Environmental Repositories Research Articles

Past anthropogenic impacts revealed by trace elements in cave guano

Natural and human-induced toxic elements can accumulate in the environment, posing significant risks to human health and ecosystems. This study explores cave bat guano, an unconventional and relatively under-researched environmental repository, to reveal historical pollution trends and sources. Through trace elements analysis of a 1.5-m-thick guano deposit from Zidită Cave (Romania), we track changes in mining and metallurgy from 1000 CE–2012. We identified substantial pollution primarily from porphyry copper and Au–Ag–Te mines, but also impacts from usage of leaded gasoline and agricultural practices. Our record shows disruptions caused by the Bubonic plague around 1250 CE and a major surge ∼ 1500 CE. After the decline triggered by the European silver market collapse in 1525 CE, our study reveals a brief mining revival. This resurgence was followed by a continuous decline lasting until the early 1800s, driven by socio-economic upheavals and recurrent outbreaks of the bubonic plagues. The Industrial Revolution sparked prolonged growth that lasted until 1989 CE, only briefly interrupted by the Great Depression and World War II. Consequently, cave bat guano proves to be a critical resource for understanding spatial pollution patterns, both locally and regionally, and for identifying specific pollution sources.

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2024 Annual Meeting

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2024 Annual Meeting

Updating International Society for Biological and Environmental Repositories Best Practices, Fifth Edition: A New Process for Relevance in an Evolving Landscape.

The recently published fifth edition of the International Society for Biological and Environmental Repositories (ISBER) Best Practices signifies a pivotal milestone in navigating the complexities of repository management. Repositories operate within a constantly evolving landscape influenced by the changing fields of biospecimen science, technology, legal requirements, and ethical considerations. This dynamic is further amplified by unprecedented local and global challenges, such as pandemics, conflicts, and supply chain disruptions. Creating this new edition required a comprehensive approach capable of delivering a focused and coherent resource reflecting the broad horizon of its diverse users. The innovative approach used the existing phased development process and integrated the canvassing of opinions, formal evaluation, and real-time collaboration platforms. Merging these techniques enabled efficient collection and effective distillation of the latest in biobanking practices, enhancing the value of the fifth edition for repositories of specimens and associated data. The expanded document is a testament to the collective efforts of many dedicated individuals who have built upon the foundations of prior editions.

The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting

The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting

The Stability of the Anti-Müllerian Hormone in Serum and Plasma Samples under Various Preanalytical Conditions.

The anti-Müllerian hormone (AMH) is a glycoprotein that plays an important role in prenatal sex differentiation. It is used as a biomarker in polycystic ovary syndrome (PCOS) diagnostics, as well as for estimating an individual's ovarian reserve and the ovarian response to hormonal stimulation during in vitro fertilization (IVF). The aim of this study was to test the stability of AMH during various preanalytical conditions that are in accordance with the ISBER (International Society for Biological and Environmental Repositories) protocol. Plasma and serum samples were taken from each of the 26 participants. The samples were then processed according to the ISBER protocol. AMH levels were measured in all the samples simultaneously using the chemiluminescent kit ACCESS AMH in a UniCel® DxI 800 Immunoassay System (Beckman Coulter, Brea, CA, USA). The study proved that AMH retains a relatively high degree of stability during repeated freezing and thawing in serum. AMH was shown to be less stable in plasma samples. Room temperature proved to be the least suitable condition for the storage of samples before performing the biomarker analysis. During the testing of storage stability at 5-7 °C, the values decreased over time for all the plasma samples but remained stable in the serum samples. We proved that AMH is highly stable under various stress conditions. The anti-Müllerian hormone retained the greatest stability in the serum samples.

Readiness for Artificial Intelligence in Biobanking

Readiness for Artificial Intelligence in Biobanking

Brief Reports Prepared by Students and Graduates of Master of Science in Biobanking.

Brief Reports Prepared by Students and Graduates of Master of Science in Biobanking.

