Modified NEBNext® VarSkip Short SARS-CoV-2 Library Prep Kit for Illumina Platforms - adapted for wastewater samples v1

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This modified protocol details methods for cDNA synthesis and library preparation for sequencing of wastewater samples containing SARS-CoV-2. The protocol is based primarily on the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L 24/96 reactions, with a few modifications. Primarily, VarSkip Short primers are used in place of the ARTIC V3 primers. These primers are available in the NEBNext®ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®); however, for optimal variant detection from wastewater, sequenced fragments should be as large as possible, so we discourage fragmentation prior to end prep. There are a couple of decision points in this protocol. Examining cDNA amplicon samples on an Agilent TapeStation system or similar fragment analyzer is extremely helpful in making these decisions.

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v2

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater; however, this protocol was written to be broadly applicable for all wastewater sequence data submissions to NCBI. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. Version updates: V2: minor edits to the BioSample and SRA templates V3: Many minor edits were made to make the protocol more broadly applicable to submitters outside of FDA's wastewater project. Updates were also made to both metadata templates, including a new attribute to the SRA metadata template, called "enrichment_kit". There are now three custom attributes we recommend populating to more specifically capture relevant methods for ww sequencing: enrichment approach, primer set, and library prep kit.

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v2

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. Version updates: V2: minor edits to the BioSample and SRA templates

Inclusive Higher Education in Russia (by the Example of the Volga Federal District)

The article covers the possibility of establishing resource centers in higher education institutions for teaching people with disabilities and health limitations. The implementation of the project «Monitoring, research and information support of activities provided by the regional resource centers of higher education for people with disabilities" is considered. The university has developed a model of information-analytical guidance to educate people with disabilities with the help of regional resource centers of higher education for people with health limitations. A number of measures for establishing educational activities at the university are presented. The main effect of the organized events by the resource training and methodological center is considered. It is the involvement of all participants of the process at all its levels in the problem of inclusive higher education. Priority activity areas of the resource training and methodological center of Minin University are highlighted. The results of the inclusive higher education on the base of Minin University were summed up.

Trends in the development of crowdfunding in the domestic business environment

The article examines the interpretation of the economic essence of crowdfunding by various scholars, its features and foreign experience of application in financing ideas and projects in various spheres of socio-economic life. In the context of globalization the opening of new markets and opportunities, intensification of capital exchange processes, the use of innovative financial solutions can have a positive impact on national competitiveness and attract small businesses and individuals with innovative ideas but do not have sufficient financial resources for their development and implementation. It is described that crowdfunding is a fundraising tool that with the help of Internet technologies allows to receive investments in a short time from a large number of people to support small or medium business projects, while crowdfunding participants are: project authors, project donors, Internet workers and the state as a regulator of these relations. The main indicators that need to be analyzed if you want to use crowdfunding as a tool of alternative financing of self-organizing economic systems, in particular are: analysis of macroeconomic indicators in the country of its application; comparison of risks of economic development and introduction of crowdfunding; creation of state measures to stimulate the economy and ensure information and financial security at all levels of crowdfunding regulation. The main models of crowdfunding that are used in world practice are described: P2P (Peer-to-Peer) for financing of individuals and P2B (Peer-to-Business) for financing of small and medium business. The main advantages and disadvantages of crowdfunding and the possibility of its application in different economies are considered. The advantages are the improvement of the project management process and increase of their efficiency through the establishment of feedback, the efficiency of which increases significantly due to the use of modern Internet technologies, which allows to transfer a significant part of project monitoring functions to investors. The disadvantage of crowdfunding is the impossibility of its application to large-scale projects that require large investments. The Strategy of the Development of the Financial Sector of Ukraine until 2025 has been studied, according to which it is envisaged to improve the regulation of the payment market infrastructure in accordance with EU standards and to create a large number of FinTech companies in Ukraine.

Creating a Corpus of Multilingual Parent-Child Speech Remotely: Lessons Learned in a Large-Scale Onscreen Picturebook Sharing Task

With lockdowns and social distancing measures in place, research teams looking to collect naturalistic parent-child speech interactions have to develop alternatives to in-lab recordings and observational studies with long-stretch recordings. We designed a novel micro-longitudinal study, the Talk Together Study, which allowed us to create a rich corpus of parent-child speech interactions in a fully online environment (N participants = 142, N recordings = 410). In this paper, we discuss the methods we used, and the lessons learned during adapting and running the study. These lessons learned cover nine domains of research design, monitoring and feedback: Recruitment strategies, Surveys and Questionnaires, Video-call scheduling, Speech elicitation tools, Videocall protocols, Participant remuneration strategies, Project monitoring, Participant retention, and Data Quality, and may be used as a primer for teams planning to conduct remote studies in the future.

RT-qPCR Detection of SARS-CoV-2 from Wastewater Using the AB 7500 v1

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol describes triplex and duplex assays for the RT-qPCR detection of the nucleocapsid region of the SARS-CoV-2 genome. These assays, along with the murine norovirus (MNV; extraction control) and crAssphage (human indicator) RT-qPCR assay (RT-qPCR Detection of Process Controls (Murine noroviurs and crAssphage) from Wastewater (protocols.io)), were developed for use on the AB 7500 platform using software version 2.0 or 2.3. All assays incorporate an internal amplification control (IC) to prevent the reporting of false negatives due to inhibition or failure of the RT-qPCR. These multiplexed detection assays were developed for the qualitative determination SARS-CoV-2 nucleocapsid gene extracted from wastewater. Valid sample results are contingent upon the detection of the MNV extraction control from the sample being tested.

RT-qPCR Detection of Process Controls (Murine noroviurs and crAssphage) from Wastewater using AB 7500 v1

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol describes the murine norovirus (MNV; extraction control) and crAssphage (human indicator) RT-qPCR assay developed for use on the AB 7500 platform using software version 2.0 or 2.3. The assay incorporates an internal amplification control (IC) to prevent the reporting of false negatives due to inhibition or failure of the RT-qPCR. This multiplexed detection assay was developed for the determination crAssphage extracted from wastewater, as an endogenous control, and MNV as an extraction control. The assay is designed to be used in conjunction with the SARS-CoV-2 RT-qPCR detection assay. Valid sample results for SARS-CoV-2 detection are contingent upon the detection of the MNV extraction control from the sample being tested.

RNA Extraction from Wastewater Concentrates Using RNeasy and Zymo Kits v1

This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR detection, library prep, genome sequencing, quality control checks, and data submission to NCBI. This method describes the extraction of RNA from viral concentrates using the RNeasy and Zymo kits.