1391. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomatoBeatriz Romero-Rodríguez, Marko Petek, Chen Jiao, Maja Križnik, Maja Zagorščak, Zhangjun Fei, Eduardo Rodríguez Bejarano, Kristina Gruden, Araceli G. Castillo, 2023, izvirni znanstveni članek Povzetek: Background Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). Results We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. Conclusion We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
Ključne besede: geminivirus, TYLCV, tomato, transcriptome, miRNA
Objavljeno v DiRROS: 15.07.2024; Ogledov: 297; Prenosov: 193
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1392. Biodiversity patterns of cyanobacterial oligotypes in lakes and rivers : results of a large-scale metabarcoding survey in the Alpine regionNico Salmaso, Serena Bernabei, Adriano Boscaini, Camilla Capelli, Leonardo Cerasino, Isabelle Domaizon, Tina Eleršek, Claudia Greco, Aleksandra Krivograd-Klemenčič, Paolo Tomassetti, Rainer Kurmayer, 2023, izvirni znanstveni članek Povzetek: In this work, we characterised the cyanobacterial communities in the plankton and littoral biofilm of 38 lakes and in the biofilm of 21 rivers in the Alps and surrounding subalpine regions by 16S rRNA gene metabarcoding. We found little overlap in the distribution of amplicon sequence variants (ASVs) between the three habitats and between water bodies. The differences were caused by environmental filtering acting on the selection of the most abundant ASVs and a high contribution of rare oligotypes. The differentiation of community and genotype composition from specific water bodies was explained to a significant extent by environmental variables and morphometry. The taxonomic consistency of ASVs classified under the same genus name was assessed by phylogenetic analyses performed on three representative dominant genera, namely Cyanobium, Tychonema and Planktothrix. The analyses revealed eco-evolutionary adaptations in lakes and rivers, including some evidence for a polyphyletic nature. Monitoring individual genotypes in relation to environmental conditions will be useful to define the ecological amplitude of these taxa. However, the persistence or ephemeral nature of some of the rarest and most unusual ASVs has remained unknown.
Ključne besede: plankton, littoral, bioflm, European Alps, phylogenetic analysis, toxigenic cyanobacteria
Objavljeno v DiRROS: 15.07.2024; Ogledov: 311; Prenosov: 217
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1393. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endospermShuang Zhang, Arindam Ghatak, Mitra Mohammadi Bazargani, Hannes Kramml, Fujuan Zang, Shuang Gao, Živa Ramšak, Kristina Gruden, Rajeev K. Varshney, Dong Jiang, Palak Chaturvedi, Wolfram Weckwerth, 2023, izvirni znanstveni članek Povzetek: The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.
Ključne besede: wheat, proteomics and metabolomics, aleurone, sub-aleurone, starchy endosperm, endosperm transfer cells
Objavljeno v DiRROS: 15.07.2024; Ogledov: 663; Prenosov: 199
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1394. Adrenal vein sampling for primary aldosteronism : a 15-year national referral center experienceTomaž Kocjan, Mojca Jensterle Sever, Gaj Vidmar, Rok Vrčkovnik, Pavel Berden, Milenko Stankovič, 2020, izvirni znanstveni članek Povzetek: Background Adrenal vein sampling (AVS) is essential for diagnostics of primary aldosteronism, distinguishing unilateral from bilateral disease and determining treatment options. We reviewed the performance of AVS for primary aldosteronism at our center during first 15 years, comparing the initial period to the period after the introduction of a dedicated radiologist. Additionally, AVS outcomes were checked against CT findings and the proportion of operated patients with proven unilateral disease was estimated. Patients and methods A retrospective cross-sectional study conducted at the national endocrine referral center included all patients with primary aldosteronism who underwent AVS after its introduction in 2004 until the end of 2018. AVS was performed sequentially during Synacthen infusion. When the ratio of cortisol concentrations from adrenal vein and inferior vena cava was at least 5, AVS was considered successful. Results Data from 235 patients were examined (168 men; age 32%73, median 56 years; BMI 18%48, median 30.4 kg/ m2). Average number of annual AVS procedures increased from 7 in the 2004%2011 period to 29 in the 2012%2018 period (p < 0.001). AVS had to be repeated in 10% of procedures; it was successful in 77% of procedures and 86% of patients. The proportion of patients with successful AVS (92% in 2012%2018 vs. 66% in 2004%2011, p < 0.001) and of successful AVS procedures (82% vs. 61%, p < 0.001) was statistically significantly higher in the recent period. Conclusions Number of AVS procedures and success rate at our center increased over time. Introduction of a dedicated radiologist and technical advance expanded and improved the AVS practice.
