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13 pages, 868 KiB  
Article
The Effect of Clarification Protocols on the Vinification of White Wines with Papain and Bromelain Immobilized on Glutaraldehyde Activated Chitosan
by Emmanuel M. Papamichael, Efstathios Hatziloukas, Amalia-Sofia Afendra, Panagiota-Yiolanda Stergiou and Violeta Maltabe
Catalysts 2024, 14(11), 788; https://doi.org/10.3390/catal14110788 - 6 Nov 2024
Viewed by 1027
Abstract
The aim of this study is the implementation of reliable, inexpensive, and practical clarification methods of white wines, without affecting their traditional organoleptic characteristics, through treatment of musts and/or white wines with immobilized papain and bromelain. In all vinifications which focused on the [...] Read more.
The aim of this study is the implementation of reliable, inexpensive, and practical clarification methods of white wines, without affecting their traditional organoleptic characteristics, through treatment of musts and/or white wines with immobilized papain and bromelain. In all vinifications which focused on the production of white wines with improved organoleptic characteristics, the yeast strain Saccharomyces cerevisiae Z622 was used. Both purified papain and bromelain were immobilized on high-molecular-weight chitosan microparticles using three different protocols. The immobilized proteases with the most effective protocol were applied to both unfermented musts and fermented wines. Control vinifications were also performed using bentonite as a clarifying agent. Quantitative analyses of the white wines were carried out at the end of the alcoholic fermentation and after six months of bottling and storage in the refrigerator. The organoleptic characteristics of the clarified white wines treated with the immobilized proteases were compared with those treated with bentonite, a blank untreated white wine sample, and a commercial sample of Debina white wine through sensory evaluation. The results showed that only the musts treated with immobilized papain before fermentation resulted in clarified white wines with stable and improved sensory characteristics, similar to those of the Debina white wine sample. Full article
(This article belongs to the Section Biocatalysis)
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22 pages, 3686 KiB  
Article
Structure–Activity Relationship of Synthetic Linear KTS-Peptides Containing Meta-Aminobenzoic Acid as Antagonists of α1β1 Integrin with Anti-Angiogenic and Melanoma Anti-Tumor Activities
by Majdi Saleem Naamneh, Tatjana Momic, Michal Klazas, Julius Grosche, Johannes A. Eble, Cezary Marcinkiewicz, Netaly Khazanov, Hanoch Senderowitz, Amnon Hoffman, Chaim Gilon, Jehoshua Katzhendler and Philip Lazarovici
Pharmaceuticals 2024, 17(5), 549; https://doi.org/10.3390/ph17050549 - 24 Apr 2024
Cited by 1 | Viewed by 2516
Abstract
To develop peptide drugs targeting integrin receptors, synthetic peptide ligands endowed with well-defined selective binding motifs are necessary. The snake venom KTS-containing disintegrins, which selectively block collagen α1β1 integrin, were used as lead compounds for the synthesis and structure–activity relationship of a series [...] Read more.
To develop peptide drugs targeting integrin receptors, synthetic peptide ligands endowed with well-defined selective binding motifs are necessary. The snake venom KTS-containing disintegrins, which selectively block collagen α1β1 integrin, were used as lead compounds for the synthesis and structure–activity relationship of a series of linear peptides containing the KTS-pharmacophore and alternating natural amino acids and 3-aminobenzoic acid (MABA). To ensure a better stiffness and metabolic stability, one, two and three MABA residues, were introduced around the KTS pharmacophore motif. Molecular dynamics simulations determined that the solution conformation of MABA peptide 4 is more compact, underwent larger conformational changes until convergence, and spent most of the time in a single cluster. The peptides’ binding affinity has been characterized by an enzyme linked immunosorbent assay in which the most potent peptide 4 inhibited with IC50 of 324 ± 8 µM and 550 ± 45 µM the binding of GST-α1-A domain to collagen IV fragment CB3, and the cell adhesion to collagen IV using α1-overexpressor cells, respectively. Docking studies and MM-GBSA calculations confirmed that peptide 4 binds a smaller region of the integrin near the collagen-binding site and penetrated deeper into the binding site near Trp1. Peptide 4 inhibited tube formation by endothelial cell migration in the Matrigel angiogenesis in vitro assay. Peptide 4 was acutely tolerated by mice, showed stability in human serum, decreased tumor volume and angiogenesis, and significantly increased the survival of mice injected with B16 melanoma cells. These findings propose that MABA-peptide 4 can further serve as an α1β1-integrin antagonist lead compound for further drug optimization in angiogenesis and cancer therapy. Full article
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22 pages, 12087 KiB  
Article
A Cloud-Based Deep Learning Framework for Downy Mildew Detection in Viticulture Using Real-Time Image Acquisition from Embedded Devices and Drones
by Sotirios Kontogiannis, Myrto Konstantinidou, Vasileios Tsioukas and Christos Pikridas
Information 2024, 15(4), 178; https://doi.org/10.3390/info15040178 - 24 Mar 2024
Cited by 12 | Viewed by 2615
Abstract
In viticulture, downy mildew is one of the most common diseases that, if not adequately treated, can diminish production yield. However, the uncontrolled use of pesticides to alleviate its occurrence can pose significant risks for farmers, consumers, and the environment. This paper presents [...] Read more.
In viticulture, downy mildew is one of the most common diseases that, if not adequately treated, can diminish production yield. However, the uncontrolled use of pesticides to alleviate its occurrence can pose significant risks for farmers, consumers, and the environment. This paper presents a new framework for the early detection and estimation of the mildew’s appearance in viticulture fields. The framework utilizes a protocol for the real-time acquisition of drones’ high-resolution RGB images and a cloud-docker-based video or image inference process using object detection CNN models. The authors implemented their framework proposition using open-source tools and experimented with their proposed implementation on the debina grape variety in Zitsa, Greece, during downy mildew outbursts. The authors present evaluation results of deep learning Faster R-CNN object detection models trained on their downy mildew annotated dataset, using the different object classifiers of VGG16, ViTDet, MobileNetV3, EfficientNet, SqueezeNet, and ResNet. The authors compare Faster R-CNN and YOLO object detectors in terms of accuracy and speed. From their experimentation, the embedded device model ViTDet showed the worst accuracy results compared to the fast inferences of YOLOv8, while MobileNetV3 significantly outperformed YOLOv8 in terms of both accuracy and speed. Regarding cloud inferences, large ResNet models performed well in terms of accuracy, while YOLOv5 faster inferences presented significant object classification losses. Full article
(This article belongs to the Special Issue Deep Learning for Image, Video and Signal Processing)
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14 pages, 858 KiB  
Article
Biostimulant Effect of Commercial Rhizobacteria Formulation on the Growth of Vitis vinifera L.: Case of Optimal and Water Deficit Conditions
by Vasileios Papantzikos, Areti Papanikou, Vasileios Stournaras, Paraskevi Mpeza, Spiridon Mantzoukas and Georgios Patakioutas
Appl. Biosci. 2024, 3(1), 151-164; https://doi.org/10.3390/applbiosci3010010 - 8 Mar 2024
Cited by 2 | Viewed by 1846
Abstract
As climate change is an imminent threat to the environment and agriculture, there is an increasing need to find immediate solutions capable of compensating for water deficits even in semi-arid conditions. This study is focused on the evaluation of the vegetative growth of [...] Read more.
