Unravelling differential Hes1 dynamics during axis elongation of mouse embryos through single-cell tracking.

The intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we have developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells.

How does an organism extract relevant information from transcription factor concentrations?

How does an organism regulate its genes? The involved regulation typically occurs in terms of a signal processing chain: an externally applied stimulus or a maternally supplied transcription factor leads to the expression of some downstream genes, which, in turn, are transcription factors for further genes. Especially during development, these transcription factors are frequently expressed in amounts where noise is still important; yet, the signals that they provide must not be lost in the noise. Thus, the organism needs to extract exactly relevant information in the signal.

Trading bits in the readout from a genetic network.

In the regulation of gene expression, information of relevance to the organism is represented by the concentrations of transcription factor molecules. To extract this information the cell must effectively "measure" these concentrations, but there are physical limits to the precision of these measurements. We use the gap gene network in the early fly embryo as an example of the tradeoff between the precision of concentration measurements and the transmission of relevant information.

Delays in Fitness Adjustment Can Lead to Coexistence of Hierarchically Interacting Species.

Organisms that exploit different environments may experience a stochastic delay in adjusting their fitness when they switch habitats. We study two such organisms whose fitness is determined by the species composition of the local environment, as they interact through a public good. We show that a delay in the fitness adjustment can lead to the coexistence of the two species in a metapopulation, although the faster-growing species always wins in well-mixed competition experiments.

Multiple scales in metapopulations of public goods producers.

Multiple scales in metapopulations can give rise to paradoxical behavior: in a conceptual model for a public goods game, the species associated with a fitness cost due to the public good production can be stabilized in the well-mixed limit due to the mere existence of these scales. The scales in this model involve a length scale corresponding to separate patches, coupled by mobility, and separate time scales for reproduction and interaction with a local environment. Contrary to the well-mixed high mobility limit, we find that for low mobilities, the interaction rate progressively stabilizes this species due to stochastic effects, and that the formation of spatial patterns is not crucial for this stabilization.

Exploiting ecology in drug pulse sequences in favour of population reduction.

A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentration of a drug (antibiotic or chemotherapeutic) as it permeates through the population and is progressively degraded. Different treatment regimes, involving single or periodical doses, are evaluated in terms of the minimal population size (a measure of the extinction probability), and the population composition (a measure of the selection pressure for resistance or tolerance during the treatment). We show that there exist timescales over which the low-stress regime is as effective as the high-stress regime, due to the competition between the two species.

Universal equation of state and pseudogap in the two-dimensional Fermi gas.

We determine the thermodynamic properties and the spectral function for a homogeneous two-dimensional Fermi gas in the normal state using the Luttinger-Ward, or self-consistent T-matrix, approach. The density equation of state deviates strongly from that of the ideal Fermi gas even for moderate interactions, and our calculations suggest that temperature has a pronounced effect on the pressure in the crossover from weak to strong coupling, consistent with recent experiments. We also compute the superfluid transition temperature for a finite system in the crossover region.

Closing the patient-oncologist communication gap: a review of historic and current efforts.

Effective communication is essential in developing any relationship--this is particularly true between oncologists and their patients. The patient-oncologist relationship is one of the most delicate in medicine, and given the strong emotions associated with cancer, successful communication plays a paramount role in the wellbeing of patients and oncologists. Significant advances to close the communication gap have occurred over the past several decades, largely by addressing deficiencies in the various stages of an oncologist's lengthy training: undergraduate medical education, residency and fellowship, and continuing medical education.

Dipolar gases in coupled one-dimensional lattices.

We consider dipolar bosons in two tubes of one-dimensional lattices, where the dipoles are aligned to be maximally repulsive and the particle filling fraction is the same in each tube. In the classical limit of zero intersite hopping, the particles arrange themselves into an ordered crystal for any rational filling fraction, forming a complete devil's staircase like in the single tube case. Turning on hopping within each tube then gives rise to a competition between the crystalline Mott phases and a liquid of defects or solitons.

Formation of β-sheets in glutamine and alanine tripeptides.

The misfolding and aggregation of proteins is associated with many different diseases including the trinucleotide repeat disorders and Prion diseases. We have studied three residue peptides comprising alanine and glutamine in order to understand the short range interactions affecting the formation of β-rich aggregates. Using infrared spectroscopy, we have found that trialanine and triglutamine form significant amounts of β-sheet, but that tripeptides containing alanine and glutamine are only able to form β-sheet if the glutamine side-chains extend outward on both faces of the sheet.

Interpolation schemes for peptide rearrangements.

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures.