---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21711'
abstract:
- lang: eng
text: 'Background: Low-volume trapping columns are essential for sample enrichment,
desalting, and injection profile focusing on nano-LC–MS-based proteomics. They
enable higher sample loading, improve chromatographic performance, and protect
the analytical column by removing salts and contaminants. Recently, monolithic
trap columns with micropillar architecture have emerged as alternatives to conventionally
packed traps. This study compares the performance of a packed and a micropillar
monolithic trap column for the analysis of tryptic peptides. Methods: A tryptic
digest of HeLa cell lysate was analyzed under identical LC–MS conditions using
both trap types. Peptides were detected at 214 nm and analyzed by nano-ESI on
a Q Exactive Plus Orbitrap. Data were searched against the human UniProt database
(February 2023) using FragPipe v20.0, and statistical evaluation of MaxLFQ intensities
was performed in Perseus using Welch’s t-test and clustering analysis. Results:
Over 2500 proteins were identified with both setups. The packed trap column yielded
more total peptides, particularly those with post-translational modifications
and higher hydrophilicity, whereas the monolithic column favored peptides of intermediate
hydrophobicity. Chromatographic profiles confirmed a slight reduction in the trapping
efficiency of hydrophilic peptides by the monolithic trap. Conclusions: Trap column
design significantly influences peptide recovery and proteome coverage.'
acknowledgement: 'The authors thank Gábor Tóth, Uppsala University, Sweden, and Armel
Nicolas, Institute for Science and Technology Austria, for their support. This research
was conducted during a student residency in Vienna under the auspices of OeAD. ZI:
ICM-2016-03196.'
article_number: '10'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jadranka
full_name: Miletić Vukajlović, Jadranka
last_name: Miletić Vukajlović
- first_name: Bojana
full_name: Ilić, Bojana
last_name: Ilić
- first_name: Bella
full_name: Bruszel, Bella
id: 70abbbb3-88ea-11ec-8e0a-e8c939944834
last_name: Bruszel
- first_name: Tanja
full_name: Panić-Janković, Tanja
last_name: Panić-Janković
- first_name: Goran
full_name: Mitulović, Goran
last_name: Mitulović
citation:
ama: Miletić Vukajlović J, Ilić B, Bruszel B, Panić-Janković T, Mitulović G. Comparison
of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar
trap columns for proteomics analyses. Proteomes. 2026;14(1). doi:10.3390/proteomes14010010
apa: Miletić Vukajlović, J., Ilić, B., Bruszel, B., Panić-Janković, T., & Mitulović,
G. (2026). Comparison of the trapping efficiency for tryptic peptides on particle-packed
and micro-pillar trap columns for proteomics analyses. Proteomes. MDPI.
https://doi.org/10.3390/proteomes14010010
chicago: Miletić Vukajlović, Jadranka, Bojana Ilić, Bella Bruszel, Tanja Panić-Janković,
and Goran Mitulović. “Comparison of the Trapping Efficiency for Tryptic Peptides
on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses.” Proteomes.
MDPI, 2026. https://doi.org/10.3390/proteomes14010010.
ieee: J. Miletić Vukajlović, B. Ilić, B. Bruszel, T. Panić-Janković, and G. Mitulović,
“Comparison of the trapping efficiency for tryptic peptides on particle-packed
and micro-pillar trap columns for proteomics analyses,” Proteomes, vol.
14, no. 1. MDPI, 2026.
ista: Miletić Vukajlović J, Ilić B, Bruszel B, Panić-Janković T, Mitulović G. 2026.
Comparison of the trapping efficiency for tryptic peptides on particle-packed
and micro-pillar trap columns for proteomics analyses. Proteomes. 14(1), 10.
mla: Miletić Vukajlović, Jadranka, et al. “Comparison of the Trapping Efficiency
for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics
Analyses.” Proteomes, vol. 14, no. 1, 10, MDPI, 2026, doi:10.3390/proteomes14010010.
short: J. Miletić Vukajlović, B. Ilić, B. Bruszel, T. Panić-Janković, G. Mitulović,
Proteomes 14 (2026).
