Are the old International Board for Plant Genetic Resources (IBPGR) base collections available through the Plant Treaty's multilateral system of access and benefit sharing? A review

In 1975, the International Board for Plant Genetic Resources created the first internationally linked system of genebanks, known as the Registry of Base Collections (RBC), to conserve plant germplasm and make it available globally for agricultural research and development. Over time, international efforts shifted away from enhancing and building the RBC toward other means to promote the conservation and sustainable use of plant genetic resources. Perhaps the most important development in this regard was the negotiation of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty or ITPGRFA) and the development of its multilateral system for access and benefit sharing (multilateral system). Our study aimed to ascertain whether the RBC materials are still being conserved/curated in the original recipient organizations. We also sought to assess whether those materials have been included in, and are available through, the ITPGRFA's multilateral system. This outcome would be significant since, in many ways, the multilateral system reflects the spirit, commitment, and objectives of the RBC, with important additional components (e.g. obligations to share monetary benefits derived from the uses of plant genetic resources for food and agriculture). We identify four levels of probability that RBC materials are included in, and available through, the multilateral system. Ultimately, we find that there is a high level of probability that approximately 80% of the RBC materials are currently available through the multilateral system. We further identify a number of possible interventions that could be made to ensure that all RBC materials are conserved and made available through the multilateral system (or on similar terms and conditions of facilitated access and benefit sharing)

Are the old International Board for Plant Genetic Resources (IBPGR) base collections available through the Plant Treaty’s multilateral system of access and benefit sharing? A review

In 1975, the International Board for Plant Genetic Resources created the first internationally linked system of genebanks, known as the Registry of Base Collections (RBC), to conserve plant germplasm and make it available globally for agricultural research and development. Over time, international efforts shifted away from enhancing and building the RBC toward other means to promote the conservation and sustainable use of plant genetic resources. Perhaps the most important development in this regard was the negotiation of the International Treaty on Plant Genetic Resources for Food and Agriculture (Plant Treaty or ITPGRFA) and the development of its multilateral system for access and benefit sharing (multilateral system). Our study aimed to ascertain whether the RBC materials are still being conserved/curated in the original recipient organizations. We also sought to assess whether those materials have been included in, and are available through, the ITPGRFA’s multilateral system. This outcome would be significant since, in many ways, the multilateral system reflects the spirit, commitment, and objectives of the RBC, with important additional components (e.g. obligations to share monetary benefits derived from the uses of plant genetic resources for food and agriculture). We identify four levels of probability that RBC materials are included in, and available through, the multilateral system. Ultimately, we find that there is a high level of probability that approximately 80% of the RBC materials are currently available through the multilateral system. We further identify a number of possible interventions that could be made to ensure that all RBC materials are conserved and made available through the multilateral system (or on similar terms and conditions of facilitated access and benefit sharing)

Structuring chemical space: similarity-based characterization of the PubChem Database

The ensemble of conceivable molecules is referred to as the Chemical Space. In this article we describe a hierarchical version of the Affinity Propagation (AP) clustering algorithm and apply it to analyze the LINGO‐based similarity matrix of a 500 000‐molecule subset of the PubChem database, which contains more than 19 million compounds. The combination of two highly efficient methods, namely the AP clustering algorithm and LINGO‐based molecular similarity calculations, allows the unbiased analysis of large databases. Hierarchical clustering generates a numerical diagonalization of the similarity matrix. The target‐independent, intrinsic structure of the database , derived without any previous information on the physical or biological properties of the compounds, maps together molecules experimentally shown to bind the same biological target or to have similar physical propertie

Podoplanin immunopositive lymphatic vessels at the implant interface in a rat model of osteoporotic fractures

Insertion of bone substitution materials accelerates healing of osteoporotic fractures. Biodegradable materials are preferred for application in osteoporotic patients to avoid a second surgery for implant replacement. Degraded implant fragments are often absorbed by macrophages that are removed from the fracture side via passage through veins or lymphatic vessels. We investigated if lymphatic vessels occur in osteoporotic bone defects and whether they are regulated by the use of different materials. To address this issue osteoporosis was induced in rats using the classical method of bilateral ovariectomy and additional calcium and vitamin deficient diet. In addition, wedge-shaped defects of 3, 4, or 5 mm were generated in the distal metaphyseal area of femur via osteotomy. The 4 mm defects were subsequently used for implantation studies where bone substitution materials of calcium phosphate cement, composites of collagen and silica, and iron foams with interconnecting pores were inserted. Different materials were partly additionally functionalized by strontium or bisphosphonate whose positive effects in osteoporosis treatment are well known. The lymphatic vessels were identified by immunohistochemistry using an antibody against podoplanin. Podoplanin immunopositive lymphatic vessels were detected in the granulation tissue filling the fracture gap, surrounding the implant and growing into the iron foam through its interconnected pores. Significant more lymphatic capillaries were counted at the implant interface of composite, strontium and bisphosphonate functionalized iron foam. A significant increase was also observed in the number of lymphatics situated in the pores of strontium coated iron foam. In conclusion, our results indicate the occurrence of lymphatic vessels in osteoporotic bone. Our results show that lymphatic vessels are localized at the implant interface and in the fracture gap where they might be involved in the removal of lymphocytes, macrophages, debris and the implants degradation products. Therefore the lymphatic vessels are involved in implant integration and fracture healing

