Function of the ypt2 gene in the exocytic pathway of Schizosaccharomyces pombe.

The ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the ypt/rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian rab8. We have introduced a mutation into the gene corresponding to a mutation identified in ypt1, in which a conserved valine residue was altered to asparagine. The mutated ypt2 gene was introduced into the S. pombe genome by gene replacement. The resulting strain was temperature-sensitive for growth. Normal growth was restored by introduction of a plasmid-borne wild-type ypt2 cDNA or by cDNA for rab8 but not by various other rab or ypt sequences. At restrictive temperature the mutant cells accumulated the secretory protein acid phosphatase in a form that appeared to be fully glycosylated and acquired a population of vesicles detectable by electron microscopy. Thus the ypt2 protein, and by inference rab8, appear to function in the last stage of the secretory pathway.     

Mesoproterozoic surface oxygenation accompanied major sedimentary manganese deposition at 1.4 and 1.1 Ga

Manganese (Mn) oxidation in marine environments requires oxygen (O₂) or other reactive oxygen species in the water column, and widespread Mn oxide deposition in ancient sedimentary rocks has long been used as a proxy for oxidation. The oxygenation of Earth's atmosphere and oceans across the Archean-Proterozoic boundary are associated with massive Mn deposits, whereas the interval from 1.8–1.0 Ga is generally believed to be a time of low atmospheric oxygen with an apparent hiatus in sedimentary Mn deposition. Here, we report geochemical and mineralogical analyses from 1.1 Ga manganiferous marine-shelf siltstones from the Bangemall Supergroup, Western Australia, which underlie recently discovered economically significant manganese deposits. Layers bearing Mn carbonate microspheres, comparable with major global Mn deposits, reveal that intense periods of sedimentary Mn deposition occurred in the late Mesoproterozoic. Iron geochemical data suggest anoxic-ferruginous seafloor conditions at the onset of Mn deposition, followed by oxic conditions in the water column as Mn deposition persisted and eventually ceased. These data imply there was spatially widespread surface oxygenation ~1.1 Ga with sufficiently oxic conditions in shelf environments to oxidize marine Mn(II). Comparable large stratiform Mn carbonate deposits also occur in ~1.4 Ga marine siltstones hosted in underlying sedimentary units. These deposits are greater or at least commensurate in scale (tonnage) to those that followed the major oxygenation transitions from the Neoproterozoic. Such a period of sedimentary manganogenesis is inconsistent with a model of persistently low O₂ throughout the entirety of the Mesoproterozoic and provides robust evidence for dynamic redox changes in the mid to late Mesoproterozoic.     

Species richness and assemblages of bats along a forest elevational transect in Papua New Guinea

Over the past decades, elevational gradients have become a powerful tool with which to understand the underlying cause(s) of biodiversity. The Mt. Wilhelm elevational transect is one such example, having been used to study the birds, insects, and plants of Papua New Guinea (PNG). However, a survey of mammals from this forest elevational transect was lacking. We thus aimed to investigate patterns in the community structure and species richness of bats (Chiroptera) along the transect, link the species to available regional data, and explain the observed patterns by including environmental characteristics. Bat assemblages were surveyed between 200 m and a timberline at 3700 m a.s.l. at eight study sites separated by 500 m in elevation. We conducted mist-netting and acoustic surveys to detect and identify species at each site. Regional data were compiled to compare local with regional diversity. Finally, biotic (i.e., food availability, habitat features) and abiotic (i.e., mean daily temperature) factors were included in our analyses to disentangle the ecological drivers underlying bat diversity. Results revealed that species richness decreases with ascending elevation and was best explained by a corresponding decrease in temperature. We observed both turnover and nestedness of the species composition at regional scale whereas turnover was dominant at local scale. Extensions and shifts of bat elevational ranges were also found in Mt. Wilhelm. Consequently, despite that the study was restricted to one mountain in PNG, it demonstrates how basic inventory surveys can be used to address ecological questions in other similar and undisturbed tropical mountains.     

