Probing the Architecture of the Budding Yeast Inner Kinetochore

Chromosome segregation must occur with fidelity to maintain genome stability and prevent aneuploid disorders. During segregation, the kinetochore is assembled onto centromeric DNA and achieves the attachment of microtubule plus ends, which provide the force to physically segregate chromosomes to opposite poles of the cell. The kinetochore is a macromolecular protein/DNA machine composed of 8-9 biochemical complexes, the DNA-binding components of which define the inner kinetochore, and the microtubule-binding components of which define the outer kinetochore. The 3D protein architecture of the inner kinetochore in living cells remains poorly understood due to the resolution limits of live-cell imaging techniques. Here, we use pairwise, in vivo fluorescence microscopy to determine the position of kinetochore components relative to the centromere specific histone H3 variant, Cse4, with nanometer resolution. In addition, we complement kinetochore focus analysis with DNA dynamics simulations to propose a connection between chromatin dynamics and the observed anisotropy of the inner kinetochore proteins, Ame1 and Cse4, relative to the outer kinetochore proteins, Ndc80 and Nuf2.Bachelor of Scienc

Identification of a selective G1-phase benzimidazolone inhibitor by a senescence-targeted virtual screen using artificial neural networks

Cellular senescence is a barrier to tumorigenesis in normal cells and tumour cells undergo senescence responses to genotoxic stimuli, which is a potential target phenotype for cancer therapy. However, in this setting, mixed-mode responses are common with apoptosis the dominant effect. Hence, more selective senescence inducers are required. Here we report a machine learning-based in silico screen to identify potential senescence agonists. We built profiles of differentially affected biological process networks from expression data obtained under induced telomere dysfunction conditions in colorectal cancer cells and matched these to a panel of 17 protein targets with confirmatory screening data in PubChem. We trained a neural network using 3517 compounds identified as active or inactive against these targets. The resulting classification model was used to screen a virtual library of ~2M lead-like compounds. 147 virtual hits were acquired for validation in growth inhibition and senescence-associated β-galactosidase (SA-β-gal) assays. Among the found hits a benzimidazolone compound, CB-20903630, had low micromolar IC50 for growth inhibition of HCT116 cells and selectively induced SA-β-gal activity in the entire treated cell population without cytotoxicity or apoptosis induction. Growth suppression was mediated by G1 blockade involving increased p21 expression and suppressed cyclin B1, CDK1 and CDC25C. Additionally, the compound inhibited growth of multicellular spheroids and caused severe retardation of population kinetics in long term treatments. Preliminary structure-activity and structure clustering analyses are reported and expression analysis of CB-20903630 against other cell cycle suppressor compounds suggested a PI3K/AKT-inhibitor-like profile in normal cells, with different pathways affected in cancer cells

Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents

Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors. Structure-based elaboration of these compounds enabled the development of a series with nanomolar affinities for fascin, good physicochemical properties and the ability to inhibit fascin-mediated bundling of filamentous actin. These compounds provide promising starting points for fascin-targeted anti-metastatic therapies

BCL11A enhancer edited hematopoietic stem cells persist in rhesus monkeys without toxicity

Gene editing of the erythroid-specific BCL11A enhancer in hematopoietic stem and progenitor cells (HSPCs) from sickle cell disease (SCD) patients induces fetal hemoglobin (HbF) without detectable toxicity as assessed by mouse xenotransplant. Here, we evaluated autologous engraftment and HbF induction potential of erythroid-specific BCL11A enhancer edited HSPCs in four non-human primates. We utilized a single guide RNA (sgRNA) with identical human and rhesus target sequences to disrupt a GATA1 binding site at the BCL11A +58 erythroid enhancer. Cas9 protein and sgRNA ribonucleoprotein complex (RNP) was electroporated into rhesus HSPCs, followed by autologous infusion after myeloablation. We found that gene edits persisted in peripheral blood (PB) and bone marrow (BM) for up to 101 weeks similarly for BCL11A enhancer or control locus (AAVS1) targeted cells. Biallelic BCL11A enhancer editing resulted in robust gamma-globin induction, with the highest levels observed during stress erythropoiesis. Indels were evenly distributed across PB and BM lineages. Off-target edits were not observed. Non-homologous end-joining repair alleles were enriched in engrafting HSCs. In summary, we find that edited HSCs can persist for at least 101 weeks post-transplant, and biallelic edited HSCs provide substantial HbF levels in PB red blood cells, together supporting further clinical translation of this approach

