Niche Expansion and Contraction in a Variable Environment

When food is abundant, sparrows are found in great variety ofhabitats and appear to specialize on particularly profitabletypes of seeds. However, during periods of food scarcity, eachsparrow species occupies a very narrow range of habitats butconsumes a great variety of seeds within each occupied habitat.As a result, average dietary overlap may underestimate the potentialfor competition for food within habitats during periods of foodshortage whereas average habitat overlap overestimates the potentialfor competition since each species occupies a different habitatduring periods of food shortage.     

Niche Overlap and Network Specialization of Flower-Visiting Bees in an Agricultural System

Different resource use strategies manifest as differences in the realized niches of species. Niche segregation may involve several dimensions of the niche, such as diet, space, and time. We measured the level of redundancy and complementarity of a bee–plant interaction network in an agricultural system. Because flower resource diversity is high and resource abundance associated with flowering phenology varies throughout the year, we hypothesized that trophic overlap in the community would be low (i.e., high niche complementarity). In contrast, we expected a combination of physiological constraints and exploitation competition to create high temporal overlap, leading to high redundancy in the time of use of floral resources. Dietary overlap was low (NO_ih?=?0.18): niches of 88% of species pairs had less than 30% overlap. In contrast, temporal overlap was intermediate (NO_ih?=?0.49): niches of 65% of species pairs had 30% to 60% overlap. Network analysis showed that bees separated their dietary niches and had intermediate complementary specialization (H₂′?=?0.46). In terms of their temporal niches (H₂′?=?0.12), bees were generalists, with high temporal redundancy. Temperature was not a key factor in the determination of niche overlap, suggesting that environmental factors do not likely have a primary role in determining high redundancy in the temporal use of floral resources. Rather, temporal overlap is likely associated with the timing of nectar production by flowers. Our results suggest that bees partition a wide variety of available floral resources, resulting in low dietary overlap and intermediate temporal overlap.     

A C4-oxidizing Lytic Polysaccharide Monooxygenase Cleaving Both Cellulose and Cello-oligosaccharides

Lignocellulosic biomass is a renewable resource that significantly can substitute fossil resources for the production of fuels, chemicals, and materials. Efficient saccharification of this biomass to fermentable sugars will be a key technology in future biorefineries. Traditionally, saccharification was thought to be accomplished by mixtures of hydrolytic enzymes. However, recently it has been shown that lytic polysaccharide monooxygenases (LPMOs) contribute to this process by catalyzing oxidative cleavage of insoluble polysaccharides utilizing a mechanism involving molecular oxygen and an electron donor. These enzymes thus represent novel tools for the saccharification of plant biomass. Most characterized LPMOs, including all reported bacterial LPMOs, form aldonic acids, i.e., products oxidized in the C1 position of the terminal sugar. Oxidation at other positions has been observed, and there has been some debate concerning the nature of this position (C4 or C6). In this study, we have characterized an LPMO from Neurospora crassa (NcLPMO9C; also known as NCU02916 and NcGH61–3). Remarkably, and in contrast to all previously characterized LPMOs, which are active only on polysaccharides, NcLPMO9C is able to cleave soluble cello-oligosaccharides as short as a tetramer, a property that allowed detailed product analysis. Using mass spectrometry and NMR, we show that the cello-oligosaccharide products released by this enzyme contain a C4 gemdiol/keto group at the nonreducing end.     

Both inhalant and intravenous uroguanylin inhibit leukotriene C4-induced airway changes

Uroguanylin, a well-known ligand of guanylyl cyclase C receptor in the gastrointestinal tissue, has recently been reported to have pulmonary effects. We investigated the inhibitory effects of uroguanylin against leukotriene C4-induced bronchoconstriction and airway microvascular leakage. Anesthetized guinea pigs, ventilated via a tracheal cannula in a plethysmograph box, were measured by pulmonary mechanics for 10 min after i.v. administering 2 microg/kg leukotriene C4. Airway microvascular leakage was assessed by extravasation of Evans blue dye into airway tissues. Both inhalant and i.v. pretreatment of uroguanylin significantly inhibited leukotriene C4-induced pulmonary changes in a dose-dependent manner, suggesting its effectiveness against an asthmatic condition.     

Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding

Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering. As crowder concentrations increased, the mean radius of gyration of FlgM first decreased but then exhibited an uptick. Ensemble optimization modeling indicated that FlgM conformations under protein crowding segregated into two distinct populations, one compacted and one extended. Coarse-grained simulations showed that compacted conformers fit into an interstitial void and occasionally bind to a surrounding crowder, whereas extended conformers snake through interstitial crevices and bind multiple crowders simultaneously. Crowder-induced conformational segregation may facilitate various cellular functions of IDPs.     

Specialization and noncompetitive resource partitioning among sponge-eating dorid nudibranchs

Summary Habitat and food resource partitioning ecologically isolate six species of Pacific Northwest dorid nudibranchs. Food resources along a gradient of sponge skeletal structure are partitioned between two exploitive guilds. The guilds are characterized by mutually exclusive predatory and digestive adaptations which allow efficient processing of sponges with poorly- or well-organized skeletons. Habitats along a depth gradient are partitioned within guilds. For a dorid species, feeding rates, extraction efficiencies and food quality are virtually identical for sponges with the appropriate extreme (either poorly- or well-organized) and intermediate skeletal organizations, but growth and reproductive rates supported by the former prey type are twice those supported by the latter prey type. Prey types with the appropriate extreme skeletal organization are thus optimal food and specialization to that food is expected. When two divergent specialist species co-occur, food resource partitioning is demonstrable but arises from self-stabilizing specializations to maximize net energy accumulation and not from competitive interactions. Habitat partitioning is viewed as arising from prey distributions and dorid physiological tolerances. This system represents an example of morphological and behavioral specializations giving rise to resource partitioning as opposed to competition giving rise to resource partitioning and subsequent morphological and behavioral specializations.     

C4 Photosynthesis Promoted Species Diversification during the Miocene Grassland Expansion

Identifying how organismal attributes and environmental change affect lineage diversification is essential to our understanding of biodiversity. With the largest phylogeny yet compiled for grasses, we present an example of a key physiological innovation that promoted high diversification rates. C₄ photosynthesis, a complex suite of traits that improves photosynthetic efficiency under conditions of drought, high temperatures, and low atmospheric CO₂, has evolved repeatedly in one lineage of grasses and was consistently associated with elevated diversification rates. In most cases there was a significant lag time between the origin of the pathway and subsequent radiations, suggesting that the ‘C₄ effect’ is complex and derives from the interplay of the C₄ syndrome with other factors. We also identified comparable radiations occurring during the same time period in C₃ Pooid grasses, a diverse, cold-adapted grassland lineage that has never evolved C₄ photosynthesis. The mid to late Miocene was an especially important period of both C₃ and C₄ grass diversification, coincident with the global development of extensive, open biomes in both warm and cool climates. As is likely true for most “key innovations”, the C₄ effect is context dependent and only relevant within a particular organismal background and when particular ecological opportunities became available.     

Unraveling 14-3-3 Proteins in C4 Panicoids with Emphasis on Model Plant Setaria italica Reveals Phosphorylation-Dependent Subcellular Localization of RS Splicing Factor

14-3-3 proteins are a large multigenic family of regulatory proteins ubiquitously found in eukaryotes. In plants, 14-3-3 proteins are reported to play significant role in both development and response to stress stimuli. Therefore, considering their importance, genome-wide analyses have been performed in many plants including Arabidopsis, rice and soybean. But, till date, no comprehensive investigation has been conducted in any C₄ panicoid crops. In view of this, the present study was performed to identify 8, 5 and 26 potential 14-3-3 gene family members in foxtail millet (Si14-3-3), sorghum (Sb14-3-3) and maize (Zm14-3-3), respectively. In silico characterization revealed large variations in their gene structures; segmental and tandem duplications have played a major role in expansion of these genes in foxtail millet and maize. Gene ontology annotation showed the participation of 14-3-3 proteins in diverse biological processes and molecular functions, and in silico expression profiling indicated their higher expression in all the investigated tissues. Comparative mapping was performed to derive the orthologous relationships between 14-3-3 genes of foxtail millet and other Poaceae members, which showed a higher, as well as similar percentage of orthology among these crops. Expression profiling of Si14-3-3 genes during different time-points of abiotic stress and hormonal treatments showed a differential expression pattern of these genes, and sub-cellular localization studies revealed the site of action of Si14-3-3 proteins within the cells. Further downstream characterization indicated the interaction of Si14-3-3 with a nucleocytoplasmic shuttling phosphoprotein (SiRSZ21A) in a phosphorylation-dependent manner, and this demonstrates that Si14-3-3 might regulate the splicing events by binding with phosphorylated SiRSZ21A. Taken together, the present study is a comprehensive analysis of 14-3-3 gene family members in foxtail millet, sorghum and maize, which provides interesting information on their gene structure, protein domains, phylogenetic and evolutionary relationships, and expression patterns during abiotic stresses and hormonal treatments, which could be useful in choosing candidate members for further functional characterization. In addition, demonstration of interaction between Si14-3-3 and SiRSZ21A provides novel clues on the involvement of 14-3-3 proteins in the splicing events.     

