Characterisation and mapping of gene Lr73 conferring seedling resistance to Puccinia triticina in common wheat

Key message

A gene conferring seedling resistance to Puccinia triticina was mapped to chromosome 2BS in the wheat Morocco. The gene was shown to be distinct and was therefore designated Lr73.

Abstract

The wheat genotype Morocco, widely susceptible to isolates of Puccinia triticina, was resistant to an Australian isolate of this pathogen collected in 2004. Genetic studies established that the resistance in Morocco was also present the Australian wheat genotypes Avocet, Halberd, Harrier, Tincurrin and a selection of cultivar Warigal lacking the resistance gene Lr20. Genetic studies based on a cross with Halberd showed that the gene is dominant and located on chromosome 2BS (XwPt8760—4 cM—Lr73—1.4 cM—XwPt8235). The gene was genetically independent of the Lr13, Lr16 and Lr23 loci, also located on chromosome 2BS, indicating that it is distinct. The locus designation Lr73 was therefore assigned. On the basis of multi-pathotype tests, it is likely Lr73 is also present in the Australian wheat cultivars Clearfield STL, Federation (with Lr10), Gatcher (with Lr10 and Lr27+Lr31), Marombi (with Lr1 and Lr37), Pugsley (with Lr1 and Lr37), Spear (with Lr1), Stiletto and Tarsa (with Lr1). Gene Lr73 is unlikely to be of value in resistance breeding. However, recognising Lr73 is important to avoid its inadvertent selection in breeding programmes. Furthermore, the apparent rarity of avirulence for genes like Lr73, sometimes referred to as “fossil” resistance genes, makes them of interest in terms of the evolution of disease resistance in host plants and of virulence in the respective rust pathogens.     

Performance of Transient Elastography for the Staging of Liver Fibrosis in Patients with Chronic Hepatitis B: A Meta-Analysis

Background

Transient elastography (TE), a non-invasive tool that measures liver stiffness, has been evaluated in meta-analyses for effectiveness in assessing liver fibrosis in European populations with chronic hepatitis C (CHC). However, these data cannot be extrapolated to populations in Asian countries, where chronic hepatitis B (CHB) is more prevalent. In this study, we performed a meta-analysis to assess the overall performance of TE for assessing liver fibrosis in patients with CHB.

Methods

Studies from the literature and international conference abstracts which enrolled only patients with CHB or performed a subgroup analysis of such patients were enrolled. Combined effects were calculated using area under the receiver operating characteristic curves (AUROC) and diagnostic accuracy values of each study.

Result

A total of 18 studies comprising 2,772 patients were analyzed. The mean AUROCs for the diagnosis of significant fibrosis (F2), severe fibrosis (F3), and cirrhosis (F4) were 0.859 (95% confidence interval [CI], 0.857–0.860), 0.887 (95% CI, 0.886–0.887), and 0.929 (95% CI, 0.928–0.929), respectively. The estimated cutoff for F2 was 7.9 (range, 6.1–11.8) kPa, with a sensitivity of 74.3% and specificity of 78.3%. For F3, the cutoff value was determined to be 8.8 (range, 8.1–9.7) kPa, with a sensitivity of 74.0% and specificity of 63.8%. The cutoff value for F4 was 11.7 (range, 7.3–17.5) kPa, with a sensitivity of 84.6% and specificity of 81.5%.

Conclusion

TE can be performed with good diagnostic accuracy for quantifying liver fibrosis in patients with CHB.     

