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.     

Integrative analysis of N-linked human glycoproteomic data sets reveals PTPRF ectodomain as a novel plasma biomarker candidate for prostate cancer

In an attempt to identify prostate cancer biomarkers with greater diagnostic and prognostic capabilities, we have developed an integrative proteomic discovery workflow focused on N-linked glycoproteins that refines the target selection process. In this work, hydrazide-based chemistry was used to identify N-linked glycopeptides from 22Rv1 prostate cancer cells cultured in vitro, which were compared with glycopeptides identified from explanted 22Rv1 murine tumor xenografts. One hundred and four human glycoproteins were identified in the former analysis and 75 in the latter, with 40 proteins overlapping between data sets. Of the 40 overlapping proteins, 80% have multiple literature references to the neoplastic process and ～40% to prostatic neoplasms. These include a number of well-known prostate cancer-associated biomarkers, such as prostate-specific membrane antigen (PSMA). By integrating gene expression data and available literature, we identified members of the overlap data set that deserve consideration as potential prostate cancer biomarkers. Specifically, the identification of the extracellular domain of protein tyrosine phosphatase receptor type F (PTPRF) was of particular interest due to the direct involvement of PTPRF in the control of β-catenin signaling, as well as dramatically elevated gene expression levels in the prostate compared to other tissues. In this investigation, we demonstrate that the PTPRF E-subunit is more abundant in human prostate tumor tissue compared to normal control and also detectable in murine plasma by immunoblot and ELISA. Specifically, PTPRF distinguishes between animals xenografted with the 22Rv1 cells and control animals as early as 14 days after implantation. This result suggests that the ectodomain of PTPRF has the potential to function as a novel plasma or tissue-based biomarker for prostate cancer. The workflow described adds to the literature of potential biomarker candidates for prostate cancer and demonstrates a pathway to developing new diagnostic assays.     

The data‐index: An author‐level metric that values impactful data and incentivizes data sharing

Author‐level metrics are a widely used measure of scientific success. The h‐index and its variants measure publication output (number of publications) and research impact (number of citations). They are often used to influence decisions, such as allocating funding or jobs. Here, we argue that the emphasis on publication output and impact hinders scientific progress in the fields of ecology and evolution because it disincentivizes two fundamental practices: generating impactful (and therefore often long‐term) datasets and sharing data. We describe a new author‐level metric, the data‐index, which values both dataset output (number of datasets) and impact (number of data‐index citations), so promotes generating and sharing data as a result. We discuss how it could be implemented and provide user guidelines. The data‐index is designed to complement other metrics of scientific success, as scientific contributions are diverse and our value system should reflect that both for the benefit of scientific progress and to create a value system that is more equitable, diverse, and inclusive. Future work should focus on promoting other scientific contributions, such as communicating science, informing policy, mentoring other scientists, and providing open‐access code and tools.     

Iron supplementation is sufficient to rescue skeletal muscle mass and function in cancer cachexia

Cachexia is a wasting syndrome characterized by devastating skeletal muscle atrophy that dramatically increases mortality in various diseases, most notably in cancer patients with a penetrance of up to 80%. Knowledge regarding the mechanism of cancer‐induced cachexia remains very scarce, making cachexia an unmet medical need. In this study, we discovered strong alterations of iron metabolism in the skeletal muscle of both cancer patients and tumor‐bearing mice, characterized by decreased iron availability in mitochondria. We found that modulation of iron levels directly influences myotube size in vitro and muscle mass in otherwise healthy mice. Furthermore, iron supplementation was sufficient to preserve both muscle function and mass, prolong survival in tumor‐bearing mice, and even rescues strength in human subjects within an unexpectedly short time frame. Importantly, iron supplementation refuels mitochondrial oxidative metabolism and energy production. Overall, our findings provide new mechanistic insights in cancer‐induced skeletal muscle wasting, and support targeting iron metabolism as a potential therapeutic option for muscle wasting diseases.     

Heterologous expression and biochemical characterisation of the recombinant β-carbonic anhydrase (MpaCA) from the warm-blooded vertebrate pathogen malassezia pachydermatis

Warm-blooded animals may have Malassezia pachydermatis on healthy skin, but changes in the skin microenvironment or host defences induce this opportunistic commensal to become pathogenic. Malassezia infections in humans and animals are commonly treated with azole antifungals. Fungistatic treatments, together with their long-term use, contribute to the selection and the establishment of drug-resistant fungi. To counteract this rising problem, researchers must find new antifungal drugs and enhance drug resistance management strategies. Cyclic adenosine monophosphate, adenylyl cyclase, and bicarbonate have been found to promote fungal virulence, adhesion, hydrolase synthesis, and host cell death. The CO₂/HCO₃^-/pH-sensing in fungi is triggered by HCO₃^- produced by metalloenzymes carbonic anhydrases (CAs, EC 4.2.1.1). It has been demonstrated that the growth of M. globosa can be inhibited in vivo by primary sulphonamides, which are the typical CA inhibitors. Here, we report the cloning, purification, and characterisation of the β-CA (MpaCA) from the pathogenic fungus M. pachydermatis, which is homologous to the enzyme encoded in the genome of M. globosa and M. restricta, that are responsible for dandruff and seborrhoeic dermatitis. Fungal CAs could be thus considered a new pharmacological target for combating fungal infections and drug resistance developed by most fungi to the already used drugs.     

