Focus Issue on Roots: Duplicate and Conquer: Multiple Homologs of PHOSPHORUS-STARVATION TOLERANCE1 Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.Increasing food production is one of the major global challenges in dealing with continuously growing population and food consumption (Godfray et al., 2010). One of the major obstacles to improve crop production in tropical regions is phosphorus (P) deficiency caused by P fixation in the soil clays. P is one of the most important plant nutrients, contributing approximately 0.2% of a plant’s dry weight, and is a component of key organic molecules such as nucleic acids, phospholipids, and ATP (Schachtman et al., 1998). On tropical soils, even when the total amount of soil P is high, its bioavailability is low due to P fixation by aluminum and iron oxides in clay minerals (Marschner, 1995) and immobilization into organic forms (Schachtman et al., 1998). Approximately half of the world’s agricultural lands occurs on low-P soils (Lynch, 2011); hence, crop adaptation to P insufficiency should be a major breeding target to enable sustainable agricultural production worldwide. In addition, because phosphate rock fertilizer is a nonrenewable resource that is being depleted by agricultural demands, increasing fertilizer prices negatively impact agriculture, particularly for small-holder farmers in developing countries in the tropics and subtropics (Cordell et al., 2009; Sattari et al., 2012). In sorghum (Sorghum bicolor), breeding strategies for low-P adaptation have been developed based on multienvironment trials in West Africa, indicating the importance of undertaking selection in low-P soil conditions (Leiser et al., 2012a, 2012b). Therefore, developing crops with greater ability to grow and maintain satisfactory yields on soils with reduced P availability is expected to substantially improve food security worldwide.Tolerance to P deficiency in plants can be achieved by mechanisms underlying both P acquisition and P internal utilization efficiency (Parentoni and Souza Junior, 2008). One of the major mechanisms that plants have evolved to overcome low-P availability is to maximize the ability of the roots to acquire and absorb P from the soil. Plants can mobilize P through the exudation of organic acids, acid phosphatases, and ribonucleases, resulting in enhanced P availability and uptake (Hinsinger, 2001; Ryan et al., 2001; Dakora and Phillips, 2002; Hammond and White, 2008; Ma et al., 2009; Pang et al., 2009). Another strategy to cope with low-P availability is to increase the soil volume accessed by root systems by forming mycorrhizal symbioses (Li et al., 2012; Smith and Smith, 2012; Rai et al., 2013). Due to low-P mobility on tropical soils, changes in root architecture and morphology enhance P uptake by facilitating soil exploration (Williamson et al., 2001; Ho et al., 2005; Walk et al., 2006; Svistoonoff et al., 2007; Lynch, 2011; Ingram et al., 2012; Niu et al., 2013). Root structural changes leading to higher P uptake include increased root hair growth (Yan et al., 2004; Haling et al., 2013; Lan et al., 2013) and length and enhancing lateral root over primary root growth (Williamson et al., 2001; Wang et al., 2013). In addition, increased root surface area is achieved by a combination of reduced root diameter and enhanced elongation of relatively thinner roots (Fitter et al., 2002). There is both intraspecific and interspecific genetic variation for P deficiency tolerance in crop species (Lynch and Brown, 2001, 2012; Mudge et al., 2002; Paszkowski et al., 2002; Rausch and Bucher, 2002; Huang et al., 2011; Zhang et al., 2011; Leiser et al., 2014a) that can be explored to develop P-efficient cultivars.In rice (Oryza sativa), Phosphorus uptake1 (Pup1), a major quantitative trait locus (QTL) for P deficiency tolerance