8 research outputs found
A new broccoli × broccoli immortal mapping population and framework genetic map: tools for breeders and complex trait analysis
No full textA unique broccoli x broccoli doubled haploid (DH) population has been created from the F-1 of a cross between two DH broccoli lines derived from cultivars Green Duke and Marathon. We genotyped 154 individuals from this population with simple sequence repeat and amplified fragment length polymorphism markers to create a B. oleracea L. var. italica 'intra-crop' specific framework linkage map. The map is composed of nine linkage groups with a total length of 946.7 cM. Previous published B. oleracea maps have been constructed using diverse crosses between morphotypes of B. oleracea; this map therefore represents a useful breeding resource for the dissection of broccoli specific traits. Phenotype data have been collected from the population over five growing seasons; the framework linkage map has been used to locate quantitative trait loci for agronomically important broccoli traits including head weight (saleable yield), head diameter, stalk diameter, weight loss and relative weight loss during storage, as well as traits for broccoli leaf architecture. This population and associated linkage map will aid breeders to directly map agronomically important traits for the improvement of elite broccoli cultivars
General runner removal and the Mullineux map
No full textAbstractWe prove a new ‘runner removal theorem’ for q-decomposition numbers of the level 1 Fock space of type Ae−1(1), generalising earlier theorems of James–Mathas and the author. By combining this with another theorem relating to the Mullineux map, we show that the problem of finding all q-decomposition numbers indexed by partitions of a given weight is a finite computation
Double haploids, markers and QTL analysis in vegetable brassicas
No full textDouble haploid (DH) plants of Brassica spp. can be produced via anther culture or culture of microspores. This paper reviews the uses of double haploids in crop improvement research in vegetable brassicas (B. oleracea). Applications of DH lines are described for breeding; construction of linkage maps; genetic analysis of quantitative traits and capturing genetic variation. The advantages and disadvantages of DH lines are discussed
Presepsin as a diagnostic and prognostic biomarker of severe bacterial infections and COVID-19
No full textWe aimed to develop presepsin as a marker of diagnosis of severe infections of either bacterial and viral origin. The derivation cohort was recruited from 173 hospitalized patients with acute pancreatitis or post-operative fever or infection suspicion aggravated by at least one sign of the quick sequential organ failure assessment (qSOFA). The first validation cohort was recruited from 57 admissions at the emergency department with at least one qSOFA sign and the second validation cohort from 115 patients with COVID-19 pneumonia. Presepsin was measured in plasma by the PATHFAST assay. Concentrations more than 350 pg/ml had sensitivity 80.2% for sepsis diagnosis in the derivation cohort (adjusted odds ratio 4.47; p < 0.0001). In the derivation cohort, sensitivity for 28-day mortality prognosis was 91.5% (adjusted odds ratio 6.82; p: 0.001). Concentrations above 350 pg/ml had sensitivity 93.3% for the diagnosis of sepsis in the first validation cohort; this was 78.3% in the second validation cohort of COVID-19 aiming at the early diagnosis of acute respiratory distress syndrome necessitating mechanical ventilation. The respective sensitivity for 28-day mortality was 85.7% and 92.3%. Presepsin may be a universal biomarker for the diagnosis of severe infections of bacterial origin and prediction of unfavorable outcome. © 2023, The Author(s)
The Cyclotomic Birman-Murakami-Wenzl Algebras
