Enumeration of Flexibacter canadensis in environmental samples by using a bacteriophage isolated from soil.

The denitrifier Flexibacter canadensis, in the presence of sulfide, can reduce N2O in the presence of concentrations of C2H2 which normally inhibit N2O reduction. Most-probable-number estimates of naturally occurring F. canadensis populations in various soils and sediments were made with a bacteriophage which is active against and specific for a strain of denitrifying F. canadensis (Is-11). Our survey suggests that F. canadensis is common in the natural environment.     

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.     

Fire as a key driver of Earth's biodiversity

Many terrestrial ecosystems are fire prone, such that their composition and structure are largely due to their fire regime. Regions subject to regular fire have exceptionally high levels of species richness and endemism, and fire has been proposed as a major driver of their diversity, within the context of climate, resource availability and environmental heterogeneity. However, current fire‐management practices rarely take into account the ecological and evolutionary roles of fire in maintaining biodiversity. Here, we focus on the mechanisms that enable fire to act as a major ecological and evolutionary force that promotes and maintains biodiversity over numerous spatiotemporal scales. From an ecological perspective, the vegetation, topography and local weather conditions during a fire generate a landscape with spatial and temporal variation in fire‐related patches (pyrodiversity), and these produce the biotic and environmental heterogeneity that drives biodiversity across local and regional scales. There have been few empirical tests of the proposition that ‘pyrodiversity begets biodiversity’ but we show that biodiversity should peak at moderately high levels of pyrodiversity. Overall species richness is greatest immediately after fire and declines monotonically over time, with postfire successional pathways dictated by animal habitat preferences and varying lifespans among resident plants. Theory and data support the ‘intermediate disturbance hypothesis’ when mean patch species diversity is correlated with mean fire intervals. Postfire persistence, recruitment and immigration allow species with different life histories to coexist. From an evolutionary perspective, fire drives population turnover and diversification by promoting a wide range of adaptive responses to particular fire regimes. Among 39 comparisons, the number of species in 26 fire‐prone lineages is much higher than that in their non‐fire‐prone sister lineages. Fire and its byproducts may have direct mutagenic effects, producing novel genotypes that can lead to trait innovation and even speciation. A paradigm shift aimed at restoring biodiversity‐maintaining fire regimes across broad landscapes is required among the fire research and management communities. This will require ecologists and other professionals to spread the burgeoning fire‐science knowledge beyond scientific publications to the broader public, politicians and media.     

Linking micro‐ and macroevolutionary perspectives to evaluate the role of Quaternary sea‐level oscillations in island diversification

With shifts in island area, isolation, and cycles of island fusion–fission, the role of Quaternary sea‐level oscillations as drivers of diversification is complex and not well understood. Here, we conduct parallel comparisons of population and species divergence between two island areas of equivalent size that have been affected differently by sea‐level oscillations, with the aim to understand the micro‐ and macroevolutionary dynamics associated with sea‐level change. Using genome‐wide datasets for a clade of seven Amphiacusta ground cricket species endemic to the Puerto Rico Bank (PRB), we found consistently deeper interspecific divergences and higher population differentiation across the unfragmented Western PRB, in comparison to the currently fragmented Eastern PRB that has experienced extreme changes in island area and connectivity during the Quaternary. We evaluate alternative hypotheses related to the microevolutionary processes (population splitting, extinction, and merging) that regulate the frequency of completed speciation across the PRB. Our results suggest that under certain combinations of archipelago characteristics and taxon traits, the repeated changes in island area and connectivity may create an opposite effect to the hypothesized “species pump” action of oscillating sea levels. Our study highlights how a microevolutionary perspective can complement current macroecological work on the Quaternary dynamics of island biodiversity.     

