Global trends of cropland phosphorus use and sustainability challenges.

To meet the growing food demand while addressing the multiple challenges of exacerbating phosphorus (P) pollution and depleting P rock reserves1-15, P use efficiency (PUE, the ratio of productive P output to P input in a defined system) in crop production needs to be improved. Although many efforts have been devoted to improving nutrient management practices on farms, few studies have examined the historical trajectories of PUE and their socioeconomic and agronomic drivers on a national scale1,2,6,7,11,16,17. Here we present a database of the P budget (the input and output of the crop production system) and PUE by country and by crop type for 1961-2019, and examine the substantial contribution of several drivers for PUE, such as economic development stages and crop portfolios. To address the P management challenges, we found that global PUE in crop production must increase to 68-81%, and recent trends indicate some meaningful progress towards this goal. However, P management challenges and opportunities in croplands vary widely among countries.

Seasonality of temperate forest photosynthesis and daytime respiration.

Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction and of remote sensing indices of global biosphere productivity. Here, we use new isotopic instrumentation to determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night-the first robust evidence of the inhibition of leaf respiration by light at the ecosystem scale. Because they do not capture this effect, standard approaches overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems.

Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar).

Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.

Diel patterns of autotrophic and heterotrophic respiration among phenological stages.

Improved understanding of the links between aboveground production and allocation of photosynthate to belowground processes and the temporal variation in those links is needed to interpret observations of belowground carbon cycling processes. Here, we show that combining a trenching manipulation with high-frequency soil respiration measurements in a temperate hardwood forest permitted identification of the temporally variable influence of roots on diel and seasonal patterns of soil respiration. The presence of roots in an untrenched plot caused larger daily amplitude and a 2-3 h delay in peak soil CO2 efflux relative to a root-free trenched plot. These effects cannot be explained by differences in soil temperature, and they were significant only when a canopy was present during the growing season. This experiment demonstrated that canopy processes affect soil CO2 efflux rates and patterns at hourly and seasonal time scales, and it provides evidence that root and microbial processes respond differently to environmental factors.

Soil respiration at mean annual temperature predicts annual total across vegetation types and biomes.

Soil respiration (SR) constitutes the largest flux of CO(2) from terrestrial ecosystems to the atmosphere. However, there still exist considerable uncertainties as to its actual magnitude, as well as its spatial and interannual variability. Based on a reanalysis and synthesis of 80 site-years for 57 forests, plantations, savannas, shrublands and grasslands from boreal to tropical climates we present evidence that total annual SR is closely related to SR at mean annual soil temperature (SR(MAT)), irrespective of the type of ecosystem and biome. This is theoretically expected for non water-limited ecosystems within most of the globally occurring range of annual temperature variability and sensitivity (Q(10)). We further show that for seasonally dry sites where annual precipitation (P) is lower than potential evapotranspiration (PET), annual SR can be predicted from wet season SR(MAT) corrected for a factor related to P/PET. Our finding indicates that it can be sufficient to measure SR(MAT) for obtaining a well constrained estimate of its annual total. This should substantially increase our capacity for assessing the spatial distribution of soil CO(2) emissions across ecosystems, landscapes and regions, and thereby contribute to improving the spatial resolution of a major component of the global carbon cycle.

A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents.

We constructed a genetic linkage map for Arctic char (Salvelinus alpinus) using two backcrosses between genetically divergent strains. Forty-six linkage groups (expected = 39-41) and 19 homeologous affinities (expected = 25) were identified using 184 microsatellites, 129 amplified fragment length polymorphisms (AFLPs), 13 type I gene markers, and one phenotypic marker, SEX. Twenty-six markers remain unlinked. Female map distance (9.92 Morgans) was substantially higher than male map distance (3.90 Morgans) based on the most complete parental information (i.e., the F1 hybrids). Female recombination rates were often significantly higher than those of males across all pairwise comparisons within homologous chromosomal segments (average female to male ratios within families was 1.69:1). The female hybrid parent had significantly higher recombination rates than the pure strain female parent. Segregation distortion was detected in four linkage groups (4, 8, 13, 20) for both families. In family 3, only the largest fish were sampled for genotyping, suggesting that segregation distortion may represent regions possessing influences on growth. In family 2, almost all cases showing segregation distortion involved markers in the female hybrid parent.

Toward automated nucleic acid enzyme selection.