As climate change is an imminent threat to the environment and agriculture, there is an increasing need to find immediate solutions capable of compensating for water deficits even in semi-arid conditions. This study is focused on the evaluation of the vegetative growth of grapevine plants Vitis vinifera L., of the Greek variety “Debina” in a water deficit environment, with the application of two bacterial-based formulations: one with Bacillus amyloliquefaciens (strain QST 713) and one with Sinorhizobium meliloti (strain cepa B2352). The two formulations were tested under rational irrigation (100% of Available Water) and deficit irrigation (57% of AW). After 140 days, plant growth parameters, such as total plant growth length, leaf area, roots, shoots, and leaves dry biomass showed better performance on treatments with plant growth-promoting rhizobacteria (PGPR) formulations under either rational or deficit irrigation conditions. In addition, the metabolic response of the grapevine plants to the deficit irrigation stress, such as the total chlorophyll, leaf relative water, total phenolic, and proline content, proved to be enriched on the treatments with PGPR formulations during this experiment. The two formulations, in conditions of abiotic stress, achieved to almost compensate for the irrigation deficit, boosting the plant metabolism. This study reveals the need for further research on PGPR biostimulants, as this first trial of these formulations on grapevine could be significant in the case of water scarcity and climate change. Full article
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38 pages, 10287 KiB  
Article
Proposed Fuzzy-Stranded-Neural Network Model That Utilizes IoT Plant-Level Sensory Monitoring and Distributed Services for the Early Detection of Downy Mildew in Viticulture
by Sotirios Kontogiannis, Stefanos Koundouras and Christos Pikridas
Computers 2024, 13(3), 63; https://doi.org/10.3390/computers13030063 - 28 Feb 2024
Cited by 7 | Viewed by 2323
Abstract
Novel monitoring architecture approaches are required to detect viticulture diseases early. Existing micro-climate decision support systems can only cope with late detection from empirical and semi-empirical models that provide less accurate results. Such models cannot alleviate precision viticulture planning and pesticide control actions, [...] Read more.
Novel monitoring architecture approaches are required to detect viticulture diseases early. Existing micro-climate decision support systems can only cope with late detection from empirical and semi-empirical models that provide less accurate results. Such models cannot alleviate precision viticulture planning and pesticide control actions, providing early reconnaissances that may trigger interventions. This paper presents a new plant-level monitoring architecture called thingsAI. The proposed system utilizes low-cost, autonomous, easy-to-install IoT sensors for vine-level monitoring, utilizing the low-power LoRaWAN protocol for sensory measurement acquisition. Facilitated by a distributed cloud architecture and open-source user interfaces, it provides state-of-the-art deep learning inference services and decision support interfaces. This paper also presents a new deep learning detection algorithm based on supervised fuzzy annotation processes, targeting downy mildew disease detection and, therefore, planning early interventions. The authors tested their proposed system and deep learning model on the grape variety of protected designation of origin called debina, cultivated in Zitsa, Greece. From their experimental results, the authors show that their proposed model can detect vine locations and timely breakpoints of mildew occurrences, which farmers can use as input for targeted intervention efforts. Full article
(This article belongs to the Special Issue Artificial Intelligence in Industrial IoT Applications)
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19 pages, 2333 KiB  
Article
Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the ‘Epirus’ Region of Greece upon Consecutive Drought Stress
by Grigorios Maniatis, Eleni Tani, Anastasios Katsileros, Evangelia V. Avramidou, Theodora Pitsoli, Efi Sarri, Maria Gerakari, Maria Goufa, Maria Panagoulakou, Konstantina Xipolitaki, Kimon Klouvatos, Stamatia Megariti, Polixeni Pappi, Ioannis E. Papadakis, Penelope J. Bebeli and Aliki Kapazoglou
Plants 2024, 13(1), 27; https://doi.org/10.3390/plants13010027 - 21 Dec 2023
Cited by 4 | Viewed by 2070
Abstract
Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars ‘Debina’ [...] Read more.
Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars ‘Debina’ and ‘Dichali’ displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on ‘Richter 110’ rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock–scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. ‘Dichali’ exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this ‘miRNA-target’ module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress. Full article
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14 pages, 1365 KiB  
Article
Use of Fe (II) and H2O2 along with Heating for the Estimation of the Browning Susceptibility of White Wine
by Sofia Voltea, Ioannis K. Karabagias and Ioannis G. Roussis
Appl. Sci. 2022, 12(9), 4422; https://doi.org/10.3390/app12094422 - 27 Apr 2022
Cited by 8 | Viewed by 1982
Abstract
The aim of the present study was to investigate if the use of Fe (II) and H2O2 (Fenton reaction) along with heating can be implicated for the rapid evaluation of the browning susceptibility of white wine. In this context, increasing [...] Read more.
