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Mateusz Wierzbicki,1 Magdalena Kot,2 Agata Lange,1 Aleksandra Kalińska,2 Marcin Gołębiewski,2 Sławomir Jaworski1 1Department of Nanobiotechnology, Warsaw University of Life Sciences, Warsaw, 02-786, Poland; 2Animal Breeding Department, Warsaw University of Life Sciences, Warsaw, 02-786, PolandCorrespondence: Sławomir Jaworski, Department of Nanobiotechnology, Warsaw University of Life Sciences, Ciszewskiego 8 street, Warsaw, 02-786, Poland, Email slawomir_jaworski@sggw.edu.plPurpose: Mastitis in dairy cows is a worldwide problem faced by dairy producers. Treatment mainly involves antibiotic therapy, however, due to widespread antibiotic resistance among bacteria, such treatments are no longer effective. For this reason, scientists are searching for new solutions to combat mastitis, which is caused by bacteria, fungi, and algae. One of the most promising solutions, nanotechnology, is attracting research due to its biocidal properties. The purpose of this research was to determine the biocidal properties of nanocomposites as a potential alternative to antibiotics in the control of mastitis, as well as to determine whether the use of nanoparticles and what concentration is safe for the breeder and the animal.Patients and Methods: In this study, the effects of Ag, Au, Cu, Fe, and Pt nanoparticles and their complexes were evaluated in relation to the survival of bacteria and fungi isolated from cattle diagnosed with mastitis, their physicochemical properties, and their toxicity to bovine and human mammary epithelial cells BME-UV1 and HMEC (human microvascular endothelial cells). Moreover, E. coli, S. aureus, C. albicans, and Prototheca sp. invasion was assessed using the alginate bead (bioprinted) model. The NPs were tested at concentrations of 25, 12.5, 6.25, 3.125, 1.56 mg/l for Au, Ag, Cu and Fe NPs, and 10, 5, 2.5, 1.25, 0.625 mg/l for Pt.Results: With the exception of Fe and Pt, all exhibited biocidal properties against isolates, while the AgCu complex had the best effect. In addition, nanoparticles showed synergistic effects, while the low concentrations had no toxic effect on BME-UV1 and HMEC cells.Conclusion: Synergistic effects of nanoparticles and no toxicity to bovine and human cells might, in the future, be an effective alternative in the fight against microorganisms responsible for mastitis, and the implementation of research results in practice would reduce the percentage of dairy cows suffering from mastitis. The problem of increasing antibiotic resistance is posing a global threat to human’s and animal’s health, and requires comprehensive research to evaluate the potential use of nanoparticles – especially their complexes – as well as to determine whether nanoparticles are safe for the breeders and the animals. The conducted series of studies allows further consideration of the use of the obtained results in practice, creating a potentially new alternative to antibiotics in the treatment and prevention of mastitis in dairy cattle.Keywords: cattle, mastitis, bacteria, fungi, nanocomposites

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINE standards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin.

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.

[2+3] Dipolar cycloadditions of aromatic nitrile oxides to abietic acid esters were investigated. The reactions showed complete site selectivity and regioselectivity, while the stereoselectivity depended on the structures of the dipolarophiles.

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).

Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

The flavor, quality, and composition of beef changes with the cattle diet regimen. The quality of meat varies, and that variability is determined by both individual and environmental factors: age, breed, live weight, fatness degree, plane of nutrition, and concentrate/roughage ratio. The strategy for the rearing and feeding of cattle for slaughter should therefore aim at reducing the saturated fatty acid content and increasing the polyunsaturated fatty acid and monounsaturated fatty acid levels. Many diseases in humans, like atherosclerosis and cardiovascular diseases, are associated with dietary fat, and their development process could take a year, the results of which can be a shorter life and its lower quality. The objective of this review was to describe the factors affecting the meat quality and fatty acid profile of the intramuscular fat of European cattle fed various diets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Sakowski, Grodkowski, Gołebiewski, Slósarz, Kostusiak, Solarczyk and Puppel.)

Background: The aim of the study was to investigate bioactive whey protein concentrations in cow's milk collected in late pasture (LP) and early indoor feeding (EIF) season from conventional and organic farms in Poland., Results: Results showed that in the LP somatic cell count (SCC) was higher under organic farming conditions. However, percentages of protein and fat were higher under conventional farming conditions. In EIF, milk from conventional dairy farms had a higher percentage of fat and lactose and a lower concentration of protein and SCC in comparison to milk from organic farms. Organic milk in LP had higher concentrations of beneficial whey proteins than conventional milk, including β-lactoglobulin (β-Lg, 4.12 vs. 2.68 g L⁻¹), lactoferrin (Lf, 334.99 vs. 188.02 mg L⁻¹), and lysozyme (Lz, 15.68 vs. 12.56 µg L⁻¹). However, conventional milk in EIF had higher concentrations of bovine serum albumin (146.47 vs. 118.65 mg L⁻¹), Lf (49 vs. 185.27 mg L⁻¹), and Lz (16.63 vs. 13.22 µg L⁻¹)., Conclusions: The results show significant differences in the investigated parameters between organic milk and milk from conventional system during EIF and LP. Moreover, extending the pasture season during EIF in organic farms decreases concentration of bioactive compounds of milk., (Copyright © 2012 Society of Chemical Industry.)

