TY  - JOUR
AU  - Patiño-Guillén, Gerardo
AU  - Pešović, Jovan
AU  - Panić, Marko
AU  - Savić-Pavićević, Dušanka
AU  - Bošković, Filip
AU  - Keyser, Ulrich Felix
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/865
AB  - Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
PB  - Nature
T2  - Nature Communications
T1  - Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination
IS  - 1
SP  - 1699
VL  - 15
DO  - 10.1038/s41467-024-45968-8
ER  - 

@article{
author = "Patiño-Guillén, Gerardo and Pešović, Jovan and Panić, Marko and Savić-Pavićević, Dušanka and Bošković, Filip and Keyser, Ulrich Felix",
year = "2024",
abstract = "Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.",
publisher = "Nature",
journal = "Nature Communications",
title = "Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination",
number = "1",
pages = "1699",
volume = "15",
doi = "10.1038/s41467-024-45968-8"
}

Patiño-Guillén, G., Pešović, J., Panić, M., Savić-Pavićević, D., Bošković, F.,& Keyser, U. F.. (2024). Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. in Nature Communications
Nature., 15(1), 1699.
https://doi.org/10.1038/s41467-024-45968-8

Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. in Nature Communications. 2024;15(1):1699.
doi:10.1038/s41467-024-45968-8 .

Patiño-Guillén, Gerardo, Pešović, Jovan, Panić, Marko, Savić-Pavićević, Dušanka, Bošković, Filip, Keyser, Ulrich Felix, "Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination" in Nature Communications, 15, no. 1 (2024):1699,
https://doi.org/10.1038/s41467-024-45968-8 . .

TY  - DATA
AU  - Patiño-Guillén, Gerardo
AU  - Pešović, Jovan
AU  - Panić, Marko
AU  - Savić-Pavićević, Dušanka
AU  - Bošković, Filip
AU  - Keyser, Ulrich Felix
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/866
AB  - This PDF file includes: → Supplementary Figures 1 to 29 → Supplementary Tables 1 to 8
PB  - Nature
T2  - Nature Communications
T1  - Supplementary Material for: Patiño-Guillén, G.; Pešović, J.; Panić, M.; Savić-Pavićević, D.; Bošković, F.; Keyser, U. F. Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination. Nat Commun 2024, 15 (1), 1699. https://doi.org/10.1038/s41467-024-45968-8.
IS  - 1
VL  - 15
DO  - 10.17863/CAM.104528
ER  - 

@misc{
author = "Patiño-Guillén, Gerardo and Pešović, Jovan and Panić, Marko and Savić-Pavićević, Dušanka and Bošković, Filip and Keyser, Ulrich Felix",
year = "2024",
abstract = "This PDF file includes: → Supplementary Figures 1 to 29 → Supplementary Tables 1 to 8",
publisher = "Nature",
journal = "Nature Communications",
title = "Supplementary Material for: Patiño-Guillén, G.; Pešović, J.; Panić, M.; Savić-Pavićević, D.; Bošković, F.; Keyser, U. F. Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination. Nat Commun 2024, 15 (1), 1699. https://doi.org/10.1038/s41467-024-45968-8.",
number = "1",
volume = "15",
doi = "10.17863/CAM.104528"
}

Patiño-Guillén, G., Pešović, J., Panić, M., Savić-Pavićević, D., Bošković, F.,& Keyser, U. F.. (2024). Supplementary Material for: Patiño-Guillén, G.; Pešović, J.; Panić, M.; Savić-Pavićević, D.; Bošković, F.; Keyser, U. F. Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination. Nat Commun 2024, 15 (1), 1699. https://doi.org/10.1038/s41467-024-45968-8.. in Nature Communications
Nature., 15(1).
https://doi.org/10.17863/CAM.104528

Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Supplementary Material for: Patiño-Guillén, G.; Pešović, J.; Panić, M.; Savić-Pavićević, D.; Bošković, F.; Keyser, U. F. Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination. Nat Commun 2024, 15 (1), 1699. https://doi.org/10.1038/s41467-024-45968-8.. in Nature Communications. 2024;15(1).
doi:10.17863/CAM.104528 .

Patiño-Guillén, Gerardo, Pešović, Jovan, Panić, Marko, Savić-Pavićević, Dušanka, Bošković, Filip, Keyser, Ulrich Felix, "Supplementary Material for: Patiño-Guillén, G.; Pešović, J.; Panić, M.; Savić-Pavićević, D.; Bošković, F.; Keyser, U. F. Single-Molecule RNA Sizing Enables Quantitative Analysis of Alternative Transcription Termination. Nat Commun 2024, 15 (1), 1699. https://doi.org/10.1038/s41467-024-45968-8." in Nature Communications, 15, no. 1 (2024),
https://doi.org/10.17863/CAM.104528 . .

