IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure

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Arabidopsis assay for mutagenicity

Four laboratories, two in the Czech Republic (Brno and Prague) and two in the CIS (Moscow and Duschanbe), participated in the International Programme on Chemical Safety's (IPCS) collaborative study to evaluate the utility of the most commonly used plant test systems, including the Arabidopsis thaliana assay, for assessign the mutagenic potential of environmental agents. Out of the five compounds evaluated in the Arabidopsis assay, three compounds, i.e., ethyl methanesulfonate, N-methyl-N-nitrosourea, and azidoglycerol, were reported to be mutagenic by all four participating laboratories. Sodium azide (NaN₃) demonstrated a negative response in all four laboratories, whereas maleic hydrazide was reported to be weakly mutagenic by one laboratory and nonmutagenic by the other three laboratories.     

Vicia faba chromosomal aberration assay

A collaborative study involving laboratories in six countries was initiated under the sponsorship of the International Programme on Chemical Safety (IPCS) to determine the sensitivity, efficiency and reliability of the Vicia faba root tip meristem chromosomal aberration assay using a standardized protocol. The six Laboratories that participated in this study were located in the Slovak Republic, India, Japan, Poland, Sweden and the USA. All laboratories adhered to a standardized protocol for the Vicia faba chromosomal aberartion assay. Four coded chemicals, azidoglycerol (AG), N-methyl-N-nitrosourea (MNU), sodium azide (NaN₃) and maleic hydrazide (MH) were tested with the Vicia faba chromosomal aberration assay. Of the four chemicals, three (MH, AG and MNU) were found to be clastogenic and gave a concentration related response. However, the results of NaN₃ were equivocal which might be explained by the stability of NaN₃. The conclusions from this study suggest that the Vicia faba chromosomal aberration bioassay is an efficient and reliable short-term bioassay for the rapid screening of chemicals for clastogenicity.     

Tradescantia micronucleus bioassay

Four coded chemicalsm azidoglycerol (AG), N-methyl-N-nitrosourea (MNU), sodium azide (NaN₃), and maleic hydrazide (MH), were tested with the Tradescantia micronucleus (Trad-MCN) bioassay by five independent laboratories from five different countries. The purpose of this international collaborative study was to evaluate four plant bioassays, of which the Trad-MCN assay was one, for their sensitivity, efficiency and reliability. The study was carried out under the sponsorship of the International Programme on Chemical Safety. All laboratories adhered to a standard Trad-MCN protocol which suggested that three replicate tests be conducted with each chemical. The results reported by all laboratories, although not equal, showed good agreement among the laboratories. In fact, all five laboratories obtained positive results with MH and MNU, while four of the five laboratories achieved positive results with NaN₃. AG was tested in only three laboratories. Two reported negative results, while one reported positive results but only at a single high dose. The data from this study suggest that under normal conditions, the Trad-MCN bioassay is an efficient and reliable short-term bioassay for clastogens. It is suitable for the rapid screening of chemicals, and also is specially qualified for in situ monitoring of ambient pollutants.     

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.The emerging problems of increased food demand, declining water tables, and increasingly unpredictable growing environments due to climate change require increasingly adaptable varieties in order to maintain high rice (Oryza sativa) yields under variable conditions. Although genotype × environment variation has typically been viewed as a challenge to plant breeding efforts (Basford and Cooper, 1998; Cooper et al., 1999), the variation across environments known as adaptive phenotypic plasticity is likely to be an important trait for future crop plants, as it increases plant fitness and survival (Nicotra and Davidson, 2010). In some future growing seasons, rice may face edaphic stresses such as drought stress (due to low rainfall or reduced availability of irrigation) and lower nutrient availability (due to decreased fertilizer or water availability), whereas in other seasons, the growing conditions may remain optimal. Specialized root architectures, although effective for a specific stress-prone environment, can be functionally maladaptive in different conditions (Ho et al., 2005; Poot and Lambers, 2008). Therefore, increased plasticity in root traits in terms of allocational, morphological, anatomical, or developmental plasticity (Sultan, 2000) could improve crop performance across future growing seasons (Aspinwall et al., 2015).A number of previous studies have reported that plasticity in certain root traits conferred improved plant performance under stress or variable growth conditions to which the crop may be exposed. Under different types of drought stress, plasticity in root length density or total root length (Kano-Nakata et al., 2011; Tran et al., 2015) and lateral root length and/or branching (Suralta et al., 2010; Kano et al., 2011; Kano-Nakata et al., 2013) has been observed to improve shoot biomass, water uptake, and photosynthesis under drought in rice. Plasticity in the level of root aerenchyma development (measured as root porosity) was reported to result in higher shoot dry matter (Niones et al., 2013) and grain yield (Niones et al., 2012) under transient drought stress in rice, and plasticity in other anatomical traits has been hypothesized as a major reason for wheat (Triticum aestivum) being more drought tolerant than rice (Kadam et al., 2015). In a set of 42 native and crop species, plasticity in root depth was a better predictor of shoot response to drought than absolute root depth (Reader et al., 1993). Under low nitrogen, plasticity in specific root area, specific root length, and root tissue density conferred the least reduction in relative growth rate in 10 perennial herbaceous species (Useche and Shipley, 2010), and plasticity in maize (Zea mays) root growth angle improved yield (Trachsel et al., 2013). These examples provide strong evidence that root phenotypic plasticity can result in improved plant performance across variable conditions that include edaphic stress and would be an effective target for crop improvement efforts.Deciphering the genetic and molecular mechanisms controlling root phenotypic plasticity will be necessary for effective selection and crop breeding efforts. Despite the likely genetic complexity behind the regulation of trait expression according to environmental conditions, phenotypic plasticity is heritable and selectable (for review, see Nicotra and Davidson, 2010). Genetic regions identified to be related to root phenotypic plasticity traits in crops include quantitative trait loci (QTLs) for root hair length plasticity in maize under low phosphorus (Zhu et al., 2005a), lateral root number plasticity in maize under low phosphorus (Zhu et al., 2005b), plasticity in aerenchyma development in response to drought stress in rice (Niones et al., 2013), and plasticity in lateral root growth in response to drought stress in rice (Niones et al., 2015). In wheat translocation lines, a plastic response of increased root biomass to drought was located to chromosome 1BS (Ehdaie et al., 2011). These identified genetic regions can be used in selection for the development of stress-tolerant crops.Future rice crops will likely experience a range of soil conditions including prolonged aerobic periods, drought stress (progressive or intermittent), low soil fertility, and flooding. Rice may be established by either transplanting or direct seeding depending upon the amount and duration of initial rainfall. Therefore, the identification of root phenotypic plasticity traits suitable for adaptability to the particular range of conditions faced by rice crops, as well as the genetic regions responsible for those plasticity traits, may facilitate selection for wide adaptation of rice genotypes to variable conditions to confer stable yield. To address these needs, this study was conducted to identify the rice root phenotypic plasticity traits conferring adaptability across variable growth conditions by comparing contrasting genotypes from crosses between traditional and modern varieties. Our aim was to effectively quantify root architectural plasticity in order to identify which root traits may play the most important roles in rice adaptability. We hypothesized that the most plastic genotypes may show the most stable yields across environments.     