Generation and Characterization of Human Heme Oxygenase-1 Transgenic Pigs

Xenotransplantation using transgenic pigs as an organ source is a promising strategy to overcome shortage of human organ for transplantation. Various genetic modifications have been tried to ameliorate xenograft rejection. In the present study we assessed effect of transgenic expression of human heme oxygenase-1 (hHO-1), an inducible protein capable of cytoprotection by scavenging reactive oxygen species and preventing apoptosis caused by cellular stress during inflammatory processes, in neonatal porcine islet-like cluster cells (NPCCs). Transduction of NPCCs with adenovirus containing hHO-1 gene significantly reduced apoptosis compared with the GFP-expressing adenovirus control after treatment with either hydrogen peroxide or hTNF-α and cycloheximide. These protective effects were diminished by co-treatment of hHO-1 antagonist, Zinc protoporphyrin IX. We also generated transgenic pigs expressing hHO-1 and analyzed expression and function of the transgene. Human HO-1 was expressed in most tissues, including the heart, kidney, lung, pancreas, spleen and skin, however, expression levels and patterns of the hHO-1 gene are not consistent in each organ. We isolate fibroblast from transgenic pigs to analyze protective effect of the hHO-1. As expected, fibroblasts derived from the hHO-1 transgenic pigs were significantly resistant to both hydrogen peroxide damage and hTNF-α and cycloheximide-mediated apoptosis when compared with wild-type fibroblasts. Furthermore, induction of RANTES in response to hTNF-α or LPS was significantly decreased in fibroblasts obtained from the hHO-1 transgenic pigs. These findings suggest that transgenic expression of hHO-1 can protect xenografts when exposed to oxidative stresses, especially from ischemia/reperfusion injury, and/or acute rejection mediated by cytokines. Accordingly, hHO-1 could be an important candidate molecule in a multi-transgenic pig strategy for xenotransplantation.     

Polymeric LabChip Real-Time PCR as a Point-of-Care-Potential Diagnostic Tool for Rapid Detection of Influenza A/H1N1 Virus in Human Clinical Specimens

It is clinically important to be able to detect influenza A/H1N1 virus using a fast, portable, and accurate system that has high specificity and sensitivity. To achieve this goal, it is necessary to develop a highly specific primer set that recognizes only influenza A viral genes and a rapid real-time PCR system that can detect even a single copy of the viral gene. In this study, we developed and validated a novel fluidic chip-type real-time PCR (LabChip real-time PCR) system that is sensitive and specific for the detection of influenza A/H1N1, including the pandemic influenza strain A/H1N1 of 2009. This LabChip real-time PCR system has several remarkable features: (1) It allows rapid quantitative analysis, requiring only 15 min to perform 30 cycles of real-time PCR. (2) It is portable, with a weight of only 5.5 kg. (3) The reaction cost is low, since it uses disposable plastic chips. (4) Its high efficiency is equivalent to that of commercially available tube-type real-time PCR systems. The developed disposable LabChip is an economic, heat-transferable, light-transparent, and easy-to-fabricate polymeric chip compared to conventional silicon- or glass-based labchip. In addition, our LabChip has large surface-to-volume ratios in micro channels that are required for overcoming time consumed for temperature control during real-time PCR. The efficiency of the LabChip real-time PCR system was confirmed using novel primer sets specifically targeted to the hemagglutinin (HA) gene of influenza A/H1N1 and clinical specimens. Eighty-five human clinical swab samples were tested using the LabChip real-time PCR. The results demonstrated 100% sensitivity and specificity, showing 72 positive and 13 negative cases. These results were identical to those from a tube-type real-time PCR system. This indicates that the novel LabChip real-time PCR may be an ultra-fast, quantitative, point-of-care-potential diagnostic tool for influenza A/H1N1 with a high sensitivity and specificity.     

Development of a deletion mutant of Pseudomonas denitrificans that does not degrade 3-hydroxypropionic acid