donated by an aus-type Indian variety, Kasalath, was mapped to the long arm of chromosome 12 (Ni et al., 1998; Wissuwa et al., 1998, 2002; Heuer et al., 2009). Near-isogenic lines bearing the Kasalath allele at Pup1 showed 3-fold higher P uptake and grain yield in low-P trials compared with the recurrent parent, cv Nipponbare, which is intolerant to P starvation (Wissuwa and Ae, 2001). Following high-resolution mapping of Pup1, comparative sequence analyses of homologous bacterial artificial chromosomes showed that a Kasalath genomic fragment contained several genes not present in cv Nipponbare, highlighting an approximately 90-kb deletion in the cv Nipponbare reference genome that encompassed the Pup1 locus (Heuer et al., 2009). Within this insertion/deletion, OsPupK46-2, a gene encoding a Ser/Thr kinase of the Receptor-like Protein Kinase LRK10L-2 subfamily, was found to enhance grain yield and P uptake in rice lines overexpressing this gene, indicating that this protein kinase underlies the Pup1 locus (Gamuyao et al., 2012). OsPupK46-2, which is now designated PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was found to be up-regulated in the root tissues of tolerant near-isogenic lines under P-deficient conditions and was shown to increase P uptake by a physiological mechanism based on the enhancement of early root growth and development. Furthermore, lines overexpressing OsPupK46-2 showed an approximately 30% grain yield increase in comparison with the null lines, suggesting that PSTOL1 has potential for molecular breeding applications to improve crop performance under low-P conditions. Consistent with the proposed physiological mechanism underlying OsPSTOL1, the superior performance of the transgenic lines was related to enhanced root dry weight, root length, and root surface area (Gamuyao et al., 2012).Sorghum is the world’s fifth most important cereal crop and is a staple food for more than half a billion people. It is widely adapted to harsh environmental conditions, and more specifically, to arid and semiarid regions of the world (Doumbia et al., 1993, 1998). It has been estimated that rice diverged from its most recent common ancestor with sorghum and maize (Zea mays) approximately 50 million years ago (Kellogg, 1998; Paterson et al., 2000, 2004; Paterson, 2008). About 60% of the genes in the sorghum genome are located in syntenic regions to rice (Paterson et al., 2009), emphasizing the potential for using comparative genomics for cross-species identification of genes underlying abiotic stress tolerance in the grass family. Here, we applied association analysis to specifically study the role of sorghum homologs of rice OsPSTOL1 in tolerance to P starvation in sorghum. Single-nucleotide polymorphisms (SNPs) within PSTOL1 homologs in sorghum, collectively designated SbPSTOL1, were significantly associated with grain yield under low-P conditions and also root morphology and root system architecture (RSA) traits phenotyped from hydroponically grown plants. Under low P, SbPSTOL1 genes increased biomass accumulation and P content in the African landrace panel and grain yield in the sorghum association panel phenotyped in a low-P Brazilian soil. This suggests a stable effect across environments and sorghum genotypes that potentially can be used for molecular breeding applications. QTL mapping with a large sorghum recombinant inbred line population was used to validate the association results, indicating that SbPSTOL1 homologs colocalize with QTLs related to root morphology and performance under low P. Our results indicate that SbPSTOL1 homologs have the ability to enhance P uptake and sorghum performance in low-P soils by a mechanism related not only to early root growth enhancement, as was the case for rice OsPSTOL1, but also by modulating RSA.     

