Movements and spatial distribution of an endangered fish (Sciaena umbra) within a marine protected area.

The brown meagre (Sciaena umbra) is an endangered species, which requires specific protection measures to ensure its conservation. These measures need to be informed by high-quality scientific knowledge on their space use patterns. Here, we used acoustic telemetry to assess its seasonal movement patterns and habitat use within a marine protected area (MPA). Our results suggested that S. umbra is a highly sedentary species (home range < 1.0 km2) and, therefore, the MPA is extensive enough to protect the local population. Their population was discretely distributed in two main areas within the MPA, which was likely a result of habitat segregation and density-dependent movements. The temporal variability of their movements further uncovered when and where spawning occurs (mainly, but probably not only, in the fully protected area in June) and indicated that spillover of this species is limited but still possible. Overall, we highlight the importance of MPAs in the recovery of S. umbra, we advocate the need to perpetuate the current national fishing bans and extend it to other countries in the Mediterranean region, and we emphasize that considering the fine-scale movements of S. umbra in future management actions is key to achieving a successful recovery of their populations.

Rhythmic properties of Sciaena umbra calls across space and time in the Mediterranean Sea.

In animals, the rhythmical properties of calls are known to be shaped by physical constraints and the necessity of conveying information. As a consequence, investigating rhythmical properties in relation to different environmental conditions can help to shed light on the relationship between environment and species behavior from an evolutionary perspective. Sciaena umbra (fam. Sciaenidae) male fish emit reproductive calls characterized by a simple isochronous, i.e., metronome-like rhythm (the so-called R-pattern). Here, S. umbra R-pattern rhythm properties were assessed and compared between four different sites located along the Mediterranean basin (Mallorca, Venice, Trieste, Crete); furthermore, for one location, two datasets collected 10 years apart were available. Recording sites differed in habitat types, vessel density and acoustic richness; despite this, S. umbra R-calls were isochronous across all locations. A degree of variability was found only when considering the beat frequency, which was temporally stable, but spatially variable, with the beat frequency being faster in one of the sites (Venice). Statistically, the beat frequency was found to be dependent on the season (i.e. month of recording) and potentially influenced by the presence of soniferous competitors and human-generated underwater noise. Overall, the general consistency in the measured rhythmical properties (isochrony and beat frequency) suggests their nature as a fitness-related trait in the context of the S. umbra reproductive behavior and calls for further evaluation as a communicative cue.

Construction and biological characterization of a cDNA infectious clone of wheat umbra-like virus in wheat and Nicotiana benthamiana.

Umbravirus-like associated RNAs (ulaRNAs) are a new group of subviral RNAs associated with plants. Little is known about the biology of ulaRNAs. We recently reported wheat umbra-like virus (WULV) from Kansas fields. In this work, we generated a full-length cDNA clone of WULV which systemically infected N. benthamiana. While agroinfiltrated leaves demonstrated severe necrosis, upper leaves were symptomless. We also showed that WULV is capable of infecting wheat in the absence of a helper virus. Furthermore, and through sap inoculation, we demonstrated that WULV is transmissible in the form of free RNA. This is the first report of a mechanically transmissible ulaRNA. Together, these findings contribute to advancing our knowledge of the biology of WULV. Moreover, the construction of the WULV infectious clone provides a valuable research tool for further investigations including the role of WULV in symptom development in interaction with other wheat viruses.

Molecular characterization of a novel umbra-like virus from Thuja orientalis (arborvitae) in South Korea.

A novel umbra-like virus was identified in arborvitae in South Korea using RNA sequencing (RNA-seq). The virus identified was tentatively named "arborvitae umbra-like virus" (AULV) and contained a 4,300-nucleotide genome organized into four non-structural open reading frames (ORFs). Cloning and Sanger sequencing were used to confirm the viral contig sequence and determine the size of the genome. Genome analysis indicated that ORF2 encodes an RNA-dependent RNA polymerase that is probably expressed through ribosomal frameshifting. ORF3 encodes a putative long-distance movement protein, while the functions of ORFs 1 and 4 are unknown. The virus lacks a coat protein gene. The genome of AULV shares 27.3%-48.4% nucleotide sequence identity with closely related umbraviruses. Phylogenetic analysis based on the complete genome sequences and amino acid sequences of the RNA-dependent RNA polymerase revealed that AULV forms a monophyletic lineage with Guiyang paspalum paspaloides tombus-like virus (GPpTV1). We suggest that AULV is a novel umbra-like virus belonging to the family Tombusviridae.

