Sea urchin Hox genes: insights into the ancestral Hox cluster

We describe the Hox cluster in the radially symmetric sea urchin and compare our findings to what is known from clusters in bilaterally symmetric animals. Several Hox genes from the direct-developing sea urchin Heliocidaris erythrogramma are described. CHEF gel analysis shows that the Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA, and only a single cluster is present, as in lower chordates and other nonvertebrate metazoans. Phylogenetic analyses of sea urchin, amphioxus, Drosophila, and selected vertebrate Hox genes confirm that the H. erythrogramma genes, and others previously cloned from other sea urchins, belong to anterior, central, and posterior groups. Despite their radial body plan and lack of cephalization, echinoderms retain at least one of the anterior group Hox genes, an orthologue of Hox3. The structure of the echinoderm Hox cluster suggests that the ancestral deuterostome had a Hox cluster more similar to the current chordate cluster than was expected Sea urchins have at least three Abd-B type genes, suggesting that Abd-B expansion began before the radiation of deuterostomes.      

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers.

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.     

Quantifying variety‐specific heat resistance and the potential for adaptation to climate change

The impact of climate change on crop yields has become widely measured; however, the linkages for winter wheat are less studied due to dramatic weather changes during the long growing season that are difficult to model. Recent research suggests significant reductions under warming. A potential adaptation strategy involves the development of heat resistant varieties by breeders, combined with alternative variety selection by producers. However, the impact of heat on specific wheat varieties remains relatively unstudied due to limited data and the complex genetic basis of heat tolerance. Here, we provide a novel econometric approach that combines field‐trial data with a genetic cluster mapping to group wheat varieties and estimate a separate extreme heat impact (temperatures over 34 °C) across 24 clusters spanning 197 varieties. We find a wide range of heterogeneous heat resistance and a trade‐off between average yield and resistance. Results suggest that recently released varieties are less heat resistant than older varieties, a pattern that also holds for on‐farm varieties. Currently released – but not yet adopted – varieties do not offer improved resistance relative to varieties currently grown on farm. Our findings suggest that warming impacts could be significantly reduced through advances in wheat breeding and/or adoption decisions by producers. However, current adaptation‐through‐adoption potential is limited under a 1 °C warming scenario as increased heat resistance cannot be achieved without a reduction in average yields.     

Replanting reduces frog diversity in oil palm

A growing body of literature has demonstrated significant biodiversity losses for many taxa when forest is converted to oil palm. However, no studies have directly investigated changes to biodiversity throughout the oil palm life cycle, in which oil palm matures for 25–30 yr before replanting. This process leads to major changes in the oil palm landscape that likely influence species assemblages and ecosystem function. We compare frog assemblages between mature (21–27‐yr old) and recently replanted (1–2‐yr old) oil palm in Sumatra, Indonesia. Across eighteen 2.25‐ha oil palm plots, we found 719 frogs from 14 species. Frog richness was 31 percent lower in replanted oil palm (nine species) than mature oil palm (13 species). Total frog abundance was 47 percent lower in replanted oil palm, and frog assemblage composition differed significantly between the two ages of oil palm. The majority of frog species were disturbance‐tolerant, although we encountered four forest‐associated frog species within mature oil palm despite a distance of 28 km between our study sites and the nearest extensive tract of forest. Although it is clear that protection of forest is of paramount importance for the conservation of tropical fauna, our results indicate that management decisions within tropical agricultural landscapes also have a profound impact on biodiversity. Practices such as staggered replanting or maintenance of connectivity among mature oil palm patches could help maintain frog diversity in the oil palm landscape.     

Rapid modulation of ultraviolet shielding in plants is influenced by solar ultraviolet radiation and linked to alterations in flavonoids

The accumulation of ultraviolet (UV)‐absorbing compounds (flavonoids and related phenylpropanoids) and the resultant decrease in epidermal UV transmittance (T_UV) are primary protective mechanisms employed by plants against potentially damaging solar UV radiation and are critical components of the overall acclimation response of plants to changing solar UV environments. Whether plants can adjust this UV sunscreen protection in response to rapid changes in UV, as occurs on a diurnal basis, is largely unexplored. Here, we use a combination of approaches to demonstrate that plants can modulate their UV‐screening properties within minutes to hours, and these changes are driven, in part, by UV radiation. For the cultivated species Abelmoschus esculentus, large (30–50%) and reversible changes in T_UV occurred on a diurnal basis, and these adjustments were associated with changes in the concentrations of whole‐leaf UV‐absorbing compounds and several quercetin glycosides. Similar results were found for two other species (Vicia faba and Solanum lycopersicum), but no such changes were detected in Zea mays. These findings reveal a much more dynamic UV‐protection mechanism than previously recognized, raise important questions concerning the costs and benefits of UV‐protection strategies in plants and have practical implications for employing UV to enhance crop vigor and quality in controlled environments.     

