Using digital technologies in viticulture and winemaking: Technological and legal realities

Any technological innovation is a step forward in the development of our society. Almost all areas of life have been affected by the digital industry. However, there are activities that are unique per se, such as winemaking. Taste and preferences of a person are built around the individuality of each of us. Nevertheless, the processes to simplify work, to obtain a high-quality product, to increase the volume of harvest, to check counterfeit products and much more can be digitalized. Change is inevitable. Any digital technology can be used for human benefit. The use of drones in the art of winemaking is already accepted and recognized. This is only one aspect of using digital technologies in winemaking. This is what the presented research paper is about

Bottlenecks in the Open-Access System: Voices from Around the Globe

A level playing field is key for global participation in science and scholarship, particularly with regard to how scientific publications are financed and subsequently accessed. However, there are potential pitfalls of the so-called "Gold" open-access (OA) route, in which author-paid publication charges cover the costs of production and publication. Gold OA plans in which author charges are required may not solve the access problem, but rather may shift the access barrier from reader to writer. Under such plans, everyone may be free to read papers, but it may still be prohibitively expensive to publish them. In a scholarly community that is increasingly global, spread over more and more regions and countries of the world, these publication access barriers may be quite significant. In the present paper, a global suite of colleagues in academe joins this debate. The group of colleagues, a network of researchers active in scholarly publishing, spans four continents and multiple disciplines in the natural sciences, humanities, and social sciences, as well as diverse political and economic situations. We believe that this global sampling of researchers can provide the nuance and perspective necessary to grasp this complex problem. The group was assembled without an attempt to achieve global coverage through random sampling. This contribution differs from other approaches to the open-access problem in several fundamental ways. (A) It is scholar-driven, and thus can represent the ‘other side of the coin' of scholarly communication. (B) It focuses on narrative report, where scholars were free to orient their responses as they saw fit, rather than being confined to binary or scalar choices. Finally, and perhaps most importantly, (C) it distinguishes among institutions and countries and situations, highlighting inequalities of access among wealthy and economically-challenged nations, and also within countries depending on the size and location of particular institutions

A Mouse to Human Search for Plasma Proteome Changes Associated with Pancreatic Tumor Development

Background: The complexity and heterogeneity of the human plasma proteome have presented significant challenges in the identification of protein changes associated with tumor development. Refined genetically engineered mouse (GEM) models of human cancer have been shown to faithfully recapitulate the molecular, biological, and clinical features of human disease. Here, we sought to exploit the merits of a well-characterized GEM model of pancreatic cancer to determine whether proteomics technologies allow identification of protein changes associated with tumor development and whether such changes are relevant to human pancreatic cancer. Methods and Findings: Plasma was sampled from mice at early and advanced stages of tumor development and from matched controls. Using a proteomic approach based on extensive protein fractionation, we confidently identified 1,442 proteins that were distributed across seven orders of magnitude of abundance in plasma. Analysis of proteins chosen on the basis of increased levels in plasma from tumor-bearing mice and corroborating protein or RNA expression in tissue documented concordance in the blood from 30 newly diagnosed patients with pancreatic cancer relative to 30 control specimens. A panel of five proteins selected on the basis of their increased level at an early stage of tumor development in the mouse was tested in a blinded study in 26 humans from the CARET (Carotene and Retinol Efficacy Trial) cohort. The panel discriminated pancreatic cancer cases from matched controls in blood specimens obtained between 7 and 13 mo prior to the development of symptoms and clinical diagnosis of pancreatic cancer. Conclusions: Our findings indicate that GEM models of cancer, in combination with in-depth proteomic analysis, provide a useful strategy to identify candidate markers applicable to human cancer with potential utility for early detection

Comprehensive analysis of WRN protein interaction network by Mass Spectrometry.