The aim of the present study was to investigate if the use of Fe (II) and H2O2 (Fenton reaction) along with heating can be implicated for the rapid evaluation of the browning susceptibility of white wine. In this context, increasing concentrations of Fe (II) and H2O2 were added to two white wines (Roditis–Malagouzia and Debina), the samples were stored at 45 °C or 18 °C, and the absorbance at 420 nm (browning index) was measured. Moreover, total sulfur dioxide, total phenolics, flavanols, hydroxycinnamates and total free sulfhydryls were assessed during storage of Roditis–Malagouzia wine samples. The results showed that the addition of Fe (II) + H2O2 mixture in white wines increases rapidly the browning index at 45 °C, indicating the ability to develop a rapid test for the estimation of the browning susceptibility of white wines. Results also showed that the level of flavanols is a suitable index to follow the forced oxidative browning of white wine by adding Fe II + H2O2 at 45 °C. Moreover, results indicated that the levels of total free sulfhydryls may be a suitable index to follow the forced oxidative browning of white wine and in general, white wine oxidation. Full article
(This article belongs to the Section Food Science and Technology)
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15 pages, 9152 KiB  
Article
A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue
by Rama Devudu Puligedda, Fetweh H. Al-Saleem, Cristoph Wirblich, Chandana Devi Kattala, Marko Jović, Laura Geiszler, Himani Devabhaktuni, Giora Z. Feuerstein, Matthias J. Schnell, Markus Sack, Lawrence L. Livornese and Scott K. Dessain
Diagnostics 2021, 11(11), 2092; https://doi.org/10.3390/diagnostics11112092 - 12 Nov 2021
Cited by 7 | Viewed by 4458
Abstract
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), [...] Read more.
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants. Full article
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12 pages, 2185 KiB  
Article
SOX2OT Long Noncoding RNA Is Regulated by the UPR in Oestrogen Receptor-Positive Breast Cancer
by Carole Ferraro-Peyret, Marjan E. Askarian-Amiri, Debina Sarkar, Wayne R. Joseph, Herah Hansji, Bruce C. Baguley and Euphemia Y. Leung
Sci 2021, 3(2), 26; https://doi.org/10.3390/sci3020026 - 26 May 2021
Cited by 3 | Viewed by 4228
Abstract
Endoplasmic reticulum (ENR) stress perturbs cell homeostasis and induces the unfolded protein response (UPR). In breast cancer, this process is activated by oestrogen deprivation and is associated with tamoxifen resistance. We present evidence that the transcription factor SOX2 and the long noncoding RNA [...] Read more.
Endoplasmic reticulum (ENR) stress perturbs cell homeostasis and induces the unfolded protein response (UPR). In breast cancer, this process is activated by oestrogen deprivation and is associated with tamoxifen resistance. We present evidence that the transcription factor SOX2 and the long noncoding RNA SOX2 overlapping transcript (SOX2OT) are upregulated in oestrogen receptor-positive (ER+) breast cancer and in response to oestrogen deprivation. We examined the effect of the UPR on SOX2 and SOX2OT expression and the effect of SOX2OT on UPR pathways in breast cancer cell lines. The induction of the UPR by thapsigargin or glucose deprivation upregulates SOX2OT expression. This upregulation is also shown with the anti-oestrogen 4OH-tamoxifen and mTOR inhibitor everolimus in ER + breast cancer cells that are sensitive to oestrogen deprivation or everolimus treatment. SOX2OT overexpression decreased BiP and PERK expression. This effect of SOX2OT overexpression was confirmed on BiP and PERK pathway by q-PCR. Our results show that a long noncoding RNA regulates the UPR and evince a new function of SOX2OT as a participant of ENR stress reprogramming of breast cancer cells. Full article
(This article belongs to the Section Biology Research and Life Sciences)
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17 pages, 1460 KiB  
Review
Circular RNAs: Potential Applications as Therapeutic Targets and Biomarkers in Breast Cancer
by Debina Sarkar and Sarah D. Diermeier
Non-Coding RNA 2021, 7(1), 2; https://doi.org/10.3390/ncrna7010002 - 5 Jan 2021
Cited by 22 | Viewed by 6647
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs that form a covalently closed loop. A number of functions and mechanisms of action for circRNAs have been reported, including as miRNA sponge, exerting transcriptional and translational regulation, interacting with proteins, and coding for [...] Read more.
