1341. PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databasesTianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa, 2022, original scientific article Abstract: PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology.
Keywords: PaintOmics 4, web tools, datasets, analysis methods, molecular biology
Published in DiRROS: 17.07.2024; Views: 287; Downloads: 217
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1344. Effect of the oral intake of astaxanthin on semen parameters in patients with oligo-astheno-teratozoospermia : a randomized double-blind placebo-controlled trialSenka Imamović-Kumalić, Irma Virant-Klun, Eda Vrtačnik-Bokal, Bojana Pinter, 2021, original scientific article Abstract: Background Higher concentrations of seminal reactive oxygen species may be related to male infertility. Astaxanthin with high antioxidant activity can have an impact on the prevention and treatment of various health conditions, including cancer. However, efficacy studies on astaxanthin in patients with oligospermia with/without astheno- or teratozoospermia (O+-A+-T) have not yet been reported. Our aim was to evaluate the effect of the oral intake of astaxanthin on semen parameters. Patients and methods In a randomized double-blind trial, 80 men with O+-A+-T were allocated to intervention with 16 mg astaxanthin orally daily or placebo. At baseline and after three months basic semen parameters, sperm deoxyribonucleic acid (DNA) fragmentation and mitochondrial membrane potential (MMP) of spermatozoa and serum follicle-stimulating hormone (FSH) value were measured. Results Analysis of the results of 72 patients completing the study (37 in the study group, 35 in the placebo group) did not show any statistically significant change, in the astaxanthin group no improvements in the total number of spermatozoa, concentration of spermatozoa, total motility of spermatozoa, morphology of spermatozoa, DNA fragmentation and mitochondrial membrane potential of spermatozoa or serum FSH were determined. In the placebo group, statistically significant changes in the total number and concentration of spermatozoa were determined. Conclusions The oral intake of astaxanthin did not affect any semen parameters in patients with O+-A+-T.
Keywords: DNA fragmentation, antioxidant, cancer
Published in DiRROS: 17.07.2024; Views: 262; Downloads: 174
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1345. Completely resected stage III melanoma controversy : 15 years of national tertiary centre experienceBarbara Perić, Sara Milićević, Andraž Perhavec, Marko Hočevar, Janez Žgajnar, 2021, original scientific article Abstract: Background Two prospective randomized studies analysing cutaneous melanoma (CM) patients with sentinel lymph node (SLN) metastases and rapid development of systemic adjuvant therapy have changed our approach to stage III CM treatment. The aim of this study was to compare results of retrospective survival analysis of stage III CM patients% treatment from Slovenian national CM register to leading international clinical guidelines. Patients and methods Since 2000, all Slovenian CM patients with primary tumour % TIb are treated at the Institute of Oncology Ljubljana and data are prospectively collected into a national CM registry. A retrospective analysis of 2426 sentinel lymph node (SLN) biopsies and 789 lymphadenectomies performed until 2015 was conducted using Kaplan-Meier survival curves and log-rank tests. Results Positive SLN was found in 519/2426 (21.4%) of patients and completion dissection (CLND) was performed in 455 patients. The 5-year overall survival (OS) of CLND group was 58% vs. 47% of metachronous metastases group (MLNM) (p = 0.003). The 5-year OS of patients with lymph node (LN) metastases and unknown primary site (UPM) was 45% vs. 21% of patients with synchronous LN metastasis. Patients with SLN tumour burden < 0.3 mm had 5-year OS similar to SLN negative patients (86% vs. 85%; p = 0.926). The 5-year OS of patients with burden > 1.0 mm was similar to the MLNM group (49% vs. 47%; p = 0.280). Conclusions Stage III melanoma patients is a heterogeneous group with significant OS differences. CLND after positive SLNB might still remain a method of treatment for selected patients with stage III.