Valuable New Leaf or Inflorescence Resistances Ensure Improved Management of White Rust (Albugo candida) in Mustard (Brassica juncea) Crops

Field resistances/susceptibilities against Albugo candida race 2V were determined for 29 Indian Brassica juncea varieties and compared with resistant varieties from China (6) and Australia (7). ‘Basanti’ (AUDPC incidence 46.7; AUDPC severity 29.2) represents the first high‐level resistance to race 2V in Indian varieties. Several others showed lower but still useful levels of resistance, including Narendra Ageti Rai‐4 (AUDPC incidence 150.6; AUDPC severity 66.8) and JM1 (AUDPC incidence 167.1; AUDPC severity 83.7). Highly susceptible Indian varieties had AUDPC incidence values >200 and severity >100. ‘Basanti’ had least stagheads/plant (0.32), while Narendra Ageti Rai‐4 had lowest % plants with stagheads (2.48). In contrast, almost half of Indian varieties had stagheads/plant >1 and % plants with stagheads >4, and >26 for ‘Kranti’. The resistance in ‘Basanti’ paves the way forward towards significantly improved white rust management in mustard in India. JM06011, JM06021, JR049 from Australia and CJB‐003 from China had zero leaf incidence. There were significant (P < 0.001) relationships between disease incidence with severity (R² 0.92), stagheads/plant (R² 0.69) and also % plants with stagheads (R² 0.60); between disease severity with stagheads/plant (R² 0.68) and also % plants with stagheads (R² 0.69); and between stagheads/plant with % plants with stagheads (R² 0.59).     

The Essential Autophagy Gene ATG7 Modulates Organ Fibrosis via Regulation of Endothelial-to-Mesenchymal Transition

Pulmonary fibrosis is a progressive disease characterized by fibroblast proliferation and excess deposition of collagen and other extracellular matrix components. Although the origin of fibroblasts is multifactorial, recent data implicate endothelial-to-mesenchymal transition as an important source of fibroblasts. We report herein that loss of the essential autophagy gene ATG7 in endothelial cells (ECs) leads to impaired autophagic flux accompanied by marked changes in EC architecture, loss of endothelial, and gain of mesenchymal markers consistent with endothelial-to-mesenchymal transition. Loss of ATG7 also up-regulates TGFβ signaling and key pro-fibrotic genes in vitro. In vivo, EC-specific ATG7 knock-out mice exhibit a basal reduction in endothelial-specific markers and demonstrate an increased susceptibility to bleomycin-induced pulmonary fibrosis and collagen accumulation. Our findings help define the role of endothelial autophagy as a potential therapeutic target to limit organ fibrosis, a condition for which presently there are no effective available treatments.     

Copy number alterations and allelic ratio in relation to recurrence of rectal cancer

Background

In rectal cancer, total mesorectal excision surgery combined with preoperative (chemo)radiotherapy reduces local recurrence rates but does not improve overall patient survival, a result that may be due to the harmful side effects and/or co-morbidity of preoperative treatment. New biomarkers are needed to facilitate identification of rectal cancer patients at high risk for local recurrent disease. This would allow for preoperative (chemo)radiotherapy to be restricted to high-risk patients, thereby reducing overtreatment and allowing personalized treatment protocols. We analyzed genome-wide DNA copy number (CN) and allelic alterations in 112 tumors from preoperatively untreated rectal cancer patients. Sixty-six patients with local and/or distant recurrent disease were compared to matched controls without recurrence. Results were validated in a second cohort of tumors from 95 matched rectal cancer patients. Additionally, we performed a meta-analysis that included 42 studies reporting on CN alterations in colorectal cancer and compared results to our own data.

Results

The genomic profiles in our study were comparable to other rectal cancer studies. Results of the meta-analysis supported the hypothesis that colon cancer and rectal cancer may be distinct disease entities. In our discovery patient study cohort, allelic retention of chromosome 7 was significantly associated with local recurrent disease. Data from the validation cohort were supportive, albeit not statistically significant, of this finding.

Conclusions

We showed that retention of heterozygosity on chromosome 7 may be associated with local recurrence in rectal cancer. Further research is warranted to elucidate the mechanisms and effect of retention of chromosome 7 on the development of local recurrent disease in rectal cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1550-0) contains supplementary material, which is available to authorized users.