resource

CBD News: Three new ratifications to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization provide significant momentum towards its entry into force. The recent ratifications by Be




resource

CBD News: Governments meet in Pyeongchang, Republic of Korea this week for discussions which will finalise preparations for the first meeting of the governing body of the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of




resource

CBD News: Governments have established firm foundations for the operation of the Nagoya Protocol on Access and Benefit-sharing of Genetic Resources, contributing to the momentum towards entry into force and setting the agenda for the first meeting of its




resource

CBD News: Opening Remarks of the Executive Secretary Mr. Dias on the Occasion of the Third Meeting of the High-Level Panel of the Second Phase of the High-Level Panel on the Global Assessment of Resources for Implementing the Strategic Plan for Biodiversi




resource

CBD News: With four new ratifications in the last week, the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization has received 66% of the necessary ratifications, with only 17 more rat




resource

CBD News: Parties to the Convention on Biological Diversity (CBD) wrapped up a weeklong meeting on implementation with recommendations on, among others, resource mobilization, technical and scientific cooperation, poverty eradication and sustainable devel




resource

CBD News: Statement by Mr. Braulio Ferreira de Souza Dias, CBD Executive Secretary, on the Occasion of the 10th Anniversary Celebrations of the International Treaty on Plant Genetic Resources for Food and Agriculture Coming into Force, Geneva, Switzerland




resource

CBD News: The Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization will enter into force on 12 October 2014 following its ratification by 51 Parties to the Convention on Biological Di




resource

CBD News: The Nagoya Protocol on Access to Genetic Resources and the Fair Equitable Sharing of Benefits Arising from their Utilization, of the Convention on Biodiversity (CBD) enters into force today, providing the world with a mechanism to ensure that ac




resource

CBD News: Governments have agreed to a series of actions that will further bolster the Nagoya Protocol on Access and Benefit Sharing, facilitate its effective implementation, and ensure that countries have the necessary resources to take the next steps to




resource

CBD News: Recognizing that wildlife is an important renewable natural resource, with economic, cultural, nutritional and recreational value to humans, Parties at the twelfth meeting of the Conference of the Parties (COP 12), held in Pyeongchang, Republic




resource

CBD News: Statement by the CBD Executive Secretary, Mr. Braulio F. de Souza Dias, at the Fifteenth Session of the Commission on Genetic Resources for Food and Agriculture, Rome, Italy, 19 - 23 January 2015




resource

CBD News: The Collaborative Partnership on Sustainable Wildlife Management (CPW) today launched the Bushmeat Sourcebook, an online resource, on the occasion of the second World Wildlife Day. The sourcebook examines bushmeat's vital contribution to f




resource

CBD News: As governments from around the world prepare to adopt the sustainable development goals and targets later this year, it is particularly fitting that this year's World Environment Day is being celebrated under the theme of resource efficiency




resource

CBD News: To support the mobilisation and alignment of technical and financial resources for priority capacity-building needs, IPBES is developing a prototype Matchmaking Facility. This Facility aims to promote and facilitate dialogue and cooperation amon




resource

CBD News: Montreal, 28 September 2015 - Two new ratifications this month to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization brings the total number of ratifications to the gr




resource

CBD News: Message of the CBD Executive Secretary, Mr. Braulio Ferreira de Souza Dias, on the occasion of the opening of the Sixth Session of the Governing Body of the International Treaty on Plant Genetic Resources for Food and Agriculture, 5 October 2015




resource

CBD News: Ambassador Mary Seet-Cheng, Chair of the East Asian Seas Partnership Council, Viet Nam Deputy Minister of Natural Resources and Environment, Chu Pham Ngoc Hien, PEMSEA Executive Director, Stephen Adrian Ross, Dr. Chua Thia-Eng, Chair Emeritus of




resource

CBD News: Following accession by Slovakia on 29 December 2015, the total number of ratifications to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization now stands at 70.




resource

CBD News: Ratifications by Togo and the United Kingdom of Great Britain and Northern Ireland has brought the total number of ratifications to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from th




resource

CBD News: Biodiversity - the diversity of life on Earth - underpins the natural resources that provide food and livelihoods throughout the world. For many women, biodiversity serves as the cornerstone of their work, their belief systems and their basic s




resource

CBD News: Forests are crucial to the sustainable management of water ecosystems and resources, and water is essential for the sustainability of forest ecosystems. Let us work together and redouble our efforts to ensure that our forests remain healthy now




resource

CBD News: Fundamental to human well-being, water resources can help create paid and decent jobs. But water is a finite and irreplaceable resource. It is only renewable if well managed. All freshwater ultimately depends on the continued healthy functionin




resource

CBD News: Following the ratification by Senegal, the total number of ratifications to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization now stands at 73. In addition, South Afr




resource

CBD News: It is a great pleasure to welcome you all to Montreal for this inaugural meeting of the Compliance Committee under the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization.