Intensive sampling of the umbra and penumbra improves clinically significant prostate cancer detection and reduces risk of grade group upgrading at radical prostatectomy.

PURPOSE: Our objective is to evaluate the clinically significant prostate cancer detection rate of overlapping and perilesional systematic biopsy cores and its impact on grade group (GG) concordance at prostatectomy. MATERIALS AND METHODS: Biopsy maps of those undergoing MRI-targeted (TB) and systematic biopsy (SB) were reviewed to reclassify systematic cores. Perilesional (PL) cores were defined as adjacent cores within 10 mm of the target lesion ("penumbra") whilst overlap (OL) cores were defined as cores within the ROI itself ("umbra"). All other cores were designated as distant cores (DC). The incremental csPCa detection rate (GG ≥ 2) and the rate of GG upgrading on prostatectomy as OL, PL and DC sequentially added to TB were determined. RESULTS: Out of the 398 patients included, the median number of OL and PL cores was 5 (IQR 4-7) and 5 (IQR 3-6) respectively. OL cores detected more csPCa than PL cores (31 vs 16%, p < 0.001). OL and PL cores improved the csPCa detection rate of TB from 34 to 39% (p < 0.001) and 37% (p = 0.001) respectively. TB+OL+PL had greater csPCa detection compared to just TB+OL (41 vs 39%, p = 0.016) and TB+PL (41 vs 37%, p < 0.001). Of the 104 patients who underwent prostatectomy, GG upgrading rate for TB+OL+PL was lower compared to TB (21 vs 36%, p < 0.001) and was not significantly different compared to TB+OL+PL+DC (21 vs 19%, p = 0.500). CONCLUSION: A biopsy strategy incorporating both intensive sampling of the umbra and penumbra improved csPCa detection and reduced risk of GG upgrading at prostatectomy.

Let them go free: Spatial behaviour following the experimental release of hatchery-reared juveniles Sciaena umbra and Dentex dentex.

As marine stocks and biodiversity are rapidly declining, the release of hatchery-reared individuals into the wild is a species conservation measure aiming at replenishing stocks of freshwater, anadromous and marine fish species. The aim of this study is to assess for the first time the post-release exploration behaviours, survival and dispersal in the wild of released hatchery-reared juveniles of D. dentex and S. umbra. For this purpose, twenty fish from each species were tagged with acoustic transmitters and released in a marine no-take zone located in Corsica (France). Most individuals were considered alive until their last detection (95% of S. umbra and 74% of D. dentex detected individuals). Fish were detected within the receiver array on average up to 11.3 (± 20.7) and 10.3 (± 10.3) days after being released for juveniles of D. dentex and S.umbra, respectively. Dentex dentex juveniles dispersed mostly southward along the shore whereas S. umbra juveniles tended to disperse along the shore both northward and southward from the acoustic receiver array. Before their rapid dispersion (i.e. within a few days) outside the studied zone, juveniles of both species displayed increasing cumulative MCP areas and increased their vertical niche revealing their gradual coverage and exploration of deeper habitats in the area. The results from our study highlighted that hatchery-reared juveniles of both species did not settle inside the studied area but seemed to start to acclimate to the natural environment. This work is a first step towards the assessment of the viability of restocking for both species.

Targeted Prostate Biopsy: Umbra, Penumbra, and Value of Perilesional Sampling.

