Setting the biological time in central and peripheral clocks during ontogenesis

In mammals, the principal circadian clock within the suprachiasmatic nucleus (SCN) entrains the phase of clocks in numerous peripheral tissues and controls the rhythmicity in various body functions. During ontogenesis, the molecular mechanism responsible for generating circadian rhythmicity develops gradually from the prenatal to the postnatal period. In the beginning, the maternal signals set the phase of the newly developing fetal and early postnatal clocks, whereas the external light-dark cycle starts to entrain the clocks only later. This minireview discusses the complexity of signaling pathways from mothers and the outside world to the fetal and newborn animals' circadian clocks.     

Recent advances in fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy is a method in which fluctuations in the fluorescence arising from a very small sample volume are correlated to obtain information about the processes giving rise to the fluctuations. Recent progress has been made in methodologies such as two-photon excitation, photon counting histogram analysis, cross-correlation, image correlation and evanescent excitation. Fluorescence correlation spectroscopy techniques have been applied to several biological processes, including fluorescent protein photodynamics, binding equilibria and kinetics, protein oligomerization, nucleic acid interactions, and membrane and intracellular dynamics.     

Development of indel markers from Citrus clementina (Rutaceae) BAC-end sequences and interspecific transferability in Citrus

? Premise of the study: Indel markers were developed from BAC-end sequences of Citrus clementina cv. Nules. Transferability and polymorphism were tested in the Citrus genus to estimate the potential of indel markers mined from a single genotype for use in genetic studies. ? Methods and Results: Using polyacrylamide gel electrophoresis and DNA silver staining, 89 indel markers were tested for their transferability and polymorphism. Thirty-eight markers were selected. Heterozygosity in C. clementina cv. Nules was confirmed for 33 of these indel pairs. A preliminary diversity study using a capillary electrophoresis fragment analyzer was conducted with 21 indels using 45 accessions representing Citrus genus diversity. Intraspecific and interspecific polymorphisms were observed. ? Conclusions: These results indicate the utility of indel markers developed from sequence data of a single genotype of interspecific origin. In Citrus, these markers will be useful for genetic mapping, germplasm characterization, and phylogenetic assignment of DNA fragments.     

Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB

SelB is a specialized translation factor that binds GTP and GDP and delivers selenocysteyl-tRNA (Sec-tRNA(Sec)) to the ribosome. By analogy to elongation factor Tu (EF-Tu), SelB is expected to control the delivery and release of Sec-tRNA(Sec) to the ribosome by the structural switch between GTP- and GDP-bound conformations. However, crystal structures of SelB suggested a similar domain arrangement in the apo form and GDP- and GTP-bound forms of the factor, raising the question of how SelB can fulfill its delivery function. Here, we studied the thermodynamics of guanine nucleotide binding to SelB by isothermal titration calorimetry in the temperature range between 10 and 25 °C using GTP, GDP, and two nonhydrolyzable GTP analogs, guanosine 5'-O-(γ-thio)triphosphate (GTPγS) and guanosine 5'-(β,γ-imido)-triphosphate (GDPNP). The binding of SelB to either guanine nucleotide is characterized by a large heat capacity change (-621, -467, -235, and -275 cal × mol(-1) × K(-1), with GTP, GTPγS, GDPNP, and GDP, respectively), associated with compensatory changes in binding entropy and enthalpy. Changes in heat capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43 or 32 amino acids buried upon binding of GTP or GTPγS, respectively, and 15-19 amino acids upon binding GDP or GDPNP. The similarity of the GTP and GDP forms in the crystal structures can be attributed to the use of GDPNP, which appears to induce a structure of SelB that is more similar to the GDP than to the GTP-bound form.     

GENOTYPE‐BY‐TEMPERATURE INTERACTIONS MAY HELP TO MAINTAIN CLONAL DIVERSITY IN ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE)

Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity. To test the influence of temperature as a selection force in continually (seasonally) changing aquatic systems we carried out reaction norms experiments on co‐occurring clonal genotypes of a ubiquitous diatom species, Asterionella formosa Hassall, across an environmentally relevant range of temperatures. We report within population genetic diversity and extensive diversity in genotype‐specific reaction norms in growth rates and cell size traits. Our results showed genotype by environment interactions, indicating that no genotype could outgrow all others across all temperature environments. Subsequently, we constructed a model to simulate the relative proportion of each genotype in a hypothetical population based on genotype and temperature‐specific population growth rates. This model was run with different seasonal temperature patterns. Our modeling exercise showed a succession of two to several genotypes becoming numerically dominant depending on the underlying temperature pattern. The results suggest that (temperature) context dependent fitness may contribute to the maintenance of genetic diversity in isolated populations of clonally reproducing microorganisms in temporally variable environments.     

Plant species coexistence at local scale in temperate swamp forest: test of habitat heterogeneity hypothesis

It has been suggested that a heterogeneous environment enhances species richness and allows for the coexistence of species. However, there is increasing evidence that environmental heterogeneity can have no effect or even a negative effect on plant species richness and plant coexistence at a local scale. We examined whether plant species richness increases with local heterogeneity in the water table depth, microtopography, pH and light availability in a swamp forest community at three local spatial scales (grain: 0.6, 1.2 and 11.4 m). We also used the variance partitioning approach to assess the relative contributions of niche-based and other spatial processes to species occurrence. We found that heterogeneity in microtopography and light availability positively correlated with species richness, in accordance with the habitat heterogeneity hypothesis. However, we recorded different heterogeneity-diversity relationships for particular functional species groups. An increase in the richness of bryophytes and woody plant species was generally related to habitat heterogeneity at all measured spatial scales, whereas a low impact on herbaceous species richness was recorded only at the 11.4 m scale. The distribution of herbaceous plants was primarily explained by other spatial processes, such as dispersal, in contrast to the occurrence of bryophytes, which was better explained by environmental factors. Our results suggest that both niche-based and other spatial processes are important determinants of the plant composition and species turnover at local spatial scales in swamp forests.