TY  - CONF
AU  - Panić, Marko
AU  - Prijić, Ivana
AU  - Simić, Mihajlo
AU  - Ćuruvija, Ivana
AU  - Lukić, Ivana
AU  - Drgačević, Luka
AU  - Kojić, Milan
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/880
AB  - Diphtheria and tetanus, once formidable causes of morbidity and mortality worldwide, have seen their threats markedly diminished through the advent and widespread use of vaccines. This review article delves into the historical journey of diphtheria and tetanus vaccines, evaluates their current status in global immunization programs, and explores future perspectives in their evolution and implementation. The inception of diphtheria and tetanus vaccines marked a pivotal shift in infectious disease control. The development of diphtheria toxoid by Emil von Behring in the late 19th century and the subsequent creation of tetanus toxoid in the early 20th century set the stage for large-scale immunization efforts. These efforts were bolstered in the mid-20th century with the integration of these toxoids into combination vaccines, notably the DTP (diphtheria-tetanus-pertussis) vaccine, facilitating broader immunization coverage and enhanced public health outcomes. Currently, the inclusion of diphtheria and tetanus vaccines in national immunization schedules has led to a significant decline in the incidence of these diseases globally. However, challenges remain, including disparities in vaccine coverage and the emergence of non-toxigenic strains causing diphtheria. The review highlights the WHO’s strategies towards achieving higher immunization coverage and the importance of maintaining high vaccination rates to prevent resurgence. Looking forward, the review discusses the ongoing research and development aimed at improving vaccine formulations, reducing adverse reactions, and enhancing the efficacy and durability of protection. Innovations such as nanoparticle vaccines and DNA vaccines are explored as potential avenues for future advancements. Additionally, the review addresses the critical role of global health governance in addressing vaccine hesitancy, improving access in low-resource settings, and coordinating responses to outbreaks. In conclusion, while the battle against diphtheria and tetanus has seen significant victories, continuous efforts in vaccine innovation, policy implementation, and global cooperation are essential to sustain these gains and achieve the ultimate goal of global eradication.
PB  - Serbian Society for Microbiology
C3  - XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
T1  - Diphtheria and tetanus vaccines: a historical overview, present achievements, and future directions
EP  - 169
SP  - 169
UR  - https://hdl.handle.net/21.15107/rcub_intor_880
ER  - 

@conference{
author = "Panić, Marko and Prijić, Ivana and Simić, Mihajlo and Ćuruvija, Ivana and Lukić, Ivana and Drgačević, Luka and Kojić, Milan",
year = "2024",
abstract = "Diphtheria and tetanus, once formidable causes of morbidity and mortality worldwide, have seen their threats markedly diminished through the advent and widespread use of vaccines. This review article delves into the historical journey of diphtheria and tetanus vaccines, evaluates their current status in global immunization programs, and explores future perspectives in their evolution and implementation. The inception of diphtheria and tetanus vaccines marked a pivotal shift in infectious disease control. The development of diphtheria toxoid by Emil von Behring in the late 19th century and the subsequent creation of tetanus toxoid in the early 20th century set the stage for large-scale immunization efforts. These efforts were bolstered in the mid-20th century with the integration of these toxoids into combination vaccines, notably the DTP (diphtheria-tetanus-pertussis) vaccine, facilitating broader immunization coverage and enhanced public health outcomes. Currently, the inclusion of diphtheria and tetanus vaccines in national immunization schedules has led to a significant decline in the incidence of these diseases globally. However, challenges remain, including disparities in vaccine coverage and the emergence of non-toxigenic strains causing diphtheria. The review highlights the WHO’s strategies towards achieving higher immunization coverage and the importance of maintaining high vaccination rates to prevent resurgence. Looking forward, the review discusses the ongoing research and development aimed at improving vaccine formulations, reducing adverse reactions, and enhancing the efficacy and durability of protection. Innovations such as nanoparticle vaccines and DNA vaccines are explored as potential avenues for future advancements. Additionally, the review addresses the critical role of global health governance in addressing vaccine hesitancy, improving access in low-resource settings, and coordinating responses to outbreaks. In conclusion, while the battle against diphtheria and tetanus has seen significant victories, continuous efforts in vaccine innovation, policy implementation, and global cooperation are essential to sustain these gains and achieve the ultimate goal of global eradication.",
publisher = "Serbian Society for Microbiology",
journal = "XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april",
title = "Diphtheria and tetanus vaccines: a historical overview, present achievements, and future directions",
pages = "169-169",
url = "https://hdl.handle.net/21.15107/rcub_intor_880"
}

Panić, M., Prijić, I., Simić, M., Ćuruvija, I., Lukić, I., Drgačević, L.,& Kojić, M.. (2024). Diphtheria and tetanus vaccines: a historical overview, present achievements, and future directions. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
Serbian Society for Microbiology., 169-169.
https://hdl.handle.net/21.15107/rcub_intor_880

Panić M, Prijić I, Simić M, Ćuruvija I, Lukić I, Drgačević L, Kojić M. Diphtheria and tetanus vaccines: a historical overview, present achievements, and future directions. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april. 2024;:169-169.
https://hdl.handle.net/21.15107/rcub_intor_880 .

Panić, Marko, Prijić, Ivana, Simić, Mihajlo, Ćuruvija, Ivana, Lukić, Ivana, Drgačević, Luka, Kojić, Milan, "Diphtheria and tetanus vaccines: a historical overview, present achievements, and future directions" in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april (2024):169-169,
https://hdl.handle.net/21.15107/rcub_intor_880 .