Fire-adapted traits of Pinus arose in the fiery Cretaceous

? The mapping of functional traits onto chronograms is an emerging approach for the identification of how agents of natural selection have shaped the evolution of organisms. Recent research has reported fire-dependent traits appearing among flowering plants from 60 million yr ago (Ma). Although there are many records of fossil charcoal in the Cretaceous (65-145 Ma), evidence of fire-dependent traits evolving in that period is lacking. ? We link the evolutionary trajectories for five fire-adapted traits in Pinaceae with paleoatmospheric conditions over the last 250 million yr to determine the time at which fire originated as a selective force in trait evolution among seed plants. ? Fire-protective thick bark originated in Pinus c. 126 Ma in association with low-intensity surface fires. More intense crown fires emerged c. 89 Ma coincident with thicker bark and branch shedding, or serotiny with branch retention as an alternative strategy. These innovations appeared at the same time as the Earth's paleoatmosphere experienced elevated oxygen levels that led to high burn probabilities during the mid-Cretaceous. ? The fiery environments of the Cretaceous strongly influenced trait evolution in Pinus. Our evidence for a strong correlation between the evolution of fire-response strategies and changes in fire regime 90-125 Ma greatly backdates the key role that fire has played in the evolution of seed plants.     

Murine embryonic antigen (SSEA-1) is expressed on human cells and structurally related human blood group antigen I is expressed on mouse embryos

The stage-specific embryonic antigen (SSEA-1), present on embryonal carcinoma cells and on murine preimplantation embryos, is defined by a monoclonal antibody. The antigenic determinant of SSEA-1 is a carbohydrate structurally related to the human blood group antigen I. Since it has been suggested that the I antigen might represent a precursor or SSEA-1, we used antibodies to SSEA-1 and to I to analyze their expression on mouse preimplantation embryos. Both are expressed on mouse embryos; moreover, I is expressed on earlier embryos than SSEA-1. The I antigen is defined by its expression on human erythrocytes; accordingly, we examined expression of I and SSEA-1 on human peripheral blood elements. We find SSEA-1 to be expressed exclusively on human granulocytes while I is found only on erythrocytes. These results suggest that these closely related antigens can be independently expressed. Analysis of the expression of I and SSEA-1 was then extended to a series of mouse and human cell lines; some express both, some express only one, and some express neither of these antigens. The activation of specific glycosyltransferases and/or glycosidases during development and differentiation appears to be the biochemical mechanism regulating expression of these antigens.     

Dissection of H-2Db-restricted cytotoxic T-lymphocyte epitopes on simian virus 40 T antigen by the use of synthetic peptides and H-2Dbm mutants.

Five distinct cytotoxic T-lymphocyte (CTL) recognition sites were identified in the simian virus 40 (SV40) T antigen by using H-2b cells that express the truncated T antigen or antigens carrying internal deletions of various sizes. Four of the CTL recognition determinants, designated sites I, II, III, and V, are H-2Db restricted, while site IV is H-2Kb restricted. The boundaries of CTL recognition sites I, II, and III, clustered in the amino-terminal half of the T antigen, were further defined by use of overlapping synthetic peptides containing amino acid sequences previously determined to be required for recognition by T-antigen site-specific CTL clones by using SV40 deletion mutants. CTL clone Y-1, which recognizes epitope I and whose reactivity is affected by deletion of residues 193 to 211 of the T antigen, responded positively to B6/PY cells preincubated with a synthetic peptide corresponding to T-antigen amino acids 205 to 219. CTL clones Y-2 and Y-3 lysed B6/PY cells preincubated with large-T peptide LT220-233. To distinguish further between epitopes II and III, Y-2 and Y-3 CTL clones were reacted with SV40-transformed cells bearing mutations in the major histocompatibility complex class I antigen. Y-2 CTL clones lysed SV40-transformed H-2Dbm13 cells (bm13SV) which carry several amino acid substitutions in the putative antigen-binding site in the alpha 2 domain of the H-2Db antigen but not bm14SV cells, which contain a single amino acid substitution in the alpha 1 domain. Y-3 CTL clones lysed both mutant transformants. Y-1 and Y-5 CTL clones failed to lyse bm13SV and bm14SV cells; however, these cells could present synthetic peptide LT205-219 to CTL clone Y-1 and peptide SV26(489-503) to CTL clone Y-5, suggesting that the endogenously processed T antigen yields fragments of sizes or sequences different from those of synthetic peptides LT205-219 and SV26(489-503).     

