1271. 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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: Corynebacterium glutamicum, indole, indole-3-glycerol phosphate lyase, tryptophan synthase α-subunit, bioprospecting, fermentative production
Objavljeno v DiRROS: 16.07.2024; Ogledov: 308; Prenosov: 215
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1272. New records of rare species in the Mediterranean Sea (May 2022)Vasiliki Kousteni, Athanasios Anastasiadis, Michel Bariche, Pietro Battaglia, Andrea Bonifazi, Ilija Ćetković, Giovanni Chimienti, Marco Colombo, Costas Constantinou, Maria Corsini-Foka, Cem Dalyan, Aikaterini Dogrammatzi, Filippo Domenichetti, Radhouan El Zrelli, Alfredo Fernández-Alías, Thodoros E. Kampouris, Lovrenc Lipej, Borut Mavrič, Ana Pešić, Domen Trkov, 2022, izvirni znanstveni članek Povzetek: This Collective Article presents new information about the occurrence of 20 taxa that belong to six Phyla: one Cnidaria, one Ctenophora, two Annelida, four Mollusca, two Arthropoda, and ten Chordata. These records were reported from ten countries from the western to the eastern Mediterranean Sea as follows: Spain: early colonization signs of the Mar Menor lagoon by the cigar jellyfish Olindias muelleri; France: second record of the sea chub of the genus Kyphosus in French Mediterranean waters; Italy: first record of the marbled crab Pachygrapsus maurus in Sardinian waters; first records of the polychaetes Malmgrenia polypapillata and Levinsenia tribranchiata in the Tyrrhenian Sea; new record of the deep-sea squid Ancistrocheirus lesueurii in the Tyrrhenian Sea; first record of the pignosed arrowtooth eel Dysomma brevirostre in the Adriatic Sea; Tunisia: first documented record of the blue butterfish Stromateus fiatola and new record of the iconic great white shark Carcharodon carcharias in the Gulf of Gabes; Slovenia: first records of the sea slug Diaphorodoris alba and the sharpnose sevengill shark Heptranchias perlo; Mon-tenegro: new record of the rare tope shark Galeorhinus galeus; Greece: new records of the rabbitfish Chimaera monstrosa and the electric ray Tetronarce nobiliana; first published record of the nuribranch Discodoris rosi; Turkey: first record of the ctenophore Hormiphora plumosa at country level; first records of the anomuran decapod Munida speciosa and the Mediterranean tripodfish, Bathypterois mediterraneus from the Levantine Sea; Cyprus: first documented record of the nuribranch Scyllaea pelagica; Leb-anon: first record of the killer whale Orcinus orca from the Levantine Sea.
Objavljeno v DiRROS: 16.07.2024; Ogledov: 341; Prenosov: 218
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1273. Evaluating seagrass meadow dynamics by integrating field-based and remote sensing techniquesDanijel Ivajnšič, Martina Orlando-Bonaca, Daša Donša, Jaša Veno Grujić, Domen Trkov, Borut Mavrič, Lovrenc Lipej, 2022, izvirni znanstveni članek Povzetek: Marine phanerogams are considered biological sentinels or indicators since any modification in seagrass meadow distribution and coverage signals negative changes in the marine environment. In recent decades, seagrass meadows have undergone global losses at accelerating rates, and almost one-third of their coverage has disappeared globally. This study focused on the dynamics of seagrass meadows in the northern Adriatic Sea, which is one of the most anthropogenically affected areas in the Mediterranean Sea. Seagrass distribution data and remote sensing products were utilized to identify the stable and dynamic parts of the seagrass ecosystem. Different seagrass species could not be distinguished with the Sentinel-2 (BOA) satellite image. However, results revealed a generally stable seagrass meadow (283.5 Ha) but, on the other hand, a stochastic behavior in seagrass meadow retraction (90.8 Ha) linked to local environmental processes associated with anthropogenic activities or climate change. If systemized, this proposed approach to monitoring seagrass meadow dynamics could be developed as a spatial decision support system for the entire Mediterranean basin. Such a tool could serve as a key element for decision makers in marine protected areas and would potentially support more effective conservation and management actions in these highly productive and important environments.
