Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.

Meristem-Specific Suppression of Mitosis and a Global Switch in Gene Expression in the Root Cap of Pea by Endogenous Signals1

Two functionally distinct sets of meristematic cells exist within root tips of pea (Pisum sativum): the root apical meristem, which gives rise to the body of the root; and the root cap meristem, which gives rise to cells that differentiate progressively through the cap and separate ultimately from its periphery as border cells. When a specific number of border cells has accumulated on the root cap periphery, mitosis within the root cap meristem, but not the apical meristem, is suppressed. When border cells are removed by immersion of the root tip in water, a transient induction of mitosis in the root cap meristem can be detected starting within 5 min. A corresponding switch in gene expression throughout the root cap occurs in parallel with the increase in mitosis, and new border cells begin to separate from the root cap periphery within 1 h. The induction of renewed border cell production is inhibited by incubating root tips in extracellular material released from border cells. The results are consistent with the hypothesis that operation of the root cap meristem and consequent turnover of the root cap is self-regulated by a signal from border cells.

Network reconstruction using knock-out and over-expression data

This paper outlines necessary and sufficient conditions for network reconstruction of linear, time-invariant systems using data from either knock-out or over-expression experiments. These structural system perturbations, which are common in biological experiments, can be formulated as unknown system inputs, allowing the network topology and dynamics to be found. We assume that only partial state measurements are available and propose an algorithm that can reconstruct the network at the level of the measured states using either time-series or steady-state data. A simulated example illustrates how the algorithm successfully reconstructs a network from data. © 2013 EUCA.

MicroRNAs in pathology and as therapeutic target in gene therapy?

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas Moniz

Monitoring changes in thioredoxin and over-oxidised peroxiredoxin in response to exercise in humans

Introduction. Peroxiredoxin (PRDX) and thioredoxin (TRX) are antioxidant proteins that control cellular signalling and redox balance, although their response to exercise is unknown. This study aimed to assess key aspects of the PRDX-TRX redox cycle in response to three different modes of exercise. Methods. Healthy males (n = 10, mean ± SD: 22 ± 3 yrs) undertook three exercise trials on separate days: two steady-state cycling trials at moderate (60% VO2MAX; 27 min, MOD) and high (80% VO2MAX; 20 min, HIGH) intensities, and a low-volume high-intensity interval training trial (10 × 1 min 90% VO2MAX, LV-HIIT). Peripheral blood mononuclear cells were assessed for TRX-1 and over-oxidised PRDX (isoforms I-IV) protein expression before, during, and 30 min following exercise (post + 30). The activities of TRX reductase (TRX-R) and the nuclear factor kappa B (NF-κB) p65 subunit were also assessed. Results. TRX-1 increased during exercise in all trials (MOD, + 84.5%; HIGH, + 64.1%; LV-HIIT, + 205.7%; p < 05), whereas over-oxidised PRDX increased during HIGH only (MOD, - 28.7%; HIGH, + 202.9%; LV-HIIT, - 22.7%; p < .05). TRX-R and NF-κB p65 activity increased during exercise in all trials, with the greatest response in TRX-R activity seen in HIGH (p < 0.05). Discussion. All trials stimulated a transient increase in TRX-1 protein expression during exercise. Only HIGH induced a transient over-oxidation of PRDX, alongside the greatest change in TRX-R activity. Future studies are needed to clarify the significance of heightened peroxide exposure during continuous high-intensity exercise and the mechanisms of PRDX-regulatory control.

Identification of differentially expressed genes associated with pathogen-host interaction in 'Villard Blanc' and its expression analysis in grapevine cultivars resistant and susceptible to downy mildew.

2011

EXPERIMENTAL INVESTIGATION OF FOLDED PLATE GIRDERS AND SLAB JOINTS USED IN MODULAR CONSTRUCTION

The folded plate girder, a newly proposed bridge girder, is investigated through this thesis. The folded plate girder is cold bent out of a single sheet of steel. The cold bending eliminates the costly and inconsistent shop welds found in traditional girders. The folded plate girder is meant for application in short span bridges. The girder was subjected to an equivalent 75 year lifetime loading to investigate the fatigue performance. The rebar detail used in the closure region between adjacent slabs has been investigated in the past by the NCHRP 12-68 project. This thesis will proposes a hooked rebar detail as a cost effective alternative to the previously recommended headed rebar detail. The proposed hooked rebar detail looks to improve upon the headed bar detail by increasing the clear cover, and reducing the cost of fabrication and shipment of the rebar. Six specimens containing closure regions are subjected to both positive and negative moment loading in order to investigate their behavior and failure modes under ultimate load.