Niche divergence and lineage diversification among closely related Sistrurus rattlesnakes

Comparing niche divergence among closely related taxa can yield important insights into the ecological distinctiveness of genetically similar forms, and identify the processes that are responsible for diversification in such organisms. Here, we apply newly developed techniques for analysing niche divergence to assess how ecologically distinct a group of closely related rattlesnakes (Sistrurus sp.) are and to explore the role that niche divergence may have played in their diversification. We find that all taxa even the most recently evolved subspecies (approximately 100,000 years old) are now ecologically distinct, implying a role for ecology in the diversification process. Statistical analysis based on comparisons with null models show that niche divergence between forms is more common than niche conservation. Finally, there is nonlinear relationship between phylogenetic and niche divergence in this group whereby niche divergence develops more rapidly between recently diverged subspecies than more distantly related forms. Overall, our results argue that ecology may play an important role in the diversification process in these snakes.     

Distribution and evolution of C4 syndrome inRhynchospora (Rhynchosporeae-Cyperaceae)

In order to elucidate the evolution of C₄ syndrome, the taxonomic relationships, leaf anatomy, and ecological and global distribution of C₃ and C₄ species in the genusRhynchospora were investigated. The anatomical observation for 181 species revealed that 26 C₄ species occurred within theCapitatae group of the subgenusHaplostyleae, a natural group showing highly advanced morphological characteristics, together with several C₃ species. In spite of there being rather few C₄ species, they possessed two kinds of Kranz anatomical structure differing from each other in the location of Kranz cells. Some C₃ species ofCapitatae showed radial arrangement in mesophyll cells surrounding vascular bundles, which is distinguished from typical non-Kranz anatomy. The C₄ species extended their ecological ranges from wet habitats to dry savanna grasslands, while the C₃ species showed the best development in wet habitats. The C₃ species were widespread from tropical to temperate regions with partial range extension into subarctic regions of both hemispheres, showing conspicuously high concentration of species in the New World, but being absent from arid climatic regions. The C₄ species were distributed mostly in tropics and subtropics, showing two separate distributional centers in South and Central America and in Tropical Asia and Australia. The range of C₄ species was nearly completely included in the C₃ range. In conclusion, it seems that inRhynchospora the C₄ syndrome evolved relatively recently, and arose in at least two separate phylogenetic trends in the tropics and the subtropics, more probably in the Neotropics.     

Distribution of transferrin C subtypes among the Bedouin and non-Bedouin populations of Jordan

The distribution of transferrin C subtypes was studied in the population of Jordan. The sample comprised 121 Bedouins and 382 other Jordanians from Amman. The frequency of TfC2 was found to be 0.26 among the Bedouins and 0.23 among the non-Bedouin population. TfD was present in low frequency (0.005) among both the Bedouin and non-Bedouin populations.     

Vertical Movement Patterns and Ontogenetic Niche Expansion in the Tiger Shark,Galeocerdo cuvier

Sharks are top predators in many marine ecosystems and can impact community dynamics, yet many shark populations are undergoing severe declines primarily due to overfishing. Obtaining species-specific knowledge on shark spatial ecology is important to implement adequate management strategies for the effective conservation of these taxa. This is particularly relevant concerning highly-mobile species that use wide home ranges comprising coastal and oceanic habitats, such as tiger sharks, Galeocerdo cuvier. We deployed satellite tags in 20 juvenile tiger sharks off northeastern Brazil to assess the effect of intrinsic and extrinsic factors on depth and temperature usage. Sharks were tracked for a total of 1184 d and used waters up to 1112 m in depth. The minimum temperature recorded equaled 4°C. All sharks had a clear preference for surface (< 5 m) waters but variability in depth usage was observed as some sharks used mostly shallow (< 60 m) waters whereas others made frequent incursions into greater depths. A diel behavioral shift was detected, with sharks spending considerably more time in surface (< 10 m) waters during the night. Moreover, a clear ontogenetic expansion in the vertical range of tiger shark habitat was observed, with generalized linear models estimating a ~4-fold increase in maximum diving depth from 150- to 300-cm size-classes. The time spent in the upper 5 m of the water column did not vary ontogenetically but shark size was the most important factor explaining the utilization of deeper water layers. Young-of-the-year tiger sharks seem to associate with shallow, neritic habitats but they progressively move into deeper oceanic habitats as they grow larger. Such an early plasticity in habitat use could endow tiger sharks with access to previously unavailable prey, thus contributing to a wider ecological niche.     