BACKGROUND: Systematic prostate biopsies add to the cancer detection rate of targeted biopsies, but the explanation for that increased sensitivity is not yet clear. OBJECTIVE: To determine and quantify the utility of perilesional biopsies in the detection of clinically significant prostate cancer (csPCa). DESIGN, SETTING, AND PARTICIPANTS: Participants were 2048 men with magnetic resonance imaging (MRI) lesions (grades 3-5) who underwent targeted and systematic prostate biopsy via MRI/ultrasound fusion at University of California Los Angeles and Cornell between 2011 and 2019. The study is a retrospective examination of prospectively acquired data. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: All biopsy cores (30191), locations of which had been stored digitally in the image-fusion device, were analyzed for tissue pathology and relationship with MRI lesions. A validated Matlab script was used to determine the distance between MRI lesions and cores containing csPCa (3552 cores from 927 men). Significance of distance measurements was determined by multilevel, multivariable logistic regression to account for within patient-biopsy correlation and control for patient characteristics. RESULTS AND LIMITATIONS: Overall, 90% (95% confidence interval [CI] = 89-91) of csPCa cores (3206/3552) were located within a radius of 10 mm from the nearest lesion: 65% (95% CI = 63-67) within the region of interest (ROI) and 26% (95% CI = 24-27) outside the ROI but within the 10-mm "penumbra." The width of the penumbra or concentric band, which enclosed 90% of csPCa, was primarily related to MRI grade of lesion: grade 5, 5 mm; grade 4, 12 mm; grade 3, 16 mm. In 18% (95% CI = 15-20) of patients (166/927), csPCa was diagnosed only by sampling outside the MRI lesion, the yield decreasing with increasing distance. Limitations of MRI interpretation and fusion biopsy performance could affect the utility of these data in individual patients. CONCLUSIONS: Perilesional biopsies, that is, samples taken from a band of 10-mm radius outside MRI lesions (the penumbra), contain most cores of csPCa that are not present within the lesion. These data may help increase the performance characteristics of targeted prostate biopsy. PATIENT SUMMARY: We studied the locations of cancer within the prostate in men undergoing magnetic resonance imaging (MRI)-guided biopsy. We found that not all cancers are located within the MRI lesion, but 90% (95% confidence interval = 89-91) of the cancers arewithin 1 cm of the lesions. Biopsies taken from both within and around MRI lesions provide greater sensitivity for cancer detection than samples taken from the lesion only.

Universal Primers for Detection of Novel Plant Capsid-Less Viruses: Papaya Umbra-like Viruses as Example.

For diagnosis of positive-sense single-stranded RNA viruses, primers are usually raised against the sequence encoding capsid proteins, since structural proteins are more conserved. This chapter focuses on the design of primers for a group of novel viruses lacking a capsid, known as papaya Umbra-like viruses (unassigned genus) associated with Papaya Sticky Disease, which represent a threat to papaya production. Based on sequence alignments of a region encoding the RNA-dependent RNA Polymerase, universal primers to detect all the known viruses from four countries are proposed. The Forward universal primer can be used in combination with clade- and subclade-specific primers for rapid virus identification. We walk the reader through downloading sequences from nucleotide databases, doing sequence alignments and phylogenetic tree construction to identify conserved and variable regions as valid primer targets; we also show how to design and analyze the primers.

Umbra: A Visual Analysis Approach for Defense Construction Against Inference Attacks on Sensitive Information.

Collecting and analyzing anonymous personal information is required as a part of data analysis processes, such as medical diagnosis and restaurant recommendation. Such data should ostensibly be stored so that specific individual information cannot be disclosed. Unfortunately, inference attacks-integrating background knowledge and intelligent models-hinder classic sanitization techniques like syntactic anonymity and differential privacy from exhaustively protecting sensitive information. As a solution, we introduce a three-stage approach empowered within a visual interface, which depicts underlying inference behaviors via a Bayesian Network and supports a customized defense against inference attacks from unknown adversaries. In particular, our approach visually explains the process details of the underlying privacy preserving models, allowing users to verify if the results sufficiently satisfy the requirements of privacy preservation. We demonstrate the effectiveness of our approach through two case studies and expert reviews.

Characterization of glutathione S-transferase enzyme from brown meagre (Sciaena umbra) and inhibitory effects of heavy metals.