TY  - CONF
AU  - Lukić, Ivana
AU  - Dragačević, Luka
AU  - Panić, Marko
AU  - Stamenković, Marina
AU  - Kojić, Milan
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/878
AB  - In the post-COVID-19 era, there has been a significant increase in the development of mRNA vaccines not only against various diseases besides SARS-CoV-2, but also to treat cancer and genetic disorders. These vaccines, revolutionizing vaccinology, offer rapid pandemic response, high efficacy, minimal side effects, and cost-effectiveness. Achieving these benefits hinges on seamlessly integrating mRNA production steps, from plasmid DNA cloning to lipid nanoparticle formulation. This overview aims to comprehend or circumvent pitfalls in plasmid DNA cloning, a critical initial step in mRNA vaccine production. The focus is on achieving accurate insert sequence and gene expression, and it highlights the critical role of plasmid DNA design in ensuring vaccine effectiveness. Our research project entitled “Role of macroautophagy in lipid nanoparticle mRNA delivery and adjuvanticity” recognized the significance of this aspect. During our research, we designed a plasmid DNA cloning vector to incorporate the GFP-SARS-CoV-2 Spike gene. The vector was carefully constructed with several key features, including a high-copy plasmid, pUC18/pUC19 vector backbone with a robust T7 promoter, origin of replication, multiple cloning sites, polyadenylation signal, and ampicillin resistance for bacterial selection. Despite careful design, challenges like poly-A tail deletion may arise, prompting the exploration of stable large-size and low-copy vectors, as well as linear and bacteriophage vectors. But, for largescale production and regulatory compliance, vector systems must be scalable and well-documented. Commercial vectors and automated synthesis facilitate gene construction, with artificial intelligence ensuring sequence accuracy. Precision is crucial for complex antigens, as seen in tuberculosis mRNA vaccine development. Addressing these challenges demands a combining of molecular biology techniques, computational tools, and collaboration with experts in microbiology, molecular biology, and vaccine development. The design’s scalability and documentation are vital for large-scale production and regulatory compliance, emphasizing the multifaceted approach required for successful mRNA vaccine development.
PB  - Serbian Society for Microbiology
C3  - XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
T1  - mRNA vaccine manufacturing – challenges in plasmid DNA cloning vector design
EP  - 157
SP  - 157
UR  - https://hdl.handle.net/21.15107/rcub_intor_878
ER  - 

@conference{
author = "Lukić, Ivana and Dragačević, Luka and Panić, Marko and Stamenković, Marina and Kojić, Milan",
year = "2024",
abstract = "In the post-COVID-19 era, there has been a significant increase in the development of mRNA vaccines not only against various diseases besides SARS-CoV-2, but also to treat cancer and genetic disorders. These vaccines, revolutionizing vaccinology, offer rapid pandemic response, high efficacy, minimal side effects, and cost-effectiveness. Achieving these benefits hinges on seamlessly integrating mRNA production steps, from plasmid DNA cloning to lipid nanoparticle formulation. This overview aims to comprehend or circumvent pitfalls in plasmid DNA cloning, a critical initial step in mRNA vaccine production. The focus is on achieving accurate insert sequence and gene expression, and it highlights the critical role of plasmid DNA design in ensuring vaccine effectiveness. Our research project entitled “Role of macroautophagy in lipid nanoparticle mRNA delivery and adjuvanticity” recognized the significance of this aspect. During our research, we designed a plasmid DNA cloning vector to incorporate the GFP-SARS-CoV-2 Spike gene. The vector was carefully constructed with several key features, including a high-copy plasmid, pUC18/pUC19 vector backbone with a robust T7 promoter, origin of replication, multiple cloning sites, polyadenylation signal, and ampicillin resistance for bacterial selection. Despite careful design, challenges like poly-A tail deletion may arise, prompting the exploration of stable large-size and low-copy vectors, as well as linear and bacteriophage vectors. But, for largescale production and regulatory compliance, vector systems must be scalable and well-documented. Commercial vectors and automated synthesis facilitate gene construction, with artificial intelligence ensuring sequence accuracy. Precision is crucial for complex antigens, as seen in tuberculosis mRNA vaccine development. Addressing these challenges demands a combining of molecular biology techniques, computational tools, and collaboration with experts in microbiology, molecular biology, and vaccine development. The design’s scalability and documentation are vital for large-scale production and regulatory compliance, emphasizing the multifaceted approach required for successful mRNA vaccine development.",
publisher = "Serbian Society for Microbiology",
journal = "XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april",
title = "mRNA vaccine manufacturing – challenges in plasmid DNA cloning vector design",
pages = "157-157",
url = "https://hdl.handle.net/21.15107/rcub_intor_878"
}

Lukić, I., Dragačević, L., Panić, M., Stamenković, M.,& Kojić, M.. (2024). mRNA vaccine manufacturing – challenges in plasmid DNA cloning vector design. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
Serbian Society for Microbiology., 157-157.
https://hdl.handle.net/21.15107/rcub_intor_878

Lukić I, Dragačević L, Panić M, Stamenković M, Kojić M. mRNA vaccine manufacturing – challenges in plasmid DNA cloning vector design. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april. 2024;:157-157.
https://hdl.handle.net/21.15107/rcub_intor_878 .

