The HOX-5 and surfeit gene clusters are linked in the proximal portion of mouse chromosome 2

Using an interspecies backcross, we have mapped the HOX-5 and surfeit (surf) gene clusters within the proximal portion of mouse chromosome 2. While the HOX-5 cluster of homeobox-containing genes has been localized to chromosome 2, bands C3-E1, by in situ hybridization, its more precise position relative to the genes and cloned markers of chromosome 2 was not known. Surfeit, a tight cluster of at least six highly conserved “housekeeping” genes, has not been previously mapped in mouse, but has been localized to human chromosome 9q, a region of the human genome with strong homology to proximal mouse chromosome 2. The data presented here place HOX-5 in the vicinity of the closely linked set of developmental mutations rachiterata, lethargic, and fidget and place surf close to the proto-oncogene Abl, near the centromere of chromosome 2.     

Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production

Microbiological investigation of anaerobic ammonium oxidizing (anammox) bacteria has until now been restricted to wastewater species. The present study describes the enrichment and characterization of two marine Scalindua species, the anammox genus that dominates almost all natural habitats investigated so far. The species were enriched from a marine sediment in the Gullmar Fjord (Sweden) using a medium based on Red Sea salt. Anammox cells comprised about 90% of the enrichment culture after 10 months. The enriched Scalindua bacteria displayed all typical features known for anammox bacteria, including turnover of hydrazine, the presence of ladderane lipids, and a compartmentalized cellular ultrastructure. The Scalindua species also showed a nitrate-dependent use of formate, acetate and propionate, and performed a formate-dependent reduction of nitrate, Fe(III) and Mn(IV). This versatile metabolism may be the basis for the global distribution and substantial contribution of the marine Scalindua anammox bacteria to the nitrogen loss from oxygen-limited marine ecosystems.     

New pathways for ammonia conversion in soil and aquatic systems

Ammonia conversion processes are essential for most soil and aquatic systems. Under natural conditions, the many possible reactions are difficult to analyze. For example, nitrification and denitrification have long been regarded as separate phenomena performed by different groups of bacteria in segregated areas of soils, sediments or aquatic systems sequentially in time. It has now been established that strict segregation in place and time of the two processes is not necessary and that both denitrifiers and nitrifiers have versatile metabolisms. However, the rates described for aerobic denitrifiers are very low compared to the rates observed under anoxic conditions. Also the rates of nitrifier denitrification are quite low, indicating that these conversions may not play an important role under natural conditions. In addition, these processes often result in the emission of quite large amounts of undesirable products, NO and N₂O. Heterotrophic nitrification might be of relevance for systems, that contain a high carbon to nitrogen ratio. Recently, a novel process (Anammox) has been discovered in which ammonium serves as the electron donor for denitrification of nitrite into dinitrogen gas. ¹⁵N labeling studies showed that hydrazine and hydroxylamine were important intermediates in this process. Enrichment cultures on ammonium, nitrite and bicarbonate resulted in the dominance of one morphotypical microorganism. The growth rate of the cultures is extremely low (doubling time 11 days), but the affinity for ammonium and nitrite and the conversion rates (9.2 10^–4 mol kg^–1 s^–1) are quite high. Some of the reported high nitrogen losses in soil and aquatic systems might be attributed to anaerobic ammonium oxidation. In addition, this conversion offers new opportunities for nitrogen removal, when it is combined with recently developed processes for partial nitrification.     

Cell-surface markers for the isolation of pancreatic cell types derived from human embryonic stem cells

Using a flow cytometry-based screen of commercial antibodies, we have identified cell-surface markers for the separation of pancreatic cell types derived from human embryonic stem (hES) cells. We show enrichment of pancreatic endoderm cells using CD142 and of endocrine cells using CD200 and CD318. After transplantation into mice, enriched pancreatic endoderm cells give rise to all the pancreatic lineages, including functional insulin-producing cells, demonstrating that they are pancreatic progenitors. In contrast, implanted, enriched polyhormonal endocrine cells principally give rise to glucagon cells. These antibodies will aid investigations that use pancreatic cells generated from pluripotent stem cells to study diabetes and pancreas biology.     

Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding

The terminal region of barley chromosome 5HL controls malt extract, diastatic power, free amino acid nitrogen, alpha-amylase activity, seed dormancy and pre-harvest sprouting. Comparative analysis of the barley and rice maps has established that the terminal region of barley chromosome 5HL is syntenic to rice chromosome 3L near the telomere end. The rice BAC (Bacterial Artificial Chromosome) sequences covering the region of chromosome 3L were used to search barley expressed sequenced tags database. Thirty-three genes were amplified by PCR (polymerase chain reaction) with the primers designed from barley ESTs (expressed sequence tag). Comparison of the sequences of the PCR generated DNA fragments revealed polymorphisms including single nucleotide polymorphism (SNP), insertions or deletions between the barley varieties. Seven new PCR based molecular markers were developed and mapped within 10 cM in three doubled haploid barley populations (Stirling × Harrington, Baudin × AC Metcalfe and Chebec × Harrington). The mapped genes maintain the micro-syntenic relationship between barley and rice. These gene specific markers provide simple and efficient tools for germplasm characterization and marker-assisted selection for barley malting quality, and ultimately lead to isolation and identification of the major gene(s) controlling multiple quality traits on barley chromosome 5HL.     

Impaired carotenogenesis can affect organization and functionality of etioplast membranes

The effects of impaired carotenogenesis on plastid membrane organization, functionality and stability were studied in etiolated barley plants grown at 20 and 30°C. The plants were treated with norflurazon or amitrole, two herbicides affecting phytoene desaturation and lycopene cyclization, respectively. At 20°C, the amitrole-treated etioplasts, which accumulated lycopene in their inner membranes, exhibited disorganized prolamellar bodies, containing a prevalent form of non-phototransformable protochlorophyllide (Pchlide). They also showed a certain difficulty in reducing the phototransformable pigment to chlorophyllide when exposed to light, and were unable to reform the active ternary complex [protochlorophyllide–oxidoreductase (POR)–Pchlide–NADPH] when placed back in darkness. No ultrastructural alterations were found in norflurazon-treated etioplasts, with carotenogenesis inhibited at the phytoene desaturation step. In these latter organelles, Pchlide, whose forms were comparable with those of the control etioplasts, was photoreduced quickly after illumination and the ternary complex was reformed during a subsequent dark period. Thus, the impaired carotenogenesis leading to the accumulation of lycopene showed greater interference with the etioplast membrane arrangement and functionality than did the earlier interruption of the biosynthetic pathway at the phytoene level. This might be due to the different interactions of the distinct carotenoid precursors with other membrane components. However, in etioplasts of norflurazon-treated plants, a rise in growth temperature caused a partial demolition of prolamellar bodies, showing a lowered thermostability of the carotenoid-deficient membranes. This latter effect strengthens the concept that a correct and complete carotenogenesis pathway, leading to the synthesis of polar carotenoids (i.e. xanthophylls), is required for the maintenance of stable plastid membranes.     

