Pachycladon species evolved traits to adapt to New Zealand habitats : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatū, New Zealand

Figures are re-used with permission.The supplementary files in Appendix 2 may be made available on request to the Library.P. cheesemanii is a close relative of A. thaliana and is an allotetraploid perennial herb that is widespread in the South Island of New Zealand. It grows at altitudes of up to 1,000 m where it is subject to relatively high levels of UV-B radiation. However, to date the origin of this species and the mechanisms underlying its tolerance to its harsh living environmental conditions such as moderate–high UV-B radiation, cold and drought is unclear. To gain the first insights into how Pachycladon copes with UV-B stress, I sequenced the P. cheesemanii genome and compared the UV-B tolerance of plants from Wye Creek (~300-m altitude) and Kingston (~500-m altitude) with that of A. thaliana from Col-0 (~100-m altitude) and Kondara (1,000–1,100-m altitude). A high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologues. A synteny analysis involving genomes from other species of the Brassicaceae family suggested that the two subgenomes of P. cheesemanii may have the same origin as species from Brassicaceae Lineage I and EII. While UV-B radiation caused greater growth reduction in A. thaliana Col-0 and Kondara than in P. cheesemanii Wye Creek, growth was not reduced in P. cheesemanii Kingston. Homologues of the A. thaliana UV-B radiation response genes have multiple copies in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii Wye Creek and Kingston may differ from that in A. thaliana. Although the P. cheesemanii genome shows close similarity with that of A. thaliana, the uniqueness of the strongly UV-B-induced UVR8-independent pathway in P. cheesemanii may help this species to tolerate relatively high UV-B radiation. Next, to understand the different stress responses of A. thaliana and P. cheesemanii, I designed a project to build multiple-stress transcriptomes for A. thaliana and P. cheesemanii. Since plant responses to salt and drought are related and have overlapping mechanisms, and salt stress can easily be applied in the laboratory, high salinity rather than drought stress was used to stress A. thaliana and P. cheesemanii plants in this study. Transcriptomes of A. thaliana and P. cheesemanii plants in response to cold, salt and UV-B radiation stresses were created. A high-quality de novo transcriptome assembly of allopolyploid P. cheesemanii was obtained by using multiple assemblers with further downstream processing. Differential expression analysis revealed a strong bias, in terms of the number of DEGs, towards upregulation in both A. thaliana and P. cheesemanii in responding to salt stress, as well as in P. cheesemanii’s cold and UV-B treatment responses. Meanwhile, in each species, a number of DEGs was shared between stresses, although the majority were unique in responding to each stress in upregulation and downregulation, respectively. Further, GO enrichment analysis revealed that these responsive genes were involved in some biological processes shared by A. thaliana and P. cheesemanii. Immune system processes, response to stimuli, signalling, developmental processes, growth, negative regulation of biological processes, multi-organism processes, biological regulation, secondary metabolic processes, cell communication, and cellular aromatic compound metabolic processes were common in the responses of both A. thaliana and P. cheesemanii to all three stresses. In both A. thaliana and P. cheesemanii, a number of these biological processes were also stress specific. First of all, in A. thaliana, cold stress may easily affect photomorphogenesis in cold responses, while the majority of the P. cheesemanii unique cold responses occurred in root differentiation, floral whorl development and regulation of programmed cell death. Second, A. thaliana responses to salt stress affected starch metabolism and lipid modification, whereas disaccharide and polysaccharide metabolism, as well as microtubule structure, were affected by salt stress uniquely in P. cheesemanii. Finally, A. thaliana responses to UV-B radiation involved a combination of physical and biological defences, including cell wall modification defence, stomatal movement, vitamin B6 metabolic processes and oxygen metabolic processes. In contrast, seed germination biological regulation was affected in P. cheesemanii under UV-B radiation stress. Further, P. cheesemanii had a larger number of unique GO enrichments in cold responses than did A. thaliana. There was a wide range of crosstalk among the biological processes in responding to the three stresses in A. thaliana, while only one main cluster was identified in crosstalk for the three stress responses in P. cheesemanii. In this main cluster, the biosynthetic process for anthocyanins was in the centre position, and it was found that multiple stress-responsive biological processes probably involved anthocyanins in P. cheesemanii. Thus, although the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies such as a highly UV-B-activated UVR8-independent pathway, allowing the plant to tolerate relatively high UV-B radiation. The stress process is highly conserved in plant species under various stresses, but species also develop a few unique characteristics that may help them adapt to their own ecological niche and survive particular environmental stresses