Lukić, Ivana, Dragačević, Luka, Panić, Marko, Stamenković, Marina, Kojić, Milan, "mRNA vaccine manufacturing – challenges in plasmid DNA cloning vector design" in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april (2024):157-157,
https://hdl.handle.net/21.15107/rcub_intor_878 .

TY  - CONF
AU  - Panić, Marko
AU  - Prijić, Ivana
AU  - Simić, Mihajlo
AU  - Lukić, Ivana
AU  - Petrušić, Marija
AU  - Živković, Irena
AU  - Kojić, Milan
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/876
AB  - Tetanus toxin, a highly potent neurotoxin produced by Clostridium tetani, is the primary agent responsible for causing tetanus. This serious, potentially fatal disease can be effectively prevented through vaccination. Thanks to successful vaccination campaigns, tetanus has become exceedingly rare in both developed and most developing countries. However, the widespread presence of C. tetani spores in the environment means that tetanus cannot be completely eradicated, underscoring the ongoing need for vaccination. Traditionally, tetanus vaccines are produced by cultivating C. tetani, extracting a crude form of the tetanus toxin, and then chemically inactivating it for use in immunization. This method has proven clinically effective and is in widespread use. A challenge with this approach, however, is that the vaccine contains hundreds of various C. tetani proteins, with the active component making up only a variable and small fraction of the overall vaccine mass. To improve the current tetanus vaccine, there is potential in the recombinant production of a genetically inactivated tetanus vaccine. Prior studies have demonstrated the feasibility of engineering the full-length tetanus toxin in E. coli, and our current work builds on this foundation. We have successfully cloned the complete tetanus toxin open reading frame into the pMAL expression vector. This step was followed by the creation of a genetically inactivated protein, achieved through standard site-directed mutagenesis which altered 8 critical amino acid residues. These mutations have been confirmed via sequencing, ensuring that the toxin is genetically inactivated and thus does not require chemical inactivation for vaccine production. Our present focus is on optimizing the expression of this protein in E. coli. Following this, we intend to conduct thorough assessments of the biochemical and immunological properties of the recombinant tetanus toxin. This research represents a promising avenue towards enhancing the efficacy and specificity of tetanus vaccines, potentially improving global health outcomes.
PB  - Serbian Society for Microbiology
C3  - XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
T1  - Exploring E. coli-based expression of genetically inactivated tetanus toxin for vaccine development
EP  - 113
SP  - 113
UR  - https://hdl.handle.net/21.15107/rcub_intor_876
ER  - 

@conference{
author = "Panić, Marko and Prijić, Ivana and Simić, Mihajlo and Lukić, Ivana and Petrušić, Marija and Živković, Irena and Kojić, Milan",
year = "2024",
abstract = "Tetanus toxin, a highly potent neurotoxin produced by Clostridium tetani, is the primary agent responsible for causing tetanus. This serious, potentially fatal disease can be effectively prevented through vaccination. Thanks to successful vaccination campaigns, tetanus has become exceedingly rare in both developed and most developing countries. However, the widespread presence of C. tetani spores in the environment means that tetanus cannot be completely eradicated, underscoring the ongoing need for vaccination. Traditionally, tetanus vaccines are produced by cultivating C. tetani, extracting a crude form of the tetanus toxin, and then chemically inactivating it for use in immunization. This method has proven clinically effective and is in widespread use. A challenge with this approach, however, is that the vaccine contains hundreds of various C. tetani proteins, with the active component making up only a variable and small fraction of the overall vaccine mass. To improve the current tetanus vaccine, there is potential in the recombinant production of a genetically inactivated tetanus vaccine. Prior studies have demonstrated the feasibility of engineering the full-length tetanus toxin in E. coli, and our current work builds on this foundation. We have successfully cloned the complete tetanus toxin open reading frame into the pMAL expression vector. This step was followed by the creation of a genetically inactivated protein, achieved through standard site-directed mutagenesis which altered 8 critical amino acid residues. These mutations have been confirmed via sequencing, ensuring that the toxin is genetically inactivated and thus does not require chemical inactivation for vaccine production. Our present focus is on optimizing the expression of this protein in E. coli. Following this, we intend to conduct thorough assessments of the biochemical and immunological properties of the recombinant tetanus toxin. This research represents a promising avenue towards enhancing the efficacy and specificity of tetanus vaccines, potentially improving global health outcomes.",
publisher = "Serbian Society for Microbiology",
journal = "XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april",
title = "Exploring E. coli-based expression of genetically inactivated tetanus toxin for vaccine development",
pages = "113-113",
url = "https://hdl.handle.net/21.15107/rcub_intor_876"
}

Panić, M., Prijić, I., Simić, M., Lukić, I., Petrušić, M., Živković, I.,& Kojić, M.. (2024). Exploring E. coli-based expression of genetically inactivated tetanus toxin for vaccine development. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
Serbian Society for Microbiology., 113-113.
https://hdl.handle.net/21.15107/rcub_intor_876

Panić M, Prijić I, Simić M, Lukić I, Petrušić M, Živković I, Kojić M. Exploring E. coli-based expression of genetically inactivated tetanus toxin for vaccine development. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april. 2024;:113-113.
https://hdl.handle.net/21.15107/rcub_intor_876 .