Photophysics of PbS Quantum Dot Films Capped with Arsenic Sulfide Ligands

PbS quantum dots (QDs) of different sizes capped with short (NH₄)₃AsS₃ inorganic ligands are produced via ligand exchange processes from oleate‐capped PbS QDs. The solid‐state photophysical properties of the control organic‐capped and the inorganic‐ligand‐capped QDs are investigated to determine their potential for optoelectronic applications. Ultrafast transient transmission shows that in the oleate‐capped QDs, carrier recombination at sub‐nanosecond scales occurs via Auger recombination, traps, and surface states. At longer times, intense signals associated with radiative recombination are obtained. After ligand exchange, the QDs become decorated with (NH₄)₃AsS₃ complexes and relaxation is dominated by efficient carrier transfer to the ligand states on timescales as fast as ≈2 ps, which competes with carrier thermalization to the QD band edge states. Recombination channels present in the oleate‐capped QDs, such as radiative and Auger recombination, appear quenched in the inorganic‐capped QDs. Evidence of efficient carrier trapping at shallow ligand states, which appears more intense under excitation above the (NH₄)₃AsS₃ gap, is provided. A detailed band diagram of the various relaxation and recombination processes is proposed that comprehensively describes the photophysics of the QD systems studied.     

A novel series of arylsulfonylthiophene-2-carboxamidine inhibitors of the complement component C1s

Inhibiting the classical pathway of complement activation by attenuating the proteolytic activity of the serine protease C1s is a potential strategy for the therapeutic intervention in disease states such as hereditary angioedema, ischemia-reperfusion injury, and acute transplant rejection. A series of arylsulfonylthiophene-2-carboxamidine inhibitors of C1s were synthesized and evaluated for C1s inhibitory activity. The most potent compound had a Ki of 10nM and >1000-fold selectivity over uPA, tPA, FX(a), thrombin, and plasmin.     

Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease

Over 1,500 variants in the ABCA4 locus cause phenotypes ranging from severe, early-onset retinal degeneration to very late-onset maculopathies. The resulting ABCA4/Stargardt disease is the most prevalent Mendelian eye disorder, although its underlying clinical heterogeneity, including penetrance of many alleles, are not well-understood. We hypothesized that a share of this complexity is explained by trans-modifiers, i.e., variants in unlinked loci, which are currently unknown. We sought to identify these by performing exome sequencing in a large cohort for a rare disease of 622 cases and compared variation in seven genes known to clinically phenocopy ABCA4 disease to cohorts of ethnically matched controls. We identified a significant enrichment of variants in 2 out of the 7 genes. Moderately rare, likely functional, variants, at the minor allele frequency (MAF) <0.005 and CADD>25, were enriched in ROM1, where 1.3% of 622 patients harbored a ROM1 variant compared to 0.3% of 10,865 controls (p = 2.41E04; OR 3.81 95% CI [1.77; 8.22]). More importantly, analysis of common variants (MAF>0.1) identified a frequent haplotype in PRPH2, tagged by the p.Asp338 variant with MAF = 0.21 in the matched general population that was significantly increased in the patient cohort, MAF 0.25, p = 0.0014. Significant differences were also observed between ABCA4 disease subgroups. In the late-onset subgroup, defined by the hypomorphic p.Asn1868Ile variant and including c.4253+43G>A, the allele frequency for the PRPH2 p.Asp338 variant was 0.15 vs 0.27 in the remaining cohort, p = 0.00057. Known functional data allowed suggesting a mechanism by which the PRPH2 haplotype influences the ABCA4 disease penetrance. These associations were replicated in an independent cohort of 408 patients. The association was highly statistically significant in the combined cohorts of 1,030 cases, p = 4.00E-05 for all patients and p = 0.00014 for the hypomorph subgroup, suggesting a substantial trans-modifying role in ABCA4 disease for both rare and common variants in two unlinked loci.     

Simulation modeling of phytoplankton dynamics in a large eutrophic river,Hungary — Danubian Phytoplankton Growth Model (DPGM)

Ecological models have often been used in order to answer questions that are in the limelight of recent researches such as the possible effects of climate change. The methodology of tactical models is a very useful tool comparison to those complex models requiring relatively large set of input parameters. In this study, a theoretical strategic model (TEGM) was adapted to the field data on the basis of a 24-year long monitoring database of phytoplankton in the Danube River at the station of Göd, Hungary (at 1669 river kilometer - hereafter referred to as “rkm”). The Danubian Phytoplankton Growth Model (DPGM) is able to describe the seasonal dynamics of phytoplankton biomass (mg L^?1) based on daily temperature, but takes the availability of light into consideration as well. In order to improve fitting, the 24-year long database was split in two parts in accordance with environmental sustainability. The period of 1979–1990 has a higher level of nutrient excess compared with that of the 1991–2002. The authors assume that, in the above-mentioned periods, phytoplankton responded to temperature in two different ways, thus two submodels were developed, DPGM-sA and DPGM-sB. Observed and simulated data correlated quite well. Findings suggest that linear temperature rise brings drastic change to phytoplankton only in case of high nutrient load and it is mostly realized through the increase of yearly total biomass.     

