Mapping global cropland and field size

A new 1 km global IIASA-IFPRI cropland percentage map for the baseline year 2005 has been developed which integrates a number of individual cropland maps at global to regional to national scales. The individual map products include existing global land cover maps such as GlobCover 2005 and MODIS v.5, regional maps such as AFRICOVER and national maps from mapping agencies and other organizations. The different products are ranked at the national level using crowdsourced data from Geo-Wiki to create a map that reflects the likelihood of cropland. Calibration with national and subnational crop statistics was then undertaken to distribute the cropland within each country and subnational unit. The new IIASA-IFPRI cropland product has been validated using very high-resolution satellite imagery via Geo-Wiki and has an overall accuracy of 82.4%. It has also been compared with the EarthStat cropland product and shows a lower root mean square error on an independent data set collected from Geo-Wiki. The first ever global field size map was produced at the same resolution as the IIASA-IFPRI cropland map based on interpolation of field size data collected via a Geo-Wiki crowdsourcing campaign. A validation exercise of the global field size map revealed satisfactory agreement with control data, particularly given the relatively modest size of the field size data set used to create the map. Both are critical inputs to global agricultural monitoring in the frame of GEOGLAM and will serve the global land modelling and integrated assessment community, in particular for improving land use models that require baseline cropland information. These products are freely available for downloading from the http://cropland.geo-wiki.org website.

Downgrading recent estimates of land available for biofuel production

Recent estimates of additional land available for bioenergy production range from 320 to 1411 million ha. These estimates were generated from four scenarios regarding the types of land suitable for bioenergy production using coarse-resolution inputs of soil productivity, slope, climate, and land cover. In this paper, these maps of land availability were assessed using high-resolution satellite imagery. Samples from these maps were selected and crowdsourcing of Google Earth images was used to determine the type of land cover and the degree of human impact. Based on this sample, a set of rules was formulated to downward adjust the original estimates for each of the four scenarios that were previously used to generate the maps of land availability for bioenergy production. The adjusted land availability estimates range from 56 to 1035 million ha depending upon the scenario and the ruleset used when the sample is corrected for bias. Large forest areas not intended for biofuel production purposes were present in all scenarios. However, these numbers should not be considered as definitive estimates but should be used to highlight the uncertainty in attempting to quantify land availability for biofuel production when using coarse-resolution inputs with implications for further policy development.

Differences in substrate specificity and kinetic properties of the recombinant hexokinases HXK1 and HXK2 from Entamoeba histolytica

Entamoeba histolytica is responsible for amoebic colitis and liver abscess in humans. Entamoeba dispar is a closely related, morphologically indistinguishable nonpathogenic species. The hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) isoenzyme patterns distinguish the pathogenic and nonpathogenic species. Both species possess two hexokinases with very similar molecular mass and different isoelectric points. In order to understand the role of the two different isoenzymes from E. histolytica, we purified the recombinant hexokinases HXK1 and HXK2 and examined substrate spectrum and kinetic properties. The two enzymes displayed similar temperature and pH optima, they were inhibited strongly by AMP and ADP, not by glucose 6-phosphate. Both enzymes phosphorylated glucose well and were unable to phosphorylate fructose or galactose. We also detected significant differences. HXK1 was more sensitive to inhibition by AMP and ADP. Mannose was phosphorylated well by HXK1, but at a much lower rate by HXK2. We attempted to expand the substrate spectrum of E. histolytica HXK1 by modifying its active site to become similar to the active site of the fructose phosphorylating yeast hexokinase PII. None of the nine mutants gained any fructokinase activity, but all of them retained at least some glucokinase and mannokinase activity. Mannokinase activity was decreased drastically by two single amino acid exchanges, both of which contributed significantly to this effect. The data indicate that a complex interaction of a number of amino acid residues is necessary for the ability to phosphorylate a given hexose.

Molecular and biochemical characterization of phosphoglucomutases from Entamoeba histolytica and Entamoeba dispar

Entamoeba histolytica and Entamoeba dispar have only recently been defined as two separate species. E. histolytica, the pathogenic species, is the microorganism causing invasive intestinal amoebiasis and/or liver abscess, while the morphologically similar E. dispar is nonpathogenic and noninvasive. The gold standard for the distinction of the two species has been the isoenzyme electrophoresis of phosphoglucomutases (EC 5.4.2.2) and hexokinases (EC 2.7.1.1), but there had also been a controversy about the possibility of a conversion of isoenzyme patterns. In this study, we cloned the phosphoglucomutase (PGM) cDNAs from the pathogenic and the nonpathogenic species. The deduced amino acid sequences were only 2.4% different. The cDNAs were expressed in Escherichia coli under the control of a T7 RNA polymerase promoter. The recombinant polypeptides displayed strong phosphoglucomutase activity, each of the recombinant enzymes comigrated with its natural counterpart from E. histolytica and E. dispar in the starch gel electrophoresis. Our results give a biochemical interpretation of the PGM isoenzyme pattern and support the clear distinction between the two species.