date_created: 2026-04-12T22:01:49Z
date_published: 2026-03-01T00:00:00Z
date_updated: 2026-05-04T10:36:21Z
day: '01'
ddc:
- '540'
department:
- _id: MassSpec
doi: 10.3390/proteomes14010010
external_id:
pmid:
- '41893725'
file:
- access_level: open_access
checksum: 1e0c66bbf4b6e0be626a8639ea664b63
content_type: application/pdf
creator: dernst
date_created: 2026-05-04T10:31:35Z
date_updated: 2026-05-04T10:31:35Z
file_id: '21790'
file_name: 2026_Proteomes_Vukajlovic.pdf
file_size: 1009723
relation: main_file
success: 1
file_date_updated: 2026-05-04T10:31:35Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proteomes
publication_identifier:
eissn:
- 2227-7382
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison of the trapping efficiency for tryptic peptides on particle-packed
and micro-pillar trap columns for proteomics analyses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21779'
abstract:
- lang: eng
text: Acidomycin is an anti-mycobacterial antibiotic with a unique mode of action,
targeting the biotin biosynthesis pathway. Despite being highly active against
mycobacteria in vitro, its development as an anti-tubercular agent has been hindered
due to suboptimal pharmacokinetics. Engineering of the acidomycin biosynthesis
may yield new analogues with improved pharmacological properties. Here, we describe
the identification of the acidomycin biosynthetic gene cluster (BGC) in a Streptomyces
bacterium isolated from the rhizosphere of Edelweiss. Notably, the acidomycin
BGC is located in proximity to the genes for the biosynthesis of stravidins, secondary
metabolites targeting a different enzyme in the biotin biosynthesis pathway, and
two genes for streptavidins, proteins that strongly bind and sequester biotin.
The identity of the acidomycin BGC was confirmed via both gene knock-out and heterologous
expression, which suggested that the fatty acid required for the formation of
acidomycin's acyl chain is most likely scavenged from the biotin biosynthesis
pathway. CRISPR/Cas9-assisted knock-out of the cytochrome P450-encoding gene in
the acidomycin BGC resulted in a significant decrease in its yield but did not
abrogate the biosynthesis completely.
acknowledgement: This work was supported by the University of Vienna. The authors
thank Anna Fabisikova from the Mass Spectrometry Centre and the team of the NMR
Centre (both of the Faculty of Chemistry, University of Vienna and members of the
Vienna Life Science Instruments) for assistance with data acquisition. Open Access
funding provided by Universitat Wien. This work was supported by Universität Wien.
article_number: e70357
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna
full_name: Vignolle, Anna
last_name: Vignolle
- first_name: Martin
full_name: Zehl, Martin
id: 8e016d5b-5d77-11f0-86d2-96cdb3922a55
last_name: Zehl
orcid: 0000-0001-9685-0373
- first_name: Jaime Felipe Guerrero
full_name: Garzón, Jaime Felipe Guerrero
last_name: Garzón
- first_name: Olha
full_name: Schneider, Olha
last_name: Schneider
- first_name: Johannes
full_name: Gafriller, Johannes
last_name: Gafriller
- first_name: Ulrike
full_name: Grienke, Ulrike
last_name: Grienke
- first_name: Rasmus H.
full_name: Kirkegaard, Rasmus H.
last_name: Kirkegaard
- first_name: Sergey B.
full_name: Zotchev, Sergey B.
last_name: Zotchev
citation:
ama: Vignolle A, Zehl M, Garzón JFG, et al. Identification and characterisation
of the gene cluster governing biosynthesis of the anti-mycobacterial antibiotic
acidomycin. Microbial Biotechnology. 2026;19(4). doi:10.1111/1751-7915.70357
apa: Vignolle, A., Zehl, M., Garzón, J. F. G., Schneider, O., Gafriller, J., Grienke,
U., … Zotchev, S. B. (2026). Identification and characterisation of the gene cluster
governing biosynthesis of the anti-mycobacterial antibiotic acidomycin. Microbial
Biotechnology. Wiley. https://doi.org/10.1111/1751-7915.70357
chicago: Vignolle, Anna, Martin Zehl, Jaime Felipe Guerrero Garzón, Olha Schneider,
Johannes Gafriller, Ulrike Grienke, Rasmus H. Kirkegaard, and Sergey B. Zotchev.