Background: So far, in research studies, the age of cows has not been considered as a factor that may influence the changes in the content of milk ingredients with antioxidant properties modified by the feed supplementation. The aim of this study was to determine the influence of supplementation on the content of ingredients having antioxidant properties and to determine the influence of the age of cows taking part in the experiment on these changes. The experiment was conducted using 20 Polish Holstein Friesian cows, 10 primiparous and 10 multiparous. The combined supplementation of fish oil and linseed constituted the experimental factor., Results: The milk of primiparous cows after 21 days of supplementation was characterised by a higher content of C18:1 trans-11, C18:2 cis-9, trans-11, α-retinol, α-tocopherol and β-lactoglobulin compared to the milk of multiparous cows, in which a higher level of lactoferrin, C20:5 and β-carotene was recorded. In both groups an increase in the total antioxidant status was noted (a higher level in the milk of primiparous cows)., Conclusions: Modification of the diet of cows with fish oil and linseed significantly influenced antioxidant properties of their milk; however, the response of multiparous and primaparous cows was noticeably different to the supplement introduced., (Copyright © 2012 Society of Chemical Industry.)

Bacteriophage bIBB29 was isolated from a whey sample originating from an industrial biotechnological process, disturbed by a bacteriophage attack. Phage bIBB29 was determined to be active against three phage-resistant strains of Lactococcus lactis. It belongs to the 936 species containing virulent phages with isometric head and short non-contractile tail. One-step growth kinetics of bIBB29 phage showed that its latent time was 23 min, and the burst size was about 130 bacteriophages. The complete nucleotide sequence of the virulent L. lactis bacteriophage bIBB29 comprises 29305 nucleotides and is the sixth phage genome of the 936 species published until now. The G+C content of the bIBB29 genome (34.7%) is similar to that of its host and also to that of other phages from the 936 species. The bIBB29 genome counts 54 open reading frames organized in three typical clusters, corresponding to the early, middle and late expressed genes. Only 20 protein products of the predicted genes were found to have their homologs among proteins with known function. The early expressed region in the genomes of 936 group members displays the highest divergence, whereas the late and middle regions share high similarities, with the exception of five genes. The genome of bIBB29 shares the highest overall nucleotide similarity with bIL170 (87%), and the lowest with phage 712 (77%). The host range analysis showed that despite the high level of similarity between the receptor binding protein (RBP) of phage bIBB29 and P475, they have a different host range. This implies that RBP is not a sufficient factor for host range.

Here we report the nucleotide sequence of pCTX-M3, a highly conjugative plasmid that is responsible for the extensive spread of the gene coding for the CTX-M-3 extended-spectrum beta-lactamase in clinical populations of the family Enterobacteriaceae in Poland. The plasmid belongs to the IncL/M incompatibility group, is 89,468 bp in size, and carries 103 putative genes. Besides bla(CTX-M-3), it also bears the bla(TEM-1), aacC2, and armA genes, as well as integronic aadA2, dfrA12, and sul1, which altogether confer resistance to the majority of beta-lactams and aminoglycosides and to trimethoprim-sulfamethoxazole. The conjugal transfer genes are organized in two blocks, tra and trb, separated by a spacer sequence where almost all antibiotic resistance genes and multiple mobile genetic elements are located. Only bla(CTX-M-3), accompanied by an ISEcp1 element, is placed separately, in a DNA fragment previously identified as a fragment of the Kluyvera ascorbata chromosome. On the basis of sequence analysis, we speculate that pCTX-M3 might have arisen from plasmid pEL60 from plant pathogen Erwinia amylovora by acquiring mobile elements with resistance genes. This suggests that plasmids of environmental bacterial strains could be the source of those plasmids now observed in bacteria pathogenic for humans.

Escherichia coli isolates recovered from patients during a clonal outbreak in a Warsaw, Poland, hospital in 1997 produced different levels of an extended-spectrum beta-lactamase (ESBL) of the SHV type. The beta-lactamase hyperproduction correlated with the multiplication of ESBL gene copies within a plasmid. Here, we present the complete nucleotide sequence of plasmid p1658/97 carried by the isolates recovered during the outbreak. The plasmid is 125,491 bp and shows a mosaic structure in which all modules constituting the plasmid core are homologous to those found in plasmids F and R100 and are separated by segments of homology to other known regions (plasmid R64, Providencia rettgeri genomic island R391, Vibrio cholerae STX transposon, Klebsiella pneumoniae or E. coli chromosomes). Plasmid p1658/97 bears two replication systems, IncFII and IncFIB; we demonstrated that both are active in E. coli. The presence of an active partition system (sopABC locus) and two postsegregational killing systems (pemIK and hok/sok) indicates that the plasmid should be stably maintained in E. coli populations. The conjugative transfer is ensured by the operons of the tra and trb genes. We also demonstrate that the plasmidic segment undergoing amplification contains the blaSHV-5 gene and is homologous to a 7.9-kb fragment of the K. pneumoniae chromosome. The amplicon displays the structure of a composite transposon of type I.