Academic literature on the topic 'Bioarchive'

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by an inflammatory process. One of the inflammation markers that can be measured is C-reactive protein (CRP). Another indicator of inflammation is malondialdehyde (MDA), though it is still uncommon to be analyzed in SLE patients. The study looked for the MDA value and found a correlation with CRP. A cross-sectional study design with a correlative analytical was performed. CRP level data was taken from Hasan Sadikin lupus registry data, and MDA levels were analyzed from a bioarchive patient’s serum. We collected the patients’ data who had CRP level from Hasan Sadikin lupus registry and analysed MDA levels from the serum sample. MDA levels were analyzed using an ELISA method. The data obtained were analyzed using the Pearson correlation and Eta correlation test. The study involved 78 data patients as subjects. It was found that the median of CRP and MDA was 0.85 mg/l and 153.10 ng/ml, respectively. These results indicate that the CRP levels in SLE patients are still within normal limits. Statistical analysis showed no correlation between CRP and MDA level (r=0.2, P>0.05). Additionally, the correlation between CRP and MDA with organ involvement, such as lupus nephritis (LN), lupus cutaneous (LC), and lupus musculoskeletal (LM), showed no correlation (Fh<Ft). There is no correlation between CRP and MDA levels in SLE patients, and specific organ involvement of the disease does not affect the correlation.

Abstract Introduction: Banked, unrelated umbilical cord blood units (CBU) are a rich source of hematopoietic stem cells for hematopoietic reconstitution. Potency assays on attached segments have been used for CBU release from the bank to the transplant center. CBUs have historically been manufactured and cryopreserved in bags with three segments (made from the tubing used to fill the bag) arranged across the top of the cassette. Prior to cryopreservation, the CBU is overwrapped, placed in a metal cassette and frozen in a control-rate freezer and submerged under liquid nitrogen for long-term storage. After cryopreservation, segments can be removed from the cassette, without disturbing the bag, for HLA typing, potency assays, or other testing. Last year, in an effort to increase the number of segments available for testing, we changed the configuration of the cryobag to create a fourth segment. To fit in the cassette, the segments were arranged with two segments across the top and two segments bent at 90 degrees to fit between the 20% and 80% portions of the bag. When performing our annual stability testing, we realized that the two distal segments, positioned between the 20% and 80% compartments yielded lower potency results than the segments positioned across the top of the cassette. We investigated this finding as described below. Method: Three large fresh CBUs were processed separately on a Sepax cell processor (Biosafe, Geneva, Switzerland) and evenly divided into two cryopreservation bags. For each CBU, one bag was created with three segments and the other bag with four segments. The cryopreservative, dimethylsulfoxide in dextran, was added at a final concentration of 10% to both bags prior to cryopreservation. Segments were positioned either across the top (3 segments) or in the bent configuration (4 segments) for each of the paired CBUs. All units were cryopreserved and stored in a Thermogenesis Bioarchive. After two weeks in storage, the CBUs were tested. The bags and segments were assayed for ALDHbr, viable CD34, CD45, glycophorin A and viability (7-AAD) along with colony forming units (CFUs), the potency assay used by our bank. Results: The segments configured across the top of the bag correlated with results from the cryobag for ALDHbr (as a percent of viable CD45+, Table 1), CD34+ (as a percent of viable CD45+) and CFU. In contrast, segments placed between the 20% and 80% compartments were significantly lower than the bag for both ALDHbr (as a percent of viable CD45+) and CFU, although CD34+ (as a percent of viable CD45+) was equivalent. Conclusions: Segments attached to CBUs can predict potency of the CBU by various parameters. However, proper placement of the segments within the cryopreservation cassette must be performed to ensure that potency measured on the segments reflects potency measured on the cord blood unit. Disclosures No relevant conflicts of interest to declare.