Panić, Marko, Prijić, Ivana, Simić, Mihajlo, Lukić, Ivana, Petrušić, Marija, Živković, Irena, Kojić, Milan, "Exploring E. coli-based expression of genetically inactivated tetanus toxin for vaccine development" in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april (2024):113-113,
https://hdl.handle.net/21.15107/rcub_intor_876 .

TY  - CONF
AU  - Lukić, Ivana
AU  - Popović, Mina
AU  - Miljković, Radmila
AU  - Tsibulskaya, Darya
AU  - Panić, Marko
AU  - Dragačević, Luka
AU  - Stojanović, Marijana
PY  - 2024
UR  - http://intor.torlakinstitut.com/handle/123456789/874
AB  - Limosilactobacillus reuteri demonstrates a significant
role in treating gastrointestinal diseases
through the synthesis of various health-promoting
factors. These include mucus-binding proteins,
reactive oxygen species-scavenging enzymes, antimicrobial
agents (reuterin is capable of inhibiting
the growth of a wide spectrum of microorganisms),
vitamins (folate and vitamin B12), and unique
exopolysaccharides. Different strains of L. reuteri
exhibit strain-specific anti-inflammatory effects,
influencing the expression of immune-related
factors such as IL-10 and TNF-α (PMID: 20798357;
PMID: 22207578). Furthermore, the mitigating
impact of L. reuteri strains on inflammation is confirmed
in vivo and in vitro with the implication of
an interaction between probiotics and immune
cells in the intestinal mucosa (PMID: 22207578).
Our study aimed to investigate the potential anti-
inflammatory effects of daily treatment with autochthonous
probiotic strain L. reuteri B2 (PMID:
33932415) could have an anti-inflammatory effect
on local immune response. In a 14-day experiment
with Intor Swiss: Albino mice (n=10), those treated
with L. reuteri B2 (5x106 CFU/mL, 100 μl) showed a
favorable impact on the gut’s inflammatory environment.
Histological analyses of colon samples
and intraperitoneal macrophages revealed lower
myeloperoxidase (MPO) activity, reduced production
of superoxide ions, IFNγ, IL-6, and TNFα, along
with an enhanced production of IL-10 in L. reuteri
B2 treated mice compared to untreated ones. Notably,
histopathological preparations did not show
significant differences between the groups. The
study suggests that L. reuteri B2 may be valuable
for further evaluation in managing, preventing,
and treating inflammatory bowel diseases. The
presented findings contribute to understanding
the specific anti-inflammatory effects of this strain
on the local immune response, supporting its potential
as a therapeutic agent.
PB  - Serbian Society for Microbiology
C3  - XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
T1  - The anti-inflammatory effect of Limosilactobacillus Reuteri b2 administration
EP  - 38
SP  - 38
UR  - https://hdl.handle.net/21.15107/rcub_intor_874
ER  - 

@conference{
author = "Lukić, Ivana and Popović, Mina and Miljković, Radmila and Tsibulskaya, Darya and Panić, Marko and Dragačević, Luka and Stojanović, Marijana",
year = "2024",
abstract = "Limosilactobacillus reuteri demonstrates a significant
role in treating gastrointestinal diseases
through the synthesis of various health-promoting
factors. These include mucus-binding proteins,
reactive oxygen species-scavenging enzymes, antimicrobial
agents (reuterin is capable of inhibiting
the growth of a wide spectrum of microorganisms),
vitamins (folate and vitamin B12), and unique
exopolysaccharides. Different strains of L. reuteri
exhibit strain-specific anti-inflammatory effects,
influencing the expression of immune-related
factors such as IL-10 and TNF-α (PMID: 20798357;
PMID: 22207578). Furthermore, the mitigating
impact of L. reuteri strains on inflammation is confirmed
in vivo and in vitro with the implication of
an interaction between probiotics and immune
cells in the intestinal mucosa (PMID: 22207578).
Our study aimed to investigate the potential anti-
inflammatory effects of daily treatment with autochthonous
probiotic strain L. reuteri B2 (PMID:
33932415) could have an anti-inflammatory effect
on local immune response. In a 14-day experiment
with Intor Swiss: Albino mice (n=10), those treated
with L. reuteri B2 (5x106 CFU/mL, 100 μl) showed a
favorable impact on the gut’s inflammatory environment.
Histological analyses of colon samples
and intraperitoneal macrophages revealed lower
myeloperoxidase (MPO) activity, reduced production
of superoxide ions, IFNγ, IL-6, and TNFα, along
with an enhanced production of IL-10 in L. reuteri
B2 treated mice compared to untreated ones. Notably,
histopathological preparations did not show
significant differences between the groups. The
study suggests that L. reuteri B2 may be valuable
for further evaluation in managing, preventing,
and treating inflammatory bowel diseases. The
presented findings contribute to understanding
the specific anti-inflammatory effects of this strain
on the local immune response, supporting its potential
as a therapeutic agent.",
publisher = "Serbian Society for Microbiology",
journal = "XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april",
title = "The anti-inflammatory effect of Limosilactobacillus Reuteri b2 administration",
pages = "38-38",
url = "https://hdl.handle.net/21.15107/rcub_intor_874"
}