Thesis (Ph.D.)--University of Washington, 2014Cells that have lost WRN function exhibit a shortened replicative lifespan, accumulation of chromosomal aberrations, and demonstrate sensitivity to a number of chemotherapeutic agents, including DNA Topoisomerase I inhibitor camptothecin (CPT). On organismal level, the lack of this protein results in the progeroid syndrome Werner Syndrome, which is characterized by increased incidence of cancers, cardiovascular disease, cataracts, and other age-associated pathologies. In this study we examined the network of proteins that associate with WRN protein, and then expanded this picture when the cells were challenged with CPT. We detail the profiling analysis used for unbiased detection of all interacting proteins using LC-MS/MS, followed by data analysis and selection of targets for follow-up. We then focus on the method development, complexities of data analysis, and application of selected reaction monitoring (SRM), a method for targeted MS. Using RNAi we demonstrate the power of this technique for relative protein quantitation of human proteins WRN and TP53, and a number of small, low-abundance seminal fluid proteins from D.melanogaster flies. SRM was applied for two studies of the WRN interactome: 1) to partially validate findings of the profiling screen after short-term treatment with CPT, and 2) to describe the dynamics of association of these proteins with WRN as a function of time, by expanding the treatment time course to 6 and 12 hours. We report on our description of WRN protein interaction complexes in unperturbed cells, and how these interaction complexes become reorganized in response to DNA damage. Our results demonstrate that the newly recruited proteins participate in chromatin remodeling, negative regulation of cell cycle progression, and double-strand break repair. We focus on 40 proteins to test their differential interaction with WRN after 1, 6, and 12 hours of treatment with CPT. We specifically focus on the functional importance of the chromatin-remodeling factors, and present the list of WRN interacting proteins that have emerged as high-priority targets for functional validation. Finally, we discuss how our work has expanded the understanding of the functional roles of WRN, and how targeted, hypothesis-driven application of mass spectrometry can be used to answer complex questions about protein interaction

Rapid Assessment of RNAi-mediated Protein Depletion by Selected Reaction Monitoring Mass Spectrometry

We describe the use of a targeted proteomics approach, selected reaction monitoring (SRM) mass spectrometry, to detect and assess RNAi-mediated depletion or “knockdown” of specific proteins from human cells and from <i>Drosophila</i> flies. This label-free approach does not require any specific reagents to confirm the depletion of RNAi target protein(s) in unfractionated cell or whole organism extracts. The protocol described here is general, can be developed rapidly, and can be multiplexed to detect and measure multiple proteins at once. Furthermore, the methodology can be extended to any tandem mass spectrometer, making it widely accessible. This methodology will be applicable to a wide range of basic science and clinical questions where RNAi-mediated protein depletion needs to be verified, or where differences in relative abundance of target proteins need to be rapidly assessed between samples

A SARS-CoV-2 Coronavirus Antigen-Detecting Half-Strip Lateral Flow Assay Towards the Development of Point of Care Tests Using Commercially Available Reagents

The SARS-CoV-2 pandemic has created an unprecedented need for rapid diagnostic testing to enable the efficient treatment and mitigation of COVID-19. The primary diagnostic tool currently employed is reverse transcription polymerase chain reaction (RT-PCR), which can have good sensitivity and excellent specificity. Unfortunately, implementation costs and logistical problems with reagents during the global SARS-CoV-2 pandemic have hindered its universal on demand adoption. Lateral flow assays (LFAs) represent a class of diagnostic that, if sufficiently clinically sensitive, may fill many of the gaps in the current RT-PCR testing regime, especially in low- and middle-income countries (LMICs). To date, many serology LFAs have been developed, though none meet the performance requirements necessary for diagnostic use cases, primarily due to the relatively long delay between infection and seroconversion. However, based on previously reported results from SARS-CoV-1, antigen-based SARS-CoV-2 assays may have significantly better clinical sensitivity than serology assays. To date, only a very small number of antigen-detecting LFAs have been developed. Development of a half-strip LFA is a useful first step in the development of any LFA format. In this paper we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. We have tested this LFA in buffer and measured an LOD of 0.62 ng/mL using an optical reader with sensitivity equivalent to a visual read. Further development, including evaluating the appropriate sample matrix, will be required for this assay approach to be made useful in a point of care setting, though this half-strip LFA may serve as a useful starting point for others developing similar tests. </p