No full textThis thesis presents a study of the cyclotomic BMW algebras, introduced by Haring-Oldenburg as a generalization of the BMW (Birman-Murakami-Wenzl) algebras related to the cyclotomic Hecke algebras of type G(k,1,n) (also known as Ariki-Koike algebras) and type B knot theory involving affine/cylindrical tangles. The motivation behind the definition of the BMW algebras may be traced back to an important problem in knot theory; namely, that of classifying knots (and links) up to isotopy. The algebraic definition of the BMW algebras uses generators and relations originally inspired by the Kauffman link invariant. They are intimately connected with the Artin braid group of type A, Iwahori-Hecke algebras of type A, and with many diagram algebras, such as the Brauer and Temperley-Lieb algebras. Geometrically, the BMW algebra is isomorphic to the Kauffman Tangle algebra. The representations and the cellularity of the BMW algebra have now been extensively studied in the literature. These algebras also feature in the theory of quantum groups, statistical mechanics, and topological quantum field theory. In view of these relationships between the BMW algebras and several objects of "type A", several authors have since naturally generalized the BMW algberas for other types of Artin groups. Motivated by knot theory associated with the Artin braid group of type B, Haring-Oldenburg introduced the cyclotomic BMW algebras B_n^k as a generalization of the BMW algebras such that the Ariki-Koike algebra h_{n,k} is a quotient of B_n^k, in the same way the Iwahori-Hecke algebra of type A is a quotient of the BMW algebra. In this thesis, we investigate the structure of these algebras and show they have a topological realization as a certain cylindrical analogue of the Kauffman Tangle algebra. In particular, they are shown to be R-free of rank k^n (2n-1)!! and bases that may be explicitly described both algebraically and diagrammatically in terms of cylindrical tangles are obtained. Unlike the BMW and Ariki-Koike algebras, one must impose extra so-called "admissibility conditions" on the parameters of the ground ring in order for these results to hold. This is due to potential torsion caused by the polynomial relation of order k imposed on one of the generators of B_n^k. It turns out that the representation theory of B_2^k is crucial in determining these conditions precisely. The representation theory of B_2^k is analysed in detail in a joint preprint with Wilcox in [45] (http://arxiv.org/abs/math/0611518). The admissibility conditions and a universal ground ring with admissible parameters are given explicitly in Chapter 3. The admissibility conditions are also closely related to the existence of a non-degenerate Markov trace function of B_n^k which is then used together with the cyclotomic Brauer algebras in the linear independency arguments contained in Chapter 4. Furthermore, in Chapter 5, we prove the cyclotomic BMW algebras are cellular, in the sense of Graham and Lehrer. The proof uses the cellularity of the Ariki-Koike algebras (Graham-Lehrer [16] and Dipper-James-Mathas [8]) and an appropriate "lifting" of a cellular basis of the Ariki-Koike algebras into B_n^k, which is compatible with a certain anti-involution of B_n^k. When k = 1, the results in this thesis specialize to those previously established for the BMW algebras by Morton-Wasserman [30], Enyang [9], and Xi [47]. REMARKS: During the writing of this thesis, Goodman and Hauschild-Mosley also attempt similar arguments to establish the freeness and diagram algebra results mentioned above. However, they withdrew their preprints ([14] and [15]), due to issues with their generic ground ring crucial to their linear independence arguments. A similar strategy to that proposed in [14], together with different trace maps and the study of rings with admissible parameters in Chapter 3, is used in establishing linear independency of our basis in Chapter 4. Since the submission of this thesis, new versions of these preprints have been released in which Goodman and Hauschild-Mosley use alternative topological and Jones basic construction theory type arguments to establish freeness of B_n^k and an isomorphism with the cyclotomic Kauffman Tangle algebra. However, they require their ground rings to be an integral domain with parameters satisfying the (slightly stronger) admissibility conditions introduced by Wilcox and the author in [45]. Also, under these conditions, Goodman has obtained cellularity results. Rui and Xu have also obtained freeness and cellularity results when k is odd, and later Rui and Si for general k, under the assumption that \delta is invertible and using another stronger condition called "u-admissibility". The methods and arguments employed are strongly influenced by those used by Ariki, Mathas and Rui [3] for the cyclotomic Nazarov-Wenzl algebras and involve the construction of seminormal representations; their preprints have recently been released on the arXiv. It should also be noted there are slight differences between the definitions of cyclotomic BMW algebras and ground rings used, as explained partly above. Furthermore, Goodman and Rui-Si-Xu use a weaker definition of cellularity, to bypass a problem discovered in their original proofs relating to the anti-involution axiom of the original Graham-Lehrer definition. This Ph.D. thesis, completed at the University of Sydney, was submitted September 2007 and passed December 2007
