Detection of Intra-Tumor Self Antigen Recognition during Melanoma Tumor Progression in Mice Using Advanced Multimode Confocal/Two Photon Microscope

Determining how tumor immunity is regulated requires understanding the extent to which the anti-tumor immune response “functions” in vivo without therapeutic intervention. To better understand this question, we developed advanced multimodal reflectance confocal/two photon fluorescence intra-vital imaging techniques to use in combination with traditional ex vivo analysis of tumor specific T cells. By transferring small numbers of melanoma-specific CD8+ T cells (Pmel-1), in an attempt to mimic physiologic conditions, we found that B16 tumor growth alone was sufficient to induce naive Pmel-1 T cell proliferation and acquisition of effector phenotype. Tumor -primed Pmel-1 T cells, are capable of killing target cells in the periphery and secrete IFNγ, but are unable to mediate tumor regression. Within the tumor, Pmel-1 T cells have highly confined mobility, displaying long term interactions with tumor cells. In contrast, adoptively transferred non tumor-specific OT-I T cells show neither confined mobility, nor long term interaction with B16 tumor cells, suggesting that intra-tumor recognition of cognate self antigen by Pmel-1 T cells occurs during tumor growth. Together, these data indicate that lack of anti-tumor efficacy is not solely due to ignorance of self antigen in the tumor microenvironment but rather to active immunosuppressive influences preventing a protective immune response

Inflammation-Associated Nitrotyrosination Affects TCR Recognition through Reduced Stability and Alteration of the Molecular Surface of the MHC Complex

Nitrotyrosination of proteins, a hallmark of inflammation, may result in the production of MHC-restricted neoantigens that can be recognized by T cells and bypass the constraints of immunological self-tolerance. Here we biochemically and structurally assessed how nitrotyrosination of the lymphocytic choriomeningitis virus (LCMV)-associated immunodominant MHC class I-restricted epitopes gp33 and gp34 alters T cell recognition in the context of both H-2Db and H-2Kb. Comparative analysis of the crystal structures of H-2Kb/gp34 and H-2Kb/NY-gp34 demonstrated that nitrotyrosination of p3Y in gp34 abrogates a hydrogen bond interaction formed with the H-2Kb residue E152. As a consequence the conformation of the TCR-interacting E152 was profoundly altered in H-2Kb/NY-gp34 when compared to H-2Kb/gp34, thereby modifying the surface of the nitrotyrosinated MHC complex. Furthermore, nitrotyrosination of gp34 resulted in structural over-packing, straining the overall conformation and considerably reducing the stability of the H-2Kb/NY-gp34 MHC complex when compared to H-2Kb/gp34. Our structural analysis also indicates that nitrotyrosination of the main TCR-interacting residue p4Y in gp33 abrogates recognition of H-2Db/gp33-NY complexes by H-2Db/gp33-specific T cells through sterical hindrance. In conclusion, this study provides the first structural and biochemical evidence for how MHC class I-restricted nitrotyrosinated neoantigens may enable viral escape and break immune tolerance

Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus

<p>Abstract</p> <p>Background</p> <p>The study of speciation in the marine realm is challenging because of the apparent absence of physical barriers to dispersal, which are one of the main drivers of genetic diversity. Although phylogeographic studies using mitochondrial DNA (mtDNA) information often reveal significant genetic heterogeneity within marine species, the evolutionary significance of such diversity is difficult to interpret with these markers. In the northwestern (NW) Pacific, several studies have emphasised the potential importance of sea-level regression during the most recent glaciations as a driver of genetic diversity in marine species. These studies have failed, however, to determine whether the period of isolation was long enough for divergence to attain speciation. Among these marine species, the cosmopolitan estuarine-dependent fish <it>Mugil cephalus </it>represents an interesting case study. Several divergent allopatric mtDNA lineages have been described in this species worldwide, and three occur in sympatry in the NW Pacific.</p> <p>Results</p> <p>Ten nuclear microsatellites were surveyed to estimate the level of genetic isolation of these lineages and determine the role of sea-level fluctuation in the evolution of NW Pacific <it>M. cephalus</it>. Three cryptic species of <it>M. cephalus </it>were identified within this region (NWP1, 2 and 3) using an assignment test on the microsatellite data. Each species corresponds with one of the three mtDNA lineages in the COI phylogenetic tree. NWP3 is the most divergent species, with a distribution range that suggests tropical affinities, while NWP1, with a northward distribution from Taiwan to Russia, is a temperate species. NWP2 is distributed along the warm Kuroshio Current. The divergence of NWP1 from NWP2 dates back to the Pleistocene epoch and probably corresponds to the separation of the Japan and China Seas when sea levels dropped. Despite their subsequent range expansion since this period of glaciation, no gene flow was observed among these three lineages, indicating that speciation has been achieved.</p> <p>Conclusions</p> <p>This study successfully identified three cryptic species in <it>M. cephalus </it>inhabiting the NW Pacific, using a combination of microsatellites and mitochondrial genetic markers. The current genetic architecture of the <it>M. cephalus </it>species complex in the NW Pacific is the result of a complex interaction of contemporary processes and historical events. Sea level and temperature fluctuations during Plio-Pleistocene epochs probably played a major role in creating the marine species diversity of the NW Pacific that is found today.</p