Lukić, I., Popović, M., Miljković, R., Tsibulskaya, D., Panić, M., Dragačević, L.,& Stojanović, M.. (2024). The anti-inflammatory effect of Limosilactobacillus Reuteri b2 administration. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april
Serbian Society for Microbiology., 38-38.
https://hdl.handle.net/21.15107/rcub_intor_874

Lukić I, Popović M, Miljković R, Tsibulskaya D, Panić M, Dragačević L, Stojanović M. The anti-inflammatory effect of Limosilactobacillus Reuteri b2 administration. in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april. 2024;:38-38.
https://hdl.handle.net/21.15107/rcub_intor_874 .

Lukić, Ivana, Popović, Mina, Miljković, Radmila, Tsibulskaya, Darya, Panić, Marko, Dragačević, Luka, Stojanović, Marijana, "The anti-inflammatory effect of Limosilactobacillus Reuteri b2 administration" in XIII Congress of microbiologists of Serbia with international participation, Mikromed regio 5, From biotechnology to human and planetary health, 4-6 april (2024):38-38,
https://hdl.handle.net/21.15107/rcub_intor_874 .

TY  - CHAP
AU  - Savić-Pavićević, Dušanka
AU  - Radenković, Lana
AU  - Velimirov, Luka
AU  - Radovanović, Nemanja
AU  - Ninković, Anastasija
AU  - Garai, Nemanja
AU  - Brkušanin, Miloš
AU  - Panić, Marko
AU  - Pešović, Jovan
PY  - 2023
UR  - http://intor.torlakinstitut.com/handle/123456789/937
AB  - Long read or third-generation sequencing produces reads from 1 kb to several Mb in length with preserved epigenetic marks, at the single-molecule level and in real-time. Single-molecule real-time sequencing (PacBio) and protein nanopore sequencing (Oxford Nanopore Technologies) are available technologies. PacBio technology is based on monitoring the nucleotide incorporation by a single DNA polymerase molecule in real time using fluorescence as a surrogate marker. PacBio HiFi reads are ~15 kb in length with >99.9% accuracy. Oxford Nanopore sequencing infers nucleotide sequence from the changes in ion current intensity while DNA passes through a stochastic sensor – a protein nanopore. It can sequence DNA fragments ranging in five orders of magnitude (20 bp to several Mb), with duplex read accuracy >99.9% when using R10.4.1 nanopores. Innovations such as a miniature device of the palm-size with a price <1000 dollars, sequencing in the field, digital enrichment of target sequences (adaptive sampling) and direct RNA sequencing have become a reality with the electronic „reading“ of nucleic acids. Long read sequencing enabled completing the human genome sequence and releasing a draft of the human pangenome reference. It has also accelerated genome sequencing of eukaryotic species. Out of 1065 genomes deposited in the NCBI database, ~1000 were sequenced since its development. The full potential of the method in studying transcriptome and epigenome will be visible in the years to come. Long read sequencing is becoming the basis of precision medicine effective for all human populations and biodiversity conservation and was announced as the method of the year 2022 according to Nature Methods.
AB  - Sekvenciranje dugih fragmenata ili treća generacija sekvenciranja u realnom vremenu produkuje očitavanja pojedinačnih molekula DNK dužineod 1 kb do nekoliko Mbsa očuvanim epigenetičkim oznakama. Dostupne tehnologije su sekvenciranje pojedinačnih molekula u realnom vremenu (eng. single-molecule real-time sequencing, PacBio) i sekvenciranje kroz proteinske nanopore (Oxford Nanopore Technologies). PacBio tehnologija zasnovana je na detekciji ugradnje nukelotida od strane pojedinačnog molekula DNK polimeraze u realnom vremenu, korišćenjem fluoresecencije kao surogat markera. PacBio HiFi očitavanja su dužine ~15 kb sa tačnošću >99,9%. Oxford Nanopore tehnologija izvodi sekvencu nukleotida iz promena u intenzitetu jonske struje dok DNK prolazi kroz stohastički senzor – proteinsku nanoporu.Može sekvencirati fragmente DNK u rasponu od pet redova veličina (20 bp do nekoliko Mb) sa tačnošću dupleks očitavanja >99,9% kada se koriste R10.4.1 nanopore. Sa elektronskim „čitanjem” nukleinskih kiselina, inovacije kao što su minijaturni uređaj veličine dlana sa cenom <1000 dolara, sekvenciranje na terenu, digitalno obogaćivanje ciljnih sekvenci (adaptivno uzorkovanje) i direktno sekvenciranje RNK, postali su stvarnost. Sekvenciranje dugih fragmenata omogućilo je kompletiranje sekvence genoma čoveka, objavljivanje drafta ljudskog pangenoma i ubrzalo je sekvenciranje genoma eukariota. Od uvođenja metode 2011. godine sekvencirano je ~1000 od 1065 genoma deponovanih u NCBI bazi. Puni potencijal metode u izučavanju transkriptoma i epigenoma biće vidljiv u godinama koje slede. Sekvenciranje dugih fragmenata postaje osnova precizne medicine efikasne za sve ljudske populacije i očuvanja biodiverziteta, i zavredelo je da bude metoda 2022. godine prema časopisu Nature Methods.
PB  - IMGGI
T1  - Sekvenciranje dugih fragmenata – sledeći nivo genomskih istraživanja
T1  - Long read sequencing – the next level in genomic research
UR  - https://hdl.handle.net/21.15107/rcub_intor_937
ER  - 