resource

CBD News: to Parties yet to ratify or accede to the Nagoya Protocol from Rafael Pacchiano Alamán, Minister for Environment and Natural, Resources, Mexico and COP 13 President and Braulio Ferreira de Souza Dias, Executive Secretary, Convention on Biol




resource

CBD News: Rafael Pacchiano Alamán, Minister of Environment and Natural Resources of Mexico, as the incoming president of the thirteenth meeting of the Conference of the Parties (COP 13) to the Convention on Biological Diversity (CBD), in a joint lett




resource

CBD News: Germany is the latest country to ratify the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization, bringing the total number of ratifications to 74. This includes 73 countrie




resource

CBD News: Montreal, 13 June 2016 - China, Finland and Zambia are the latest countries to ratify the ground-breaking Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization, bringing the




resource

CBD News: Belgium and Bulgaria are the latest countries to ratify the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD), bringing th




resource

CBD News: France, Mali, the Netherlands, the Republic of Moldova and Sweden are the latest countries to ratify the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization, bringing the t




resource

CBD News: Biodiversity, the variety of life on Earth, provides us with a wealth of natural resources that are extremely important for the tourism sector.




resource

CBD News: This week marks the two-year anniversary of the entry into force of the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity.




resource

CBD News: It is a great pleasure to participate in this session of the Commission on Genetic Resources for Food and Agriculture and to discuss opportunities to further integrate biodiversity within the agriculture and food production sectors.




resource

CBD News: On the occasion of the International Day for Biological Diversity, Japan became the latest country to ratify the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization, bring




resource

CBD News: On Friday, 19 May 2017, the Republic of Korea became the 98th country to ratify the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization.




resource

CBD News: On the 5th of June 2017, Kuwait ratified the Nagoya Protocol on Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization, an agreement under the Convention on Biological Diversity, bri




resource

CBD News: The international community has long recognized the interdependence of all countries with regard to plant genetic resources for food and agriculture and their relevance to FAO as well as the Convention on Biological Diversity (CBD) and its Nagoy




resource

CBD News: A Memorandum of Cooperation (MoC) geared towards enhancing cooperation between the Secretariats of the Convention on Biological Diversity (CBD) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture was signed today




resource

CBD News: Germany has published the first report on the utilization of genetic resources through the Access and Benefit-sharing (ABS) Clearing-House by issuing a checkpoint communiqué concerning research on ants from South Africa. This was rapidly fo




resource

Development of a novel {beta}-1,6-glucan-specific detection system using functionally-modified recombinant endo-{beta}-1,6-glucanase [Methods and Resources]

β-1,3-d-Glucan is a ubiquitous glucose polymer produced by plants, bacteria, and most fungi. It has been used as a diagnostic tool in patients with invasive mycoses via a highly-sensitive reagent consisting of the blood coagulation system of horseshoe crab. However, no method is currently available for measuring β-1,6-glucan, another primary β-glucan structure of fungal polysaccharides. Herein, we describe the development of an economical and highly-sensitive and specific assay for β-1,6-glucan using a modified recombinant endo-β-1,6-glucanase having diminished glucan hydrolase activity. The purified β-1,6-glucanase derivative bound to the β-1,6-glucan pustulan with a KD of 16.4 nm. We validated the specificity of this β-1,6-glucan probe by demonstrating its ability to detect cell wall β-1,6-glucan from both yeast and hyphal forms of the opportunistic fungal pathogen Candida albicans, without any detectable binding to glucan lacking the long β-1,6-glucan branch. We developed a sandwich ELISA-like assay with a low limit of quantification for pustulan (1.5 pg/ml), and we successfully employed this assay in the quantification of extracellular β-1,6-glucan released by >250 patient-derived strains of different Candida species (including Candida auris) in culture supernatant in vitro. We also used this assay to measure β-1,6-glucan in vivo in the serum and in several organs in a mouse model of systemic candidiasis. Our work describes a reliable method for β-1,6-glucan detection, which may prove useful for the diagnosis of invasive fungal infections.




resource

Integration and Application of Knowledge, Experience and Resources Supporting Students with Special Educational Needs in the Epidemic




resource

Position statement addresses difficult issue: allocating scare resources in COVID-19 era

(American Geriatrics Society) The COVID-19 pandemic has placed unprecedented pressure on societies worldwide, given the pandemic's rapid, often deadly spread. In health care, the pandemic has raised the pressing question of how society should allocate scarce resources during a crisis. This is the question experts addressed today in a new position statement published by the American Geriatrics Society (AGS) in the Journal of the American Geriatrics Society (DOI: 10.1111/jgs.16537).




resource

Fashion Brands Repurpose Resources to Offer Aid in the COVID-19 Crisis

Retail giants like Yoox Net-a-Porter Group and Brooks Brothers quickly pivoted to offer life-saving services.