“Identification and Characterisation of the Gene Cluster Governing Biosynthesis
of the Anti-Mycobacterial Antibiotic Acidomycin.” Microbial Biotechnology.
Wiley, 2026. https://doi.org/10.1111/1751-7915.70357.
ieee: A. Vignolle et al., “Identification and characterisation of the gene
cluster governing biosynthesis of the anti-mycobacterial antibiotic acidomycin,”
Microbial Biotechnology, vol. 19, no. 4. Wiley, 2026.
ista: Vignolle A, Zehl M, Garzón JFG, Schneider O, Gafriller J, Grienke U, Kirkegaard
RH, Zotchev SB. 2026. Identification and characterisation of the gene cluster
governing biosynthesis of the anti-mycobacterial antibiotic acidomycin. Microbial
Biotechnology. 19(4), e70357.
mla: Vignolle, Anna, et al. “Identification and Characterisation of the Gene Cluster
Governing Biosynthesis of the Anti-Mycobacterial Antibiotic Acidomycin.” Microbial
Biotechnology, vol. 19, no. 4, e70357, Wiley, 2026, doi:10.1111/1751-7915.70357.
short: A. Vignolle, M. Zehl, J.F.G. Garzón, O. Schneider, J. Gafriller, U. Grienke,
R.H. Kirkegaard, S.B. Zotchev, Microbial Biotechnology 19 (2026).
date_created: 2026-05-03T22:01:37Z
date_published: 2026-04-01T00:00:00Z
date_updated: 2026-05-07T08:22:41Z
day: '01'
ddc:
- '570'
department:
- _id: MassSpec
doi: 10.1111/1751-7915.70357
external_id:
pmid:
- '42036976'
file:
- access_level: open_access
checksum: 8c8aa660cef5394167e06f187adbabf0
content_type: application/pdf
creator: dernst
date_created: 2026-05-07T08:21:06Z
date_updated: 2026-05-07T08:21:06Z
file_id: '21835'
file_name: 2026_MicrobialBiotechnology_Vignolle.pdf
file_size: 575492
relation: main_file
success: 1
file_date_updated: 2026-05-07T08:21:06Z
has_accepted_license: '1'
intvolume: ' 19'
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Microbial Biotechnology
publication_identifier:
eissn:
- 1751-7915
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Identification and characterisation of the gene cluster governing biosynthesis
of the anti-mycobacterial antibiotic acidomycin
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21953'
abstract:
- lang: eng
text: Several Streptomyces strains were isolated from freshwater sediments collected
in the Laxenburg ponds (Lower Austria). Genome sequencing and bioinformatics analyses
revealed biosynthetic gene clusters (BGCs) that may specify production of chemically
diverse secondary metabolites. Various culture conditions were employed to induce
metabolite production, and subsequent LC-MS analyses facilitated the identification
of the produced compounds and their correlation with the corresponding BGCs. These
analyses of sediment-derived Streptomyces spp. highlight their extensive biosynthetic
potential, revealing a diverse range of bioactive secondary metabolites, including
siderophores, antibiotics, and other compounds with potential therapeutic applications.
Genomes of two Streptomyces isolates, one of them representing a potentially new
species, harbored several uncharacterized BGCs that may specify biosynthesis of
novel secondary metabolites. Although targeted overexpression of pathway-specific
regulators from these BGCs did not yield additional metabolites, whereas knockout
experiments led to metabolic changes, presumably reflecting regulatory or compensatory
interactions between multiple biosynthetic pathways. Continued exploration of
these strains and their BGCs may lead to the discovery of new bioactive molecules
with pharmaceutical and biotechnological applications.
acknowledgement: "The computational results of this work have been achieved using
the Life Science Compute Cluster (LiSC) of the University of Vienna. We additionally
thank Julia Ramesmayer for assistance during DNA extraction and sample preparation
for long-read sequencing. Support from the Mass Spectrometry Centre of the Faculty
of Chemistry, University of Vienna, is thankfully acknowledged.\r\nThe author(s)
declared that financial support was received for this work and/or its publication.