Methods for automation of nucleic acid selections are being developed. The selection of aptamers has been successfully automated using a Biomek 2000 workstation. Several binding species with nanomolar affinities were isolated from diverse populations. Automation of a deoxyribozyme ligase selection is in progress. The process requires eleven times more robotic manipulations than an aptamer selection. The random sequence pool contained a 5' iodine residue and the ligation substrate contained a 3' phosphorothioate. Initially, a manual deoxyribozyme ligase selection was performed. Thirteen rounds of selection yielded ligators with a 400-fold increase in activity over the initial pool. Several difficulties were encountered during the automation of DNA catalyst selection, including effectively washing bead-bound DNA, pipetting 50% glycerol solutions, purifying single strand DNA, and monitoring the progress of the selection as it is performed. Nonetheless, automated selection experiments for deoxyribozyme ligases were carried out starting from either a naive pool or round eight of the manually selected pool. In both instances, the first round of selection revealed an increase in ligase activity. However, this activity was lost in subsequent rounds. A possible cause could be mispriming during the unmonitored PCR reactions. Potential solutions include pool redesign, fewer PCR cycles, and integration of a fluorescence microtiter plate reader to allow robotic 'observation' of the selections as they progress.

Glycobiology of Plasmodium falciparum.

The human malaria parasite, Plasmodium falciparum, has as its only glycoconjugate GPI anchors. These structures, present in essentially all parasite surface proteins, are associated with disease pathology. In contrast, the parasite depends for essential recognition events on saccharides associated with host cell glycoproteins and proteoglycans.

Control of cation concentrations in stream waters by surface soil processes in an Amazonian watershed.

The chemical composition of ground waters and stream waters is thought to be determined primarily by weathering of parent rock. In relatively young soils such as those occurring in most temperate ecosystems, dissolution of primary minerals by carbonic acid is the predominant weathering pathway that liberates Ca2+, Mg2+ and K+ and generates alkalinity in the hydrosphere. But control of water chemistry in old and highly weathered soils that have lost reservoirs of primary minerals (a common feature of many tropical soils) is less well understood. Here we present soil and water chemistry data from a 10,000-hectare watershed on highly weathered soil in the Brazilian Amazon. Streamwater cation concentrations and alkalinity are positively correlated to each other and to streamwater discharge, suggesting that cations and bicarbonate are mainly flushed from surface soil layers by rainfall rather than being the products of deep soil weathering carried by groundwater flow. These patterns contrast with the seasonal patterns widely recognized in temperate ecosystems with less strongly weathered soils. In this particular watershed, partial forest clearing and burning 30 years previously enriched the soils in cations and so may have increased the observed wet season leaching of cations. Nevertheless, annual inputs and outputs of cations from the watershed are low and nearly balanced, and thus soil cations from forest burning will remain available for forest regrowth over the next few decades. Our observations suggest that increased root and microbial respiration during the wet season generates CO2 that drives cation-bicarbonate leaching, resulting in a biologically mediated process of surface soil exchange controlling the streamwater inputs of cations and alkalinity from these highly weathered soils.

Emissions of nitrous oxide and nitric oxide from soils of native and exotic ecosystems of the Amazon and Cerrado regions of Brazil.

This paper reviews reports of nitrous oxide (N2O) and nitric oxide (NO) emissions from soils of the Amazon and Cerrado regions of Brazil. N2O is a stable greenhouse gas in the troposphere and participates in ozone-destroying reactions in the stratosphere, whereas NO participates in tropospheric photochemical reactions that produce ozone. Tropical forests and savannas are important sources of atmospheric N2O and NO, but rapid land use change could be affecting these soil emissions of N oxide gases. The five published estimates for annual emissions of N2O from soils of mature Amazonian forests are remarkably consistent, ranging from 1.4 to 2.4 kg N ha(-1) year(-1), with a mean of 2.0 kg N ha(-1) year(-1). Estimates of annual emissions of NO from Amazonian forests are also remarkably similar, ranging from 1.4 to 1.7 kg N ha(-1) year(-1), with a mean of 1.5 kg N ha(-1) year(-1). Although a doubling or tripling of N2O has been observed in some young (< or = 2 years) cattle pastures relative to mature forests, most Amazonian pastures have lower emissions than the forests that they replace, indicating that forest-to-pasture conversion has, on balance, probably reduced regional emissions slightly (<10%). Secondary forests also have lower soil emissions than mature forests. The same patterns apply for NO emissions in Amazonia. At the only site in Cerrado where vegetation measurements have been made N2O emissions were below detection limits and NO emissions were modest (approximately 0.4 kg N ha(-1) year(-1)). Emissions of NO doubled after fire and increased by a factor of ten after wetting dry soil, but these pulses lasted only a few hours to days. As in Amazonian pastures, NO emissions appear to decline with pasture age. Detectable emissions of N2O have been measured in soybean and corn fields in the Cerrado region, but they are modest relative to fluxes measured in more humid tropical agricultural regions. No measurements of NO from agricultural soils in the Cerrado region have been made, but we speculate that they could be more important than N2O emissions in this relatively dry climate. While a consistent pattern is emerging from these studies in the Amazon region, far too few data exist for the Cerrado region to assess the impact of land use changes on N oxide emissions.