Keywords: cutaneous melanoma, surgery treatment, sentinel node biopsy
Published in DiRROS: 17.07.2024; Views: 295; Downloads: 153
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1346. Poročilo o preskusu št.: LVG 2024-061 : vzorec št. 2024/00310Nikica Ogris, 2024, expertise, arbitration decision Keywords: varstvo gozdov, morfološke analize, črna jelša, Alnus glutinosa, list, rja, gliva, Melampsoridium betulinum
Published in DiRROS: 17.07.2024; Views: 285; Downloads: 124
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1347. Systematic comparison of nanopore and illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approachAnja Pecman, Ian Adams, Ion Gutiérrez-Aguirre, Adrian Fox, Neil Boonham, Maja Ravnikar, Denis Kutnjak, 2022, original scientific article Abstract: High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology for the first time and 11 plant viruses with different genome organizations. For all samples, sequencing libraries for the MiSeq were prepared from ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) and for MinION sequencing, direct RNA sequencing of totRNA was used. Moreover, for one of the samples, which contained five different plant viruses and a viroid, three additional variations of sample preparation for MinION sequencing were also used: direct RNA sequencing of rRNA-depleted totRNA, cDNA-PCR sequencing of totRNA, and cDNA-PCR sequencing of rRNA-depleted totRNA. Whilst direct RNA sequencing of total RNA was the quickest of the tested approaches, it was also the least sensitive: using this approach, we failed to detect only one virus that was present in a sample at an extremely low titer. All other MinION sequencing approaches showed improved performance with outcomes similar to Illumina sequencing, with cDNA-PCR sequencing of rRNA-depleted totRNA showing the best performance amongst tested nanopore MinION sequencing approaches. Moreover, when enough sequencing data were generated, high-quality consensus viral genome sequences could be reconstructed from MinION sequencing data, with high identity to the ones generated from Illumina data. The results of this study implicate that, when an appropriate sample and library preparation are selected, nanopore MinION sequencing could be used for the detection of plant viruses and viroids with similar performance as Illumina sequencing. Taken as a balance of practicality and performance, this suggests that MinION sequencing may be an ideal tool for fast and affordable virus diagnostics.
Keywords: high-throughput sequencing, plant virus, viroid detection, comparison, nanopore MinION sequencing, illumina MiSeq sequencing
Published in DiRROS: 16.07.2024; Views: 334; Downloads: 211
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1348. Diversity of dinoflagellate symbionts in scyphozoan hosts from shallow environments : the Mediterranean Sea and Cabo Frio (Rio de Janeiro, Brazil)Lucija Raspor Dall'Olio, Alfred Beran, Vesna Flander-Putrle, Alenka Malej, Andreja Ramšak, 2022, original scientific article Abstract: Symbiotic scyphozoan jellyfish are poorly understood in terms of their symbionts and traits, as well as the ecological significance of this association. Dinoflagellate symbionts of the medusae Cotylorhiza tuberculata, Phyllorhiza punctata, and Cassiopea xamachana collected in the Mediterranean Sea and Cabo Frio (Rio de Janeiro, Brazil) were phylogenetically identified based on 28S rDNA and ITS2 haplotypes. The studied medusae harbour only one phylotype of symbionts in a time, but scyphozoan jellyfishes can associate with several types of symbionts. This study confirmed that the main symbionts of investigated scyphozoans belong to the genera Symbiodinium, Philozoon, and Breviolum. The associations between dinoflagellate symbionts and Cotylorhiza tuberculata changed from year to year, hosting Philozoon one year and Breviolum another. Invasive species in the Mediterranean Sea Phyllorhiza punctata harboured dinoflagellate symbionts of genus Symbiodinium as in the native areal. Pigment analysis of two shallow-water symbiont species Breviolum sp. and Philozoon medusarum revealed characteristic profiles for each genus.
Keywords: symbiodiniaceae, scyphozoa, 28S rDNA, ITS2, cultivation, pigments, marine biology
Published in DiRROS: 16.07.2024; Views: 336; Downloads: 184
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1349. 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, original scientific article Abstract: 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.
Keywords: glioblastoma, natural killer cells, translational oncology
Published in DiRROS: 16.07.2024; Views: 324; Downloads: 264
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1350. Fermentative indole production via bacterial tryptophan synthase alpha subunit and plant indole-3-glycerol phosphate lyase enzymesLenny Ferrer, Melanie Mindt, Maria Suarez-Diez, Tatjana Jilg, Maja Zagorščak, Jin-Ho Lee, Kristina Gruden, Volker F. Wendisch, Katarina Cankar, 2022, original scientific article Abstract: Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L–1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat.
Keywords: Corynebacterium glutamicum, indole, indole-3-glycerol phosphate lyase, tryptophan synthase α-subunit, bioprospecting, fermentative production
Published in DiRROS: 16.07.2024; Views: 323; Downloads: 221
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