This work was supported by the University of Vienna via the Research Platform Secondary
Metabolomes of Bacterial Communities (MetaBac). Open access funding provided by
University of Vienna. "
article_number: '1793713'
article_processing_charge: Yes
article_type: original
author:
- first_name: Inmaculada
full_name: Tocino-Márquez, Inmaculada
last_name: Tocino-Márquez
- first_name: Martin
full_name: Zehl, Martin
id: 8e016d5b-5d77-11f0-86d2-96cdb3922a55
last_name: Zehl
orcid: 0000-0001-9685-0373
- first_name: Jovana
full_name: Batajic, Jovana
last_name: Batajic
- first_name: Joana
full_name: Séneca, Joana
last_name: Séneca
- first_name: Petra
full_name: Pjevac, Petra
last_name: Pjevac
- first_name: José
full_name: Murillo-Alba, José
last_name: Murillo-Alba
- first_name: Jesús
full_name: Martín, Jesús
last_name: Martín
- first_name: Olga N.
full_name: Sekurova, Olga N.
last_name: Sekurova
- first_name: Sergey B.
full_name: Zotchev, Sergey B.
last_name: Zotchev
citation:
ama: Tocino-Márquez I, Zehl M, Batajic J, et al. Unveiling the genomes and secondary
metabolomes of Streptomyces spp. from freshwater sediments. Frontiers in Microbiology.
2026;17. doi:10.3389/fmicb.2026.1793713
apa: Tocino-Márquez, I., Zehl, M., Batajic, J., Séneca, J., Pjevac, P., Murillo-Alba,
J., … Zotchev, S. B. (2026). Unveiling the genomes and secondary metabolomes of
Streptomyces spp. from freshwater sediments. Frontiers in Microbiology.
Frontiers Media. https://doi.org/10.3389/fmicb.2026.1793713
chicago: Tocino-Márquez, Inmaculada, Martin Zehl, Jovana Batajic, Joana Séneca,
Petra Pjevac, José Murillo-Alba, Jesús Martín, Olga N. Sekurova, and Sergey B.
Zotchev. “Unveiling the Genomes and Secondary Metabolomes of Streptomyces Spp.
from Freshwater Sediments.” Frontiers in Microbiology. Frontiers Media,
2026. https://doi.org/10.3389/fmicb.2026.1793713.
ieee: I. Tocino-Márquez et al., “Unveiling the genomes and secondary metabolomes
of Streptomyces spp. from freshwater sediments,” Frontiers in Microbiology,
vol. 17. Frontiers Media, 2026.
ista: Tocino-Márquez I, Zehl M, Batajic J, Séneca J, Pjevac P, Murillo-Alba J, Martín
J, Sekurova ON, Zotchev SB. 2026. Unveiling the genomes and secondary metabolomes
of Streptomyces spp. from freshwater sediments. Frontiers in Microbiology. 17,
1793713.
mla: Tocino-Márquez, Inmaculada, et al. “Unveiling the Genomes and Secondary Metabolomes
of Streptomyces Spp. from Freshwater Sediments.” Frontiers in Microbiology,
vol. 17, 1793713, Frontiers Media, 2026, doi:10.3389/fmicb.2026.1793713.
short: I. Tocino-Márquez, M. Zehl, J. Batajic, J. Séneca, P. Pjevac, J. Murillo-Alba,
J. Martín, O.N. Sekurova, S.B. Zotchev, Frontiers in Microbiology 17 (2026).
date_created: 2026-06-08T08:34:10Z
date_published: 2026-04-20T00:00:00Z
date_updated: 2026-06-10T07:49:04Z
day: '20'
ddc:
- '572'
department:
- _id: MassSpec
doi: 10.3389/fmicb.2026.1793713
external_id:
pmid:
- '42088272'
file:
- access_level: open_access
checksum: 31fb6b98c8a6d4007cb21808c6d2d9e3
content_type: application/pdf
creator: dernst
date_created: 2026-06-10T07:46:30Z
date_updated: 2026-06-10T07:46:30Z
file_id: '21989'
file_name: 2026_FrontiersMicrobiology_TocinoMarquez.pdf
file_size: 3582644
relation: main_file
success: 1
file_date_updated: 2026-06-10T07:46:30Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Microbiology
publication_identifier:
issn:
- 1664-302X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
status: public
title: Unveiling the genomes and secondary metabolomes of Streptomyces spp. from freshwater
sediments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2026'
...