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Background: Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. // Methods: We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung's disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. // Findings: We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung's disease) from 264 hospitals (89 in high-income countries, 166 in middle-income countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in low-income countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. // Interpretation: Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between low-income, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Planetary Migration in Protoplanetary Disks

The known exoplanet population displays a great diversity of orbital architectures, and explaining the origin of this is a major challenge for planet formation theories. The gravitational interaction between young planets and their protoplanetary disks provides one way in which planetary orbits can be shaped during the formation epoch. Disk-planet interactions are strongly influenced by the structure and physical processes that drive the evolution of the protoplanetary disk. In this review we focus on how disk-planet interactions drive the migration of planets when different assumptions are made about the physics of angular momentum transport, and how it drives accretion flows in protoplanetary disk models. In particular, we consider migration in discs where: (i) accretion flows arise because turbulence diffusively transports angular momentum; (ii) laminar accretion flows are confined to thin, ionised layers near disk surfaces and are driven by the launching of magneto-centrifugal winds, with the midplane being completely inert; (iii) laminar accretion flows pervade the full column density of the disc, and are driven by a combination of large scale horizontal and vertical magnetic fields

The application of various chemicals to cuts made in the stem bases of Brachystegia spiciformis (Benth.) Troupin and Terminalia sericea Burch. ex DC

Picloram-potassium and various mixtures of picloram with 2,4-D amine, 2,4,5-T ester alone were injected into incisions made in the cambium of standing Brachystegia spiciformis and Julbernadia globiflora trees. Each arboriciade was tested at a range of application rates, at different times of the year and at three different sites fir each species. Picloram potassium and 2,4,5-T ester were also tested on Terminalia sericea trees. Glyphosphate, MCPA, mixtures of mecoprop and 2,4,5T amine and different mixtures of 2,4-T ester with 2,4,5-T ester, cacodylic acid and Tandex were tested on B. spiciformis and J. globiflora trees at one site and only in January. Arboricides containing picloram, with or without the addition of 2,4-D or 2,4,5-T, were the most effective chemicals for the control for trees. Higher applications rates were required to kill B. spiciformis and J. globiflora between May and October when they were not actively growing. T. sericea trees were susceptible to arboricide treatment throughout the year. The response of individual trees to treatment with arboricides appears to be related to size.Picloram-kalium en verskillende mengsels met picloram met 2,4-D amien, 2,4,5-T ester of amien, of 2,4,5-T ester alleenlik is in snitte wat in die kambium van Brachystegia spiciformis en Julbernardia globiflora bome gemaak is, ingespuit. Elke boomonkruiddoder is teen 'n reeks van toedieningsvlakke op verskillende tye van die jaar en op drie verskillende persele vir elke spesie, getoets. Picloram-kalium en 2,4,5-T ester is ook op Terminalia sericea bome getoets. Glyphosphate, MCPA, mengsel van mecoprop en 2,4,5-T amien en verskeie mengsels van 2,4-D ester met 2,4,5-T ester, cacodylic suur en Tandex is op B. spiciformis end J. globoflora bome op een perseel en slegs in Januarie, getoets. Boomonkruiddoder me tpicloram, sonder of met addisionele 2,4-D of 2,4,5-T, was die mees doeltreffende chemikali&#235 vir die beheer van bome gewees. Ho&#235r toedieningsvlakke was nodig om B. spiciformis en J. globiflora tussen Mei en Oktober, wanneer hulle nie in 'n aktiewe groeifase is nie, te dood. T. sericea bome was gevoelig vir boomonkruiddoder dwarsdeur die jaar. Die reaksie van alleenstaande bome op behandeling met boomonkruiddoder is verwant aan boomgrootte.Keywords: arboricides, bush control, cacodylic acid, glyphosphate, mecoprop, MCPA, picloram, stem injection, Tandex, 2,4-D, 2,4,5-TJournal of the Grassland Society of southern Africa 7(2):116–12

The role of

No Abstract. African Journal of Range and Forage Science Vol. 18 (1)1983: pp.151_15

Towards a method of assessing the veld condition of the Valley Bushveld in the Eastern Cape.

Reports the results of an investigation conducted to develop a method of scoring bushveld according to its productive condition; Currently, no technique is available for assessing the condition of Valley Bushveld in the Eastern Cape. The objective of this investigation was to develop a method of scoring bushveld according to its productive condition. It was established, through principal component analysis that, while bushveld condition is negatively related to the percentage of Lycium austrinum, it is positively related to tree density, foliage volume below 1,5m, the percentage of Portulacaria afra, Euphorbia spp. and Schotia afra. Furthermore, it was established that species such as Brachylaena ilicifolia, Rhigozum obovatum, Zygophyllum morgsana and Azima tetracantha are indicative of important differences within the Valley Bushveld. From these variables a tentative technique was developed to score the condition of Valley Bushveld.Keywords: azima tetracantha; brachylaena ilicifolia; Browse; Cluster analysis; Eastern Cape; euphorbia; method; portulacaria; portulacaria afra; Principal component analysis; rhigozum obovatum; schotia afra; south africa; Species composition; technique; Tree density; Valley Bushveld; Veld assessments; veld condition; Veld conditions; zygophyllum morgsanaJournal of the Grassland Society of Southern Africa