The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting “Biobanking: Shaping the Scientific Journey”In‐Person: May 17 – 20, 2022Atlanta, Georgia, USAVirtual: June 14 – 15, 2022

Biopreservation and BiobankingAhead of Print The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting “Biobanking: Shaping the Scientific Journey”In‐Person: May 17 – 20, 2022Atlanta, Georgia, USAVirtual: June 14 – 15, 2022The abstracts that follow demonstrate the broad range of timely issues addressed in the contributed oral and poster presentations at ISBER's 2022 Annual Meeting & Exhibits.Published Online:5 May 2022https://doi.org/10.1089/bio.2022.29104.abstractsAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetails Volume 0Issue 0 InformationCopyright 2021, Mary Ann Liebert, Inc., publishersTo cite this article:The International Society for Biological and Environmental Repositories Presents Abstracts from Its Annual Meeting “Biobanking: Shaping the Scientific Journey”In‐Person: May 17 – 20, 2022Atlanta, Georgia, USAVirtual: June 14 – 15, 2022.Biopreservation and Biobanking.ahead of printhttp://doi.org/10.1089/bio.2022.29104.abstractsOnline Ahead of Print:May 5, 2022PDF download

An overview of the National Biobank of the National Health Laboratory Service: a South African national treasure for biological resources

Abstract The National Biobank of the National Health Laboratory Service (NHLS) is a national treasure established to serve as support infrastructure for the provision of high quality human biological materials for research purposes and it represents the first of its kind in South Africa. This article aims to demonstrate the alignment of the NHLS Biobank to international best practices and guidelines with reference to the 13 sections of the International Society of Biological and Environmental Repositories (ISBER) Best Practices for Repositories (4th ed.). The NHLS Biobank has implemented procedures and management strategies that are technical best practices covering the lifecycle of biobanking (collection, processing, storage and dissemination of human biological materials) while having respect for ethical and regulatory processes, upholding the interest of the donors. ISBER best practices are invaluable sources of guidance and benchmarking on the guiding principles has enabled the NHLS Biobank to develop into an entity with infrastructure and operational activities that support its short-term and long-term objectives that are set out in the business plan.

The Ocean Genome Legacy: A Genomic Resource Repository for Marine Life.

The Ocean Genome Legacy: A Genomic Resource Repository for Marine Life.