A SARS-CoV-2 Coronavirus Nucleocapsid Protein Antigen-Detecting Lateral Flow Assay

Inexpensive, simple, rapid diagnostics are necessary for efficient detection, treatment and mitigation of COVID‑19. Currently, the primary diagnostic tool being utilized is reverse transcription polymerase chain reaction (RT-PCR). RT-PCR delivers results with good sensitivity and excellent specificity, but is expensive, prone to access challenges and is often slowed by transport to centralized testing laboratories. Antigen-based assays are inexpensive and can be rapidly mass-produced and deployed, with lateral flow assays (LFAs) being the most common inexpensive antigen test. To date, few antigen-detecting LFAs for COVID-19 have been commercialized. Herein, we present an open source LFA using commercially available antibodies and materials for the detection of SARS-CoV-2. Using an optical reader with comparable sensitivity to a visual read, the LFA yielded a Limit of Detection (LOD) of 23 TCID50/mL (95% CI of 9.1 to 37 TCID50/mL), equivalent to 1.4x105 copies/mL (95% CI of 5.5x104 to 2.3x105 copies/mL) irradiated virus in pooled nasal matrix. This LOD meets the criteria suggested by WHO for diagnosis of acute SARS-CoV-2 infection in a point of care format. A clinical evaluation and further testing is ongoing.</p

Bottlenecks in the Open-Access System: Voices from Around the Globe

A level playing field is key for global participation in science and scholarship, particularly with regard to how scientific publications are financed and subsequently accessed. However, there are potential pitfalls of the so-called “Gold” open-access (OA) route, in which author-paid publication charges cover the costs of production and publication. Gold OA plans in which author charges are required may not solve the access problem, but rather may shift the access barrier from reader to writer. Under such plans, everyone may be free to read papers, but it may still be prohibitively expensive to publish them. In a scholarly community that is increasingly global, spread over more and more regions and countries of the world, these publication access barriers may be quite significant. In the present paper, a global suite of colleagues in academe joins this debate. The group of colleagues, a network of researchers active in scholarly publishing, spans four continents and multiple disciplines in the natural sciences, humanities, and social sciences, as well as diverse political and economic situations. We believe that this global sampling of researchers can provide the nuance and perspective necessary to grasp this complex problem. The group was assembled without an attempt to achieve global coverage through random sampling. This contribution differs from other approaches to the open-access problem in several fundamental ways. (A) It is scholar-driven, and thus can represent the ‘other side of the coin’ of scholarly communication. (B) It focuses on narrative report, where scholars were free to orient their responses as they saw fit, rather than being confined to binary or scalar choices. Finally, and perhaps most importantly, (C) it distinguishes among institutions and countries and situations, highlighting inequalities of access among wealthy and economically-challenged nations, and also within countries depending on the size and location of particular institutions

Antibody Screening Results for Anti-Nucleocapsid Antibodies Towards the Development of a SARS-CoV-2 Nucleocapsid Protein Antigen Detecting Lateral Flow Assay

The global COVID-19 pandemic has created an urgent demand for large numbers of inexpensive, accurate, rapid, point-of-care diagnostic tests. Analyte-based assays are suitably inexpensive and can be rapidly mass-produced, but for sufficiently accurate performance they require highly optimized antibodies and assay conditions. We used an automated liquid handling system, customized to handle arrays of lateral flow immunoassay (LFA) tests in a high-throughput screen, to identify anti-nucleocapsid antibodies that will perform optimally in an LFA. We tested 1021 anti-nucleocapsid antibody pairs as LFA capture and detection reagents with the goal of highlighting pairs that have the greatest affinity for unique epitopes of the nucleocapsid protein of SARS-CoV-2 within the LFA format. In contrast to traditional antibody screening methods (e.g., ELISA, bio-layer interferometry), the method described here integrates real-time reaction kinetics with transport in, and immobilization directly onto, nitrocellulose. We have identified several candidate antibody pairs that are suitable for further development of an LFA for SARS-CoV-2.</p