Controlling the Reactivity of Silicate and Aluminate Glasses in Aqueous Alkaline Environments

Production of cement, the binder component of concrete, accounts for an estimated 9% of global CO2 emissions. To improve sustainability of cement and concrete use, two strategies have emerged: (1) to consume less cement by partially replacing it with supplementary cementing materials (SCMs), or (2) to consume less concrete by improving its durability (e.g., as hindered by reactive aggregates). Many such SCMs and reactive aggregates are well-represented as amorphous aluminosilicates. The current research investigates simplified metrics that reflect the composition and structure of these aluminosilicates while enabling prediction of their aqueous reactivity in alkaline environments, and the associated impact on cement paste and mortar properties. New means to control aluminosilicate reactivity are developed, alongside improved understandings that will aid in the future use of data-driven learning tools to study and solve similar material problems

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

$\textbf{BACKGROUND}$: The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - "Immunoseq". $\textbf{RESULTS}$: We performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations. $\textbf{CONCLUSIONS}$: We show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells.This work was supported by grants from the Canadian Institute of Health Research (CIHR), the UK Medical Research Council (G1100125), the Swedish Research Council (DO283001) and Knut and Alice Wallenberg Foundation (KAW). We also acknowledge the use of subjects from the Cambridge BioResource and the support of the Cambridge NIHR Biomedical Research Centre. AM was supported by the Fond de Recherche Santé Québec Doctoral training award. TP and CL holds a Canada Research Chair

A transcriptional timetable of autumn senescence

BACKGROUND: We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. RESULTS: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. CONCLUSIONS: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components

Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development

AGAMOUS clade genes encode MADS box transcription factors that have been shown to play critical roles in many aspects of flower and fruit development in angiosperms. Tomato possesses two representatives of this lineage, TOMATO AGAMOUS (TAG1) and TOMATO AGAMOUS-LIKE1 (TAGL1), allowing for an analysis of diversification of function after gene duplication. Using RNAi (RNA interference) silencing, transgenic tomato lines that specifically down-regulate either TAGL1 or TAG1 transcript accumulation have been produced. TAGL1 RNAi lines show no defects in stamen or carpel identity, but show defects in fruit ripening. In contrast TAG1 RNAi lines show defects in stamen and carpel development. In addition TAG1 RNAi lines produce red ripe fruit, although they are defective in determinacy and produce ectopic internal fruit structures. e2814, an EMS- (ethyl methane sulphonate) induced mutation that is temperature sensitive and produces fruit phenotypes similar to that of TAG1 RNAi lines, was also characterized. Neither TAG1 nor TAGL1 expression is disrupted in the e2814 mutant, suggesting that the gene corresponding to the e2814 mutant represents a distinct locus that is likely to be functionally downstream of TAG1 and TAGL1. Based on these analyses, possible modes by which these gene duplicates have diversified in terms of their functions and regulatory roles are discussed

Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus

Objectives: Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of systemic lupus erythematosus (SLE) and rheumatoid arthritis. A20 is a negative regulator of NF-κB but the role of its DUB domain and related genetic variants remain unclear. We aimed to study the functional effects of A20 DUB-domain alterations in immune cells and understand its link to SLE pathogenesis. Methods: CRISPR/Cas9 was used to generate human U937 monocytes with A20 DUB-inactivating C103A knock-in (KI) mutation. Whole genome RNA-sequencing was used to identify differentially expressed genes between WT and C103A KI cells. Functional studies were performed in A20 C103A U937 cells and in immune cells from A20 C103A mice and genotyped healthy individuals with A20 DUB polymorphism rs2230926. Neutrophil extracellular trap (NET) formation was addressed ex vivo in neutrophils from A20 C103A mice and SLE-patients with rs2230926. Results: Genetic disruption of A20 DUB domain in human and murine myeloid cells did not give rise to enhanced NF-κB signalling. Instead, cells with C103A mutation or rs2230926 polymorphism presented an upregulated expression of PADI4, an enzyme regulating protein citrullination and NET formation, two key mechanisms in autoimmune pathology. A20 C103A cells exhibited enhanced protein citrullination and extracellular trap formation, which could be suppressed by selective PAD4 inhibition. Moreover, SLE-patients with rs2230926 showed increased NETs and increased frequency of autoantibodies to citrullinated epitopes. Conclusions: We propose that genetic alterations disrupting the A20 DUB domain mediate increased susceptibility to SLE through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation