Definition of Naturally Processed Peptides Reveals Convergent Presentation of Autoantigenic Topoisomerase I Epitopes in Scleroderma.

ObjectiveAutoimmune responses to DNA topoisomerase I (topo I) are found in a subset of scleroderma patients who are at high risk for interstitial lung disease (ILD) and mortality. Anti-topo I antibodies (ATAs) are associated with specific HLA-DRB1 alleles, and the frequency of HLA-DR-restricted topo I-specific CD4+ T cells is associated with the presence, severity, and progression of ILD. Although this strongly implicates the presentation of topo I peptides by HLA-DR in scleroderma pathogenesis, the processing and presentation of topo I has not been studied.MethodsWe developed a natural antigen processing assay (NAPA) to identify putative CD4+ T cell epitopes of topo I presented by monocyte-derived dendritic cells (mo-DCs) from 6 ATA-positive patients with scleroderma. Mo-DCs were pulsed with topo I protein, HLA-DR-peptide complexes were isolated, and eluted peptides were analyzed by mass spectrometry. We then examined the ability of these naturally presented peptides to induce CD4+ T cell activation in 11 ATA-positive and 11 ATA-negative scleroderma patients.ResultsWe found that a common set of 10 topo I epitopes was presented by Mo-DCs from scleroderma patients with diverse HLA-DR variants. Sequence analysis revealed shared peptide-binding motifs within the HLA-DRβ chains of ATA-positive patients and a subset of topo I epitopes with distinct sets of anchor residues capable of binding to multiple different HLA-DR variants. The NAPA-derived epitopes elicited robust CD4+ T cell responses in 73% of ATA-positive patients (8 of 11), and the number of epitopes recognized correlated with ILD severity (P = 0.025).ConclusionThese findings mechanistically implicate the presentation of a convergent set of topo I epitopes in the development of scleroderma

Synthesis Report: Implementing a Regional, Indigenous-Led and Sustainability-Informed Impact Assessment in Ontario’s Ring of Fire

Background: the issue Development in Ontario’s “Ring of Fire”, a significant deposit of minerals, including chromite, located in the boreal region of the far north of the province, has been on the table for many years. Despite the fact that successive governments have hyped the value of the resources, the remoteness and lack of infrastructure, as well as the inability of governments to obtain the buy-in of all of the First Nations communities in the region, has left the Ring of Fire undeveloped. Thus, Ontario’s far north remains one of the world’s largest, most intact ecological systems. The boreal forest and peatlands play key roles in regulating the climate. Proposed mining in this region has generated significant controversy and conflict because the potential for wealth generation is accompanied by the potential for significant and possibly serious negative impacts and cumulative effects, as recently-proposed infrastructure developments quite literally ‘pave the way’ for multiple mines and generations of extraction. The proposals also present a likelihood of inequitably distributed benefits and risks at a variety of physical and temporal scales, with remote Anishinaabe and Anishini communities and their ways of life particularly vulnerable in this regard. These communities are already experiencing an ongoing state of social emergency with youth suicide, addiction and housing crises, as well as a persistent lack of essential community infrastructure, including safe drinking water. For many years, analysts and First Nations leaders have been calling for a regional process in order to broadly assess the expected impacts of the proposed developments in the Ring of Fire. They have noted the complexity of the contemplated infrastructure decisions, the potential for lasting negative impacts, and vast cumulative effects. And yet, without this framework in place, provincial and federal impact assessment (IA) regimes are currently proceeding to assess two individual road proposals that threaten to open the region up to mining. Objectives With this research, our team has synthesized knowledge across a range of areas, including Indigenous-led IA, regional and strategic approaches to IA, and the use of gender-based analysis plus in IA, and applied it to the example of Ontario’s Ring of Fire. In doing so, our primary aim has been to develop, test, and propose a workable plan for how such an approach could be adopted in the specific context of Ontario’s Far North. Methodology Our team began with a period of background preparation and literature review, including following the developments in the region over the fall months, including the progression of the project-level assessments that were being conducted at the federal and provincial levels for the Marten Falls Community Access Road and the Webequie Supply Road. The PI conducted a community visit, workshop and some interviews in collaboration with Neskantaga First Nation in November 2019. Subsequent to that visit, the team collaboratively prepared three draft models for how a regional IA could be implemented in partnership with an Indigenous Governing Authority (IGA) in the region. The team convened a day-long meeting with 14 community representatives, elders and leaders from Neskantaga First Nation in Thunder Bay on January 23, 2020 to discuss, debate and refine the models. The discussion was audio-recorded with permission, transcribed and coded. From there, the team finalized our recommendations and began drafting this report. Key messages The key messages communicated to us by knowledge holders, elders, and leadership in the community engagement sessions included: • The people in the communities are the real authority; the grassroots and the elders must be heard for any process to be legitimate; • The appropriate Indigenous Governing Authority (IGA) must be a collective of affected First Nations, rather than one of the existing tribal councils or regional organizations, such as NAN or Matawa (on the basis of ecological connectivity and socio-cultural impacts related to probable infrastructure locations); • An Elders Advisory Council should be an integral element at all stages of decision-making; • The ongoing state of social emergency must be addressed first, before new projects can be adequately considered. Communities must be satisfied that any potential new projects or infrastructure will mitigate the crises, and enhance long-term social, cultural and ecological sustainability; and, • Any regional approaches need to provide a framework that can effectively guide project-level assessments and approvals, which in turn lead into community-level consent processes, in line with local protocols. Results The recommended model includes a semi-permanent Ring of Fire Commission to be established by agreement between the federal Minister of Environment and Climate Change and an Indigenous Governing Authority made up of impacted and interested First Nations. The Commission, in conjunction with an Elder Advisory Council, should develop a framework for cumulative effects; baseline data (including on the ongoing social emergency); criteria for a modified ‘positive contribution to sustainability’ test; and a regional plan. Under the umbrella of the Commission, we recommend a joint panel review process for making subsequent decisions about individual projects proposed for the region, within the parameters established by the Commission. Decisions on individual projects will subsequently be made independently by each relevant governing authority. For more information, contact Professor Dayna Nadine Scott, [email protected]

Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters

Here we show how a simple inorganic salt can spontaneously form autocatalytic sets of replicating inorganic molecules that work via molecular recognition based on the {PMo12} ≡ [PMo12O40]3– Keggin ion, and {Mo36} ≡ [H3Mo57M6(NO)6O183(H2O)18]22– cluster. These small clusters are able to catalyze their own formation via an autocatalytic network, which subsequently template the assembly of gigantic molybdenum-blue wheel {Mo154} ≡ [Mo154O462H14(H2O)70]14–, {Mo132} ≡ [MoVI72MoV60O372(CH3COO)30(H2O)72]42– ball-shaped species containing 154 and 132 molybdenum atoms, and a {PMo12}⊂{Mo124Ce4} ≡ [H16MoVI100MoV24Ce4O376(H2O)56 (PMoVI10MoV2O40)(C6H12N2O4S2)4]5– nanostructure. Kinetic investigations revealed key traits of autocatalytic systems including molecular recognition and kinetic saturation. A stochastic model confirms the presence of an autocatalytic network involving molecular recognition and assembly processes, where the larger clusters are the only products stabilized by the cycle, isolated due to a critical transition in the network

Plasma proteome correlates of lipid and lipoprotein: biomarkers of metabolic diversity and inflammation in children of rural Nepal.

Proteins involved in lipoprotein metabolism can modulate cardiovascular health. While often measured to assess adult metabolic diseases, little is known about the proteomes of lipoproteins and their relation to metabolic dysregulation and underlying inflammation in undernourished child populations. The objective of this population study was to globally characterize plasma proteins systemically associated with HDL, LDL, and triglycerides in 500 Nepalese children. Abnormal lipid profiles characterized by elevated plasma triglycerides and low HDL-cholesterol (HDL-C) concentrations were common, especially in children with subclinical inflammation. Among 982 proteins analyzed, the relative abundance of 11, 12, and 52 plasma proteins was correlated with LDL-cholesterol (r = -0.43∼0.70), triglycerides (r = -0.39∼0.53), and HDL-C (r = -0.49∼0.79) concentrations, respectively. These proteins included apolipoproteins and numerous unexpected intracellular and extracellular matrix binding proteins, likely originating in hepatic and peripheral tissues. Relative abundance of two-thirds of the HDL proteome varied with inflammation, with acute phase reactants higher by 4∼40%, and proteins involved in HDL biosynthesis, cholesterol efflux, vitamin transport, angiogenesis, and tissue repair lower by 3∼20%. Untargeted plasma proteomics detects comprehensive sets of both known and novel lipoprotein-associated proteins likely reflecting systemic regulation of lipoprotein metabolism and vascular homeostasis. Inflammation-altered distributions of the HDL proteome may be predisposing undernourished populations to early chronic disease