Ključne besede: Adriatic Sea, seagrass meadow, change analysis, Cimodocea nodosa, image classifiers, Sentinel-2, marine biology, hydrobiology
Objavljeno v DiRROS: 16.07.2024; Ogledov: 272; Prenosov: 200
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1274. Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the oceanMario Pinto, Zihao Zhao, Katja Klun, Eugen Libowitzky, Gerhard J. Herndl, 2022, izvirni znanstveni članek Povzetek: Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analyzed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for 2 years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harbored genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase, respectively. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This report identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential for utilizing LDPE-associated compounds as carbon and energy source.
IMPORTANCE Low-density polyethylene (LDPE) is one of the most used plastics worldwide, and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements, and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After 2 years of incubation, two of the microbial communities exhibited very similar taxonomic compositions mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean that might have the potential to degrade LDPE-associated compounds and that alkane degradation pathways might be involved.
Ključne besede: LDPE, ocean, biodegradation, biofilms, metagenomics
Objavljeno v DiRROS: 16.07.2024; Ogledov: 368; Prenosov: 195
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1275. Inventory and DNA-barcode library of ground-dwelling predatory arthropods from Krokar virgin forest, SloveniaŽan Kuralt, Urška Ratajc, Neža Pajek Arambašić, Maja Ferle, Matic Gabor, Ivan Kos, 2022, izvirni znanstveni članek Povzetek: Background
At a time of immense human pressure on nature and the resulting global environmental changes, the inventory of biota - especially of undisturbed natural areas - is of unprecedented value as it provides a baseline for future research. Krokar, an example of such an undisturbed area, is the largest virgin forest remnant in Slovenia. It is located in the Dinaric Alps, which are believed to harbour the most diverse fauna of soil invertebrates in Europe. Nevertheless, the soil fauna of the Krokar virgin forest has not been thoroughly studied. Moreover, modern taxonomic approaches often rely on genetic information (e.g. DNA-barcodes), while extensive reference libraries from the Dinaric area are lacking. Our work, therefore, focused on addressing this lack of faunistic and genetic data from the Dinaric area.
New information
A total of 2336 specimens belonging to 100 taxa (45 spiders, 30 centipedes, 25 ground-dwelling beetles) were collected and deposited to GBIF. DNA-barcodes of 124 specimens belonging to 73 species were successfully obtained and deposited in GenBank and BOLD databases.
Ključne besede: zoology, faunistics, primary forest, Slovenia
Objavljeno v DiRROS: 16.07.2024; Ogledov: 284; Prenosov: 136
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1276. A new obligate groundwater species of Asellus (Isopoda, Asellidae) from IranMohammad Javad Malek-Hosseini, Jure Jugovic, Yaser Fatemi, Matjaž Kuntner, Rok Kostanjšek, Christophe J. Douady, Florian Malard, 2022, izvirni znanstveni članek Povzetek: With only 43 described stygobionts and only two isopod species the obligate groundwater fauna of Iran, a vast country with over 10% of limestone surface, is inadequately known. Here, we report the discovery of Asellus ismailsezarii sp. nov. from Zagros mountains, the first eyeless and depigmented asellid isopod from Iran. The new species is morphologically similar to Asellus monticola Birstein, 1932, but it is eyeless and fully depigmented, has a slightly curved pereopod IV and does not bear any setae on proximal margins of exopodite of pleopods IV and V. Species phylogenetic relationships using original and datamined mitochondrial DNA and nuclear rDNA, and estimation of molecular divergences with other Asellus species, suggest that A. ismailsezarii sp. nov. is sister to a larger clade that also contains the European A. aquaticus species complex. Surface populations of Asellus have colonized groundwater at multiple occasions and localities, both in Europe and Asia, giving rise to species and subspecies that have evolved troglomorphisms, such as depigmentation and loss of eyes. Of the 37 formally described species and subspecies of Asellus, 15 are from groundwater, including A. ismailsezarii sp. nov. We predict that many more obligate groundwater Asellus taxa are yet to be discovered in Asia.
