Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.     

Intracellular measurement of ammonium in Chara corallina using ion-selective microelectrodes

The study of ammonium (NH₄ ⁺) transport across plant cell membranes requires accurate measurement of NH₄ ⁺ gradients across subcellular gradients. We have developed an ammonium-selective microelectrode based on the ionophore nonactin. This electrode can detect NH₄ ⁺ activities (a_NH4) in vivo in the millimolar range in the presence of cytosolic levels of potassium, the main interfering ion. The electrode was used to measure intracellular a_NH4 in internodal cells of the giant alga Chara corallina. Results from cells incubated in media supplemented with 1 mM NH₄ ⁺ produced two populations, with means of 7.3 and 30.8 mM, respectively. HPLC analysis of vacuolar sap suggests the higher population represents vacuolar impalements, and the lower population can thus be assumed to be cytosolic. These results suggest a four-fold accumulation of NH₄ ⁺ in the vacuolar compartment of Chara. This revised version was published online in June 2006 with corrections to the Cover Date.     

Characterization of Tiki,a New Family of Wnt-specific Metalloproteases

The Wnt family of secreted glycolipoproteins plays pivotal roles in development and human diseases. Tiki family proteins were identified as novel Wnt inhibitors that act by cleaving the Wnt amino-terminal region to inactivate specific Wnt ligands. Tiki represents a new metalloprotease family that is dependent on Mn²⁺/Co²⁺ but lacks known metalloprotease motifs. The Tiki extracellular domain shares homology with bacterial TraB/PrgY proteins, known for their roles in the inhibition of mating pheromones. The TIKI/TraB fold is predicted to be distantly related to structures of additional bacterial proteins and may use a core β-sheet within an α+β-fold to coordinate conserved residues for catalysis. In this study, using assays for Wnt3a cleavage and signaling inhibition, we performed mutagenesis analyses of human TIKI2 to examine the structural prediction and identify the active site residues. We also established an in vitro assay for TIKI2 protease activity using FRET peptide substrates derived from the cleavage motifs of Wnt3a and Xenopus wnt8 (Xwnt8). We further identified two pairs of potential disulfide bonds that reside outside the β-sheet catalytic core but likely assist the folding of the TIKI domain. Finally, we systematically analyzed TIKI2 cleavage of the 19 human WNT proteins, of which we identified 10 as potential TIKI2 substrates, revealing the hydrophobic nature of Tiki cleavage sites. Our study provides insights into the Tiki family of proteases and its Wnt substrates.     

The use of historical environmental monitoring data to test predictions on cross-scale ecological responses to alterations in river flows

Determination of ecological responses to river flows is fundamental to understanding how flow-dependent ecosystems have been altered by regulation, water diversions and climate change, and how to effect river restoration. Knowledge of ecohydrological relationships can support water management and policy, but this is not always the case. Management rules have tended to be developed ahead of scientific knowledge. The lag between practice and knowledge could be addressed by using historical monitoring data on ecological responses to changes in flows to determine significant empirical ecohydrological relationships, as an adjunct to investigating responses prospectively. This possibility was explored in the Murray–Darling Basin, Australia. We assessed 359 data sets collected during monitoring programs across the basin. Of these, only 32 (9%) were considered useful, based on a match between the scale at which sampling was done and ecological responses are likely to occur, and used to test flow–ecology predictions for phytoplankton, macroinvertebrates, fishes, waterbirds, floodplain trees, basin-scale vegetation and estuarine biota. We found relationships between flow and ecological responses were likely to be more strongly supported for large, long-lived, widespread biota (waterbirds, basin-scale vegetation, native fishes), than for more narrowly distributed (e.g. estuarine fishes) or smaller, short-lived organisms (e.g. phytoplankton, macroinvertebrates). This pattern is attributed to a mismatch between the design of monitoring programs and the response time frames of individual biota and processes, and to the use of local river discharge as a primary predictor variable when, for many biotic groups, other predictors need to be considered.     

Satellite tracking and diving behaviour of sub-adult narwhals (<Emphasis Type="Italic">Monodon monoceros</Emphasis>) in Svalbard,Norway

Three juvenile narwhals captured during August 1998 in the northeast of Svalbard, Norway, were equipped with satellite-relayed data loggers (SRDLs) that transmitted diving and swim-speed data, in addition to location, for up to 46 days. A total of 1,354 complete dive cycles were recorded. Most of the diving was shallow and of short duration. Maximum recorded dive depth was 546 m, maximum recorded dive duration was 24.8 min, and maximum recorded swim-speed was 4.7 ms⁻¹. Ascent speed, vertical ascent speed, descent speed and vertical descent speed were all significantly higher during deep dives (>200 m) than for shallow dives (<200 m). In addition both ascent and descent angles were much steeper for deep dives than during shallow dives. Most of the shallow diving seemed to be associated with travelling, with the animal shifting between various locations, while the deep diving (often to the bottom) for extended periods in some specific areas might have been associated with foraging. Even though the sample size in this study is small, the data are the first information available for movements and diving behaviour of narwhals near Svalbard.     

Intramolecular carboxylate catalysis in the depurination of a 7-methylguanosine derivative

We have compared the pH-independent rates of glycosidic hydrolysis in a carboxylate-bearing 7-methylguanosine derivative with those of a reference compound and with that of 7-methylguanosine itself. A syn-oriented carboxylate group affords catalysis in the hydrolysis reaction, although the instability of 7-alkylguanosines above pH 7 severely limits the useful pH range that could be studied. The effect of the carboxylate near neutral pH can be viewed in three different ways: it provides a 3-fold acceleration as compared to underivatized 7-methylguanosine, an approximately 30-fold acceleration when the decelerating effect of the ketal group is considered, and because of slow decomposition of the reference compound under the reaction conditions, we conclude that the carboxylate provides an acceleration of ≥43-fold as compared to the protio reference compound.     

Molecular cloning and characterization of complementary deoxyribonucleic acids corresponding to bovine trophoblast protein-1: a comparison with ovine trophoblast protein-1 and bovine interferon-alpha II

Bovine trophoblast protein-1 (bTP-1) is a secreted glycoprotein that consists of several forms differing slightly in mol wt and isoelectric point. It is produced by bovine conceptuses after about day 15 of pregnancy and is believed to play a key role in signalling the presence of an embryo to the mother. In this study, a series of recombinant cDNA clones corresponding to the mRNA for bTP-1 have been isolated from cDNA libraries representing day 18-19 bovine conceptus poly(A)+ mRNA. Base sequencing of several cDNAs indicated that multiple mRNAs for bTP-1 exist. Northern blotting and primer extension experiments showed that the mRNAs average about 1 kilobase in length. One apparently full-length cDNA clone consisted of 1035 bases up to the beginning of the poly(A) tail. It contained an open reading frame of 195 codons which began at a position 79 bases from the 5' end. Its entire sequence was 85% identical to that of a cDNA for the immunologically related ovine trophoblast protein-1 (oTP-1) and about 79% identical to that for a bovine interferon-alpha II (IFN alpha II). The highest conservation of sequence (greater than 90%) was noted in the 3'-untranslated sequences of the bTP-1 and oTP-1 cDNAs. The deduced amino acid sequence of bTP-1 shared 80% identity with oTP-1, between 45-55% with human, rodent, porcine, and bovine IFNs of the alpha 1 subfamily and about 70% with a bovine IFN alpha II. A single potential site for N-glycosylation was noted at Asn78. These results show that bTP-1, like its ovine counterpart oTP-1, is structurally related to the IFN alpha S. We suggest that these embryonic IFNs play a role in controlling immunoreactions at the trophoblast-uterus interface as well as triggering other maternal responses to pregnancy.     

Molecular characterization and genetic mapping of two clusters of genes encoding chlorophyll a/b-binding proteins in Lycopersicon esculentum (tomato)

We have constructed a tomato genomic library in the λ Charon 4 phage vector. The library was screened with a pea cDNA probe encoding a chlorophyll a/b-binding protein (CAB), and several recombinant phages containing tomato CAB genes were isolated and characterized by restriction mapping, heteroduplex analysis and nucleotide sequencing. Two phages with overlapping segments of the tomato genome contain a total of four CAB genes, all arranged in tandem. A third phage contains three CAB genes, two arranged in tandem and one in opposite orientation, and an additional, truncated CAB gene. Genetic mapping experiments showed that the four CAB genes on the first two phages belong to a locus, previously designated Cab-1, on chromosome 2. The CAB genes from the third phage belong to the Cab-3 locus on chromosome 3. Complete sequence determination of two CAB genes, one from each locus, and additional sequence determination of about 50% of each of the other five CAB genes showed that each gene within a CAB locus is more similar to other CAB genes in the same locus than it is to the CAB genes from the second locus. Furthermore, the polypeptides encoded by Cab-1 genes diverge significantly from those encoded by Cab-3 genes in the domains of transit peptide and the N terminus of the mature polypeptide but are essentially identical in the rest of the sequence.     

Two new dinosaur tracksites from the Lower Cretaceous Jiaguan Formation of Sichuan Basin,China: specific preservation and ichnotaxonomy

Two new dinosaur tracksites are reported from the Lower Cretaceous Jiaguan Formation in the Sichuan Basin, Qijiang District of Chongqing. These are the Gaoqing-Yongsheng and the Huibu tracksites, which represent the 13th and 14th reports from this formation. The Gaoqing-Yongsheng tracksite reveals the trackway of a large biped (ornithopod) in association with isolated sauropod tracks and large indeterminate undertracks with radial cracks. These features are preserved as natural casts with pebble infillings in a coarse, cross bedded and very thick bedded sandstone sequence. The Huibu tracksite reveals isolated theropod tracks and ornithopod tracks, the latter having a quadripartite, Caririchnium-like morphology, preserved in a thin bedded sandstone sequence with intercalated mudstone.     

Metabolic engineering of Escherichia coli for 1-butanol production

Compared to ethanol, butanol offers many advantages as a substitute for gasoline because of higher energy content and higher hydrophobicity. Typically, 1-butanol is produced by Clostridium in a mixed-product fermentation. To facilitate strain improvement for specificity and productivity, we engineered a synthetic pathway in Escherichia coli and demonstrated the production of 1-butanol from this non-native user-friendly host. Alternative genes and competing pathway deletions were evaluated for 1-butanol production. Results show promise for using E. coli for 1-butanol production.