Outcomes Following Anterior Cruciate Ligament Reconstruction with Patellar Tendon vs Hamstring Autografts: A Systematic Review of Randomized Controlled Trials with a Mean Follow-up of 15 Years

BACKGROUND: The two most common surgical treatment modalities for anterior cruciate ligament reconstruction (ACL), patellar tendon (PT) and hamstring tendon (HS) autografts, have been shown to have outcomes that are both similar and favorable; however, many of these are short or intermediate-term. The objective of this systematic review is to evaluate randomized controlled trials (RCTs) with a minimum 10-year follow-up data to compare the long-term outcomes of ACL reconstructions performed using PT and HS autografts. METHODS: This systematic review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. A search of three databases (PubMed, Cochrane and EMBASE) was performed to identify RCTs with a minimum of 10-year follow-up that compared clinical and/or functional outcomes between PT and HS autografts. RESULTS: Four RCTs with a total of 299 patients were included in the study. The mean follow-up ranged from 10.2 to 17 years (mean, 14.79 years). No significant differences in knee laxity or clinical outcome scores were demonstrated in any of the studies. One study found that PT autografts were significantly more likely to have osteoarthritis identified by radiographic findings. Two studies found that patients with PT autografts reported increase kneeling pain, while none of the four studies reported a difference in anterior knee pain. There were no significant differences in graft failure rates. CONCLUSION: This review demonstrates no long-term difference in clinical or functional outcomes between PT and HS autografts. However, radiographic and subjective outcomes indicate that patients with PT autografts may experience greater kneeling pain and osteoarthritis. Therefore, orthopedic surgeons should consider patient-centric factors when discussing graft options with patients

Transitory FGF treatment results in the long-lasting suppression of the proliferative response to repeated FGF stimulation.

FGF applied as a single growth factor to quiescent mouse fibroblasts induces a round of DNA replication, however continuous stimulation results in arrest in the G1 phase of the next cell cycle. We hypothesized that FGF stimulation induces the establishment of cell memory, which prevents the proliferative response to repeated or continuous FGF application. When a 2-5 day quiescence period was introduced between primary and repeated FGF treatments, fibroblasts failed to efficiently replicate in response to secondary FGF application. The establishment of “FGF memory” during the first FGF stimulation did not require DNA synthesis, but was dependent on the activity of FGF receptors, MEK, p38 MAPK and NFκB signaling, and protein synthesis. While secondary stimulation resulted in strongly decreased replication rate, we did not observe any attenuation of morphological changes, Erk1/2 phosphorylation and cyclin D1 induction. However, secondary FGF stimulation failed to induce the expression of cyclin A, which is critical for the progression from G1 to S phase. Treatment of cells with a broad range histone deacetylase inhibitor during the primary FGF stimulation rescued the proliferative response to the secondary FGF treatment suggesting that the establishment of “FGF memory” may be based on epigenetic changes. We suggest that “FGF memory” can prevent the hyperplastic response to cell damage and inflammation, which are associated with an enhanced FGF production and secretion. “FGF memory” may present a natural obstacle to the efficient application of recombinant FGFs for the treament of ulcers, ischemias and wounds

Precise breakpoint detection in a patient with 9p- syndrome

We present a case of 9p- syndrome with a complex chromosomal event originally characterized by the classical karyotype approach as 46,XX,der(9)t(9;13)(p23;q13). We used advanced technologies (Bionano Genomics genome imaging and 10× Genomics sequencing) to characterize the location of the translocation and accompanying deletion on Chromosome 9 and duplication on Chromosome 13 with single-nucleotide breakpoint resolution. The translocation breakpoint was at Chr 9:190938 and Chr 13:50850492, the deletion at Chr 9:1-190938, and the duplication at Chr 13:50850492-114364328. We identified genes in the deletion and duplication regions that are known to be associated with this patient\u27s phenotype (e.g.