Abstract The Cord Blood Banks (CBB) wishing to be affiliated to NETCORD must demonstrate that they adopted the Fact-Netcord standards for collection, processing, quality control testing, storage, selection and release for their cord blood units (CBU). The best way to provide these assurances is to obtain FACT accreditation label. The Besancon Cord Blood Bank initiated this quality approach in January 2004 and was inspected on-site in June 2004.Initial internal audits revealed major deficiencies in specific Quality Management areas and the lack of an efficient documentation system together with adequate standard operating procedures and documented validation studies for each step of the process. Adequate labelling, conformity with good transport practices and post-transplantation clinical data recovery were also areas to be improved. Moreover, in order to clarify the different pathways of material, cell products, staff, or wastes, several building works modifications had to be undertaken. Several major improvements were performed during those six months of Fact accreditation project. The Assurance Quality Information System was significantly upgraded to control all the major elements of assurance quality (staff formation, material, premises, alarms, cleaning, records, and quality control testing) by implementing a computerised Oracle-based application. Morover, all documentation was implemented on an intranet network and is now easily accessible to all the staff wherever in the facility. In order to improve the volume of CBU, a weigh-and-mix machine used for blood donor harvesting procedure was tailored for specific CBU collection. To improve the conditions of transport we set up special containers with controlled temperature continuously monitored. Finally, major validation study was performed on a short period, aiming at demonstrating efficiency and reproducibility of the overall CBU process. In brief, eligible mothers, who give their informed consent, are accepted for CB donation after a medical interview. Collection is performed with the placenta in utero. The delay between collection and processing must not exceed 24hrs. CBU volumes are reduced using Sepax© (Biosafe, Switzerland) technology for long-term storage in a Bioarchive© (Thermogenesis, CA, USA). Quality controls include testing maternal blood samples for infectious markers (HIV, HCV, HBV, HTLV, syphilis) and the presence of IGg- and IgM-antibodies against toxoplasmosis, EBV and CMV on the day of birth and after a quarantine period of at least 60 days. No active infectious disease is mandatory. A baby’s clinical examination is performed at the same time point. Microbiological tests on the CBU must be negative. In addition, our CBB requires a minimal collection volume of 80 ml and a minimum of 2 x 106 CD34 cells for CBU qualification. We implemented a systematic cord blood haemoglobin analysis and tested systematically cord blood plasma for viral infection by genomic detection. Finally, our bank obtained its FACT accreditation on May 2nd 2005, validating our strategy. This achievement had a great impact on CBB staff, desiring to maintain and improve their know how. On June 30th 2005, 5045 CBU were registered at French marrow registry and 273 (5%) were transplanted, 142 (52%) in France and 131 (48%) in other countries. This high 5% transplantation rate may be due to the stringent initial quality controls requirements.

Abstract Abstract 3023 Background: The segment attached to the freezing bag is considered an important source of cells for testing the quality of a cryopreserved CBU prior to release for transplantation. CB banks test cells from the segment for CD34+ cell count, viability and colony forming units (CFU) as surrogates of potency of the frozen products. The NCBP reported results of 384 segments of CBU processed with the AutoExpress (AXP) system (Albano et al, ASH 2011). Average segment CD34+ viability was 96% (SD:+/− 3.3%) and correlation with the CBU pre-cryopreservation viable CD34+ counts (vCD34; R2:0.9) and CFU (R2:0.6) were excellent. Segment vCD34+ and CFU also correlated highly with each other (R2:0.69). As of 08/2012, 1056 segments from NCBP AXP CBU have been evaluated with average CD34+ cell viability of 96% (SD:+/− 3.1). However, how the segment results compare to those obtained from the CBU at the transplant center is not established. Methods: To evaluate whether the segment could predict the post-thaw CBU vCD34+ counts, viability and CFU at MSKCC, we compared the post-thaw results of 37 NCBP CBU, AXP-processed and stored in BioArchive freezers, shipped, and thawed at MSKCC, with the information from their respective segments tested at NCBP prior to CBU release and the pre-cryopreservation data. Segment CD34+ counts and viability were evaluated by flow cytometry and 7-AAD exclusion using a single platform and the ISHAGE gating strategy. Segment CFU were evaluated using the NCBP CFU high resolution digital imaging technology (Albano et al, ASH 2008). The segment viable cells/ul were used to estimate