@inbook{
author = "Savić-Pavićević, Dušanka and Radenković, Lana and Velimirov, Luka and Radovanović, Nemanja and Ninković, Anastasija and Garai, Nemanja and Brkušanin, Miloš and Panić, Marko and Pešović, Jovan",
year = "2023",
abstract = "Long read or third-generation sequencing produces reads from 1 kb to several Mb in length with preserved epigenetic marks, at the single-molecule level and in real-time. Single-molecule real-time sequencing (PacBio) and protein nanopore sequencing (Oxford Nanopore Technologies) are available technologies. PacBio technology is based on monitoring the nucleotide incorporation by a single DNA polymerase molecule in real time using fluorescence as a surrogate marker. PacBio HiFi reads are ~15 kb in length with >99.9% accuracy. Oxford Nanopore sequencing infers nucleotide sequence from the changes in ion current intensity while DNA passes through a stochastic sensor – a protein nanopore. It can sequence DNA fragments ranging in five orders of magnitude (20 bp to several Mb), with duplex read accuracy >99.9% when using R10.4.1 nanopores. Innovations such as a miniature device of the palm-size with a price <1000 dollars, sequencing in the field, digital enrichment of target sequences (adaptive sampling) and direct RNA sequencing have become a reality with the electronic „reading“ of nucleic acids. Long read sequencing enabled completing the human genome sequence and releasing a draft of the human pangenome reference. It has also accelerated genome sequencing of eukaryotic species. Out of 1065 genomes deposited in the NCBI database, ~1000 were sequenced since its development. The full potential of the method in studying transcriptome and epigenome will be visible in the years to come. Long read sequencing is becoming the basis of precision medicine effective for all human populations and biodiversity conservation and was announced as the method of the year 2022 according to Nature Methods., Sekvenciranje dugih fragmenata ili treća generacija sekvenciranja u realnom vremenu produkuje očitavanja pojedinačnih molekula DNK dužineod 1 kb do nekoliko Mbsa očuvanim epigenetičkim oznakama. Dostupne tehnologije su sekvenciranje pojedinačnih molekula u realnom vremenu (eng. single-molecule real-time sequencing, PacBio) i sekvenciranje kroz proteinske nanopore (Oxford Nanopore Technologies). PacBio tehnologija zasnovana je na detekciji ugradnje nukelotida od strane pojedinačnog molekula DNK polimeraze u realnom vremenu, korišćenjem fluoresecencije kao surogat markera. PacBio HiFi očitavanja su dužine ~15 kb sa tačnošću >99,9%. Oxford Nanopore tehnologija izvodi sekvencu nukleotida iz promena u intenzitetu jonske struje dok DNK prolazi kroz stohastički senzor – proteinsku nanoporu.Može sekvencirati fragmente DNK u rasponu od pet redova veličina (20 bp do nekoliko Mb) sa tačnošću dupleks očitavanja >99,9% kada se koriste R10.4.1 nanopore. Sa elektronskim „čitanjem” nukleinskih kiselina, inovacije kao što su minijaturni uređaj veličine dlana sa cenom <1000 dolara, sekvenciranje na terenu, digitalno obogaćivanje ciljnih sekvenci (adaptivno uzorkovanje) i direktno sekvenciranje RNK, postali su stvarnost. Sekvenciranje dugih fragmenata omogućilo je kompletiranje sekvence genoma čoveka, objavljivanje drafta ljudskog pangenoma i ubrzalo je sekvenciranje genoma eukariota. Od uvođenja metode 2011. godine sekvencirano je ~1000 od 1065 genoma deponovanih u NCBI bazi. Puni potencijal metode u izučavanju transkriptoma i epigenoma biće vidljiv u godinama koje slede. Sekvenciranje dugih fragmenata postaje osnova precizne medicine efikasne za sve ljudske populacije i očuvanja biodiverziteta, i zavredelo je da bude metoda 2022. godine prema časopisu Nature Methods.",
publisher = "IMGGI",
booktitle = "Sekvenciranje dugih fragmenata – sledeći nivo genomskih istraživanja, Long read sequencing – the next level in genomic research",
url = "https://hdl.handle.net/21.15107/rcub_intor_937"
}

Savić-Pavićević, D., Radenković, L., Velimirov, L., Radovanović, N., Ninković, A., Garai, N., Brkušanin, M., Panić, M.,& Pešović, J.. (2023). Sekvenciranje dugih fragmenata – sledeći nivo genomskih istraživanja. 
IMGGI..
https://hdl.handle.net/21.15107/rcub_intor_937

Savić-Pavićević D, Radenković L, Velimirov L, Radovanović N, Ninković A, Garai N, Brkušanin M, Panić M, Pešović J. Sekvenciranje dugih fragmenata – sledeći nivo genomskih istraživanja. 2023;.
https://hdl.handle.net/21.15107/rcub_intor_937 .