R&D modes and firm performance in high-tech companies: A research based on cross-boundary ambidexterity and network structures

This paper draws on the cross-boundary ambidexterity theory to propose that four different R&D modes impact firm performance differently and that cooperative network structure moderates the above relationships. The theoretical model is tested by using financial and patent data of 587 high-tech firms for 10 consecutive years in China. We find that different R&D modes have different impacts on a firm’s financial and innovative performance, and network structure plays different moderating roles. Practically, this work guides high-tech enterprises to optimize their resource allocation, select the most appropriate R&D mode, and establish efficient cooperative networks

Gut microbiome: A potential indicator for predicting treatment outcomes in major depressive disorder

The therapeutic outcomes in major depressive disorder (MDD), one of the most common and heterogeneous mental illnesses, are affected by factors that remain unclear and often yield unsatisfactory results. Herein, we characterized the composition and metabolic function of the gut microbiota of patients with MDD during antidepressant treatment, based on 16S rRNA sequencing and metabolomics. The microbial signatures at baseline differed significantly between responder and non-responder groups. The gut microbiota of the non-responder group was mainly characterized by increased relative abundances of the phylum Actinobacteria, families Christensenellaceae and Eggerthellaceae, and genera Adlercreutzia and Christensenellaceae R7 group compared to that of the responder group. Additionally, the gut microbiota composition of the responder and non-responder groups differed significantly before and after treatment, especially at the genus level. Moreover, 20 differential metabolites between the responder and non-responder groups were identified that were mainly involved in lipid metabolism (cholestane steroids and steroid esters). Eggerthellaceae and Adlercreutzia displayed strong co-occurrence relationships with certain metabolites, suggesting alternations in the gut microbiome, and associated metabolites may be potential mediators of successful antidepressant treatment. Overall, our study demonstrates that alterations in gut microbiota composition and metabolic function might be relevant to the response to antidepressants, thereby providing insight into mechanisms responsible for their efficacy

Atherosclerosis T1-weighted characterization (CATCH): evaluation of the accuracy for identifying intraplaque hemorrhage with histological validation in carotid and coronary artery specimens

Background: Coronary high intensity plaques (CHIPs) detected using cardiovascular magnetic resonance (CMR) coronary atherosclerosis T1-weighted characterization with integrated anatomical reference (CATCH) have been shown to be positively associated with high-risk morphology observed on intracoronary optical coherence tomography (OCT). This study sought to validate whether CHIPs detected on CATCH indicate the presence of intraplaque hemorrhage (IPH) through ex vivo imaging of carotid and coronary plaque specimens, with histopathology as the standard reference. Methods: Ten patients scheduled to undergo carotid endarterectomy underwent CMR with the conventional T1-weighted (T1w) sequence. Eleven carotid atherosclerotic plaques removed at carotid endarterectomy and six coronary artery endarterectomy specimens removed from patients undergoing coronary artery bypass grafting (CABG) were scanned ex vivo using both the conventional T1w sequence and CATCH. Both in vivo and ex vivo images were examined for the presence of IPH. The sensitivity, specificity, and Cohen Kappa (k) value of each scan were calculated using matched histological sections as the reference. k value between each scan in the discrimination of IPH was also computed. Results: A total of 236 in vivo locations, 328 ex vivo and matching histology locations were included for the analysis. Sensitivity, specificity, and k value were 76.7%, 95.3%, and 0.75 for in vivo T1w imaging, 77.2%, 97.4%, and 0.78 for ex vivo T1w imaging, and 95.0%, 92.1%, and 0.84 for ex vivo CATCH, respectively. Moderate agreement was reached between in vivo T1w imaging, ex vivo T1w imaging, and ex vivo CATCH for the detection of IPH: between in vivo T1w imaging and ex vivo CATCH (k = 0.68), between ex vivo T1w imaging and ex vivo CATCH (k = 0.74), between in vivo T1w imaging and ex vivo T1w imaging (k = 0.83). None of the coronary artery plaque locations showed IPH. Conclusion: This study demonstrated that carotid CHIPs detected by CATCH can be used to assess for IPH, a high-risk plaque feature