Glycosylphosphatidylinositol anchors of Plasmodium falciparum: molecular characterization and naturally elicited antibody response that may provide immunity to malaria pathogenesis.

Induction of proinflammatory cytokine responses by glycosylphosphatidylinositols (GPIs) of intraerythrocytic Plasmodium falciparum is believed to contribute to malaria pathogenesis. In this study, we purified the GPIs of P. falciparum to homogeneity and determined their structures by biochemical degradations and mass spectrometry. The parasite GPIs differ from those of the host in that they contain palmitic (major) and myristic (minor) acids at C-2 of inositol, predominantly C18:0 and C18:1 at sn-1 and sn-2, respectively, and do not contain additional phosphoethanolamine substitution in their core glycan structures. The purified parasite GPIs can induce tumor necrosis factor alpha release from macrophages. We also report a new finding that adults who have resistance to clinical malaria contain high levels of persistent anti-GPI antibodies, whereas susceptible children lack or have low levels of short-lived antibody response. Individuals who were not exposed to the malaria parasite completely lack anti-GPI antibodies. Absence of a persistent anti-GPI antibody response correlated with malaria-specific anemia and fever, suggesting that anti-GPI antibodies provide protection against clinical malaria. The antibodies are mainly directed against the acylated phosphoinositol portion of GPIs. These results are likely to be valuable in studies aimed at the evaluation of chemically defined structures for toxicity versus immunogenicity with implications for the development of GPI-based therapies or vaccines.

Developmental stage-specific biosynthesis of glycosylphosphatidylinositol anchors in intraerythrocytic Plasmodium falciparum and its inhibition in a novel manner by mannosamine.

Glycosylphosphatidylinositols (GPIs) are the major glycoconjugates in intraerythrocytic stage Plasmodium falciparum. Several functional proteins including merozoite surface protein 1 are anchored to the cell surface by GPI modification, and GPIs are vital to the parasite. Here, we studied the developmental stage-specific biosynthesis of GPIs by intraerythrocytic P. falciparum. The parasite synthesizes GPIs exclusively during the maturation of early trophozoites to late trophozoites but not during the development of rings to early trophozoites or late trophozoites to schizonts and merozoites. Mannosamine, an inhibitor of GPI biosynthesis, inhibits the growth of the parasite specifically at the trophozoite stage, preventing further development to schizonts and causing death. Mannosamine has no effect on the development of either rings to early trophozoites or late trophozoites to schizonts and merozoites. The analysis of GPIs and proteins synthesized by the parasite in the presence of mannosamine demonstrates that the effect is because of the inhibition of GPI biosynthesis. The data also show that mannosamine inhibits GPI biosynthesis by interfering with the addition of mannose to an inositol-acylated GlcN-phosphatidylinositol (PI) intermediate, which is distinctively different from the pattern seen in other organisms. In other systems, mannosamine inhibits GPI biosynthesis by interfering with either the transfer of a mannose residue to the Manalpha1-6Manalpha1-4GlcN-PI intermediate or the formation of ManN-Man-GlcN-PI, an aberrant GPI intermediate, which cannot be a substrate for further addition of mannose. Thus, the parasite GPI biosynthetic pathway could be a specific target for antimalarial drug development.

CFTR antisense phosphorothioate oligodeoxynucleotides (S-ODns) induce tracheo-bronchial mucin (TBM) mRNA expression in human airway mucosa.

Mucus hypersecretion is a critical component of cystic fibrosis (CF) pathogenesis. The effects of dysfunction of the cystic fibrosis transmembrane regulator (CFTR) on mucin expression were examined using the tracheo-bronchial mucin (TBM) gene as an indicator. TBM mRNA expression was assessed in a human bronchial epithelial cell line (HBE1) and human nasal mucosal explants in vitro. Antisense phosphorothioate oligodeoxynucleotides (S-ODN) to TBM suppressed baseline expression of TBM mRNA in both systems, but had no effect on glyceraldehyde phosphate dehydrogenase mRNA (GAPDH) expression. Sense and missense (multiple scrambled control oligonucleotides) S-ODNs had no effect. 8Br-cAMP and PGE1 significantly elevated TBM mRNA expression. These increases were also specifically inhibited by the antisense S-ODNs. In order to induce a CF-like state, S-ODN to CFTR were added to explants. Antisense CFTR S-ODNs were anticipated to reduce the expression of cellular CFTR protein, and the level of CFTR function. Antisense, but not sense or missense, CFTR S-ODN significantly increased TBM mRNA expression. These data suggest that mucin hypersecretion in CF may be a direct consequence of CFTR dysfunction; the specific mechanism through which this effect is mediated is not known.

