of training new generations of microbiologists. We do not want to finish without inviting all the members of the SEM to get to know us and to form part of our specialized group, which is open to all topics in microbiology.

Twitter

https://twitter.com/MicroMolSEM

Tools for bioinformatics analysis

Analysis software packages

• Galaxy.
• GeneInfinity.
• Online Bioinformatics Resources Collection (OBRC).
• Sequence Manipulation Suite (SMS2).

Multiple sequence alignment

Local multiple alignment programs

• L-align (actually, it is not multiple, is paired).

Progressive multiple alignment programs

• Clustal W2 (EMBL) (Wageningen) (GenomeNet).
• Clustal W (download).

Repetitive multiple alignment programs

• DiAlign (References).
• DiAlign-TX (Reference).
• MultAlin

Combined Multiple Alignment Programs

• Clustal Omega (EBI, Pasteur).
• COBALT (NCBI).
• MUSCLE (MUltiple Sequence Comparison by Log- Expectation, (EBI), (original), (Wageningen).
• ProbCons (Stanford, Max-Planck).

• T-COFFEE on (EBI) (Wageningen).

Jalview (JAVA application for visualization of alignments)

Restriction analysis of DNA fragments

• Hypertext DNA Sequence Display.
• Restriction Mapper.
• Web Cutter 2.0 Works best with Explorer.
• Watcut.

The Antibody Resource Page

Virtual library about Microbiology and Virology

BLAST at the NCBI

• Comparisons with DNA databases (BLAST N).
• Comparisons with protein databases (BLAST P).
• Comparisons with repeated search protein databases (PSI-BLAST).
• Comparisons with databases of conserved domains (RPS-BLAST).
• Comparison of two DNA or protein sequences with each other (BLAST-2).
• Comparison of a small fragment with the database (BLAST-short).
• BLAST-X.
• T-BLAST-N.
• T-BLAST-X.

Search for MOTIVES in proteins (Secondary databases)

• CDD (Conserved Domain Database).
• INTERPRO (INTEgrated documentation Resource for PROtein families).
• MOTIF Search.
• PFAM (Protein Family Alignments using hMMs).
• PRINTS (Protein Pingerprints).
• PRODOM (PROtein DOMain Database).
• ASK (Dictionary of Protein Sites and Patterns).
• SMART (Simple Modular Architecture Research Tool).

Download programs (EBI, Genamics, Kropinsky)

Oligonucleotide design (jPCR), (NCBI), (EXAMPLE 3 v4.0 MIT) O (FIRST3 Plus) (PRIMER3plus)

Dot Matrix Alignments (DOTLET)

COME IN

• General tools.
• ENTER-DNA (search for DNA sequences).
• ENTER 3D Structures (search for three-dimensional structures, precise Cn3D) (Cn3Dlocal).
• ENTER-Proteinas (search for protein sequences).
• ENTER-Genomas (search for whole genome sequences).

Sequence assembly

• CAP3. (Article).
• CAP3 at the Pasteur Institute.
• CAP3 at IFOM.
• CAP3 in the Rhône-Alpes Pole of Bioinformatics.
• Contig Viewer (installable for Linux).
• EGassembler.

Phylogeny

• Phylip.
• Download of WebPhylip.
• Other programs phylogeny.
• Download of MEGA5.

Genomics and functional analysis

• ENSEMBL (European Bioinformatics Institute).
• Come in genomes.
• Gene Ontology (GO).
• Genomes on line (GOLD).
• KEGG (Kyoto Encyclopedia of Genes and Genomes).
• Module networks.
• NCBI Genome Data Viewer.
• Stanford Genomic Resources.

Tools in EMBL

• BLAST.
• WUBlast with post-processing.
• ClustalW.
• FastA nucleotide.
• FastA protein.

Tools in the NCBI

• learning (Phylogenetic classification of proteins).
• ORF Finder (search for ORFs).
• VecScreen (determination of the presence of vector DNA, polylinkers or adapters).

Protein identification by peptide fingerprint

• MASCOT.

Interaction protein (databases)

• DIP (Database of Interacting Proteins).

MEDLINE (PUBMED)

Microarrays de ADN

• Affymetrix.
• GLUE and R.
• Basic information about microarrays.

Protein secondary structure prediction

• JPred3.
• PredictProtein.
• PSI-Pred.

Prediction of 3D protein structure

• 3D-PSSM.
• Phyre2 (Protein Homology/analogY Recognition Engine v.2.0).
• SWISSMODEL.

Prediction of genes y ORFs in genomic DNA

• AUGUSTUS.
• FGENESH. (Article).
• FrameD. (Article).
• GeneID.
• GeneMarkS (> 1 Mbp) (Article).
• GENSCAN at the Pastor Institute (Article).
• GenomeScan.
• GLIMMER-M.
• HMMgene.
• ORF-FINDER.
• t-RNA-Scan.

Prediction of chimeras in DNA sequences

• Bellerophon

Prediction of promoter sequences in DNA

• Neural Network Promoter Prediction.
• Promoter 2.0 Prediction Server.
• Transcription factor binding sites (TFSiteScan).

Prediction of signals in proteins

• NetPhos (Phosphorylation sites in eukaryotic proteins).
• Signal IP (Signal peptides).
• SPLIT (Membrane Protein Secondary Structure Prediction Server).
• TMHMM Server (Transmembrane propellers).

Protein Data Bank (PDB) (3D structures of proteins, requires JAVA)

Codon usage

• • GRAPHICAL CODON USAGE ANALYZER.
  • CODON ADAPTATION TOOL.
  • OPTIMIZER (Optimization of DNA and protein sequences).
  • CODON USAGE DATABASE .

Utilities in the network

• Center for Biological Sequence Analysis (CBS).
• Kropinsky.
• MolBiolNet.
• Softberry.
• Free software on the net about Molecular Biology