Neuronal Nicotinic Receptor Deficits in Alzheimer Patients with the Swedish Amyloid Precursor Protein 670/671 Mutation

Abstract : The influence of β‐amyloid on cholinergic neurotransmission was studied by measuring alterations in nicotinic acetylcholine receptors (nAChRs) in autopsy brain tissue from subjects carrying the Swedish amyloid precursor protein (APP) 670/671 mutation. Significant reductions in numbers of nAChRs were observed in various cortical regions of the Swedish 670/671 APP mutation family subjects (‐73 to ‐87%) as well as in sporadic Alzheimer's disease (AD) cases (‐37 to ‐57%) using the nicotinic agonists [³H]epibatidine and [³H]nicotine, which bind with high affinity to both α3 and α4 and to α4 nAChR subtypes, respectively. Saturation binding studies with [³epibatidine revealed two binding sites in the parietal cortex of AD subjects and controls. A significant decrease in B_max (‐82%) for the high‐affinity site was observed in APP 670/671 subjects with no change in K_D compared with controls (0.018 nM APP 670/671 ; 0.036 nM control). The highest load of neuronal plaques (NPs) was observed in the parietal cortex of APP 670/671 brains, whereas the number of [³H]nicotine binding sites was less impaired compared with other cortical brain regions. Except for a positive significant correlation between the number of [³H]nicotine binding sites and number of NPs in the parietal cortex, no strict correlation was observed between nAChR deficits and the presence of NPs and neurofibrillary tangles, suggesting that these different processes may be closely related but not strictly dependent on each other.     

QUALITATIVE AND QUANTITATIVE OBSERVATIONS ON AQUATIC ALGAL COMMUNITIES AND RECOLONIZATION WITHIN THE BLAST ZONE OF MT. ST. HELENS, 1980 AND 19811

Despite the destruction and total rearrangement of much of the area north of Mt St. Helens, many different species of algae became established in the aquatic systems located in the blast zone within 3–4 months after the eruption of May 18, 1980. Initial sites of intense algal activity were found in benthic regions associated with warm springs and in the littoral and phytoplanktonic communities of some small lakes. In the summers of 1980–81, overall phytoplankton numbers and activity were low in the large lakes closest to the crater (e.g. Spirit Lake). However, diatoms, blue-green and green algal isolates from these lakes were obtained in laboratory cultures on a reduced inorganic medium used to enumerate metal and sulfur oxidizing bacteria. Species of Nodularia, Pseudanabaena, Anabaena, Oscillatoria, Nitzschia, Tribonema, Chlamydomonas, Chlorella, and microflagellates (predominantly cryptomonads) were among the more common forms found in preserved samples or isolated in cultures.     

Age-Related Differences in Synaptosomal Peroxidative Damage and Membrane Properties

Young, adult, and old rats were used to study the effect of age on the integrity and functioning of brain synaptosomes. An evaluation was made of the differences in lipid composition, membrane fluidity, Na+, K(+)-ATPase activity, and susceptibility to in vitro lipid peroxidation. There was an age-related increase in synaptosomal free fatty acids, with no modification in acyl chain composition, and a decrease in membrane phospholipids which increased the cholesterol/phospholipid mole ratio. With altered lipid composition, there was a corresponding age-dependent decrease in membrane fluidity, a reduction of Na+, K(+)-ATPase activity, and an overall greater susceptibility to in vitro lipid peroxidation. Furthermore, lipid peroxidation promoted strong modifications of the membrane fluidity, lipid composition, and Na+,K(+)-ATPase activity just as aging did, thus indicating a possible contribution of oxidative damage to ageing processes. The cases studied revealed that the greater responsiveness of old membranes to in vitro lipid peroxidation resulted in the highest degree of membrane alteration, indicating that all pathological states known to promote a peroxidative injury can have even more dramatic consequences when they take place in old brain.     

Yeast artificial chromosome-based genome mapping: Some lessons from Xq24–q28

Yeast artificial chromosomes (YACs) have recently provided a potential route to long-range coverage of complex genomes in contiguous cloned DNA. In a pilot project for 50 Mb (1.5% of the human genome), a variety of techniques have been applied to assemble Xq24–q28 YAC contigs up to 8 Mb in length and assess their quality. The results indicate the relative strength of several approaches and support the adequacy of YAC-based methods for mapping the human genome.