1. Controlling gene expression with deep generative design of regulatory DNAJan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K. Speicher, Christoph S. Börlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt P. Dubhashi, Verena Siewers, Florian David Fitz, Jens Nielsen, Aleksej Zelezniak, 2022, izvirni znanstveni članek Povzetek: Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random DNA libraries, which limits the designs to span merely a short section of the promoter and restricts their control of gene expression. Here, we prototype a deep learning strategy based on generative adversarial networks (GAN) by learning directly from genomic and transcriptomic data. Our ExpressionGAN can traverse the entire regulatory sequence-expression landscape in a gene-specific manner, generating regulatory DNA with prespecified target mRNA levels spanning the whole gene regulatory structure including coding and adjacent non-coding regions. Despite high sequence divergence from natural DNA, in vivo measurements show that 57% of the highly-expressed synthetic sequences surpass the expression levels of highly-expressed natural controls. This demonstrates the applicability and relevance of deep generative design to expand our knowledge and control of gene expression regulation in any desired organism, condition or tissue.
Objavljeno v DiRROS: 17.07.2024; Ogledov: 0; Prenosov: 1
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2. Infiltrating natural killer cells bind, lyse and increase chemotherapy efficacy in glioblastoma stem-like tumorospheresBarbara Breznik, Meng-Wei Ko, Christopher Tse, Po-Chun Chen, Emanuela Senjor, Bernarda Majc, Anamarija Habič, Nicolas Angelillis, Metka Novak, Vera Župunski, Jernej Mlakar, David Nathanson, Anahid Jewett, 2022, izvirni znanstveni članek Povzetek: Glioblastomas remain the most lethal primary brain tumors. Natural killer (NK) cell-based therapy is a promising immunotherapeutic strategy in the treatment of glioblastomas, since these cells can select and lyse therapy-resistant glioblastoma stem-like cells (GSLCs). Immunotherapy with super-charged NK cells has a potential as antitumor approach since we found their efficiency to kill patient-derived GSLCs in 2D and 3D models, potentially reversing the immunosuppression also seen in the patients. In addition to their potent cytotoxicity, NK cells secrete IFN-γ, upregulate GSLC surface expression of CD54 and MHC class I and increase sensitivity of GSLCs to chemotherapeutic drugs. Moreover, NK cell localization in peri-vascular regions in glioblastoma tissues and their close contact with GSLCs in tumorospheres suggests their ability to infiltrate glioblastoma tumors and target GSLCs. Due to GSLC heterogeneity and plasticity in regards to their stage of differentiation personalized immunotherapeutic strategies should be designed to effectively target glioblastomas.
Ključne besede: glioblastoma, natural killer cells, translational oncology
Objavljeno v DiRROS: 16.07.2024; Ogledov: 17; Prenosov: 2
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3. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by subgroup 2 R2R3-MYBs in grapevineLuis Orduña, Miaomiao Li, David Navarro-Payá, Chen Zhang, A. Santiago, Pablo Romero, Živa Ramšak, Gabriele Magon, Janine Höll, Patrick Merz, Kristina Gruden, Alessandro Vannozzi, Dario Cantu, Jochen Bogs, Darren C. J. Wong, Shao-shan Carol Huang, José Tomás Matus, 2022, izvirni znanstveni članek Povzetek: The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
Ključne besede: secondary metabolism, regulatory networks, transcription factors, transcriptional regulation, DNA affinity purification sequencing
Objavljeno v DiRROS: 16.07.2024; Ogledov: 11; Prenosov: 4
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4. Detection of the endangered stone crayfish Austropotamobius torrentium (Schrank, 1803) and its congeneric A. pallipes in its last italian biotope by eDNA analysisChiara Manfrin, Massimo Zanetti, David Stanković, Umberto Fattori, Victoria Bertucci-Maresca, Piero G. Giulianini, Alberto Pallavicini, 2022, izvirni znanstveni članek Povzetek: The stone crayfish, Austropotamobius torrentium, is a European freshwater crayfish. Although this species is relatively widespread throughout the continent, it is undergoing significant declines throughout its range. However, as the decline rates have not been quantified in detail, this species is classified as data deficient by the IUCN Red List of Threatened Species. The present study describes the development and validation of two species-specific assays based on hydrolysis probe chemistry for the detection of A. torrentium and A. pallipes environmental DNA (eDNA) in water samples collected in the Julian Alps of Italy (Friuli Venezia Giulia). The eDNA-based method was applied to 14 sites within the Danubian Slizza basin, known to be inhabited by A. torrentium, but with insufficient information on their distribution. In addition, one station in the Tagliamento River basin was sampled to test the performance of the A. pallipes probe. The presence of A. torrentium is confirmed at 6 out of 15 sites. At four of these sites, A. torrentium is detected for the first time. In contrast, the presence of A. torrentium was not detected at two sites already known to harbour the species. Finally, the presence of A. pallipes was confirmed in the station belonging to the Tagliamento basin. The methodology described, which allows the distinction between the two species, paves the way for the parallel detection of the stone crayfish and the white-clawed crayfish (A. pallipes) through eDNA analysis.