Modification and preservation of environmental signals in speleothems

Speleothems are primarily studied in order to generate archives of climatic change and results have led to significant advances in identifying and dating major shifts in the climate system. However, the climatological meaning of many speleothem records cannot be interpreted unequivocally; this is particularly so for more subtle shifts and shorter time periods, but the use of multiple proxies and improving understanding of formation mechanisms offers a clear way forward. An explicit description of speleothem records as time series draws attention to the nature and importance of the signal filtering processes by which the weather, the seasons and longer-term climatic and other environmental fluctuations become encoded in speleothems. We distinguish five sources of variation that influence speleothem geochemistry: atmospheric, vegetation/soil, karstic aquifer, primary speleothem crystal growth and secondary alteration and give specific examples of their influence. The direct role of climate diminishes progressively through these five factors. \ud \ud We identify and review a number of processes identified in recent and current work that bear significantly on the conventional interpretation of speleothem records, for example: \ud \ud 1) speleothem geochemistry can vary seasonally and hence a research need is to establish the proportion of growth attributable to different seasons and whether this varies over time. \ud \ud 2) whereas there has traditionally been a focus on monthly mean Ã�´18O data of atmospheric moisture, current work emphasizes the importance of understanding the synoptic processes that lead to characteristic isotope signals, since changing relative abundance of different weather types might 1Corresponding author, fax +44(0)1214145528, E-mail: [email protected] control their variation on the longer-term. \ud \ud 3) the ecosystem and soil zone overlying the cave fundamentally imprint the carbon and trace element signals and can show characteristic variations with time. \ud \ud 4) new modelling on aquifer plumbing allows quantification of the effects of aquifer mixing. \ud \ud 5) recent work has emphasized the importance and seasonal variability of CO2-degassing leading to calcite precipitation upflow of a depositional site on carbon isotope and trace element composition of speleothems. \ud \ud 6) Although much is known about the chemical partitioning between water and stalagmites, variability in relation to crystal growth mechanisms and kinetics is a research frontier. \ud \ud 7) Aragonite is susceptible to conversion to calcite with major loss of chemical information, but the controls on the rate of this process are obscure. \ud \ud Analytical factors are critical to generate high-resolution speleothem records. A variety of methods of trace element analysis are available, but standardization is a common problem with the most rapid methods. New stable isotope data on Irish stalagmite CC3 compares rapid laser-ablation techniques with the conventional analysis of micromilled powders and ion microprobe methods. A high degree of comparability between techniques for Ã�´18O is found on the mm-cm scale, but a previously described high-amplitude oxygen isotope excursion around 8.3 ka is identified as an analytical artefact related to fractionation of the laser-analysis associated with sample cracking. High-frequency variability of not less than 0.5o/oo may be an inherent feature of speleothem Ã�´18O records

Surface-atmosphere fluxes of volatile organic compounds in Beijing

Mixing ratios of volatile organic compounds (VOCs) were recorded in two field campaigns in central Beijing as part of the Air Pollution and Human Health in a Chinese Megacity (APHH) project. These data were used to calculate, for the first time in Beijing, the surface-atmosphere fluxes of VOCs using eddy covariance, giving a top-down estimation of VOC emissions from a central area of the city. The results were then used to evaluate the accuracy of the Multi-resolution Emission Inventory for China (MEIC). The APHH winter and summer campaigns took place in November and December 2016 and May and June 2017, respectively. The largest VOC fluxes observed were of small oxygenated compounds such as methanol, ethanol + formic acid and acetaldehyde, with average emission rates of 8.31±8.5, 3.97±3.9 and 1.83±2.0nmolm-2s-1, respectively, in the summer. A large flux of isoprene was observed in the summer, with an average emission rate of 5.31±7.7nmolm-2s-1. While oxygenated VOCs made up 60% of the molar VOC flux measured, when fluxes were scaled by ozone formation potential and peroxyacyl nitrate (PAN) formation potential the high reactivity of isoprene and monoterpenes meant that these species represented 30% and 28% of the flux contribution to ozone and PAN formation potential, respectively. Comparison of measured fluxes with the emission inventory showed that the inventory failed to capture the magnitude of VOC emissions at the local scale

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Low impact sampling of speleothems – reconciling scientific study with cave conservation

Speleothems are increasingly valued as important paleoclimate archives and yet the removal of samples from caves can come at a cost to natural heritage, impacting delicate environments with limited mechanisms for repair. Conservation of cave environments is a key responsibility for scientists and, with this in mind, we are working to develop and implement techniques that allow us to extract valuable scientific data, with minimal impact. In this study, we demonstrate the utility of low-impact reconnaissance dating surveys on caves in southern Tasmania and southwest Western Australia as a precursor to the removal of stalagmites for paleoclimate reconstruction. Small flakes of calcite were discretely extracted from the base and tip of fallen stalagmites and dated using U-Th techniques. We specifically targeted stalagmites that have naturally fallen or been previously broken by human interference, to further reduce our impact on the caves. This approach provides maximum and minimum age constraints for each stalagmite and valuable information of growth frequencies without the need to remove whole samples from the cave. Selecting the most appropriate samples to analyze based on reconnaissance ages greatly reduces the quantity of speleothem material to be removed from a cave to locate a desired interval of past time, mitigating the impacts of the research. Moreover, the reconnaissance age data enable us to build an archive of speleothem ages from the cave for future scientific research and to provide information on the age and nature of cave development, useful for cave management purposes and other studies. To assess the accuracy of this method we compared the reconnaissance age with the results of a detailed age evaluation on a small number of stalagmites removed from the caves. We have found this method to be effective and has allowed us to successfully identify several stalagmites suitable for our scientific objectives

Identification of a selective G1-phase benzimidazolone inhibitor by a senescence-targeted virtual screen using artificial neural networks

Microarray data for associated publication. Accession number in the Gene Expression Omnibus is GSE72621