Clonal Expansion of Both Modern and Ancient Genotypes of Mycobacterium tuberculosis in Southern Taiwan

We present the first comprehensive analysis of Mycobacterium tuberculosis isolates circulating in the Kaohsiung region of southern Taiwan. The major spoligotypes found in the 224 isolates studied were Beijing lineages (n = 97; 43.3%), EAI lineages (n = 72; 32.1%) and Haarlem lineages (n = 18; 8.0%). By 24 MIRU-VNTR typing, 174 patterns were identified, including 24 clusters of 74 isolates and 150 unique patterns. The combination of spoligotyping and 12-MIRU-VNTR revealed that 129 (57.6%) of the 224 isolates were clustered in 18 genotypes. Moreover, 63.6% (7/11) of infected persons younger than 30 years had a Beijing strain, which could suggest recent spread among younger persons by this family of TB strains in Kaohsiung. Among the 94 Beijing family (SIT1, SIT250 and SIT1674) isolates further analyzed for SNPs by mass spectrometry, the most frequent strain found was ST10 (n = 49; 52%), followed by ST22 (n = 17; 18%) and ST19 (n = 11; 12%). Among the EAI-Manila family isolates analyzed by region deletion-based subtyping, the most frequent strain found was RD type 1 (n = 63; 87.5%), followed by RD type 2 (n = 9; 12.5%). In our previous study, the proportion of modern Beijing strains (52.5%) in northern Taiwan was significantly higher than the proportion of EAI strains (11%). In contrast, in the present study, EAI strains comprised up to 32% of Beijing strains in southern Taiwan. In conclusion, both ‘modern’ (Beijing) and ‘ancient’ (EAI) M. tuberculosis strains are prevalent in the Kaohsiung region, perhaps suggesting that both strains are somehow more adapted to southern Taiwan. It will be interesting to investigate the dynamics of the lineage composition by different selection pressures.     

Distribution of complement protein C4 concentrations in bovine plasma

Complement component C4 concentrations were measured in 40 pure bred Hereford cattle and 40 cattle from a mixed breed herd. Significant differences were not observed between the two groups studied nor between bulls and cows. However, the distribution of C4 concentrations was relatively disperse and appeared polymodal suggesting the presence of two isotypes of C4. Polyacrylamide gel electrophoresis of immunoprecipitated bovine C4 showed many samples to have two C4 alpha chains differing in relative molecular mass by about 1800. Isoelectric focusing of bovine plasma in agarose gels followed by immunofixation with specific anti-C4 antisera revealed two populations of native C4 differing in pI by about 0.3 pH unit. An association between the type of C4 alpha chain present and the pI of the native C4 molecule was observed. Collectively these findings indicate the presence of two structural C4 genetic loci in cattle.     

Distribution of complement protein C4 concentrations in bovine plasma

Complement component C4 concentrations were measured in 40 pure bred Hereford cattle and 40 cattle from a mixed breed herd. Significant differences were not observed between the two groups studied nor between bulls and cows. However, the distribution of C4 concentrations was relatively disperse and appeared polymodal suggesting the presence of two isotypes of C4. Polyacrylamide gel electrophoresis of immunoprecipitated bovine C4 showed many samples to have two C4 α chains differing in relative molecular mass by about 1800. Isoelectric focusing of bovine plasma in agarose gels followed by immunofixation with specific anti-C4 antisera revealed two populations of native C4 differing in pI by about 0.3 pH unit. An association between the type of C4 α chain present and the pI of the native C4 molecule was observed. Collectively these findings indicate the presence of two structural C4 genetic loci in cattle.