resource

OpenDose: open access resources for nuclear medicine dosimetry

Background: Radiopharmaceutical dosimetry depends on the localization in space and time of radioactive sources and requires the estimation of the amount of energy emitted by the sources deposited within targets. In particular, when computing resources are not accessible, this task can be carried out using precomputed tables of Specific Absorbed Fractions (SAFs) or S values based on dosimetric models. The OpenDose collaboration aims to generate and make freely available a range of dosimetric data and tools. Methods: OpenDose brings together resources and expertise from 18 international teams to produce and compare traceable dosimetric data using 6 of the most popular Monte Carlo codes in radiation transport (EGSnrc/EGS++, FLUKA, GATE, Geant4, MCNP/MCNPX and PENELOPE). SAFs are uploaded, together with their associated statistical uncertainties, in a relational database. S values are then calculated from mono-energetic SAFs, based on the radioisotope decay data presented in the International Commission on Radiological Protection (ICRP) publication 107. Results: The OpenDose collaboration produced SAFs for all source regions and targets combinations of the two ICRP 110 adult reference models. SAFs computed from the different Monte Carlo codes were in good agreement at all energies, with standard deviations below individual statistical uncertainties. Calculated S values were in good agreement with OLINDA 2 (commercial) and IDAC 2.1 (free) software. A dedicated website (www.opendose.org) has been developed to provide easy and open access to all data. Conclusion: The OpenDose website allows the display and download of SAFs and the corresponding S values for 1252 radionuclides. The OpenDose collaboration, open to new research teams, will extend data production to other dosimetric models and implement new free features, such as online dosimetric tools and patient-specific absorbed dose calculation software, together with educational resources.




resource

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition [Technological Innovation and Resources]

In bottom-up, label-free discovery proteomics, biological samples are acquired in a data-dependent (DDA) or data-independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at high quantitative quality. DIA profiles of complex biological matrices such as tissues or cells can contain quantitative interferences, and the interferences at the MS1 and the MS2 signals are often independent. When comparing biological conditions, the interferences can compromise the detection of differential peptide or protein abundance and lead to false positive or false negative conclusions.

We hypothesized that the combined use of MS1 and MS2 quantitative signals could improve our ability to detect differentially abundant proteins. Therefore, we developed a statistical procedure incorporating both MS1 and MS2 quantitative information of DIA. We benchmarked the performance of the MS1-MS2-combined method to the individual use of MS1 or MS2 in DIA using four previously published controlled mixtures, as well as in two previously unpublished controlled mixtures. In the majority of the comparisons, the combined method outperformed the individual use of MS1 or MS2. This was particularly true for comparisons with low fold changes, few replicates, and situations where MS1 and MS2 were of similar quality. When applied to a previously unpublished investigation of lung cancer, the MS1-MS2-combined method increased the coverage of known activated pathways.

Since recent technological developments continue to increase the quality of MS1 signals (e.g. using the BoxCar scan mode for Orbitrap instruments), the combination of the MS1 and MS2 information has a high potential for future statistical analysis of DIA data.




resource

Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics [Technological Innovation and Resources]

Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.




resource

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands [Technological Innovation and Resources]

The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.




resource

MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity [Technological Innovation and Resources]

Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link information from both MS2 and MS3 level. However, the current cross-link search algorithm available for MS2-MS3 strategy follows a "MS2-centric" approach and suffers from a high rate of mis-identified cross-links. We demonstrate the problem using two new quality assessment metrics ["fraction of mis-identifications" (FMI) and "fraction of interprotein cross-links from known interactions" (FKI)]. We then address this problem, by designing a novel "MS3-centric" approach for cross-link identification and implementing it as a search engine named MaXLinker. MaXLinker outperforms the currently popular search engine with a lower mis-identification rate, and higher sensitivity and specificity. Moreover, we performed human proteome-wide cross-linking mass spectrometry using K562 cells. Employing MaXLinker, we identified a comprehensive set of 9319 unique cross-links at 1% false discovery rate, comprising 8051 intraprotein and 1268 interprotein cross-links. Finally, we experimentally validated the quality of a large number of novel interactions identified in our study, providing a conclusive evidence for MaXLinker's robust performance.




resource

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation [Technological Innovation and Resources]

The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration. Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducible protein-concentration measurements in biological specimens collected via microsampling. The dried blood spot (DBS) microsampling technique can be performed non-invasively without the expertise of a phlebotomist, and can enhance analyte stability which facilitate the application of this technique in retrospective studies while providing lower storage and shipping costs, because cold-chain logistics can be eliminated. Thus, precise, sensitive, and multiplexed methods for measuring protein concentrations in DBSs can be used for de novo biomarker discovery and for biomarker quantification or verification experiments. To achieve this goal, MRM assays were developed for multiplexed concentration measurement of proteins in DBSs.

The lower limit of quantification (LLOQ) was found to have a median total coefficient of variation (CV) of 18% for 245 proteins, whereas the median LLOQ was 5 fmol of peptide injected on column, and the median inter-day CV over 4 days for measuring endogenous protein concentration was 8%. The majority (88%) of the assays displayed parallelism, whereas the peptide standards remained stable throughout the assay workflow and after exposure to multiple freeze-thaw cycles. For 190 proteins, the measured protein concentrations remained stable in DBS stored at ambient laboratory temperature for up to 2 months. Finally, the developed assays were used to measure the concentration ranges for 200 proteins in twenty same sex, same race and age matched individuals.