the total vCD34 and CFU for the respective CBU. At MSKCC, CBU underwent thaw and albumin reconstitution with 8-fold dilution (10% Dextran 40; 25% albumin) as previously reported (Barker et al, BBMT 2009;15(12):1596–602). Duplicate samples were evaluated by flow cytometry within two hours. Four color flow cytometry using a dual platform was performed to measure CD45+/CD34+/CD3+ cell counts; CD34+ cell viability was assessed using a modified ISHAGE strategy (Scaradavou et al, BBMT 2010;16(4):560–8). CFU assays were performed using 1×105cells plated in duplicate and growth was evaluated at 14 days. All CBU were part of double unit grafts. Results: Consistent with prior NCBP data, segment vCD34+ cell counts correlated well with segment CFU (R2:0.89, p< 0.01; N=21). Additionally, high correlation of vCD34+ cell counts and CFU were seen between the pre-cryopreservation CBU and the segment (p<0.01, Table). Importantly, despite the differences in testing laboratories and gating strategies, the number of vCD34+ cells in the CBU post-thaw correlated with the pre-cryopreservation vCD34+ counts, as well as those from the segment (Table). Average decrease in post-thaw CBU CD34+ cell viability compared to that of the segment was 1.4% (SD:+/− 3.7%, N: 37). Although statistically significant (p: 0.029), this difference was not clinically relevant: the range of change was -10% to +4.8% and the lowest CBU CD34+ viability was 86% (Figure). Post-thaw CBU total CFU and CFUGM did not correlate with pre-cryopreservation values (Table), probably reflecting high inter-laboratory assay variability. Segment CFU and CFUGM correlation with the post-thaw values was significant although the R2was weak. The ratio of post-thaw to segment vCD34 cells (median: 1.3; SD:+/− 0.47) indicated that the segment calculation may underestimate CBU cell content. The median ratio of post-thaw to segment colony-forming cells was 0.54 for total CFU (SD:+/− 0.63) and 0.5 for CFUGM (SD:+/− 0.96). The lower CFU than vCD34 ratio may be explained, in part, by the fact that 7-AAD detects dead cells but not apoptotic; apoptotic cells are counted as alive by flow cytometry but do not have functionality and do not generate CFU in culture. Conclusions: Our results indicate that testing of CBU segments can measure accurately the potency of the frozen CB products. Moreover, the results demonstrate that CBU quality can be maintained following albumin-dextran reconstitution. These findings reflect the cryopreservation procedures, freezing bags and reconstitution method described; whether they can be applied to other CB banks or transplant center laboratories requires further investigation. Disclosures: No relevant conflicts of interest to declare.

Abstract. Mussel shells are potential bioarchives of proxies for changes of the physico-chemical conditions in the bivalve's habitat. One such proxy is the distribution of the Rare Earths and Yttrium (REY) in seawater, as REY speciation in seawater is sensitive to pH and temperature variations, due to the impact of these parameters on the activity of CO32− in seawater. We present a new protocol for sample preparation and determination of REY concentrations in bivalve shells, that includes sample treatment with NaOCl followed by REY separation and preconcentration. The data obtained was further used to calculate REY partition coefficients between shells of M. edulis and ambient seawater, and acquired results were then used in the investigation of the potential effects of pH and temperature on REY partitioning. Shells of M. edulis mussels from the North Sea show consistent shale-normalized ("SN") REY patterns that increase from the light REY to the middle REY and decrease from the middle REY to the heavy REY. Despite being different to the general seawater REYSN pattern, the shells still display distinct REY features of seawater such as a negative CeSN anomaly and small positive YSN and GdSN anomalies. Apparent partition coefficients for the REY between the shell and seawater (appDREYshell/seawater) are low and decrease strongly from the light REY (4.04 for La) to the heavy REY (0.34 for Lu). However, assuming that only the free REY3+ are incorporated into the shell, appDREY3&amp;plus;shell/seawater values are higher and rather similar for all REY (102.46 for La; 113.44 for Lu), but show a slight maximum at Tb (199.18). Although the impact of vital effects i.e. REY speciation in a mussel's extrapallial fluid from which the carbonate minerals precipitate, cannot be quantified yet, it appears that M. edulis shells are bioarchives of some REY features of seawater. We modelled the REYSN patterns of a hypothetical mussel shell at pH 8.2 and 7.6 and at temperatures of 25 and 5 °C assuming that only REY3+ are incorporated into the carbonate's crystal lattice. The results suggest that with lower pH, REY concentrations in a shells increase, but with little effect on the shape of the REYSN patterns, while a temperature change has an impact on the REYSN pattern, but only minor effects on REY concentrations.