Glutathione S-transferase (GST) detoxifies a broad spectrum of xenobiotics, especially in chemotherapeutic drugs, endogenous molecules, and environmental pollutants. Since the enzyme metabolizes toxic compounds, it has been extensively studied in many living things including aquatic organisms. In the current study, the GST enzyme was purified from brown meagre (Sciaena umbra) muscle tissue for the first time. Then, kinetic parameters of the enzyme were determined as optimum ionic strength: 20 mM Tris/HCl, optimum pH: 7.0 (Tris/HCl), and optimum substrate concentration: 3.125 mM. Eventually, inhibitory effects of the heavy metals were evaluated. IC50 values of the tested metal ions were calculated to be 0.1112, 0.6113, 0.727, and 0.7774 mM for Cd2+ , Fe3+ , Ag+ , and Cu2+ , respectively. Our results show that these heavy metals inhibit GST at very low concentrations which could cause dangerous results for aquatic systems.

DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows.

Genome sizes of eukaryotic organisms vary substantially, with whole-genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and Umbra pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5 and 5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in U. limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.

Genome characterization of fig umbra-like virus.

The complete genome of a new umbra-like virus from edible fig (Ficus carica) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is "fig umbra-like virus" (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CYVaV). In addition, phylogenetic trees based on whole-genome nucleotide sequences and amino acid sequences of the RNA-dependent RNA polymerase showed that FULV forms a monophyletic lineage with CYVaV and other umbra-like viruses. Based on the demarcation criteria of the genus Umbravirus, and lack of two umbravirus ORFs, we propose that FULV is a putative new member of the umbra-like virus clade within the family Tombusviridae.

Does Sciaena umbra (Linnaeus 1758) otolith protect tissues against nephropathy, oxidative stress and inflammation induced by ethylene glycol?

Sciaena umbra is a species of fish with large otoliths. These otoliths are used for treatment of kidney stone disease with high morbidity among the public. In present study, the first group was determined as a control. Group 2 was applied to rats by adding 1% ethylene glycol to drinking water. Group 3 rats were given 50 mg/kg otolith by gavage daily. Group 4 rats were administered by adding ethylene glycol and otolith was given. Group 5 rats were added ethylene glycol for the first 30 days. Then next 15 days, the rats were given only otolith. the Serum CREA and BUN levels and urine calcium, phosphate and pH levels were determined to be damaged by ethylene glycol. Free radicals and oxidative damage caused by ethylene glycol were determined from oxidative/antioxidative parameters. Ethylene glycol has also been shown to be inflammatory. There is no positive effect on oxidative stress. From the levels of TNF-α and IL-1ß in renal tissue, SUO has shown the triggering effect of inflammation. All data indicate that otolith is not an agent that can be used in nephropathy in the kidney. It is thought that caution should be exercised regarding its use.

Purification, compositional analysis, and anticoagulant capacity of chondroitin sulfate/dermatan sulfate from bone of corb (Sciaena umbra).

Chondroitin sulfate/dermatan sulfate (CS/DS) were isolated and purified for the first time from the bone of corb (Sciaena umbra) (CBG) and their chemical composition and anticoagulant activity were assessed. Infrared spectrum and agarose-gel electrophoresis for extracted CS/DS were also investigated. The results showed that the purified CS/DS obtained at a yield of 10% contains about 31.28% sulfate and an average molecular mass of 23.35 kDa. Disaccharide analysis indicated that CBG was composed of monosulfated disaccharides in positions 6 and 4 of the N-acetylgalactosamine (8.6% and 40.0%, respectively) and disulfated disaccharides in different percentages. The charge density was 1.4 and the ratio of 4:6 sulfated residues was equal to 4.64. Chondroitinase AC showed that the purified CS/DS contained mainly 74% CS and 26% DS. Moreover, the new CS/DS extracted from bone of corb showed a strong anticoagulant effect through activated partial thrombosis time (aPTT), thrombin time (TT) and prothrombin time (PT). In fact, CBG prolonged significantly (p < 0.05), aPTT and PT about 2.62 and 1.26 fold, respectively, greater than that of the negative control at a concentration of 1000 µg/mL. However, TT assay of CBG was prolonged 3.53 fold compared with the control at 100 µg/mL. The purified CS/DS displayed a promising anticoagulant potential, which may be used as a novel and soothing drug.