Waterfowl distribution and productivity in the Prairie Pothole Region of Canada: tools for conservation planning

Species conservation requires an understanding of the factors and interactions affecting species distribution and behavior, habitat availability and use, and corresponding vital rates at multiple temporal and spatial scales. Opportunities to investigate these relationships across broad geographic regions are rare. We combined long-term waterfowl population surveys, and studies of habitat use and breeding success, to develop models that identify and incorporate these interactions for upland-nesting waterfowl in the Prairie Pothole Region (PPR) of Canada. Specifically, we used data from the annual Waterfowl Breeding Population and Habitat Survey (1961–2009) at the survey segment level and associated habitat covariates to model and map the long-term average duck density across the Canadian PPR. We analyzed nest location and fate data from approximately 25,000 duck nests found during 3 multi-year nesting studies (1994–2011) to model factors associated with nest survival and habitat selection through the nesting season for the 5 most common upland nesting duck species: mallard (Anas platyrhynchos), gadwall (Mareca strepera), blue-winged teal (Spatula discors), northern shoveler (Spatula clypeata), and northern pintail (Anas acuta). Duck density was highly variable across the Canadian PPR, reflecting positive responses to local wetland area and count, and amounts of cropland and grassland, a regional positive response to latitude, and a negative response to local amounts of tree cover. Nest survival was affected by temporal and spatial variables at multiple scales. Specifically, nest survival demonstrated interactive effects among species, nest initiation date, and nesting cover type and was influenced by relative annual wetness, population density, and surrounding landscape composition at landscape scales, and broad geographic gradients (east-west and north-south). Likewise, species-specific probability of nest habitat selection was influenced by timing of nest initiation, population density, relative annual wetness, herbaceous cover, and tree cover in the surrounding landscape, and location within the Canadian PPR. We combined these models, with estimates of breeding effort (nesting, renesting, and nest attempts) from existing literature, in a stochastic conservation planning model that estimates nest distribution and success given spatiotemporal variation in duck density, habitat availability, and influential covariates. We demonstrate the use of this model by examining various conservation planning scenarios. These models allow estimation of local, landscape, and regional influence of conservation investments and other landscape changes on the productivity of breeding duck populations across the PPR of Canada. These models lay the groundwork for the incorporation of conservation delivery costs for full return-on-investment analyses and scenario analyses of climate, habitat, and land use change in regional and continental population models.     

Distribution of the reef manta ray Mobula alfredi and the oceanic manta ray Mobula birostris in the Philippines: a collaborative effort for conservation

Little is known about manta ray population size, structure and connectivity in the Philippines. In collaboration with dive operators, non-governmental organizations and authorities, sightings of manta rays were collated into a single national database. Using in-water photographs and videos gathered through citizen science and dedicated research efforts, this study compiled sightings between 2004 and 2020, showing 22 separate sites throughout the archipelago with manta rays present. A total of 392 individual reef manta rays (Mobula alfredi) and 107 oceanic manta rays (Mobula birostris) were identified from the collected footage. Four specific sites in the provinces of Masbate and Palawan together hosted 89% of all identified individuals and accounted for 95% of sightings, highlighting these areas are key aggregation sites. This study also reports the movements of M. birostris within the Philippines, based on photo-identification of three individuals moving 150 km between Cebu and Masbate. Despite the growing number of recreational divers in Daanbantayan and San Jacinto, an 80% decline in M. birostris sightings was observed at these sites. To ensure effective future conservation, it is recommended that efforts focus on the identification and protection of manta ray hotspots and migratory corridors, the creation of a sustainable tourism framework and, most important, the implementation of mitigation strategies to reduce fisheries interactions.     

Direct assessment of mineral phosphorus availability to tropical crops using 32P labelled compounds

The availability to plants of phosphorus (P) derived from sparingly soluble iron and aluminium phosphates was directly assessed with ³²P labelled compounds in two glasshouse trials.In the first experiment, the comparative availability of all mineral phosphate (P) compounds to maize increased with time (14 to 42 days post emergence) and plant total P uptake, but P source did not affect the growth or total plant uptake of P. The comparative availability of the amorphous AlPO₄ (Al-P), crystalline AlPO₄ (variscite), amorphous FePO₄ (Fe-P), and crystalline FePO₄ (strengite) compared to KH₂PO₄ (=100) was 53.1, 3.4, 38.9, and 1.9%, respectively. In the second experiment, the availability of Fe-P, strengite, and KH₂PO₄ to several topical crop species was examined. There was no difference between maize, sorghum, mungbean, cowpea or soybean in their ability to utilise Fe-P or KH₂PO₄, although maize utilised strengite more than the other species. The major difference between these species in their ability to acquire P appears to be a difference in ability to locate soluble soil P rather than differences in their ability to access different pools of soil P.The advantages of using neutron irradiation to directly measure P absorption from mineral P compounds over traditional methodologies is discussed.     

Identification of NADPH:protochlorophyllide oxidoreductases A and B: a branched pathway for light-dependent chlorophyll biosynthesis in Arabidopsis thaliana.