Ključne besede: angiography, adrenal gland, endocrine disorders
Objavljeno v DiRROS: 15.07.2024; Ogledov: 357; Prenosov: 172
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1396. ▫$[^{18}\mathrm F]$▫FDG PET immunotherapy radiomics signature (iRADIOMICS) predicts response of non-small-cell lung cancer patients treated with pembrolizumabDamijan Valentinuzzi, Martina Vrankar, Nina Boc, Valentina Ahac, Žiga Zupančič, Mojca Unk, Katja Škalič, Ivana Žagar, Andrej Studen, Urban Simončič, Jens C. Eickhoff, Robert Jeraj, 2020, izvirni znanstveni članek Ključne besede: medical physics, medical imaging, oncology
Objavljeno v DiRROS: 15.07.2024; Ogledov: 303; Prenosov: 103
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1397. Influence of concurrent capecitabine based chemoradiotherapy with bevacizumab on the survival rate, late toxicity and health-related quality of life in locally advanced rectal cancer : a prospective phase II CRAB trialVaneja Velenik, Vesna Zadnik, Mirko Omejc, Jan Grosek, Mojca Tuta, 2020, izvirni znanstveni članek Povzetek: Few studies reported early results on efficacy, toxicity of combined modality treatment for locally advanced rectal cancer (LARC) by adding bevacizumab to preoperative chemoradiotherapy, but long-term data on survival, and late complications are lacking. Further, none of the studies reported on the assessment of quality of life (QOL). Patients and methods. After more than 5 years of follow-up, we updated the results of our previous phase II trial in 61 patients with LARC treated with neoadjuvant capecitabine, radiotherapy and bevacizumab (CRAB study) before surgery and adjuvant chemotherapy. Secondary endpoints of updated analysis were local control (LC), disease free (DFS) and overall survival (OS), late toxicity and longitudinal health related QOL (before starting the treatment and one year after the treatment) with questionnaire EORTC QLQ-C30 and EORTC QLQ-CR38. Results. Median follow-up was 67 months. During the follow-up period, 16 patients (26.7%) died. The 5-year OS, DFS and LC rate were 72.2%, 70% and 92.4%. Patients with pathological positive nodes or pathological T3%4 tumors had significantly worse survival than patients with pathological negative nodes or T0%2 tumors. Nine patients (14.8%) developed grade % 3 late complications of combined modality treatment, first event 12 months and last 87 months after operation (median time 48 months). Based on EORTC QLQ-C30 scores one year after treatment there were no significant changes in global QOL and three symptoms (pain, insomnia and diarrhea), but physical and social functioning significantly decreased. Based on QLQ-CR38 scores body image scores significantly increase, problems with weight loss significantly decrease, but sexual dysfunction in men and chemotherapy side effects significantly increase. Conclusions. Patients with LARC and high risk factors, such as positive pathological lymph nodes and high pathological T stage, deserve more aggressive treatment in the light of improving long-term survival results. Patients after multimodality treatment should be given greater attention to the regulation of individual aspects of quality of life and the occurrence of late side effects.
Ključne besede: rectal cancer, bevacizumab, preoperative chemoradiotherapy
Objavljeno v DiRROS: 15.07.2024; Ogledov: 294; Prenosov: 118
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1398. Adaptive visual quality inspection based on defect prediction from production parametersZvezdan Lončarević, Simon Reberšek, Samo Šela, Jure Skvarč, Aleš Ude, Andrej Gams, 2024, izvirni znanstveni članek Povzetek: At the end of a production process, the manufactured products must usually be visually inspected to ensure their quality. Often, it is necessary to inspect the final product from several viewpoints. However, the inspection of all possible aspects might take too long and thus create a bottleneck in the production process. In this paper we propose and evaluate a methodology for adaptive, robot-aided visual quality inspection. With the proposed method, the most probable defects are first predicted based on the production process parameters. A suitable classifier for defect prediction is learnt in an unsupervised manner from a database that includes the produced parts and the associated parameters.Arobot then steers the camera only towards viewpoints associated with predicted defects, which implies that the trajectories of robot motion for the inspection might be different for every product. To enable dynamic planning of camera trajectories, we describe a methodology for evaluation and selection of the most appropriate autonomous motion planner. The proposed defect prediction approach was compared to other methods and evaluated on the products from a real-world production line for injection moulding, which was implemented for a producer of parts in the automotive industry.