Highlights from 2022: Innovations in Digital Health, Diagnostics, and Biomarkers

The second volume of Innovations in Digital Health, Diagnostics and Biomarkers (IDDB) has successfully come to a close. The Journal was launched during a historic pandemic, and as the fields of biomedical research and healthcare are now moving into a transition period (from the pandemic emergency towards a new normal), it is evident that the pandemic has been a universal catalyst for innovative thinking. During such transition, drivers for change have ranged from introducing new technologies to developing new operating frameworks for existing capacities, anchored in a context-dependent manner. Thus, the emerging innovations vary and often reflect a regionally defined and fragmented set of requirements.Notwithstanding the latter, manuscripts published in IDDB demonstrate wide interest in digital health, diagnostics, and biomarkers research, which defines the publishing niche that we are developing through a consistent multidisciplinary approach .[1] For example, original research by Liang et al.[2] reported the phototoxicity sensitivity for cells grown in vitro, and Pardes et al.[3] introduced the use of a mobile health platform for remote assessment of suicidal ideation, depression, and anxiety. The team of Qu et al.[4] provided a detailed review of innovative technologies for healthcare application, pointing out existing gaps, challenges, and opportunities, as well as identifying key areas where immersive technologies can impact healthcare provision. Additional articles by Medina et al.,[5] and Kozlakidis et al.[6] showcase focused areas of scientific activity, namely construction and application of biobank infrastructure for infectious diseases and a state-of-the-art review of betel nut use, respectively.Innovations are often fuelled by individual perspectives, as they emerge over a specific field of scientific activity, such as in this case. The editorial by Cheong and Wang[7] describes the Chinese experience with digital health applications in public health interventions. The commentary by Xu[8] focuses on aspects of biopsy specimen acquisition during longitudinal sampling. The inclusion of such diverse subjects and expertise is one of the unique advantages of publishing with IDDB, reducing institutional blocks that stifle further connections and limits creativity. The transdisciplinary nature of innovation is aptly demonstrated in the three related manuscripts by Arnholdt-Schmitt et al.[9–11], where original observations regarding balancing of reactive oxygen and nitrogen species (ROS and RNS, respectively) in plants, which contributes to shaping a foundational mechanism of health resilience. This group conducted pilot testing of early metabolic responses in cultured primary target cells infected with influenza H3N2 and SARS-CoV-2.The achievements made by scientists are also reported in international conference proceedings. One example is the 2021 International Society for Biological and Environmental Repositories (ISBER) virtual workshop proceedings by Ivanova and Katsaounis.[12] This report summarizes key barriers, challenges, and perceptions to digital innovations with respect to informed consent in biobanking (and wider implications for longitudinal sampling and organ donation). Additionally, IDDB has been privileged to publish the abstracts presented at the 2022 Advancing Healthcare Innovation Summit (AHIS)[13] in Cincinnati, OH, USA. As with the manuscripts mentioned above, abstracts from AHIS represent a wide geographical and subject coverage, having healthcare innovation and a strong belief in the potential impact of such innovation as their common denominator.I would personally like to thank the Journal staff for their tireless support during this second year (including social media support for @EditorsIDDB). I thank my Associate Editor, Dr Daniel Catchpoole, and the entire editorial board for continuous encouragement and scientific direction of the Journal as it continues to develop. We are excited to have two young professionals (Drs Beheshta Paiman and Gowhar Rashid) who recently joined IDDB as part of a year-long editorial fellowship. A special mention should be made for the Innovative Healthcare Institute (IHCI) that shoulders the cost of operations and publication under the leadership of Dr. Abdulrahman Jazieh. Finally, I gratefully acknowledge the many reviewers[14] who actively supported the peer-review process, which was applied to all manuscripts alike and has resulted in stronger contributions to the body of literature on healthcare innovations.

Workshop Proceedings: Informed Consent in Biobanking–from the Key Barriers, Challenges, and Perceptions to Digital Innovations

Workshop Proceedings: Informed Consent in Biobanking–from the Key Barriers, Challenges, and Perceptions to Digital Innovations

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2021 Virtual Symposium In partnership with UHN Biospecimen Services October 4 – 5, 2021

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2021 Virtual Symposium In partnership with UHN Biospecimen Services October 4 – 5, 2021

Machine Learning as a Service for DiSSCo’s Digital Specimen Architecture

International mass digitization efforts through infrastructures like the European Distributed System of Scientific Collections (DiSSCo), the US resource for Digitization of Biodiversity Collections (iDigBio), the National Specimen Information Infrastructure (NSII) of China, and Australia’s digitization of National Research Collections (NRCA Digital) make geo- and biodiversity specimen data freely, fully and directly accessible. Complementary, overarching infrastructure initiatives like the European Open Science Cloud (EOSC) were established to enable mutual integration, interoperability and reusability of multidisciplinary data streams including biodiversity, Earth system and life sciences (De Smedt et al. 2020). Natural Science Collections (NSC) are of particular importance for such multidisciplinary and internationally linked infrastructures, since they provide hard scientific evidence by allowing direct traceability of derived data (e.g., images, sequences, measurements) to physical specimens and material samples in NSC. To open up the large amounts of trait and habitat data and to link these data to digital resources like sequence databases (e.g., ENA), taxonomic infrastructures (e.g., GBIF) or environmental repositories (e.g., PANGAEA), proper annotation of specimen data with rich (meta)data early in the digitization process is required, next to bridging technologies to facilitate the reuse of these data. This was addressed in recent studies (Younis et al. 2018, Younis et al. 2020), where we employed computational image processing and artificial intelligence technologies (Deep Learning) for the classification and extraction of features like organs and morphological traits from digitized collection data (with a focus on herbarium sheets). However, such applications of artificial intelligence are rarely—this applies both for (sub-symbolic) machine learning and (symbolic) ontology-based annotations—integrated in the workflows of NSC’s management systems, which are the essential repositories for the aforementioned integration of data streams. This was the motivation for the development of a Deep Learning-based trait extraction and coherent Digital Specimen (DS) annotation service providing “Machine learning as a Service” (MLaaS) with a special focus on interoperability with the core services of DiSSCo, notably the DS Repository (nsidr.org) and the Specimen Data Refinery (Walton et al. 2020), as well as reusability within the data fabric of EOSC. Taking up the use case to detect and classify regions of interest (ROI) on herbarium scans, we demonstrate a MLaaS prototype for DiSSCo involving the digital object framework, Cordra, for the management of DS as well as instant annotation of digital objects with extracted trait features (and ROIs) based on the DS specification openDS (Islam et al. 2020). Source code available at: https://github.com/jgrieb/plant-detection-service