Differential Gene Expression and Adherence of Escherichia coli O157:H7 In Vitro and in Ligated Pig Intestines

BACKGROUND: Escherichia coli O157:H7 strain 86-24 grown in MacConkey broth (MB) shows almost no adherence to cultured epithelial cells but adheres well in pig ligated intestines. This study investigated the mechanisms associated with the difference between in-vitro and in-vivo adherence of the MB culture. METHODOLOGY/PRINCIPAL FINDINGS: It was found that decreased adherence in vitro by bacteria grown in MB was mainly due to lactose, possibly implicating the involvement of carbon catabolite repression (CCR). Expression of selected virulence-related genes associated with adherence and CCR was then examined by quantitative PCR. When bacteria were grown in MB and Brain Heart Infusion with NaHCO(3) (BHIN) plus lactose, pH was reduced to 5.5-5.9 and there was a significant decrease in expression of the locus of enterocyte effacement (LEE) genes eae, tir, espD, grlA/R and ler, and an increase in cya (cAMP), and two negative regulators of the LEE, gadE and hfq. Putative virulence genes stcE, hlyA, ent and nleA were also decreased in vitro. Reversal of these changes was noted for bacteria recovered from the intestine, where transcripts for qseF and fis and putative virulence factors AidA(15), TerC and Ent/EspL2 were significantly increased, and transcripts for AIDA(48), Iha, UreC, Efa1A, Efa1B, ToxB, EhxA, StcE, NleA and NleB were expressed at high levels. CONCLUSIONS/SIGNIFICANCE: Presence of lactose resulted in decreased expression of LEE genes and the failure of EHEC O157:H7 to adhere to epithelial cells in vitro but this repression was overcome in vivo. CCR and/or acidic pH may have played a role in repression of the LEE genes. Bacterial pathogens need to integrate their nutritional metabolism with expression of virulence genes but little is known of how this is done in E. coli O157:H7. This study indicates one aspect of the subject that should be investigated further

A Generalized Alternating Linearization Bundle Method for Structured Convex Optimization with Inexact First-Order Oracles

In this paper, we consider a class of structured optimization problems whose objective function is the summation of two convex functions: f and h, which are not necessarily differentiable. We focus particularly on the case where the function f is general and its exact first-order information (function value and subgradient) may be difficult to obtain, while the function h is relatively simple. We propose a generalized alternating linearization bundle method for solving this class of problems, which can handle inexact first-order information of on-demand accuracy. The inexact information can be very general, which covers various oracles, such as inexact, partially inexact and asymptotically exact oracles, and so forth. At each iteration, the algorithm solves two interrelated subproblems: one aims to find the proximal point of the polyhedron model of f plus the linearization of h; the other aims to find the proximal point of the linearization of f plus h. We establish global convergence of the algorithm under different types of inexactness. Finally, some preliminary numerical results on a set of two-stage stochastic linear programming problems show that our method is very encouraging

Hyperspectral Target Detection via Adaptive Information—Theoretic Metric Learning with Local Constraints

By using the high spectral resolution, hyperspectral images (HSIs) provide significant information for target detection, which is of great interest in HSI processing. However, most classical target detection methods may only perform well based on certain assumptions. Simultaneously, using limited numbers of target samples and preserving the discriminative information is also a challenging problem in hyperspectral target detection. To overcome these shortcomings, this paper proposes a novel adaptive information-theoretic metric learning with local constraints (ITML-ALC) for hyperspectral target detection. The proposed method firstly uses the information-theoretic metric learning (ITML) method as the objective function for learning a Mahalanobis distance to separate similar and dissimilar point-pairs without certain assumptions, needing fewer adjusted parameters. Then, adaptively local constraints are applied to shrink the distances between samples of similar pairs and expand the distances between samples of dissimilar pairs. Finally, target detection decision can be made by considering both the threshold and the changes between the distances before and after metric learning. Experimental results demonstrate that the proposed method can obviously separate target samples from background ones and outperform both the state-of-the-art target detection algorithms and the other classical metric learning methods