Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks

We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a dynamically determinant subnetwork, we explore the robustness of transcriptional regulation as a function of the type of Boolean functions used in the model that mimic the influence of regulating agents on the transcription level of a gene. We compare the results obtained for the actual yeast network with those from two different model networks, one with similar in-degree distribution as the yeast and random otherwise, and another due to Balcan et al., where the global topology of the yeast network is reproduced faithfully. We, surprisingly, find that the first set of model networks better reproduce the results found with the actual yeast network, even though the Balcan et al. model networks are structurally more similar to that of yeast.Comment: 7 pages, 4 figures, To appear in Int. J. Bifurcation and Chaos, typos were corrected and 2 references were adde

Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling

Diverse animal taxa metamorphose between larval and juvenile phases in response to bacteria. Although bacteria-induced metamorphosis is widespread among metazoans, little is known about the molecular changes that occur in the animal upon stimulation by bacteria. Larvae of the tubeworm Hydroides elegans metamorphose in response to surface-bound Pseudoalteromonas luteoviolacea bacteria, producing ordered arrays of phage tail-like metamorphosis-associated contractile structures (MACs). Sequencing the Hydroides genome and transcripts during five developmental stages revealed that MACs induce the regulation of groups of genes important for tissue remodeling, innate immunity, and mitogen-activated protein kinase (MAPK) signaling. Using two MAC mutations that block P. luteoviolacea from inducing settlement or metamorphosis and three MAPK inhibitors, we established a sequence of bacteria-induced metamorphic events: MACs induce larval settlement; then, particular properties of MACs encoded by a specific locus in P. luteoviolacea initiate cilia loss and activate metamorphosis-associated transcription; finally, signaling through p38 and c-Jun N-terminal kinase (JNK) MAPK pathways alters gene expression and leads to morphological changes upon initiation of metamorphosis. Our results reveal that the intricate interaction between Hydroides and P. luteoviolacea can be dissected using genomic, genetic, and pharmacological tools. Hydroides' dependency on bacteria for metamorphosis highlights the importance of external stimuli to orchestrate animal development. The conservation of Hydroides genome content with distantly related deuterostomes (urchins, sea squirts, and humans) suggests that mechanisms of bacteria-induced metamorphosis in Hydroides may have conserved features in diverse animals. As a major biofouling agent, insight into the triggers of Hydroides metamorphosis might lead to practical strategies for fouling control

Thermodynamics and Universality for Mean Field Quantum Spin Glasses

We study aspects of the thermodynamics of quantum versions of spin glasses. By means of the Lie-Trotter formula for exponential sums of operators, we adapt methods used to analyze classical spin glass models to answer analogous questions about quantum models.Comment: 17 page

Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures

Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm Hydroides elegans, a significant biofouling agent, require contact with surface-bound bacteria to undergo metamorphosis; however, the mechanisms that underpin this microbially mediated developmental transition have been enigmatic. Here, we show that a marine bacterium, Pseudoalteromonas luteoviolacea, produces arrays of phage tail–like structures that trigger metamorphosis of H. elegans. These arrays comprise about 100 contractile structures with outward-facing baseplates, linked by tail fibers and a dynamic hexagonal net. Not only do these arrays suggest a novel form of bacterium-animal interaction, they provide an entry point to understanding how marine biofilms can trigger animal development

THE ASSOCIATION BETWEEN STATIC FOOT POSTURE AND PEAK PATELLAR TENDON FORCE DURING SINGLE-LEG LANDINGS: PRELIMINARY FINDINGS

Patellar tendinopathy is particularly prevalent in jumping-sport athletes and develops due to chronic overloading without appropriate load modification. Pronated and supinated foot postures have been suggested to be associated with the development of the injury. This study aimed to investigate the association between static foot posture, measured using the Foot Posture Index (FPI), and peak patellar tendon force during single-leg drop landings. Kinetic and kinematic data were collected during a single-leg landing task and used to estimate peak patellar tendon force. There was no statistically significant association between FPI and peak patellar tendon force during landing (p = 0.910). Further research investigating how foot posture may affect lower limb loading during landing is required to inform pre-screening and rehabilitation protocols for jumping sport athletes

The DEEP2 Redshift Survey: Lyman Alpha Emitters in the Spectroscopic Database

We present the first results of a search for Lyman-alpha emitters (LAEs) in the DEEP2 spectroscopic database that uses a search technique that is different from but complementary to traditional narrowband imaging surveys. We have visually inspected ~20% of the available DEEP2 spectroscopic data and have found nine high-quality LAEs with clearly asymmetric line profiles and an additional ten objects of lower quality, some of which may also be LAEs. Our survey is most sensitive to LAEs at z=4.4-4.9 and that is indeed where all but one of our high-quality objects are found. We find the number density of our spectroscopically-discovered LAEs to be consistent with those found in narrowband imaging searches. The combined, averaged spectrum of our nine high-quality objects is well fit by a two-component model, with a second, lower-amplitude component redshifted by ~420 km/s with respect to the primary Lyman-alpha line, consistent with large-scale outflows from these objects. We conclude by discussing the advantages and future prospects of blank-sky spectroscopic surveys for high-z LAEs.Comment: Accepted for publication in Ap

Which Method-Stereotype Changes are Indicators of Code Smells?

A study of how method roles evolve during the lifetime of a software system is presented. Evolution is examined by analyzing when the stereotype of a method changes. Stereotypes provide a high-level categorization of a method\u27s behavior and role, and also provide insight into how a method interacts with its environment and carries out tasks. The study covers 50 open-source systems and 6 closed-source systems. Results show that method behavior with respect to stereotype is highly stable and constant over time. Overall, out of all the history examined, only about 10% of changes to methods result in a change in their stereotype. Examples of methods that change stereotype are further examined. A select number of these types of changes are indicators of code smells

The DEEP2 Galaxy Redshift Survey: Mean Ages and Metallicities of Red Field Galaxies at z ~ 0.9 from Stacked Keck/DEIMOS Spectra

As part of the DEEP2 galaxy redshift survey, we analyze absorption line strengths in stacked Keck/DEIMOS spectra of red field galaxies with weak to no emission lines, at redshifts 0.7 <= z <= 1. Comparison with models of stellar population synthesis shows that red galaxies at z ~ 0.9 have mean luminosity-weighted ages of the order of only 1 Gyr and at least solar metallicities. This result cannot be reconciled with a scenario where all stars evolved passively after forming at very high z. Rather, a significant fraction of stars can be no more than 1 Gyr old, which means that star formation continued to at least z ~ 1.2. Furthermore, a comparison of these distant galaxies with a local SDSS sample, using stellar populations synthesis models, shows that the drop in the equivalent width of Hdelta from z ~ 0.9 to 0.1 is less than predicted by passively evolving models. This admits of two interpretations: either each individual galaxy experiences continuing low-level star formation, or the red-sequence galaxy population from z ~ 0.9 to 0.1 is continually being added to by new galaxies with younger stars.Comment: A few typos were corrected and numbers in Table 1 were revise

Tools to Ease the Choice and Design of Protein Crystallisation Experiments

The process of macromolecular crystallisation almost always begins by setting up crystallisation trials using commercial or other premade screens, followed by cycles of optimisation where the crystallisation cocktails are focused towards a particular small region of chemical space. The screening process is relatively straightforward, but still requires an understanding of the plethora of commercially available screens. Optimisation is complicated by requiring both the design and preparation of the appropriate secondary screens. Software has been developed in the C3 lab to aid the process of choosing initial screens, to analyse the results of the initial trials, and to design and describe how to prepare optimisation screens