Cloud Optimized Raster Encoding (CORE): A Web-Native Streamable Format for Large Environmental Time Series

The Environmental Data Portal EnviDat aims to fuse data publication repository functionalities with next-generation web-based environmental geospatial information systems (web-EGIS) and Earth Observation (EO) data cube functionalities. User requirements related to mapping and visualization represent a major challenge for current environmental data portals. The new Cloud Optimized Raster Encoding (CORE) format enables an efficient storage and management of gridded data by applying video encoding algorithms. Inspired by the cloud optimized GeoTIFF (COG) format, the design of CORE is based on the same principles that enable efficient workflows on the cloud, addressing web-EGIS visualization challenges for large environmental time series in geosciences. CORE is a web-native streamable format that can compactly contain raster imagery as a data hypercube. It enables simultaneous exchange, preservation, and fast visualization of time series raster data in environmental repositories. The CORE format specifications are open source and can be used by other platforms to manage and visualize large environmental time series.

Letter to the editor: ISBER Two Decades and Beyond: Honoring Our Past, Celebrating the Present, and Envisioning Our Future.

Biopreservation and BiobankingVol. 19, No. 4 Review ArticlesFree AccessLetter to the editor: ISBER Two Decades and Beyond: Honoring Our Past, Celebrating the Present, and Envisioning Our FutureDebra Leiolani Garcia and Zisis KozlakidisDebra Leiolani GarciaAddress correspondence to:, Debra Leiolani Garcia, MPA, San Mateo, CA 94401, USA E-mail Address: dleiolani@gmail.comPrivate Consultant, San Mateo, California, USA.ISBER President (2019–2020).Search for more papers by this author and Zisis KozlakidisInternational Agency for Research on Cancer, World Health Organization, Lyon, France.ISBER President (2017–2018).Search for more papers by this authorPublished Online:13 Aug 2021https://doi.org/10.1089/bio.2021.29088.dlgAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail As the International Society of Biological and Environmental Repositories (ISBER) celebrated its 20th anniversary, it was essential for its members to look back and reflect on how the society started and continues to grow as a global resource and collective force in the biobanking arena. ISBER strives to connect biobanks and related fields around the world to ensure quality through standardization and harmonization of biobanking practices. We have witnessed during the past 20 years that biobanking is being recognized as an indispensable research infrastructure activity underpinning scientific breakthroughs.As we reviewed our history, it became apparent that ISBER should capture the valuable work of its membership and the global biobanking community in an e-book highlighting its history and achievements (www.isber.org/resource/resmgr/20annibook/20thAnniversaryBook-ISBER-v0.pdf).The first edition of the e-book was initiated at the celebration of the 20th anniversary of the society and provides the inspiration for many more years to come. It articulates the distilled efforts and history of ISBER over the past two decades, the different individuals who have shaped the society into its current form, as well as the many efforts to investigate the diverse aspects ISBER as an active inclusive society, run by its members and responding to the evolving needs of the biobanking field as a whole.The history of ISBER is proof of how an important idea, such as the development of a society focused on the quality of biological research materials and biobanking, can come to realization, be expressed by a scientific journal,1 and eventually mature when there is committed leadership supported by interested, experienced, and enthusiastic members, all aided by a dedicated administrative staff. ISBER was created to be an international forum, creating opportunities for networking, education, and innovation by providing harmonized approaches to emerging challenges in repositories, as well as fostering ideas to create new solutions. Today, continuing on those footsteps, the primary goals of the society include creating educational and training opportunities; providing a forum for dissemination of state-of-the-art policies, processes, and research findings; and showcasing innovative technologies, products, and services.Two decades is a very short period of time for a global concept to become established and flourish, such that it is now considered an infrastructural component vital to delivering modern precision research. This sustained growth of biobanking and its eventual acceptance as a discipline form part of ISBER's legacy. Since 1999, academia, biobankers, patient advocates, industry and state representatives, lawyers, and others with an interest in biobanking have met at least once per year during the ISBER annual meeting to share and expand their expert knowledge in the field. This global focal point of ISBER meetings has created a strong foundation for the regular exchange of experiences, networking opportunities, as well as the development of best practices educational tools with a global reach, especially as the biobanking field develops in Asia, Eastern Europe, Africa, and South America.2ISBER is proud of its many accomplishments over the past 20 years. It will continue to move forward with strong, visionary, and thought-provoking leadership, along with its supportive management. The society will continue its onward stride into its third decade as the premier global forum that addresses the harmonization of scientific, technical, legal, and ethical issues relevant to repositories of biological and environmental specimens.DisclaimerWhere authors are identified as personnel of the International Agency for Research on Cancer/WHO, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy, or views of the International Agency for Research on Cancer/WHO.