Inflammatory Cytokines in General and Central Obesity and Modulating Effects of Physical Activity

Context Chronic systemic inflammation in obesity originates from local immune responses in visceral adipose tissue. However, assessment of a broad range of inflammation-mediating cytokines and their relationship to physical activity and adipometrics has scarcely been reported to date. Objective To characterize the profile of a broad range of pro-and anti-inflammatory cytokines and the impact of physical activity and energy expenditure in individuals with general obesity, central obesity, and non-obese subjects. Design, Setting, and Participants A cross-sectional study comprising 117 obese patients (body mass index (BMI) >= 30) and 83 non-obese community-based volunteers. Main Outcomes Measures Serum levels of interleukin (IL)-2, IL-4, IL-5, IL-10, IL-12, IL-13, granulocyte-macrophage colony-stimulating factor (GM-CSF),interferon (IFN)-gamma and tumor necrosis factor (TNF)-alpha were measured. Physical activity and energy expenditure (MET) were assessed with actigraphy. Adipometrics comprised BMI, weight, abdominal-, waist-and hip-circumference, waist to hip ratio (WHR),and waist-to-height-ratio (WHtR). Results General obesity was associated with significantly elevated levels of IL-5, IL-10, IL-12, IL-13, IFN-gamma and TNF-alpha, central obesity with significantly elevated IL-5, IL-10, IL-12, IL-13 and IFN-gamma-levels. In participants with general obesity, levels of IL-4, IL-10 and IL-13 were significantly elevated in participants with low physical activity, even when controlled for BMI which was negatively associated with physical acitivity. Cytokines significantly correlated with adipometrics, particularly in obese participants. Conclusions Results confirm up-regulation of certain pro-and anti-inflammatory cytokines in obesity. In obese subjects, physical activity may lower levels and thus reduce pro-inflammatory effects of cytokines that may link obesity, insulin resistance and diabetes

Transcriptional Analysis of Shewanella oneidensis MR-1 with an Electrode Compared to Fe(III)Citrate or Oxygen as Terminal Electron Acceptor

Shewanella oneidensis is a target of extensive research in the fields of bioelectrochemical systems and bioremediation because of its versatile metabolic capabilities, especially with regard to respiration with extracellular electron acceptors. The physiological activity of S. oneidensis to respire at electrodes is of great interest, but the growth conditions in thin-layer biofilms make physiological analyses experimentally challenging. Here, we took a global approach to evaluate physiological activity with an electrode as terminal electron acceptor for the generation of electric current. We performed expression analysis with DNA microarrays to compare the overall gene expression with an electrode to that with soluble iron(III) or oxygen as the electron acceptor and applied new hierarchical model-based statistics for the differential expression analysis. We confirmed the differential expression of many genes that have previously been reported to be involved in electrode respiration, such as the entire mtr operon. We also formulate hypotheses on other possible gene involvements in electrode respiration, for example, a role of ScyA in inter-protein electron transfer and a regulatory role of the cbb3-type cytochrome c oxidase under anaerobic conditions. Further, we hypothesize that electrode respiration imposes a significant stress on S. oneidensis, resulting in higher energetic costs for electrode respiration than for soluble iron(III) respiration, which fosters a higher metabolic turnover to cover energy needs. Our hypotheses now require experimental verification, but this expression analysis provides a fundamental platform for further studies into the molecular mechanisms of S. oneidensis electron transfer and the physiologically special situation of growth on a poised-potential surface

Testing a Short Nuclear Marker for Inferring Staphylinid Beetle Diversity in an African Tropical Rain Forest

The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, there are only few attempts to use DNA markers for inventorying all animal species found in environmental samples to describe variations of biodiversity patterns.In this study, an analysis of the nuclear D3 region of the 28S rRNA gene to delimit species-like units is compared to results based on distinction of morphospecies. Data derived from both approaches are used to assess diversity and composition of staphylinid beetle communities of a Guineo-Congolian rain forest in Kenya. Beetles were collected with a standardized sampling design across six transects in primary and secondary forests using pitfall traps. Sequences could be obtained of 99% of all individuals. In total, 76 molecular operational taxonomic units (MOTUs) were found in contrast to 70 discernible morphospecies. Despite this difference both approaches revealed highly similar biodiversity patterns, with species richness being equal in primary and secondary forests, but with divergent species communities in different habitats. The D3-MOTU approach proved to be an efficient tool for biodiversity analyses.Our data illustrate that the use of MOTUs as a proxy for species can provide an alternative to morphospecies identification for the analysis of changes in community structure of hyperdiverse insect taxa. The efficient amplification of the D3-marker and the ability of the D3-MOTUs to reveal similar biodiversity patterns as analyses of morphospecies recommend its use in future molecular studies on biodiversity