Dans le contexte des changements climatiques, les écosystèmes marins arctiques sont confrontés à des modifications environnementales accélérés, dont les conséquences sur les communautés biotiques sont encore débattues. La diminution du couvert de glace, l’augmentation de la turbidité et des apports d’eau douce vont affecter les producteurs primaires arctiques, avec des effets en cascade sur un processus-clé de ces écosystèmes : la relation trophique entre producteurs primaires et consommateurs benthiques (à laquelle se réfère généralement l’expression « couplage pélagos-benthos »). L’étude directe de ces interactions complexes n’est pas aisée dans ces milieux. Le modèle biologique des bivalves filtreurs peut permettre de contourner ces problèmes en remplissant une fonction d’ « intermédiaire » pour la compréhension de ces processus écologiques. Parmi les avantages de ce modèle d’étude, il y a tout d’abord le fait que ces organismes enregistrent au sein de leur coquille, dans les couches de biocarbonates, certaines dynamiques de leurs environnements. Les informations contenues dans ces « bioarchives » sont interprétées grâce aux méthodes de la sclérochronologie et de la sclérochimie et concernent une fenêtre temporelle correspondante à la vie des individus (de quelques années à plus que 500 ans). Un autre avantage de ce modèle biologique est que, s’agissant d’organismes qui sont des consommateurs primaires, l’étude de leur régime alimentaire peut apporter des éléments sur la relation trophique avec les producteurs primaires. Avec les méthodes de l’écologie trophique, en particulier les acides gras et les isotopes stables, l’étude des tissus permet d’obtenir des informations sur les sources assimilées à l’échelle de quelques semaines/mois. L’objectif de cette thèse est de tester le potentiel des bivalves Astarte moerchi (complexe borealis) comme modèle biologique pour l’étude des écosystèmes marins arctiques. Pour ce faire, une approche couplée est utilisée combinant l’analyse de la coquille par les méthodes de la sclérochronologie et de la sclérochimie (ratios élémentaires) et l’analyse des tissus par les méthodes de l’écologie trophique (acides gras, isotopes stable du carbone et de l’azote, isotopes du carbone sur acides gras individuels). Deux populations actuelles d’Astarte moerchi ont été étudiées dans deux fjords présentant des caractéristiques environnementales contrastées : le Young Sound au Nord-Est du Groenland (considéré comme fjord « arctique ») et le Kongsfjorden à l’Ouest de l’Archipel du Svalbard (considéré comme site « sub-arctique »). L’étude des tissus d’A. moerchi a permis de mettre en évidence la plasticité trophique de cette espèce, avec des différences dans les sources d’alimentation de deux populations liées aux dynamiques locales de production primaire. L’étude de la coquille d’A. moerchi a permis de : a) corroborer l’hypothèse de la formation annuelle des stries de croissance, confirmant la longévité de cette espèce pouvant atteindre 150 ans ; b) montrer l’intérêt potentiel de l’étude des ratios élémentaires dans les biocarbonates et en particulier du ratio Barium sur Calcium (Ba/Ca), qui pourrait être relié aux efflorescences phytoplanctoniques et c) montrer que les conditions environnementales contrastées du site arctique et sub-arctique se traduisent dans des patrons de croissance coquillère différents. Des perspectives pour l’utilisation ultérieure de ce modèle en écologie sont discutées. Pour conclure, une réflexion épistémologique est amorcée sur la spécificité du modèle biologique d’étude des bivalves filtreurs. En opposition à une notion plus classique d’ « organisme modèle » utilisée en biologie expérimentale, nous proposons que les bivalves filtreurs (à l’instar d’autres « bioarchives » comme les arbres, des coraux et des algues corallines) appartiennent à une catégorie de modèles biologiques qu’on pourrait qualifier « in situ » et qui semble être spécifique à la discipline écologique
In the context of climate change, Arctic marine ecosystems are affected by rapid environmental modifications, whose effects on biotic communities are still debated. The sea-ice decline and the increase in freshwater inputs and turbidity are likely to impact Arctic primary producers, with cascade effects on a key-process in those ecosystems: the trophic relationship between primary producers and benthic consumers (generally referred as “pelagic-benthic coupling”). The direct study of such complex interaction is not straightforward in the Arctic. The biological model of filter-feeding bivalves offers the possibility to get around these problems, allowing to study those ecological processes indirectly. Among the advantages of this model, there is first of all the fact that these organisms record in their shell, in the carbonate layers, some dynamics of their environments. The information recorded in such “bioarchives” are interpreted through the methods of sclerochronology and sclerochemistry and relate to a time window corresponding to the organism lifespan (from some years to more than 500 years). Given that these organisms are primary consumers, another advantage of this biological model is that the study of their diet can provide information about the trophic relationship with primary producers. With the methods of trophic ecology, especially fatty acids and stable isotopes, the study of the tissues allows the investigation of sources assimilated at a timescale of weeks/months.The main objective of this thesis is to test the potential of bivalves Astarte moerchi (borealis complex) as a biological model for the study of marine Arctic ecosystems. A coupled approach is used to combine shell