Ključne besede: robot learning, robotic quality inspection, visual quality inspection, injection moulding, production parameters, robot motion planning
Objavljeno v DiRROS: 15.07.2024; Ogledov: 316; Prenosov: 218
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1399. Embedded complex curves in the affine planeAntonio Alarcón, Franc Forstnerič, 2024, izvirni znanstveni članek Povzetek: This paper brings several contributions to the classical Forster-Bell-Narasimhan conjecture and the Yang problem concerning the existence of proper and almost proper (hence complete) injective holomorphic immersions of open Riemann surfaces in the affine plane ${\mathbb C}^2$ satisfying interpolation and hitting conditions. We also show that in every compact Riemann surface there is a Cantor set whose complement admits a proper holomorphic embedding in ${\mathbb C}^2$. The focal point is a lemma saying the following. Given a compact bordered Riemann surface, $M$, a closed discrete subset $E$ of its interior ${\mathring M}=M\setminus bM$, a compact subset $K\subset {\mathring M}\setminus E$ without holes in $\mathring M$, and a ${\cal C}^1$ embedding $f: M\hookrightarrow \mathbb C^2$ which is holomorphic in $\mathring M$, we can approximate $f$ uniformly on $K$ by a holomorphic embedding $F: bM\hookrightarrow {\mathbb C}^2$ which maps $E\cup bM$ out of a given ball and satisfies some interpolation conditions.
Ključne besede: Riemann surfaces, complex curves, complete holomorphic embedding
Objavljeno v DiRROS: 15.07.2024; Ogledov: 269; Prenosov: 149
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1400. Transarterial embolization of the external carotid artery in the treatment of life-threatening haemorrhage following blunt maxillofacial traumaČrt Langel, Dimitrij Lovrič, Urša Boneš, Tomislav Mirković, Primož Gradišek, Anita Mrvar Brečko, Katarina Šurlan Popović, 2020, pregledni znanstveni članek Povzetek: Background. Severe bleeding after blunt maxillofacial trauma is a rare but life-threatening event. Non-responders to conventional treatment options with surgically inaccessible bleeding points can be treated by transarterial embolization (TAE) of the external carotid artery (ECA) or its branches. Case series on such embolizations are small; considering the relatively high incidence of maxillofacial trauma, the ECA TAE procedure has been hypothesized either underused or underreported. In addition, the literature on the ECA TAE using novel non-adhesive liquid embolization agents is remarkably scarce.Patients and methods. PubMed review was performed to identify the ECA TAE literature in the context of blunt maxillofacial trauma. If available, the location of the ECA injury, the location of embolization, the chosen embolization agent, and efficacy and safety of the TAE were noted for each case. Survival prognostic factors were also reviewed. Additionally, we present an illustrative TAE case using a precipitating hydrophobic injectable liquid (PHIL) to safely and effectively control a massive bleeding originating bilaterally in the ECA territories.Results and conclusions. Based on a review of 205 cases, the efficacy of TAE was 79.4-100%, while the rate of major complications was about 2-4%. Successful TAE haemostasis, Glasgow Coma Scale score >- 8 at presentation, injury severity score <- 32, shock index <- 1.1 before TAE and <- 0.8 after TAE were significantly correlated with higher survival rate. PHIL allowed for fast yet punctilious application, thus saving invaluable time in life-threatening situations while simultaneously diminishing the possibility of inadvertent injection into the ECA-internal carotid artery (ICA) anastomoses.
Ključne besede: maxillofacial trauma, external carotid artery injury, intractable bleeding
Objavljeno v DiRROS: 12.07.2024; Ogledov: 284; Prenosov: 151
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