Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.

Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.

Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence-based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitivity domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel WHy-like protein (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in Escherichia coli significantly protected the recombinant host against cold and freeze stress.

Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.

The Act will have implications for all research activities that involve the collection, processing, and storage of personal information. POPIA provides for the development of Codes of Conduct to guide the interpretation of the Act with respect to a particular sector or class of information. 1 Codes of Conduct are particularly important for providing for prior authorisations in terms of Section 57 of POPIA for the sector to which it applies. Prior authorisations are required for using unique identifiers of personal information in data processing activities, and for sharing special personal information or the personal information of children with countries outside of South Africa that do not have adequate data protection laws. In order to understand and functionally interpret the provisions of POPIA for the research community in the Republic of South Africa (South Africa), the Academy of Science of South Africa (ASSAf) is leading a process to develop a Code of Conduct (Code) for research under the Act. A Code can be developed by the Information Regulator or by a public or private body deemed 'sufficiently representative' of the bodies in respect of the particular class of information or sector to which the Code will apply. During 2020, ASSAf was approached by scientists in South Africa to consider the development of a Code for research, and public events were held during Open Access Week in October 2020, and Science Forum South Africa in December 2020, to further discuss the role of ASSAf in this regard. A Commentary published in this issue sets out the full rationale for the development of the Code by ASSAf and details the consultation process to date. 2 Within the research setting, POPIA regulates the processing of personal information for research purposes, and the flow of data across South Africa's borders to ensure that any limitations on the right to privacy are justified and aimed at protecting other important rights and interests. The new regulatory system that POPIA establishes will function alongside other legislation and regulatory structures governing research in South Africa, as outlined below. The law which takes precedent will be that which provides the most comprehensive protections to the rights of individuals in South Africa.This paper sets out the key discussion points in relation to the development of the Code. It is intended as a paper that can support further stakeholder consultation and public engagement in the process of developing a Code which meets the needs, and is representative of, the South African research community.

This study describes the roles of laboratory information management systems (LIMS) in multi-site genetics studies in Africa. We used the HiGeneS Africa project as a case study. The study participants were recruited in six African countries between 2019 to 2021. The Baobab LIMS, a server–client-based system (an African-led innovation) was used for the coordination of the biospecimen. The development phase of the LIMS showcased the team formation, data collection, biospecimen collection, and shipment strategies. The implementation phase showcased the biospecimen registration, processing, and quality control (QC) analytics. The sample QC was done using Nanodrop, Qubit, and PicoGreen/gDNATapestation assays. The results showed that a total of 3144 study participants were recruited from Cameroon, Ghana, Mali, Rwanda, Senegal, and South Africa. The biospecimen registration provided a comprehensive registry that included patient demographics, genetic information, and clinical and blood/saliva samples from the proband and family relatives. The QC analyzes identified 30 samples that failed QC, linked to overdue storage in the freezer before DNA extraction. The LIMS components implemented in this project formed a structure that can be upscaled to artificial intelligence-based LIMS. In conclusion, this study represents the largest and the most diverse collection of biospecimens for the genetic study of hearing impairment in Africa to date. A well-characterized LIMS should be recommended for multi-site molecular studies, particularly in Africa, to enhance African participation in global genomic medicine.

The Protection of Personal Information Act (POPIA) [No.4 of 2013] is the first comprehensive data protection regulation to be passed in South Africa and it gives effect to the right to informational privacy derived from the constitutional right to privacy It is due to come into force in 2020, and seeks to regulate the processing of personal information in South Africa, regulate the flow of personal information across South Africa’s borders, and ensure that any limitations on the right to privacy are justified and aimed at protecting other important rights and interests. Although it was not drafted with health research in mind, POPIA will have an impact on the sharing of health data for research, in particular biorepositories. It is now timely to consider the impact of POPIA on biorepositories, and the necessary changes to their access and sharing arrangements prior to POPIA coming into force.

Jerome Amir Singh's affiliation was erroneously given as: Centre for Medical Ethics and Law, Stellenbosch University, Stellenbosch, South Africa. Thecorrect affiliation is: School of Law, Howard College, University of KwaZulu-Natal, Durban, South Africa. The error appears in the Discussion Document by Adams et al. [https://doi.org/10.17159/sajs.2021/10933] on Page 1 under Affiliations (no. 22) and on Page 11 in the table under Authors' information, as well as in the accompanying Commentary by Adams et al. [https://doi.org/10.17159/sajs.2021/10935] in Table 1 on Page 3.