Savić-Pavićević, Dušanka, Radenković, Lana, Velimirov, Luka, Radovanović, Nemanja, Ninković, Anastasija, Garai, Nemanja, Brkušanin, Miloš, Panić, Marko, Pešović, Jovan, "Sekvenciranje dugih fragmenata – sledeći nivo genomskih istraživanja" (2023),
https://hdl.handle.net/21.15107/rcub_intor_937 .

TY  - CONF
AU  - Vlijm, Rifka
AU  - Li, Xue
AU  - Panić, Marko
AU  - Rüthnick, Diana
AU  - Hata, Shoji
AU  - Herrmannsdörfer, Frank
AU  - Kuner, Thomas
AU  - Heilemann, Mike
AU  - Engelhardt, Johann
AU  - Hell, Stefan W.
AU  - Schiebel, Elmar
PY  - 2018
UR  - http://intor.torlakinstitut.com/handle/123456789/843
AB  - The centrosome linker proteins C-Nap1, rootletin and CEP68 connect the
two centrosomes of a cell during interphase into one microtubule organizing centre. This coupling is important for cell migration, cilia formation and timing of mitotic spindle formation. Very little is known about
the structure of the centrosome linker. Here, we used STimulated Emission Depletion (STED)microscopy to show that each C-Nap1 ring at the
proximal end of the two centrioles organizes a rootletin ring and in addition multiple rootletin fibres that radiate outwards from the ring into the
cytoplasm. Rootletin filaments have a repeat organization of 75 nm and
bind CEP68 via its C-terminal spectrin repeat containing region in 75
nm intervals. CEP68 is essential in forming rootletin filaments that branch
off centrioles and modulates the thickness of rootletin fibres. Thus, the
centrosome linker consists of a vast network of repeating rootletin units
with C-Nap1 as ring organizer and CEP68 as filament modulator. The
punctual contact model is consistent with the biological properties of
the centrosome linker.
PB  - Biophysical Society
PB  - Elsevier
C3  - Biophysical Journal
T1  - STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles
IS  - 3
SP  - 535a
VL  - 114
DO  - 10.1016/j.bpj.2017.11.2926
ER  - 

@conference{
author = "Vlijm, Rifka and Li, Xue and Panić, Marko and Rüthnick, Diana and Hata, Shoji and Herrmannsdörfer, Frank and Kuner, Thomas and Heilemann, Mike and Engelhardt, Johann and Hell, Stefan W. and Schiebel, Elmar",
year = "2018",
abstract = "The centrosome linker proteins C-Nap1, rootletin and CEP68 connect the
two centrosomes of a cell during interphase into one microtubule organizing centre. This coupling is important for cell migration, cilia formation and timing of mitotic spindle formation. Very little is known about
the structure of the centrosome linker. Here, we used STimulated Emission Depletion (STED)microscopy to show that each C-Nap1 ring at the
proximal end of the two centrioles organizes a rootletin ring and in addition multiple rootletin fibres that radiate outwards from the ring into the
cytoplasm. Rootletin filaments have a repeat organization of 75 nm and
bind CEP68 via its C-terminal spectrin repeat containing region in 75
nm intervals. CEP68 is essential in forming rootletin filaments that branch
off centrioles and modulates the thickness of rootletin fibres. Thus, the
centrosome linker consists of a vast network of repeating rootletin units
with C-Nap1 as ring organizer and CEP68 as filament modulator. The
punctual contact model is consistent with the biological properties of
the centrosome linker.",
publisher = "Biophysical Society, Elsevier",
journal = "Biophysical Journal",
title = "STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles",
number = "3",
pages = "535a",
volume = "114",
doi = "10.1016/j.bpj.2017.11.2926"
}

Vlijm, R., Li, X., Panić, M., Rüthnick, D., Hata, S., Herrmannsdörfer, F., Kuner, T., Heilemann, M., Engelhardt, J., Hell, S. W.,& Schiebel, E.. (2018). STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles. in Biophysical Journal
Biophysical Society., 114(3), 535a.
https://doi.org/10.1016/j.bpj.2017.11.2926

Vlijm R, Li X, Panić M, Rüthnick D, Hata S, Herrmannsdörfer F, Kuner T, Heilemann M, Engelhardt J, Hell SW, Schiebel E. STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles. in Biophysical Journal. 2018;114(3):535a.
doi:10.1016/j.bpj.2017.11.2926 .

Vlijm, Rifka, Li, Xue, Panić, Marko, Rüthnick, Diana, Hata, Shoji, Herrmannsdörfer, Frank, Kuner, Thomas, Heilemann, Mike, Engelhardt, Johann, Hell, Stefan W., Schiebel, Elmar, "STED Nanoscopy of the Centrosome Linker Reveals a CEP68-Organized, Periodic Rootletin Network Anchored to a C-Nap1 Ring at Centrioles" in Biophysical Journal, 114, no. 3 (2018):535a,
https://doi.org/10.1016/j.bpj.2017.11.2926 . .