analysis by the methods of sclerochronology and sclerochemistry (elemental ratios) and tissue analysis by the methods of trophic ecology (fatty acids, carbon and nitrogen stable isotopes, compound-specific carbon stable isotopes on individual fatty acids). Two living A. moerchi populations have been studied in two fjords presenting contrasted environmental conditions: Young Sound in North-East Greenland (considered as “Arctic” site) and Kongsfjorden in the West coast of the Svalbard Archipelago (considered as a “sub-Arctic” site). The study of the tissues of A. moerchi allowed to show the trophic plasticity of this species, with differences in food sources of the two populations linked to local primary production dynamics. The analysis of the shell of A. moerchi allowed to: a) corroborate the hypothesis of annual growth lines formation, thus confirming the longevity of this species that can attain 150 years; b) show the potential interest of the analysis of elemental ratios and particularly the ratio between Barium and Calcium (Ba/Ca), which could be relied to phytoplanktonic blooms and c) show that contrasted environmental conditions in the Arctic and sub-Arctic sites result in different shell growth patterns. Some perspectives for the further use of this model study in ecology are discussed. To conclude, an epistemological reflection is sketched about the specificity of the biological model study of filter-feeding bivalves. In contrast to the classical notion of “model organism” used in experimental biology, we suggest that filter-feeding bivalves (as well as other “bioarchives” like trees, corals and coralline algae) belong to a category of biological models that could be named “in situ” and seems specific to the ecological discipline

Biogeochemical tracers and sclerochronologies are used to answer many ecological questions that require linking organisms with the environment. Calcified hard parts of organisms that remain chemically inert after formation are particularly advantageous for extracting information (e.g. otoliths, shells, coral) on both the organism and the environment. These structures have growth increments enabling time-resolved information to be extracted on a range of time-scales (sub-daily to centennial). For my research, otoliths (fish earstones) were chosen as an environmental proxy, as they contain both biogeochemical (i.e. radiocarbon and trace elements) and sclerochronological (i.e. growth) signals that reflect environmental change in marine systems. My overarching aim is to use otolith-based proxy records to provide new data describing environmental change in marine systems of southern Australia and New Zealand. More specifically, I employ biogeochemical tracers and sclerochronologies to: (1) detect changes in radiocarbon transport through time in marine waters; (2) establish a radiocarbon record for upwelled waters in the southeastern Indian Ocean; (3) examine local and regional effects of climate forcing on fish growth, and (4) determine the physiological controls acting upon trace element assimilation into otoliths and the differences in chemical constituents of an upwelled water mass. Otoliths of deep water fish – ocean perch from the genus Helicolenus – are used in all applications and originate from areas along southern Australia and New Zealand. Thus, the biogeochemical and sclerochronological data derived from these fish describe changes occurring in the marine environments of the southwest Pacific and southeastern Indian Oceans. Radiocarbon records from the otoliths of H. barathri, combined with published records of other fish species in the southwest Pacific Ocean, show transport of the bomb radiocarbon signal from marine surface waters to depths approaching 1000 m. Transports lags ranging from 5 to 20 years are documented, and radiocarbon reservoir ages are calculated for water masses associated with the Tasman Sea. Radiocarbon measurements from H. percoides, in an upwelling area along the southern coast of Australian (southeastern Indian Ocean), are the very first radiocarbon time series documented for the region and reflect the lower radiocarbon values expected for seasonally upwelled water. Long term growth responses resulting from sclerochronologies from a Helicolenus species complex from southern Australia to New Zealand are compared across regions and species with broad- and local-scale climatic/oceanographic variables using univariate mixed effects models. These data demonstrate how broad scale climate patterns and weather can have additive or synergistic effects on the local environment, which are reflected in the growth of the fish. Biogeochemical tracers (Na, Sr, Mg, Ba, Li) and sclerochronologies (growth) are also extracted from otoliths of the same fish in this upwelling region. These data are used simultaneously in combination with univariate and multivariate mixed effects modelling to describe physiological and environmental controls on otolith chemistry. Temporal signals within these data are correlated with seasonal upwelling events. Ba:Ca and Li:Ca are more influenced by the environment, while Sr:Ca and Na:Ca are controlled by physiological processes. Ba:Ca negatively tracks upwelling events, suggesting an upwelled water mass not enriched in Ba. Li:Ca correlates positively with chlorophyll-a, indicating a possible proxy for marine productivity. Thus, the overarching aim of this research has been achieved: biogeochemical tracers and sclerochronologies derived from Helicolenus otoliths have provided new data describing environmental change in marine systems of southern Australia and New Zealand.
Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 2015.