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases

Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and plant defense responses to diseases. The 140 EST-contigs identified through the keyword NBS-LRR were classified according to function. This classification allowed association of the predicted products of EST-contigs with biological processes, including host defense and apoptosis, and with molecular functions such as nucleotide binding and signal transducer activity. Fisher's exact test was used to examine the significance of differences in contig expression between libraries representing the responses to biotic stress challenges and other libraries from the BCGP. This analysis revealed seven contigs highly similar to catalase, chitinase, protein with a BURP domain and unknown proteins. The involvement of these coffee proteins in plant responses to disease is discussed.     

EglD, a putative endoglucanase, with an expansin like domain is localized in the conidial cell wall of Aspergillus nidulans

Although the process of conidial germination in filamentous fungi has been extensively studied, many aspects remain to be elucidated since the asexual spore or conidium is vital in their life cycle. Breakage and reformation of cell wall polymer bonds along with the maintenance of cell wall plasticity during conidia germination depend upon a range of hydrolytic enzymes whose activity is analogous to that of expansins, a highly conserved group of plant cell wall proteins with characteristic wall loosening activity. In the current study, we identified and characterized the eglD gene in Aspergillus nidulans, an expansin-like gene the product of which shows strong similarities with bacterial and fungal endo-beta1,4-glucanases. However, we failed to show such activity in vitro. The eglD gene is constitutively expressed in all developmental stages and compartments of A. nidulans asexual life cycle. However, the EglD protein is exclusively present in conidial cell walls. The role of the EglD protein in morphogenesis, growth and germination rate of conidia was investigated. Our results show that EglD is a conidial cell wall localized expansin-like protein, which could be involved in cell wall remodeling during germination.     

Identification of the extracellular polysaccharide produced by the snow mold fungus Microdochium nivale

A water-insoluble, extracellular polysaccharide was isolated from the culture medium of the snow mold fungus, Microdochium nivale, that had been cultivated in potato/dextrose broth. The polysaccharide consisted of glucose only. Its Fourier transform infrared spectrum showed a beta configuration of the C1 position of glucose. Linkage analysis of the polysaccharide showed that it had a linear structure of -(14)-linked glucose. The polysaccharide was therefore identified as cellulose. This is the first report of extracellular cellulose occurring in fungi.     

Immunocytochemical evidence for an NMDA1 receptor subunit in dissociated cells of<Emphasis Type="Italic"> Hydra vulgaris</Emphasis>

We have previously reported immunocytochemical, biochemical, behavioral, and electrophysiological evidence for glutamatergic transmission through (±)--amino-3-hydroxy-5-methyl-isoxazole-4-propionic acid (AMPA)/kainate receptors in hydra. We now report specific localization of the N-Methyl-D-aspartic acid receptor subunit 1 (NMDAR1) in epithelial, nerve, nematocytes, and interstitial cells of hydra. Macerates of tentacle/hypostome pieces of Hydra vulgaris were prepared on agar-coated slides, fixed with buffered formaldehyde/glutaraldehyde, and fluorescently labeled with monoclonal antibodies against mammalian NMDAR1. Negative controls omitted primary antibody. Digital images were recorded and analyzed. Specific localized and intense labeling was found in ectodermal battery cells, other epithelial cells, nematocytes, interstitial cells, and sensory and ganglionic nerve cells, and in battery cells was associated with enclosed nematocytes and neurons. The labeling of myonemes was more diffuse and less intense. In nerve and sensory cells, punctate labeling was prominent on cell bodies. These results are consistent with our earlier evidence for glutamatergic neurotransmission and kainate/NMDA regulation of stenotele discharge. They support other behavioral and biochemical evidence for a D-serine-sensitive, strychnine-insensitive, glycine receptor in hydra and suggest that the glutamatergic AMPA/kainate-NMDA system is an early evolved, phylogenetically old, behavioral control mechanism.