Illumination releases the arrest in chlorophyll (Chl) biosynthesis in etiolated angiosperm seedlings through the enzymatic photoreduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the first light-dependent step in chloroplast biogenesis. NADPH: Pchlide oxidoreductase (POR, EC 1.3.1.33), a nuclear-encoded plastid-localized enzyme, mediates this unique photoreduction. Paradoxically, light also triggers a drastic decrease in the amounts of POR activity and protein before the Chl accumulation rate reaches its maximum during greening. While investigating this seeming contradiction, we identified two distinct Arabidopsis thaliana genes encoding POR, in contrast to previous reports of only one gene in angiosperms. The genes, designated PorA and PorB, by analogy to the principal members of the phytochrome photoreceptor gene family, display dramatically different patterns of light and developmental regulation. PorA mRNA disappears within the first 4 h of greening, whereas PorB mRNA persists even after 16 h of illumination, mirroring the behavior of two distinct POR protein species. Experiments designed to help define the functions of POR A and POR B demonstrate exclusive expression of PorA in young seedlings and of PorB both in seedlings and in adult plants. Accordingly, we propose the existence of a branched light-dependent Chl biosynthesis pathway in which POR A performs a specialized function restricted to the initial stages of greening and POR B maintains Chl levels throughout angiosperm development.     

Cytotoxicity of Nephrotoxic Fungal Toxins to Kidney-derived LLC-PK1 and OK Cell Lines

The nephrotoxic fungal toxins ochratoxin A (OA), ochratoxin B (OB) and citrinin (CIT) are natural contaminants of foods and feeds. While cytotoxicity assays have proven useful for establishing relative toxicity and structure–function relationships within groups of fungal toxins, a drawback of in vitro bioassays is their susceptibility to variation depending on endpoint, target cell, and dosing strategy. These variables were explored for OA, OB, CIT using two continuous kidney cell lines (LLC-PK₁ and OK) and four cytotoxicity assay endpoints. The nephrotoxic antibiotic gentamicin was used as a positive control for cytotoxicity throughout. In general, fungal toxin-induced cytotoxicity was more pronounced in LLC-PK₁ cultures using mitochondrial dehydrogenase inhibition (MTT assay) as the endpoint. Altered dosing strategy, but not seeding density, consistently influenced cytotoxicity: CIT was more toxic to cells when added at the time of seeding, whereas OA was more toxic when added 24 h after cultures were seeded. Toxicity rankings for the fungal toxins were consistent with in vivo studies and were, in order of most to least toxic, OA>OB>CIT. The data indicate that LLC-PK₁ and OK cells compare favorably to existing models in terms of sensitivity to nephrotoxic fungal toxins, but also that relatively minor changes in assay protocols can affect the cytotoxicity of individual toxins and comparative toxicity within a group of toxins.     

Cytogenetics for the model system Arabidopsis thaliana

A detailed karyotype of Arabidopsis thaliana is presented using meiotic pachytene cells in combination with fluorescence in situ hybridization. The lengths of the five pachytene bivalents varied between 50 and 80 μm, which is 20–25 times longer than mitotic metaphase chromosomes. The analysis confirms that the two longest chromosomes (1 and 5) are metacentric and the two shortest chromosomes (2 and 4) are acrocentric and carry NORs subterminally in their short arms, while chromosome 3 is submetacentric and medium sized. Detailed mapping of the centromere position further revealed that the length variation between the pachytene bivalents comes from the short arms. Individual chromosomes were unambiguously identified by their combinations of relative lengths, arm-ratios, presence of NOR knobs and FISH signals with a 5S rDNA probe and chromosome specific DNA probes. Polymorphisms were found among six ecotypes with respect to the number and map positions of 5S rDNA loci. All ecotypes contain 5S rDNA in the short arms of chromosomes 4 and 5. Three different patterns were observed regarding the presence and position of a 5S rDNA locus on chromosome 3. Repetitive DNA clones enabled us to subdivide the pericentromeric heterochromatin into a central domain, characterized by pAL1 and 106B repeats, which accommodate the functional centromere and two flanking domains, characterized by the 17 A20 repeat sequences. The upper flanking domains of chromosomes 4 and 5, and in some ecotypes also chromosome 3, contain a 5S rDNA locus. The detection of unique cosmids and YAC sequences demonstrates that detailed physical mapping of Arabidopsis chromosomes by cytogenetic techniques is feasible. Together with the presented karyotype this makes Arabidopsis a model system for detailed cytogenetic mapping.