The transcriptome of Populus in elevated CO2 reveals increased anthocyanin biosynthesis during delayed autumnal senescence
No full textThe delay in autumnal senescence that has occurred in recent decades has been linked to rising temperatures. Here, we suggest that increasing atmospheric CO2 may partly account for delayed autumnal senescence and for the first time, through transcriptome analysis, identify gene expression changes associated with this delay.Using a plantation of Populus × euramericana grown in elevated [CO2] (e[CO2]) with free-air CO2 enrichment (FACE) technology, we investigated the molecular and biochemical basis of this response. A Populus cDNA microarray was used to identify genes representing multiple biochemical pathways influenced by e[CO2] during senescence. Gene expression changes were confirmed through real-time quantitative PCR, and leaf biochemical assays.Pathways for secondary metabolism and glycolysis were significantly up-regulated by e[CO2] during senescence, in particular, those related to anthocyanin biosynthesis. Expressed sequence tags (ESTs) representing the two most significantly up-regulated transcripts in e[CO2], LDOX (leucoanthocyanidin dioxgenase) and DFR (dihydroflavonol reductase), gave (e[CO2]/ambient CO2 (a[CO2])) expression ratios of 39.6 and 19.3, respectively.We showed that in e[CO2] there was increased autumnal leaf sugar accumulation and up-regulation of genes determining anthocyanin biosynthesis which, we propose, prolongs leaf longevity during natural autumnal senescence.<br/
The function and origin of the CD4+ T cell in the classical Hodgkin lymphoma microenvironment
No full textPhDClassical Hodgkin lymphoma (CHL) is a germinal centre B cell malignancy where the bulk of the tumour comprises a non-clonal immune infiltrate enriched for CD4+ T cells. The role of these cells in the pathophysiology of CHL is poorly understood. Biomarkers predictive of clinical outcome in CHL are limited. This thesis examines microenvironment biomarkers with the goal of identifying the 10-20% of patients who are not cured by conventional therapy, and also investigates the function of the CD4+ T cell in CHL.
The prognostic power of FOXP3, a marker of regulatory T cells, CD68, a macrophage marker and CD20, a B cell marker, is validated in a new patient cohort and for the first time CD68 and FOXP3 are combined in a statistically robust scoring system. The data presented challenge the assumption that the microenvironment is Th2-polarised or senescent and demonstrates relative over-expression of T-BET, a Th1 marker and under-expression of PD1, a marker of senescence/exhaustion, with little evidence for Th2 marker expression. A cytokine-enriched in vitro culture system was developed demonstrating superior proliferation and longevity of CHL-derived T cells compared to non-malignant tissue-derived controls. These cells sustain expression of markers associated with proliferation and longevity (e.g. CD27, CD28) and remain functional (express cytokines) for many weeks. A panel of CD4+ T cell-specific markers was determined capable of differentiating CHL-derived from non-malignant or non-Hodgkin lymphoma-derived CD4+ T cells, in which markers of central memory (CD62L and CCR7) and early activation (CD69) are over-represented and markers of senescence (CD57 and PD1) are under-represented. Cytokine profiles were found to resemble Th1 (expression of IL2, IFN- and TNF expression) rather than Th2 (IL4, IL13, IL21, IL10 and IL6) responses.
The data presented confirm a new prognostic biomarker signature and show a Th1 rather than Th2-dominated microenvironment enriched for cytokine-secreting functional effector CD4+ T cells and long-lived, proliferative cells resembling central memory cells rather than hypoproliferative, anergic, non-functional T cells