The potential and realized spread of wildfires across Canada

Given that they can burn for weeks or months, wildfires in temperate and boreal forests may become immense (eg., 10⁰ – 10⁴ km²). However, during the period within which a large fire is ‘active’, not all days experience weather that is conducive to fire spread; indeed most of the spread occurs on a small proportion (e.g., 1 – 15 days) of not necessarily consecutive days during the active period. This study examines and compares the Canada‐wide patterns in fire‐conducive weather (‘potential’ spread) and the spread that occurs on the ground (‘realized’ spread). Results show substantial variability in distributions of potential and realized spread days across Canada. Both potential and realized spread are higher in western than in eastern Canada; however, whereas potential spread generally decreases from south to north, there is no such pattern with realized spread. The realized‐to‐potential fire‐spread ratio is considerably higher in northern Canada than in the south, indicating that proportionally more fire‐conducive days translate into fire progression. An exploration of environmental correlates to spread show that there may be a few factors compensating for the lower potential spread in northern Canada: a greater proportion of coniferous (i.e., more flammable) vegetation, lesser human impacts (i.e., less fragmented landscapes), sufficient fire ignitions, and intense droughts. Because a linear relationship exists between the frequency distributions of potential spread days and realized spread days in a fire zone, it is possible to obtain one from the other using a simple conversion factor. Our methodology thus provides a means to estimate realized fire spread from weather‐based data in regions where fire databases are poor, which may improve our ability to predict future fire activity.     

Animal movements in fire‐prone landscapes

Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire‐prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer‐term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire‐prone ecosystems.     

Reproducibility of protein identification of selected cell types in Barrett's esophagus analyzed by combining laser-capture microdissection and mass spectrometry

Barrett's esophagus (BE) is associated with increased risk of esophageal adenocarcinoma (EAC) and characterized by replacement of normal esophageal squamous epithelium by columnar epithelium. These alterations are also reflected in changes in the protein-expression profiles of the cell types involved. To separately investigate the proteomes of selected cell-types we combined laser-capture microdissection (LCM) and liquid chromatography-mass spectrometry (LC-MS). Aims were to determine the sensitivity, specificity, and technical reproducibility of the sampling method, and the biological variability within and between biopsies and patients. Frozen biopsies were cryo-sectioned, samples of around 2000 epithelial or stroma cells microdissected, digested and measured by Orbitrap LC-MS. Proteins were then identified by MS/MS database search and quantified by label-free analysis. An average of 366 protein-groups were identified per sample, and more protein-groups were found in epithelial samples than in stromal samples (442 vs 301, p < 0.0001). Altogether, 1254 distinct protein-groups were found, 289 and 88 of them significantly more often in epithelial and stroma samples, respectively. We assessed five different types of reproducibilities (run-to-run, intrabiopsy, biopsy-to-biopsy, experiment-to-experiment, and patient-to-patient) for protein identification and protein quantification. Reproducibility of protein identification ranged from 78 to 57%, and standard deviation of protein quantification was on patient-to-patient level four times higher than for run-to-run. We conclude that sampling around 2000 cells requires groups of 32 samples to detect significant, over 10-fold differences in protein abundances and thus creates a successful compromise between throughput and quality of results. We therefore believe that this method is suitable for investigating protein-expression profiles during carcinogenesis.     

Feeding ecology of Lilian’s Lovebird Agapornis lilianae in Liwonde National Park,Malawi

Lilian's Lovebird Agapornis lilianae is a small, near-threatened parrot resident in mopane Colophospermum mopane woodlands. We investigated its diet and foraging behaviour in Liwonde National Park, Malawi. We expected that Lilian's Lovebirds would show little specialisation for a particular food source but generally feed on available seeds, fruits, flowers and other items as observed in other lovebirds. Lilian's Lovebirds fed on 30 different plant species. Lilian's Lovebirds were observed feeding in six habitat types in Liwonde National Park and adjacent areas during the wet season, and four in the dry season. In the wet season lovebirds (23% of observations) foraged in grassy wetland (dambo) areas the most, whilst in the dry season they foraged in grasslands with tree cover (18%) the most. In mopane woodland, foraging flock sizes differed significantly between the wet (mean = 19.8 ± 1.0 lovebirds) and dry season (mean = 33.6 ± 2.3 lovebirds). Grass seeds were lovebirds’ main food source from December to June. The nutritional analysis of preferred foods showed that grass seeds have a relatively high protein and energy content. Grass seed availability is reduced with savanna burning and so early season burning (before May–June) in areas in and outside the park is not recommended.