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2021 Annual Meeting Connect and Collaborate through Biobanking: Powering Innovation and Discovery May 10–14, 2021

The International Society for Biological and Environmental Repositories Presents Abstracts from Its 2021 Annual Meeting Connect and Collaborate through Biobanking: Powering Innovation and Discovery May 10–14, 2021

Collection and storage of DNA-containing biomaterial and isolated DNA

The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.

Biobanking in the COVID-19 Era and Beyond: Part 2. A Set of Tool Implementation Case Studies.

The COVID-19 era has brought about a number of novel challenges for the global biobanking community. An array of diverse tools (e.g., standards, best practices, and plans) exists to support quality and fitness-for-purpose in biobank operations. The International Society for Biological and Environmental Repositories (ISBER) COVID-19 Response Task Force has set out to identify needs and gaps in these tools and make recommendations for the next generation of available tools, having closely examined the COVID-19-related challenges. While conducting this work to examine the relationships between tools and biobank adaptability, a subgroup of the task force conducted a parallel effort to develop and describe individual COVID-19 era case studies based on a number of operating biobanks. Each case study presents a different combination of implemented tools. Observations and lessons learned from these case studies are provided, and experiences with tool implementation are discussed. This information is supplemented by data relating to tool usefulness that was obtained through an ISBER survey discussed in a companion article. The knowledge gained from this study will be combined with other task force efforts to make recommendations to better position the biobanking community in their response to future emergencies.

Biobanking in the COVID-19 Era and Beyond: Part 1. How Early Experiences Can Translate into Actionable Wisdom.

The era of COVID-19 has brought about a number of novel challenges for the global biobanking community. To better position the biobanking community to cope with current and future challenges, the International Society for Biological and Environmental Repositories (ISBER) COVID-19 Response Task Force was convened to identify needs and gaps in biobanking tools (existing resources that support good practice), for example, standards, best practices, business, etc. and to make recommendations to benefit the community. Toward these goals, the Task Force assembled a set of questions to explore individual biobanks' experiences, with emphasis on identification of key challenges and approaches, including tools employed. A survey was designed with the use of these questions and administered by ISBER. This article presents a summary of the aggregated data obtained from the survey responses, illustrating some of the major issues encountered and identifying which tools the survey respondents found most useful. In particular, this article focuses on the challenges identified during the early months of the COVID-19 era. Recommendations are provided to support biobank emergency preparedness for the future, address lessons learned, and propose solutions to bridge identified gaps. The analysis and the complete survey dataset will also inform the larger Task Force goal to develop specific tool recommendations.