Skeletal records of community-level bleaching in Porites corals from Palau

Tropical Pacific sea surface temperature is projected to rise an additional 2–3 °C by the end of this century, driving an increase in the frequency and intensity of coral bleaching. With significant global coral reef cover already lost due to bleaching-induced mortality, efforts are underway to identify thermally tolerant coral communities that might survive projected warming. Massive, long-lived corals accrete skeletal bands of anomalously high density in response to episodes of thermal stress. These “stress bands” are potentially valuable proxies for thermal tolerance, but to date their application to questions of community bleaching history has been limited. Ecological surveys recorded bleaching of coral communities across the Palau archipelago during the 1998 and 2010 warm events. Between 2011 and 2015, we extracted skeletal cores from living Porites colonies at 10 sites spanning barrier reef and lagoon environments and quantified the proportion of stress bands present in each population during bleaching years. Across Palau, the prevalence of stress bands tracked the severity of thermal stress, with more stress bands occurring in 1998 (degree heating weeks = 13.57 °C-week) than during the less severe 2010 event (degree heating weeks = 4.86 °C-week). Stress band prevalence also varied by reef type, as more corals on the exposed barrier reef formed stress bands than did corals from sheltered lagoon environments. Comparison of Porites stress band prevalence with bleaching survey data revealed a strong correlation between percent community bleaching and the proportion of colonies with stress bands in each year. Conversely, annual calcification rates did not decline consistently during bleaching years nor did annually resolved calcification histories always track interannual variability in temperature. Our data suggest that stress bands in massive corals contain valuable information about spatial and temporal trends in coral reef bleaching and can aid in conservation efforts to identify temperature-tolerant coral reef communities.

     

Interaction of terminal transferase with single-stranded DNA

A 58-kDa monomer of terminal transferase was isolated from calf thymus using a monoclonal antibody affinity column. The enzymatic activity was comparable to that of the 44-kDa alpha beta dimer isolated by conventional methods. Binding of the two enzyme forms to single-stranded DNA was monitored by fluorescence. The site size of both forms was approximately 11 +/- 2 nucleotides. Binding of the 44-kDa alpha beta dimer to polydeoxyadenosine was examined under several conditions. The cooperativity parameter increased from about 90 in the presence of Mg2+ to 300-400 in the absence of Mg2+. The observed dissociation constant of 3-5 microM was essentially independent of salt concentration, whereas the intrinsic dissociation constant decreased about 5-fold in the presence of Mg2+. The binding parameters of the 58-kDa monomer were independent of buffer composition and were similar to those of the 44-kDa alpha beta dimer in the presence of Mg2+. These results indicate that the additional 14-kDa peptide sequences present in the high molecular mass monomer form are not part of the DNA-binding site of terminal transferase.     

Comparison of approaches to the instrumental response function in fluorescence decay measurements

Deconvolution of pulse fluorometry data requires knowledge of the instrumental response, which is not directly observable in some circumstances. Various procedures for approaching the instrumental response function were evaluated for nanosecond fluorescence decay data analyzed by nonlinear least squares, including the commonly used time shift correction and several reference fluorophore methods. A new reference fluorophore technique using a Monte Carlo convolution is introduced and tested. The correction for scattered light in several reference techniques is also presented. The random convolution and one other reference fluorophore method consistently gave superior results over a wide range of experimental conditions.     

Isotypes of spontaneous and mitogen-induced autoantibodies in SLE-prone mice

A common cellular abnormality of all murine strains prone to systemic lupus erythematosus (SLE) is an increased spontaneous polyclonal expansion of B cells. Our findings support the existence of this SLE-associated abnormality because the numbers of B lymphocytes secreting all the different IgG subclasses and IgM in spleens of all lupus-prone mice are elevated, compared to levels of normal splenic immunoglobulin-producing cells. We also report that 1) spontaneous polyclonal stimulation of immunoglobulin in autoimmune mice is preferential for subclass, and that the preferentially stimulated isotypes in each SLE strain consistently dominate both circulating and kidney-deposited immune complexes; 2) distinct patterns of isotype preference exist among the autoimmune strains determined by inherent B cell proliferative abnormalities or by B cell proliferation affected by thymus-derived lymphocytes; and 3) chronic administration of the TI B cell mitogen Lipid A in late-life SLE-prone mice induces an early-life glomerulonephritis with auto-antibodies of an isotype composition characteristic of those spontaneously produced by inherently abnormal B cells of early-life lupus mice.