Molecular biology of the hexokinase isoenzyme pattern that distinguishes pathogenic Entamoeba histolytica from nonpathogenic Entamoeba dispar

The electrophoretic patterns of hexokinase and phosphoglucomutase have been widely used to distinguish Entamoeba histolytica from Entamoeba dispar isolates. Although E. histolytica and E. dispar, previously called pathogenic and nonpathogenic Entamoeba histolytica, differ clearly in sequences of many homologous genes, a conversion between the two has been reported by several laboratories, in each case showing the conversion of hexokinase (ATP, D-hexose 6-phosphotransferase, EC 2.7.1.1) isoenzyme patterns. An apparent mobility shift of this enzyme may either be due to posttranslational modification or processing, or to the appearance of a new isoform encoded by a second gene. In this study we observed that the four observed bands in the isoenzyme patterns of pathogenic and nonpathogenic forms of Entamoeba were correlated with four different cDNAs, and that the four recombinant hexokinases produced in Escherichia coli comigrated with their natural counterparts. Polymerase chain reaction (PCR) experiments did not reveal hidden genes which might be responsible for conversion phenomena. These results strongly support the redefinition of pathogenic and nonpathogenic Entamoeba histolytica as two closely related species Entamoeba histolytica and Entamoeba dispar.

Value of neutrophil CD16 expression for detection of left shift and acute-phase response

Fc gamma RIII (CD16) expression of neutrophil granulocytes was measured in 156 patients by means of fluorescence-labeled antibodies with a flow cytometer. Results were compared with (1) 400-cell manual differential count; (2) left shift flagging on hematology analyzers; (3) absolute neutrophil count; and (4) acute-phase protein levels. Asynchrony was noted between neutrophil CD16 expression and microscopically defined neutrophil stage, particularly in heavily left-shifted samples, which made it impossible to reliably enumerate immature neutrophils on the basis of CD16 expression. According to receiver operating characteristics, the absolute count of CD16-negative neutrophils was highly discriminatory for detection of left shift, with an area under the curve (AUC) of 0.842 +/- 0.03 (SE) and maximum efficiency of 81% +/- 3%, but absolute neutrophil count was not significantly inferior (0.821 +/- 0.03 and 76% +/- 3%). STKS and SE9000 flagging demonstrated efficiency of 76% +/- 3% and 81% +/- 3%, respectively. For detection of acute-phase response, absolute neutrophil count (AUC, 0.836 +/- 0.04; maximum efficiency, 80% +/- 4%) outperformed both quantitative neutrophil CD16 expression (0.760 +/- 0.05; 75% +/- 4%) and absolute CD16-negative neutrophil count (0.757 +/- 0.05; 71% +/- 4%); absolute band count performed similarly (0.853 +/- 0.04; 79% +/- 4%) and showed high efficiency at high sensitivity and specificity. Efficiency of analyzer flagging for detection of acute-phase response was not superior to absolute neutrophil count (STKS, 77% +/- 4%; SE9000, 78% +/- 4%). In conclusion, the diagnostic value of measuring neutrophil CD16 expression was generally similar to that of less complicated analytes.

The basic isoform of profilin in pathogenic Entamoeba histolytica. cDNA cloning, heterologous expression, and actin-binding properties

In the human parasite Entamoeba histolytica, components of the cytoskeleton are involved in the pathogenicity by their contribution to immune evasion by antibody capping and shedding. In this study, we focus on profilin as a central regulatory component of the cytoskeleton. Profilin was isolated from trophozoites of the pathogenic E. histolytica strain SFL-3, and partial amino acid sequences were used to devise a probe for isolating a profilin cDNA. The deduced complete primary structure was divergent: plant profilins with amino acid sequence identities in the range 33-38% were more closely related than the mammalian profilins with sequence identities 21-28%. The cDNA was expressed as a nonfusion protein in Escherichia coli. Isoelectric focussing of the natural profilin isolated from E. histolytica showed two isoforms with different isoelectric points; the recombinant profilin migrated with the basic isoform. In a blot overlay experiment, purified 125I-labeled recombinant profilin bound not only to plant actin, but also to mammalian actin, demonstrating that cytoskeletal components from distantly related organisms with divergent primary structures can be compatible.