Interploid St. Augustinegrass [<Emphasis Type="Italic">Stenotaphrum secundatum</Emphasis> (Walt.) Kuntze] hybrids recovered by embryo rescue

St. Augustinegrass is one of the most important warm season turfgrasses in the southern United States because of its shade tolerance. Most cultivars are diploids (2n = 2x = 18) and are susceptible to various diseases and insects. Polyploid cultivars in the species have some resistance to pests, but most lack cold tolerance. In this study, eight polyploid genotypes were crossed with six diploid cultivars to transfer pest resistance to the diploids. Because interploid crosses often result in aborted seed, it was necessary to use in vitro techniques. Using embryo rescue, 268 plants were recovered from 2,463 emasculated and pollinated florets (10.88% crossability). Because of the heterogeneous nature of the species, these purported hybrids could not be verified by phenotype. DNA markers were used for hybrid identification. A subset of 25 plants from crosses between the aneuploid cultivar Floratam (2n = 4x = 32) and five diploid cultivars were analyzed using 144 expressed sequence tags–simple sequence repeats (EST-SSRs) developed from buffelgrass cDNA sequence data. Chi-square tests for paternal-specific markers revealed that all analyzed progeny were true F₁ hybrids and none originated from self-fertilization or unintended outcrossing. In addition to identifying DNA polymorphism, the EST-SSRs revealed that genetic variation exists among all analyzed cultivars and is not partitioned between ploidy levels. The findings demonstrate that these embryo rescue techniques will enable the entire spectrum of St. Augustinegrass genetic variation to be better used through the recovery of interploid hybrids.     

The origin of the Adams-Schuster difference spectrum of oxyhemoglobin.

The characteristic difference spectrum reported by Adams and Schuster (Biochem. Biophys. Res. Commun. 1974, $\text{58}$, 525) on the addition of inositol hexaphosphate to oxyhemoglobin is similar to the difference spectrum between (i) isolated α- and β-chains, (ii) α- and β-semihemoglobins, (iii) addition of inorganic phosphate to oxyhemoglobin, (v) change in temperature of a solution of oxyhemoglobin, (v) change in pH of carp carboxyhemoglobin and (vi) addition of inositol hexaphosphate to α-semihemoglobin. The spectrum may also be generated by differentiation of the spectra of oxyhemoglobin and carboxyhemoglobin, implying that the common feature of the results reported above is a shift in the position of the absorption bands. This shift may arise from several causes and so its interpretation is uncertain.     

Lifelong choline supplementation ameliorates Alzheimer’s disease pathology and associated cognitive deficits by attenuating microglia activation

Currently, there are no effective therapies to ameliorate the pathological progression of Alzheimer's disease (AD). Evidence suggests that environmental factors may contribute to AD. Notably, dietary nutrients are suggested to play a key role in mediating mechanisms associated with brain function. Choline is a B‐like vitamin nutrient found in common foods that is important in various cell functions. It serves as a methyl donor and as a precursor for production of cell membranes. Choline is also the precursor for acetylcholine, a neurotransmitter which activates the alpha7 nicotinic acetylcholine receptor (α7nAchR), and also acts as an agonist for the Sigma‐1 R (σ1R). These receptors regulate CNS immune response, and their dysregulation contributes to AD pathogenesis. Here, we tested whether dietary choline supplementation throughout life reduces AD‐like pathology and rescues memory deficits in the APP/PS1 mouse model of AD. We exposed female APP/PS1 and NonTg mice to either a control choline (1.1 g/kg choline chloride) or a choline‐supplemented diet (5.0 g/kg choline chloride) from 2.5 to 10 months of age. Mice were tested in the Morris water maze to assess spatial memory followed by neuropathological evaluation. Lifelong choline supplementation significantly reduced amyloid‐β plaque load and improved spatial memory in APP/PS1 mice. Mechanistically, these changes were linked to a decrease of the amyloidogenic processing of APP, reductions in disease‐associated microglial activation, and a downregulation of the α7nAch and σ1 receptors. Our results demonstrate that lifelong choline supplementation produces profound benefits and suggest that simply modifying diet throughout life may reduce AD pathology.