Circular RNAs (circRNAs) are a class of non-coding RNAs that form a covalently closed loop. A number of functions and mechanisms of action for circRNAs have been reported, including as miRNA sponge, exerting transcriptional and translational regulation, interacting with proteins, and coding for peptides. CircRNA dysregulation has also been implicated in many cancers, such as breast cancer. Their relatively high stability and presence in bodily fluids makes cancer-associated circRNAs promising candidates as a new biomarker. In this review, we summarize the research undertaken on circRNAs associated with breast cancer, discuss circRNAs as biomarkers, and present circRNA-based therapeutic approaches. Full article
(This article belongs to the Section Clinical Applications of Non-Coding RNA)
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4 pages, 506 KiB  
Correction
Correction: Sarkar, D., et al. Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing. Int. J. Mol. Sci. 2017, 18, 1378
by Debina Sarkar, Ali Oghabian, Pasani K. Bodiyabadu, Wayne R. Joseph, Euphemia Y. Leung, Graeme J. Finlay, Bruce C. Baguley and Marjan E. Askarian-Amiri
Int. J. Mol. Sci. 2018, 19(5), 1343; https://doi.org/10.3390/ijms19051343 - 2 May 2018
Cited by 1 | Viewed by 3624
(This article belongs to the Collection Regulation by Non-coding RNAs)
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18 pages, 1186 KiB  
Article
Multiple Isoforms of ANRIL in Melanoma Cells: Structural Complexity Suggests Variations in Processing
by Debina Sarkar, Ali Oghabian, Pasani K. Bodiyabadu, Wayne R. Joseph, Euphemia Y. Leung, Graeme J. Finlay, Bruce C. Baguley and Marjan E. Askarian-Amiri
Int. J. Mol. Sci. 2017, 18(7), 1378; https://doi.org/10.3390/ijms18071378 - 27 Jun 2017
Cited by 34 | Viewed by 6531 | Correction
Abstract
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation [...] Read more.
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation of ANRIL transcripts remains incomplete. Several functions have been associated with ANRIL. In our judgement, studies on ANRIL functionality are premature pending a more complete appreciation of the profusion of isoforms. We found differential expression of ANRIL exons, which indicates that multiple isoforms exist in melanoma cells. In addition to linear isoforms, we identified circular forms of ANRIL (circANRIL). Further characterisation of circANRIL in two patient-derived metastatic melanoma cell lines (NZM7 and NZM37) revealed the existence of a rich assortment of circular isoforms. Moreover, in the two melanoma cell lines investigated, the complements of circANRIL isoforms were almost completely different. Novel exons were also discovered. We also found the family of linear ANRIL was enriched in the nucleus, whilst the circular isoforms were enriched in the cytoplasm and they differed markedly in stability. With respect to the variable processing of circANRIL species, bioinformatic analysis indicated that intronic Arthrobacter luteus (Alu) restriction endonuclease inverted repeats and exon skipping were not involved in selection of back-spliced exon junctions. Based on our findings, we hypothesise that “ANRIL” has wholly distinct dual sets of functions in melanoma. This reveals the dynamic nature of the locus and constitutes a basis for investigating the functions of ANRIL in melanoma. Full article
(This article belongs to the Collection Regulation by Non-coding RNAs)
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