Chromatin insulator and the promoter targeting sequence modulate the timing of long-range enhancer-promoter interactions in the Drosophila embryo

The homeotic genes are essential to the patterning of the anterior-posterior axis along the developing Drosophila embryo. The expression timing and levels of these genes are crucial for the correct specification of segmental identity. The Abdominal-B (Abd-B) gene is first detected in the most posterior abdominal segments at high levels and gradually appears in progressively anterior abdominal segments in lower amounts. Regulatory mutations affecting this expression pattern produce homeotic transformations in the abdomen. The promoter targeting sequences (PTS) from Abd-B locus overcome the enhancer blocking effect of insulators and facilitate long-range enhancer-promoter interactions in transgenic flies (1, 2). In this study, we found that transgene activation by the IAB5 enhancer can be delayed by inserting a 9.5 kb 3′ Abd-B regulatory region containing the Frontabdominal-8 (Fab-8) insulator and the PTS element. We found that the delay is caused by the PTS and an insulator, and it is not specific to the enhancer or the promoter tested. Based on these findings, we hypothesize that the delay of remote enhancers is responsible for the Abd-B expression pattern, which is at least in part due to the regulatory activities of the PTS elements and chromatin boundaries.     

Stem turnover strategy of multiple-stemmed woody plants

We have investigated stem turnover strategy for Lindera umbellata, an understory shrub that sprouts from its rootstock under natural conditions to replace constituent stems, on the basis of the hypothesis that the multiple-stemmed form of woody species is an adaptation enabling efficient reproduction in high-stress environments. We tested the hypothesis that the timing of stem replacement maximizes sexual reproduction for the shrub. We developed a model for the time of optimum replacement of a stem by a daughter stem which maximizes the sexual reproduction of a shrub and tested the model using L. umbellata growing in the field. From the model, the optimum time of replacement of a stem with a daughter stem is when cumulative sexual reproduction per unit time for the stem is maximum. In practice, this will be the last age (t _opt) at which annual sexual reproduction in a stem can potentially exceed cumulative sexual reproduction per unit time for the stem. Half of the stems died at almost t _opt and had sexually mature daughter stems at that time. Other stems, however, died at times more remote from t _opt when daughter stems were sexually immature. It is thought that normal replacement of the latter stems was prevented by accidents such as breakage. We conclude that clumps of L. umbellata achieve efficient sexual reproduction by stem replacement at the optimum time, although accidents can, to some extent, determine when the stem actually dies.     

Plant pathogens drive density-dependent seedling mortality in a tropical tree

One explanation for the extraordinary diversity of tropical forest trees is that density-dependent mortality from herbivores or pathogens puts locally rare species at an advantage. Density-dependent mortality of seeds and small seedlings is particularly intense in tropical forests, but its causes remain uncertain. Here, we show experimentally that pathogens from the Oomycota are associated with intense mortality in seedlings of a neotropical tree, Sebastiana longicuspis . Seedlings in untreated plots experienced eight times higher mortality compared with seedlings in plots treated with fungicide. Mortality was strongly density dependent: in fungicide-treated plots survival was unaffected by density, but survival in unsprayed plots was over three times higher at low density. Density-dependent mortality observed in a simultaneous, non-manipulative study was highly transient, suggesting that short-term observational studies may underestimate the intensity and form of pathogen-induced mortality. If such effects are widespread, plant pathogens may play a key role in maintaining and structuring tropical diversity.     

Integrating multiple disturbance aspects: management of an invasive thistle,Carduus nutans

Background and Aims

Disturbances occur in most ecological systems, and play an important role in biological invasions. We delimit five key disturbance aspects: intensity, frequency, timing, duration and extent. Few studies address more than one of these aspects, yet interactions and interdependence between aspects may lead to complex outcomes.

Methods

In a two-cohort experimental study, we examined how multiple aspects (intensity, frequency and timing) of a mowing disturbance regime affect the survival, phenology, growth and reproduction of an invasive thistle Carduus nutans (musk thistle).

Key Results

Our results show that high intensity and late timing strongly delay flowering phenology and reduce plant survival, capitulum production and plant height. A significant interaction between intensity and timing further magnifies the main effects. Unexpectedly, high frequency alone did not effectively reduce reproduction. However, a study examining only frequency and intensity, and not timing, would have erroneously attributed the importance of timing to frequency.

Conclusions

We used management of an invasive species as an example to demonstrate the importance of a multiple-aspect disturbance framework. Failure to consider possible interactions, and the inherent interdependence of certain aspects, could result in misinterpretation and inappropriate management efforts. This framework can be broadly applied to improve our understanding of disturbance effects on individual responses, population dynamics and community composition.     

The autumn effect: timing of physical dormancy break in seeds of two winter annual species of Geraniaceae by a stepwise process

Background and Aims

The involvement of two steps in the physical dormancy (PY)-breaking process previously has been demonstrated in seeds of Fabaceae and Convolvulaceae. Even though there is a claim for a moisture-controlled stepwise PY-breaking in some species of Geraniaceae, no study has evaluated the role of temperature in the PY-breaking process in this family. The aim of this study was to determine whether a temperature-controlled stepwise PY-breaking process occurs in seeds of the winter annuals Geranium carolinianum and G. dissectum.

Methods

Seeds of G. carolinianum and G. dissectum were stored under different temperature regimes to test the effect of storage temperature on PY-break. The role of temperature and moisture regimes in regulating PY-break was investigated by treatments simulating natural conditions. Greenhouse (non-heated) experiments on seed germination and burial experiments (outdoors) were carried out to determine the PY-breaking behaviour in the natural habitat.