Glycosylation and proteolytic processing of 70 kDa C-terminal recombinant polypeptides of Plasmodium falciparum merozoite surface protein 1 expressed in mammalian cells.

The cDNAs that encode the 70 kDa C-terminal portion of Plasmodium falciparum merozoite surface protein 1 (MSP-1), with or without an N-terminal signal peptide sequence and C-terminal glycosylphosphatidylinositol (GPI) signal sequence of MSP-1, were expressed in mammalian cell lines via recombinant vaccinia virus. The polypeptides were studied with respect to the nature of glycosylation, localization, and proteolytic processing. The polypeptides derived from the cDNAs that contained the N-terminal signal peptide were modified with N -linked high mannose type structures and low levels of O -linked oligosaccharides, whereas the polypeptides from the cDNAs that lacked the signal peptide were not glycosylated. The GPI anchor moiety is either absent or present at a very low level in the polypeptide expressed from the cDNA that contained both the signal peptide and GPI signal sequences. Together, these data establish that whereas the signal peptide of MSP-1 is functional, the GPI anchor signal is either nonfunctional or poorly functional in mammalian cells. The polypeptides expressed from the cDNAs that contained the signal peptide were proteolytically cleaved at their C-termini, whereas the polypeptides expressed from the cDNAs that lacked the signal peptide were uncleaved. While the polypeptide expressed from the cDNA containing both the signal peptide and GPI anchor signal was truncated by approximately 14 kDa at the C-terminus, the polypeptide derived from the cDNA with only the signal peptide was processed to remove approximately 6 kDa, also from the C-terminus. Furthermore, the polypeptides derived from cDNAs that lacked the signal peptide were exclusively localized intra-cellularly, the polypeptides from cDNAs that contained the signal peptide were predominantly intracellular, with low levels on the cell surface; none of the polypeptides was secreted into the culture medium to a detectable level. These results suggest that N -glycosylation alone is not sufficient for the efficient extracellular transport of the recombinant MSP-1 polypeptides through the secretory pathway in mammalian cells.

Cloning and characterization of the merozoite surface antigen 1 gene of Plasmodium berghei.

Merozoite surface antigen 1 (MSA1) is a promising candidate for vaccine development against malaria parasites. Here, we report the complete nucleotide sequence of the gene encoding the precursor to this major surface antigen of Plasmodium berghei strain ANKA using cDNA library screening and polymerase chain reaction techniques. A single open reading frame of 5,376 basepairs encoding a protein with a calculated molecular mass of 197 kD was defined. The protein contains a putative signal peptide of 19 amino acids, a membrane anchor sequence of 18 residues, and shows two epidermal growth factor-like domains rich in Cys residues at the C-terminus. There are four repeat sequences of oligopeptides in the molecule: tetrapeptide (Ser-Thr-Thr-Thr), tripeptide (Pro-Thr-Pro and Pro-Ala-Ala), and dipeptide (Ser-Gly). Furthermore, three nine-residue stretches of a motif (Ala-Ser-Asn-Pro-Gly-Ala-Ser-Ala-Ser) are located near each other. All of these repeat sequences are unexceptionally located in the variable regions when compared with other MSA1 molecules. The molecule displays 79% overall identity to the analogous antigen of P. yoelii yoelii strain YM, 70% to that of P. chabaudi chabaudi strain AS, and 38% to that of P. falciparum strain Wellcome.

Protein glycosylation in the malaria parasite.

The nature and extent of glycosylation in Plasmodium falciparum has long been controversial. It has been widely believed that O-glycosylation is the major carbohydrate modification in the intraerythrocytic stage of P. falciparum and that the parasite has no N-glycosylation capacity. Contrary to this, recent studies have demonstrated that P. falciparum has a low N-glycosylation capability, and O-glycosylation is either absent or present at an extremely low level, whereas glycosylphosphatidylinositol (GPI) anchor modification is common and is the major carbohydrate modification in parasite proteins. The GPI anchor moieties are essential for parasite survival. The parasite GPI anchors can activate signaling pathways in host cells, and thereby induce the expression of inflammatory cytokines, adhesion molecules and induced nitric oxide synthase (iNOS). This might cause erythrocyte sequestration, hypoglycemia, triglyceride lipogenesis and immune dysregulation. Thus, the parasite GPI anchor structure and biosynthetic pathways are attractive targets for antimalarial and/or antiparasite drug development, as discussed here by Channe Gowda and Eugene Davidson.