Objavljeno v DiRROS: 16.07.2024; Ogledov: 11; Prenosov: 3
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5. Experimental validation of Monte Carlo based treatment planning system in bone density equivalent mediaĐeni Smilović Radojčić, Božidar Casar, David Rajlić, Manda Švabić Kolacio, Ignasi Méndez Carot, Nevena Obajdin, Dea Dundara Debeljuh, Slaven Jurković, 2020, izvirni znanstveni članek Objavljeno v DiRROS: 16.07.2024; Ogledov: 12; Prenosov: 4
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6. An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populationsJody Robbemont, Sam van Veldhuijzen, Steven J. R. Allain, Johanna Ambu, Ryan Boyle, David Stanković, 2023, izvirni znanstveni članek Povzetek: Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.
Ključne besede: citizen science, Ichthyosaura alpestris, invasive species, mtDNA barcoding, skin swabbing
Objavljeno v DiRROS: 12.07.2024; Ogledov: 56; Prenosov: 34
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7. Evaluation of the rbcL marker for metabarcoding of marine diatoms and inference of population structure of selected generaTimotej Turk Dermastia, Ivano Vascotto, Janja Francé, David Stanković, Patricija Mozetič, 2023, izvirni znanstveni članek Povzetek: Diatoms are one of the most important phytoplankton groups in the world’s oceans. There are responsible for up to 40% of the photosynthetic activity in the Ocean, and they play an important role in the silicon and carbon cycles by decoupling carbon from atmospheric interactions through sinking and export. These processes are strongly influenced by the taxonomic composition of diatom assemblages. Traditionally, these have been assessed using microscopy, which in some cases is not reliable or reproducible. Next-generation sequencing enabled us to study diversity in a high-throughput manner and uncover new distribution patterns and diversity. However, phylogenetic markers used for this purpose, such as various 18S rDNA regions, are often insufficient because they cannot distinguish between some taxa. In this work, we demonstrate the performance of the chloroplast-encoded rbcL marker for metabarcoding marine diatoms compared to microscopy and 18S-V9 metabarcoding using a series of monthly samples from the Gulf of Trieste (GoT), northern Adriatic Sea. We demonstrate that rbcL is able to detect more taxa compared to 18S-V9 metabarcoding or microscopy, while the overall structure of the diatom assemblage was comparable to the other two methods with some variations, that were taxon dependent. In total, 6 new genera and 22 new diatom species for the study region were identified. We were able to spot misidentification of genera obtained with microscopy such as Pseudo-nitzschia galaxiae, which was mistaken for Cylindrotheca closterium, as well as genera that were completely overlooked, such as Minidiscus and several genera from the Cymatosiraceae family. Furthermore, on the example of two well-studied genera in the region, namely Chaetoceros and particularly Pseudo-nitzschia, we show how the rbcL method can be used to infer even deeper phylogenetic and ecologically significant differences at the species population level. Despite a very thorough community analysis obtained by rbcL the incompleteness of reference databases was still evident, and we shed light on possible improvements. Our work has further implications for studies dealing with taxa distribution and population structure, as well as carbon and silica flux models and networks.
Ključne besede: rbcL, metabarcoding, monitoring, diatoms, population genetics, Pseudo-nitzschia, Adriatic
Objavljeno v DiRROS: 12.07.2024; Ogledov: 47; Prenosov: 20
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8. Artificial intelligence (AI) and strategic planning process within VUCA environments : a ǂresearch agenda and guidelinesRoberto Biloslavo, David A. Edgar, Erhan Aydin, Çağri Bulut, 2024, izvirni znanstveni članek Povzetek: Purpose – This study demonstrates how artificial intelligence (AI) shapes the strategic planning process in
volatile, uncertain, complex and ambiguous (VUCA) business environments.Having adopted various domains
of the Cynefin framework, the research explores AI’s transformative potential and provide insights regarding
how organisations can harness AI-driven solutions for strategic planning.
Design/methodology/approach –This conceptual papertheorises the role of AIin strategic planning process
in a VUCA world by integrating extant knowledge across multiple literature streams. The “model paper”
approach was adopted to provide a theoretical framework predicting relationships among considered concepts.