Pseudomonas denitrificans is a gram-negative bacterium that can produce vitamin B₁₂ under aerobic conditions. Recently, recombinant strains of P. denitrificans overexpressing a vitamin B₁₂-dependent glycerol dehydratase (DhaB) were developed to produce 3-hydroxypropionic acid (3-HP) from glycerol. The recombinant P. denitrificans could produce 3-HP successfully under aerobic conditions without an exogenous supply of vitamin B₁₂, but the 3-HP produced disappeared during extended cultivation due to the 3-HP degradation activity in this strain. This study developed mutant strains of P. denitrificans that do not degrade 3-HP. The following eight candidate enzymes, which might be responsible for 3-HP degradation, were selected, cloned, and studied for their activity in Escherichia coli: four (putative) 3-hydroxyisobutyrate dehydrogenases (3HIBDH), a putative 3-HP dehydrogenase (3HPDH), an alcohol dehydrogenase (ADH), and two choline dehydrogenases (CHDH). Among them, 3HIBDHI, 3HIBDHIV, and 3HPDH exhibited 3-HP degrading activity when expressed heterologously in E. coli. When 3hpdh alone or along with 3hibdhIV were disrupted from P. denitrificans, the mutant P. denitrificans exhibited greatly reduced 3-HP degradation activity that could not grow on 3-HP as the sole carbon and energy source. When the double mutant P. denitrificans Δ3hpdhΔ3hibdhIV was transformed with DhaB, an improved 3-HP yield (0.78 mol/mol) compared to that of the wild-type counterpart (0.45 mol/mol) was obtained from a 24-h flask culture. This study indicates that 3hpdh and 3hibdhIV (to a lesser extent) are mainly responsible for 3-HP degradation in P. denitrificans and their deletion can prevent 3-HP degradation during its production by recombinant P. denitrificans.     

Nitrogen biofiltration capacities and photosynthetic activity of Pyropia yezoensis Ueda (Bangiales,Rhodophyta): groundwork to validate its potential in integrated multi-trophic aquaculture (IMTA)

Porphyra spp. (currently Porphyra and Pyropia) are major sources of seafood globally. In this study, we investigated the effects of ammonium concentration, water temperature, and thallus stocking density on N-ammonium uptake rate (NUR), tissue nutrients content, N–NH₄ ⁺ filtration efficiency (NUE: nitrogen uptake efficiency %) of Pyropia yezoensis at a laboratory scale and in a mesoscale to evaluate the potential of this species as a biofilter. Additionally, photosynthetic activity was examined using Diving-PAM fluorometer to evaluate the health status. At a laboratory scale, the NUR and tissue nitrogen (N) content of P. yezoensis increased with increasing NH₄ ⁺ concentrations in the medium. The NUR at thallus stocking densities of 5 and 10 g fresh weight (FW) L^–1 were significantly higher than that at 20 g FW L^–1. Effective quantum yield (? F/F’ _m ) and tissue N content was significantly higher at all stocking densities than that at the beginning of experiment. The NUE was over 90 % at 10 and 17 °C, while all thalli cultured at 25 °C died after 5 days. In a mesoscale, the NUE at a thallus stocking density of 10.0 g FW L^–1 was significantly higher than that at a stocking density of 5.0 g FW L^–1. No differences in the NUE occurred between 10 °C and 17 °C. Photosynthetic activity (?F/F’_m and rETR_max) of P. yezoensis at optimal culture condition (10–12 °C and 10 g FW L^–1) increased over time through the experiment. This indicates that thallus was healthy during culture and chlorophyll a fluorescence can be as a monitoring tool for evaluating the physiological status of seaweeds in an integrated multi-trophic aquaculture.     

Whole-genome sequencing of matched primary and metastatic hepatocellular carcinomas

Background

To gain biological insights into lung metastases from hepatocellular carcinoma (HCC), we compared the whole-genome sequencing profiles of primary HCC and paired lung metastases.

Methods

We used whole-genome sequencing at 33X-43X coverage to profile somatic mutations in primary HCC (HBV+) and metachronous lung metastases (> 2 years interval).

Results

In total, 5,027-13,961 and 5,275-12,624 somatic single-nucleotide variants (SNVs) were detected in primary HCC and lung metastases, respectively. Generally, 38.88-78.49% of SNVs detected in metastases were present in primary tumors. We identified 65–221 structural variations (SVs) in primary tumors and 60–232 SVs in metastases. Comparison of these SVs shows very similar and largely overlapped mutated segments between primary and metastatic tumors. Copy number alterations between primary and metastatic pairs were also found to be closely related. Together, these preservations in genomic profiles from liver primary tumors to metachronous lung metastases indicate that the genomic features during tumorigenesis may be retained during metastasis.

Conclusions

We found very similar genomic alterations between primary and metastatic tumors, with a few mutations found specifically in lung metastases, which may explain the clinical observation that both primary and metastatic tumors are usually sensitive or resistant to the same systemic treatments.