Habitat use of the European mudminnow Umbra krameri and association with other fish species in a disconnected Danube side arm.

Fish assemblages along the longitudinal course of an old, disconnected and modified side arm of the Danube floodplain downstream of Vienna, Austria, as well as habitat structure, hydro-morphological and hydro-chemical factors, were investigated in order to analyse the key environmental determinants of the European mudminnow Umbra krameri. Generally, U. krameri was the most abundant species in the system. It occurred in disconnected ditches, ponds and pools with dense reed belts and comparatively low nutrient content, indicating its natural association with marsh habitats. At infrequently disturbed sites it was associated with a small group of stagnophilious and highly specialized species with adaptations to strong oxygen fluctuations. At frequently flooded sites, the species was absent or occurred in low abundances, indicating its adaptation to water bodies in older successional stages and its low competitive power in permanently connected floodplain habitats.

Seasonal variation in baseline and maximum whole-body glucocorticoid concentrations in a small-bodied stream fish independent of habitat quality.

Alterations to natural habitats are becoming more common due to changes in anthropogenic land use. As such, there is increasing interest in determining how wild animals adapt and respond to environmental stressors. The glucocorticoid (GC) stress response enables animals to react appropriately to environmental challenges but can be affected by many factors, two of which are habitat quality and time of year (i.e., season). This study tested whether baseline and maximum (stress-induced) whole-body cortisol concentrations varied in relation to habitat quality and season using wild central mudminnows (Umbra limi) collected from two connected streams differing in habitat quality in each of four seasons. Overall, baseline and maximum cortisol levels did not differ significantly between the two systems but there was evidence of a seasonal effect. Baseline cortisol levels in the fall and summer were significantly (P<0.01) lower than those in winter and spring and maximum cortisol levels in the summer were significantly lower (P<0.01) than those in the spring. Inconsistent with the prevailing paradigm, our results indicate that habitat quality does not always influence baseline GCs or the stress response. In contrast, baseline and maximum GCs in this species do vary seasonally. As such, seasonality should be considered in the interpretation of stress response data especially when using small-bodied stream fish as biological indicators.

Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792) in a Fragmented Landscape: Implications for Conservation Management.

The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80-90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.

Genetic and morphological variability of the European mudminnow Umbra krameri (Teleostei, Umbridae) in Serbia and in Bosnia and Herzegovina, a basis for future conservation activities.

As a basis for future conservation activities, the genetic and external body morphology variability of the European mudminnow Umbra krameri, a highly endangered fish species in Serbia and in Bosnia and Herzegovina, was determined for existing populations with the use of molecular markers (mitochondrial and microsatellite DNA) and geometric morphometric methods. Mitochondrial DNA cytochrome b gene analysis revealed two previously undescribed haplotypes: Da1 (the Lugomir population from the Danube River basin) and Sa1 (the Bakreni Batar and the Gromizelj populations from the Sava River system), with a corresponding genetic distance of 0·7%. Paired values of FST and DAS distances for microsatellite marker data show that the difference between the Danube and the Sava populations is seven to nine times higher than the difference between the populations within the Sava River system. Geometric morphometric analyses also support a clear separation of the Lugomir population from the Bakreni Batar and the Gromizelj populations. The analysis of the body shape variation, however, indicates a significant difference between the two genetically indistinguishable Sava populations. The observed genetic and phenetic relationships of the analysed mudminnow populations most probably represent a consequence of historical, geographical and ecological factors. These results will offer guidelines for future protection, conservation and sustainable management of this species in the region.

New distribution data and population structure of the European mudminnow Umbra krameri in Serbia and Bosnia and Herzegovina.

Seventy-six individuals of the European mudminnow Umbra krameri from two recent populations from Serbia (Bakreni Batar and Lugomir) and one from Bosnia and Herzegovina (Gromizelj) were analysed for habitat preferences and population structure. The population from Lugomir is a newly recorded population in Serbia. Besides this new record, it is noteworthy that all three studied locations are outside the currently known species distribution range limits.