Key Results

Irrespective of moisture conditions, sensitivity to the PY-breaking step in seeds of G. carolinianum was induced at temperatures ≥20 °C, and exposure to temperatures ≤20 °C made the sensitive seeds permeable. Sensitivity of seeds increased with time. In G. dissectum, PY-break occurred at temperatures ≥20 °C in a single step under constant wet or dry conditions and in two steps under alternate wet–dry conditions if seeds were initially kept wet.

Conclusions

Timing of seed germination with the onset of autumn can be explained by PY-breaking processes involving (a) two temperature-dependent steps in G. carolinianum and (b) one or two moisture-dependent step(s) along with the inability to germinate under high temperatures in G. dissectum. Geraniaceae is the third of 18 families with PY in which a two-step PY-breaking process has been demonstrated.     

Effect of undernutrition on deciduous tooth emergence among Rajput children of Shimla District of Himachal Pradesh, India

This article examines the influence of nutritional status on the emergence of deciduous dentition in a cross-sectional sample of 510 rural Rajput children from the Jubbal and Kotkhai Tehsils, Shimla District, Himachal Pradesh, India. The nutritional status of each child was evaluated using Z-scores of height/supine length-for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ). The effects of sex and side on deciduous dental emergence were not statistically significant. Partial correlation indicates that the number of emerged teeth (T) was more strongly correlated with height than with other anthropometric variables. In most age groups, the stunted boys and girls (HAZ <-2) had fewer emerged teeth than nonstunted age peers (HAZ >-2). The mean T in underweight children was also less than that of the normal children, with a few exceptions. The stunted children have a significantly greater likelihood of delayed emergence of deciduous dentition. Measures of linear growth status are more closely related to dental development than measures of growth in mass. The findings indicate that even moderate undernutrition can delay deciduous tooth emergence.     

Replicating Life Cycle of Early‐Maturing Species in the Timing of Restoration Seeding Improves Establishment and Community Diversity

Tallgrass prairie is among the most endangered ecosystems in North America. High‐diversity restorations protect remnant habitat and expand native communities. Excluding land acquisition, the most expensive step in restoration is procuring seed. Given this cost, managers want to maximize seedling establishment. Native species that flower and ripen early in the growing season are included in a diverse seeding mix but as a group they have not successfully established. For early‐maturing species, the practice of storing seeds in a cold room from harvest until sowing in the dormant season effectively eliminates exposure to the summer conditions seeds would naturally have in the wild. In this study, we compared the effect of summer sowing timing and winter sowing timing on establishment in field conditions. In August 2004 and December 2004, we broadcast a seed mix of seven early‐maturing species: Antennaria plantaginifolia (L.) Richardson. (Pussy toes), Arabis lyrata L. (Sand cress), Carex swanii (Fernald) Mack. (Downy green sedge), Hymenopappus scabiosaeus L'Hér. (Old plainsman), Lupinus perennis L. ssp. perennis var. occidentalis S. Watson. (Wild lupine), Phlox bifida Beck. (Sand phlox) and Hesperostipa spartea (Trin.) Barkworth. (Porcupine grass). We collected data on establishment and reproductive success at 12 time points from June 2005 until October 2008. Species established one growing season sooner when planted at the summer sowing time, and diversity in the summer sowing plots was higher after 4 years. Quicker establishment may have benefits such as providing early competition from weeds that may outweigh additional effort required to ensure timely planting.     

Interval timing in genetically modified mice: a simple paradigm

We describe a behavioral screen for the quantitative study of interval timing and interval memory in mice. Mice learn to switch from a short-latency feeding station to a long-latency station when the short latency has passed without a feeding. The psychometric function is the cumulative distribution of switch latencies. Its median measures timing accuracy and its interquartile interval measures timing precision. Next, using this behavioral paradigm, we have examined mice with a gene knockout of the receptor for gastrin-releasing peptide that show enhanced (i.e. prolonged) freezing in fear conditioning. We have tested the hypothesis that the mutants freeze longer because they are more uncertain than wild types about when to expect the electric shock. The knockouts however show normal accuracy and precision in timing, so we have rejected this alternative hypothesis. Last, we conduct the pharmacological validation of our behavioral screen using d -amphetamine and methamphetamine. We suggest including the analysis of interval timing and temporal memory in tests of genetically modified mice for learning and memory and argue that our paradigm allows this to be done simply and efficiently.     

Upregulation of the let-7 microRNA with precocious development in lin-12/Notch hypermorphic Caenorhabditis elegans mutants

The lin-12/Notch signaling pathway is conserved from worms to humans and is a master regulator of metazoan development. Here, we demonstrate that lin-12/Notch gain-of-function (gf) animals display precocious alae at the L4 larval stage with a significant increase in let-7 expression levels. Furthermore, lin-12(gf) animals display a precocious and higher level of let-7 gfp transgene expression in seam cells at L3 stage. Interestingly, lin-12(gf) mutant rescued the lethal phenotype of let-7 mutants similar to other known heterochronic mutants. We propose that lin-12/Notch signaling pathway functions in late developmental timing, upstream of or in parallel to the let-7 heterochronic pathway. Importantly, the human microRNA let-7a was also upregulated in various human cell lines in response to Notch1 activation, suggesting an evolutionarily conserved cross-talk between let-7 and the canonical lin-12/Notch signaling pathway.