Molecular analysis of two hexokinase isoenzymes from Entamoeba histolytica

The zymodemes, electrophoretic patterns of hexokinase, phosphoglucomutase and glucose phosphate isomerase isoenzymes, have been widely used to determine the pathogenicity of Entamoeba histolytica isolates. Although pathogenic and nonpathogenic forms of E. histolytica differ clearly in sequences of many homologous genes, a conversion between pathogenic and nonpathogenic zymodemes has been reported by several laboratories. To approach the question what might be the basis for the observed conversion, we examined the molecular biology of the hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) isoenzymes in pathogenic E. histolytica. We isolated two different cDNAs pHXK1 and pHXK2 coding for polypeptides with significant sequence similarity to hexokinases and deduced molecular masses of 49.8 kDa and 49.4 kDa. The two hexokinase sequences differed by 11% on the amino acid and by 8% on the nucleotide level. Expression of the cDNAs in Escherichia coli as nonfusion proteins gave two polypeptides with hexokinase activity. The recombinant Hxk1 and Hxk2 polypeptides comigrated with the more basic and more acidic isoforms of pathogenic amoebae in starch gel electrophoresis, as well as in low and high resolution isoelectric focussing gels. This identified the observed hexokinase isoenzymes of pathogenic E. histolytica as the products of two genes, hxk1 and hxk2.

Pathogenic Entamoeba histolytica: cDNA cloning of a histone H3 with a divergent primary structure

Entamoeba histolytica has an unusual nuclear structure characterized by a low degree of chromatin condensation and the absence of stainable metaphase chromosomes. Although nucleosome-like particles were observed, no information about histones was available so far. In this paper we describe a cDNA clone with significant homology to H3 histones that was isolated from a library of pathogenic E. histolytica. The complete cDNA encodes a 15-kDa polypeptide, which like the histone sequence from Volvox carteri is shorter by one residue than the human homologue. The amino acid sequence has only 69% identity with human H3.3 histone and 67% identity with the human H3.1 histone. This is the highest degree of sequence divergence observed for any eukaryote H3 histone sequence. Our results indicate that this divergence may contribute to the unusual chromatin structure of E. histolytica.

Molecular characterization of the cDNA coding for translation elongation factor-2 of pathogenic Entamoeba histolytica

To investigate the humoral immune response of patients with amoebic dysentry against Entamoeba histolytica, immunoglobulin G (IgG)-immunopositive cDNA clones from the pathogenic strain SFL-3 were examined. A large part of the IgG-positive cDNA clones obtained with one serum encoded highly conserved intracellular proteins. A clone was found that was homologous to translation elongation factor-2 (EF-2). Sequence analysis of the EF-2 cDNA showed 63.6% amino acid sequence identity with the human homologue. The deduced protein sequence has a length of 840 amino acid residues with a molecular mass of 93.3 kD. The 3' and 5' untranslated regions of the mRNA are relatively short as shown for other genes of E. histolytica. A genomic clone was used to analyze the region upstream of the translation initiation codon. The codon distribution of EF-2 and other published E. histolytica sequences reflects the high A/T content. The codons for different amino acids are biased to a widely differing extent.

Humoral immune response against a 70-kilodalton heat shock protein of Entamoeba histolytica in a group of patients with invasive amoebiasis

In order to investigate the humoral immune response against Entamoeba histolytica a lambda ZapII cDNA library was constructed from trophozoites of the pathogenic E. histolytica strain SFL-3. The library was screened with serum IgG from a patient with invasive amoebiasis. Forty-nine immunopositive lambda clones were isolated and partial sequences from the inserts were obtained. By comparison of the sequences with the merged database MIPSX from the Martinsried Institute for Protein Sequences we were able to identify homologous proteins for 36 of the clones. Twenty-six of the clones encoded intracellular proteins, among these, the major part (16 clones) were highly homologous to the eukaryotic 70-kDa heat shock proteins (Hsps). The open reading frame of one complete clone encodes a protein of 656 amino acid residues of 71.5 kDa which has 69.8% sequence identity with the human Hsp70 protein. In a larger screening experiment only 3 out of 12 patients detected with their IgG the phage which expressed the 70-kDa heat shock protein(s).