Findings – The paper highlights potential application of the Cynefin framework to manage complexities in
strategic decision-making process, the transformative impact of AI at different stages of strategic planning,
the required strategic planning characteristics within VUCA to be supported by AI and the attendant
challenges posed by AI integration in the uncertain business landscape.
Originality/value –This study pioneers a theoretical exploration of AI’s role in strategic planning within the
VUCA business landscape, guided by the Cynefin framework. Thus, it enriches scholarly discourse and
expands knowledge frontiers.
Ključne besede: artificial intelligence, strategic planning, VUCA
Objavljeno v DiRROS: 12.07.2024; Ogledov: 48; Prenosov: 11
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9. A new perspective on the molecular dating of the stone crayfsh with an extended phylogeographic information on the speciesDavid Stanković, Katarina Zorić, Simona Đuretanović, Gorana Stamenković, Marija Ilić, Vanja Marković, Saša Marić, 2024, izvirni znanstveni članek Povzetek: Reconstructing the origin and historical
biogeography of the Austropotamobius torrentium is
hampered by insufcient phylogeographic coverage
of the Balkans and deep contradictions in previous
molecular dating. The present work extends the phylogeographic coverage to Serbia, a country crucial for
understanding the species southward dispersal. Our
analysis revealed that the Southern Balkans lineage
occurs in most of the country, the Central and southeastern Europe lineage is restricted to the southwest
and northeast of the country, while a single population in the north of the country harbors the Lika and
Dalmatia lineage, which was previously thought to be
restricted to the northern-central Dinarides. Dataset
expansion led to revised phylogenetic relationships,
which indicated that the Apuseni lineage is not nested
within Northern-central Dinarides lineages but arose
after the most basal split within Austropotamobius
torrentium. This ‘Apuseni frst’ phylogeny provides
a new perspective for molecular dating, according to
which the split between Austropotamobius pallipes
and A. torrentium took place in the Late Oligocene,
while the formation of the phyletic lineages and the
dispersal from the Dinarides to Serbia occurred in
the late Miocene and is probably associated with the
complex and protracted process of disintegration of
the Neogene freshwater lakes in southeastern Europe.
Ključne besede: Austropotamobius torrentium, Austropotamobius bihariensis, divergence time estimation conficts, historical biogeography, neogene lakes, Serbia
Objavljeno v DiRROS: 09.07.2024; Ogledov: 68; Prenosov: 36
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10. Dendritic cell profiles in the inflamed colonic mucosa predict the responses to tumor necrosis factor alpha inhibitors in inflammatory bowel diseaseNataša Smrekar, David Drobne, Lojze Šmid, Ivan Ferkolj, Borut Štabuc, Alojz Ihan, Andreja Nataša Kopitar, 2018, izvirni znanstveni članek Povzetek: Background Dendritic cells play crucial roles in the control of inflammation and immune tolerance in the gut. We aimed to investigate the effects of tumor necrosis factor alpha (TNFa) inhibitors on intestinal dendritic cells in patients with inflammatory bowel disease and the potential role of intestinal dendritic cells in predicting the response to treatment. Patients and methods Intestinal biopsies were obtained from 30 patients with inflammatory bowel disease before and after treatment with TNFa inhibitors. The proportions of lamina propria dendritic cell phenotypes were analysed using flow cytometry. Disease activity was endoscopically assessed at baseline and after the induction treatment. Results At baseline, the proportion of conventional dendritic cells was higher in the inflamed mucosa (7.8%) compared to the uninflamed mucosa (4.5%) (p = 0.003), and the proportion of CD103+ dendritic cells was lower in the inflamed mucosa (47.1%) versus the uninflamed mucosa (57.3%) (p = 0.03). After 12 weeks of treatment, the proportion of conventional dendritic cells in the inflamed mucosa decreased from 7.8% to 4.5% (p = 0.014), whereas the proportion of CD103+ dendritic cells remained unchanged. Eighteen out of 30 (60%) patients responded to their treatment by week 12. Responders had a significantly higher proportion of conventional dendritic cells (9.16% vs 4.4%, p < 0.01) with higher expression of HLA-DR (median fluorescent intensity [MFI] 12152 vs 8837, p = 0.038) in the inflamed mucosa before treatment compared to nonresponders. Conclusions A proportion of conventional dendritic cells above 7% in the inflamed inflammatory bowel disease mucosa before treatment predicts an endoscopic response to TNFa inhibitors.
Ključne besede: inflammatory bowel disease, dendritic cells, colon cancer
Objavljeno v DiRROS: 02.07.2024; Ogledov: 133; Prenosov: 68
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