Antibiotic susceptibility patterns and resistance genes of starter cultures and probiotic bacteria used in food

A survey of starter and probiotic cultures was carried out to determine the current antibiotic resistance situation in microbial food additives in Switzerland. Two hundred isolates from 90 different sources were typed by molecular and other methods to belong to the genera Lactobacillus (74 samples), Staphylococcus (33 samples), Bifidobacterium (6 samples), Pediococcus (5 samples), or were categorized as lactococci or streptococci (82 samples). They were screened for phenotypic resistances to 20 antibiotics by the disk diffusion method. Twenty-seven isolates exhibiting resistances that are not an intrinsic feature of the respective genera were further analyzed by microarray hybridization as a tool to trace back phenotypic resistances to specific genetic determinants. Their presence was finally verified by PCR amplification or Southern hybridization. These studies resulted in the detection of the tetracycline resistance gene tet(K) in 5 Staphylococcus isolates used as meat starter cultures, the tetracycline resistance gene tet(W) in the probiotic cultures Bifidobacterium lactis DSM 10140 and Lactobacillus reuteri SD 2112 (residing on a plasmid), and the lincosamide resistance gene lnu(A) (formerly linA) in L. reuteri SD 2112.

Efficiency and catch dynamics of collapsible square and conical pots used in the red king crab (Paralithodes camtschaticus) fishery

We compared the capture efficiency and catch dynamics of collapsible square and conical pots used in resource assessment and harvesting of red king crabs (Paralithodes camtschaticus [Tilesius, 1815]) in the Barents Sea. After two days of soaking, square pots caught three times as many crabs as conical pots, and their catches consisted of a higher proportion of male crabs and male crabs larger than 160 mm carapace length compared to the catches in the conical pots. Catches in the square pots did not increase as soak times were increased beyond two days, which indicates equilibrium between the rate of entries into and the rate of exits from the pots. Catches in conical pots, however, increased with increasing soak times up to eight days, the longest soak time examined in this study. These findings demonstrate the higher efficiency of square pots and the importance of understanding catch dynamics when making population assessments based on catchper-unit-of-effort data. The favorable catch characteristics and handling properties of the collapsible square pot may make this pot design suitable for other crab fisheries, as well.

Chemical effects of cationic surfactant and anionic surfactant used in organically modified montmorillonites on degradation and fire retardancy of polyamide 12 nanocomposites

Three kinds of organically modified Na+-montmorillonites (OMMTs), including two kinds of octadecylammonium modified montmorillonite with different contents of octadecylammonium and a kind of sodium dodecylsulfonate (SDSo) modified montmorillonite, were used to prepare polyamide 12 (PA12)/OMMT nanocomposites. Effects of the modifiers on degradation and fire retardancy of PA12/OMMT nanocomposites were investigated. Acid sites formed in cationic surfactant modified MMT via Hoffman decomposition could accelerate degradation of PA12 at high temperature. However, catalytic effect of the acid sites on carbonization of the degradation products promoted char barrier formation, which reduced heat release rate (HRR). Higher content of cationic surfactant in OMMT is beneficial to fire retardancy of PA12 nanocomposites and the dispersion states of OMMT have assistant effects. In contrast, Na+-montmorillonite (Na-MMT) and anionic surfactant modified MMT (a-MMT) could not form acid sites on the MMT layers; in this case, fire retardancy of PA12/Na-MMT appears to have no improvement and PA12/a-MMT appears to have limited improvement.

Sensory information and associative cues used in food detection by wild vervet monkeys.

Understanding animals' spatial perception is a critical step toward discerning their cognitive processes. The spatial sense is multimodal and based on both the external world and mental representations of that world. Navigation in each species depends upon its evolutionary history, physiology, and ecological niche. We carried out foraging experiments on wild vervet monkeys (Chlorocebus pygerythrus) at Lake Nabugabo, Uganda, to determine the types of cues used to detect food and whether associative cues could be used to find hidden food. Our first and second set of experiments differentiated between vervets' use of global spatial cues (including the arrangement of feeding platforms within the surrounding vegetation) and/or local layout cues (the position of platforms relative to one another), relative to the use of goal-object cues on each platform. Our third experiment provided an associative cue to the presence of food with global spatial, local layout, and goal-object cues disguised. Vervets located food above chance levels when goal-object cues and associative cues were present, and visual signals were the predominant goal-object cues that they attended to. With similar sample sizes and methods as previous studies on New World monkeys, vervets were not able to locate food using only global spatial cues and local layout cues, unlike all five species of platyrrhines thus far tested. Relative to these platyrrhines, the spatial location of food may need to stay the same for a longer time period before vervets encode this information, and goal-object cues may be more salient for them in small-scale space.