Ključne besede: Asia, groundwater, molecular phylogeny, taxonomy, troglomorphy
Objavljeno v DiRROS: 16.07.2024; Ogledov: 292; Prenosov: 216
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1277. Risk perception associated with an emerging agri-food risk in Europe : plant viruses in agricultureJohny Hilaire, Sophie Tindale, Glyn Jones, Gabriela Pingarron-Cardenas, Katarina Bačnik, Mercy Ojo, Lynn J. Frewer, 2022, izvirni znanstveni članek Povzetek: Background
Research into public risk perceptions associated with emerging risks in agriculture and supply chains has focused on technological risks, zoonotic diseases, and food integrity, but infrequently on naturally occurring diseases in plants. Plant virus infections account for global economic losses estimated at $30 billion annually and are responsible for nearly 50% of plant diseases worldwide, threatening global food security. This research aimed to understand public perceptions of emerging risks and benefits associated with plant viruses in agriculture in Belgium, Slovenia, Spain, and the UK.
Methods
Online qualitative semi-structured interviews with 80 European consumers were conducted, including 20 participants in each of Belgium, Slovenia, the UK, and Spain. Microsoft Streams was used to transcribe the interview data, and NVivo was utilized to code the transcripts and analyze the data.
Results
The results indicate that, while study participants were relatively unfamiliar with the plant viruses and their potential impacts, plant viruses evoked perceived risks in a similar way to other emerging risks in the agri-food sector. These included risks to environment and human health, and the economic functioning of the relevant supply chain. Some participants perceived both risks and benefits to be associated with plant viruses. Benefits were perceived to be associated with improved plant resistance to viruses.
Conclusions
The results provide the basis for risk regulation, policy, and communication developments. Risk communication needs to take account of both risk and benefit perceptions, as well as the observation that plant viruses are perceived as an emerging, rather than an established, understood, and controlled risk. Some participants indicated the need for risk–benefit communication strategies to be developed, including information about the impacts of the risks, and associated mitigation strategies. Participants perceived that responsibility for control of plant viruses should be conferred on actors within the supply chain, in particular primary producers, although policy support (for example, financial incentivization) should be provided to improve their motivation to instigate risk mitigation activities.
Ključne besede: consumer, disease, food security, supply chain, policy
Objavljeno v DiRROS: 16.07.2024; Ogledov: 322; Prenosov: 171
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1278. 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: 280; Prenosov: 188
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1279. 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: 298; Prenosov: 170
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1280. Fast assay to predict multipotent mesenchymal stromal cell replicative senescence dynamicsKatja Kološa, Aleš Leskovšek, Teja Rajar, Tamara Lah Turnšek, 2022, izvirni znanstveni članek Povzetek: The major obstacle to the application of mesenchymal stromal cells (MSCs) in regenerative medicine is the expansion of the donor-derived cells in vitro to obtain high cell numbers in the shortest possible time. However, MSCs gradually undergo replicative senescence after a variable number of divisions that reduce their therapeutic efficacy, which needs to be determined before administration. The authors developed a fast and simple evaluation assay testing two senescence inducers, mitoxantrone (Mxt) and trichostatin A (TSA), to predict the onset of spontaneous replicative senescence of adipose-derived mesenchymal stromal cells (ASCs) and have confirmed the correlation between induced senescence and spontaneous replicative senescence in the assay using Mxt. This protocol facilitates the standardization of therapeutic ASCs and MSCs from other origins before application.
Ključne besede: adipose mesenchymal stromal (stem) cells (ASCs), cell longevity, induced senescence, mesenchymal stromal (stem) cells (MSCs), mitoxantrone, replicative senescence, trichostatin A
Objavljeno v DiRROS: 16.07.2024; Ogledov: 305; Prenosov: 147
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