Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution

Background: The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. / Results: We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. / Conclusions: Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates

Magnetic Resonance Spectroscopy discriminates the response to microglial stimulation of wild type and Alzheimer's disease models.

Microglia activation has emerged as a potential key factor in the pathogenesis of Alzheimers disease. Metabolite levels assessed by magnetic resonance spectroscopy (MRS) are used as markers of neuroinflammation in neurodegenerative diseases, but how they relate to microglial activation in health and chronic disease is incompletely understood. Using MRS, we monitored the brain metabolic response to lipopolysaccharides (LPS)-induced microglia activation in vivo in a transgenic mouse model of Alzheimers disease (APP/PS1) and healthy controls (wild-type (WT) littermates) over 4 hours. We assessed reactive gliosis by immunohistochemistry and correlated metabolic and histological measures. In WT mice, LPS induced a microglial phenotype consistent with activation, associated with a sustained increase in macromolecule and lipid levels (ML9). This effect was not seen in APP/PS1 mice, where LPS did not lead to a microglial response measured by histology, but induced a late increase in the putative inflammation marker myoinositol (mI) and metabolic changes in total creatine and taurine previously reported to be associated with amyloid load. We argue that ML9 and mI distinguish the response of WT and APP/PS1 mice to immune mediators. Lipid and macromolecule levels may represent a biomarker of activation of healthy microglia, while mI may not be a glial marker

Resolving the Fast Kinetics of Cooperative Binding: Ca2+ Buffering by Calretinin

Cooperativity is one of the most important properties of molecular interactions in biological systems. It is the ability to influence ligand binding at one site of a macromolecule by previous ligand binding at another site of the same molecule. As a consequence, the affinity of the macromolecule for the ligand is either decreased (negative cooperativity) or increased (positive cooperativity). Over the last 100 years, O2 binding to hemoglobin has served as the paradigm for cooperative ligand binding and allosteric modulation, and four practical models were developed to quantitatively describe the mechanism: the Hill, the Adair-Klotz, the Monod-Wyman-Changeux, and the Koshland-Némethy-Filmer models. The predictions of these models apply under static conditions when the binding reactions are at equilibrium. However, in a physiological setting, e.g., inside a cell, the timing and dynamics of the binding events are essential. Hence, it is necessary to determine the dynamic properties of cooperative binding to fully understand the physiological implications of cooperativity. To date, the Monod-Wyman-Changeux model was applied to determine the kinetics of cooperative binding to biologically active molecules. In this model, cooperativity is established by postulating two allosteric isoforms with different binding properties. However, these studies were limited to special cases, where transition rates between allosteric isoforms are much slower than the binding rates or where binding and unbinding rates could be measured independently. For all other cases, the complex mathematical description precludes straightforward interpretations. Here, we report on calculating for the first time the fast dynamics of a cooperative binding process, the binding of Ca2+ to calretinin. Calretinin is a Ca2+-binding protein with four cooperative binding sites and one independent binding site. The Ca2+ binding to calretinin was assessed by measuring the decay of free Ca2+ using a fast fluorescent Ca2+ indicator following rapid (<50-μs rise time) Ca2+ concentration jumps induced by uncaging Ca2+ from DM-nitrophen. To unravel the kinetics of cooperative binding, we devised several approaches based on known cooperative binding models, resulting in a novel and relatively simple model. This model revealed unexpected and highly specific nonlinear properties of cellular Ca2+ regulation by calretinin. The association rate of Ca2+ with calretinin speeds up as the free Ca2+ concentration increases from cytoplasmic resting conditions (∼100 nM) to approximately 1 μM. As a consequence, the Ca2+ buffering speed of calretinin highly depends on the prevailing Ca2+ concentration prior to a perturbation. In addition to providing a novel mode of action of cellular Ca2+ buffering, our model extends the analysis of cooperativity beyond the static steady-state condition, providing a powerful tool for the investigation of the dynamics and functional significance of cooperative binding in general

Interaction-induced chaos in a two-electron quantum-dot system

A quasi-one-dimensional quantum dot containing two interacting electrons is analyzed in search of signatures of chaos. The two-electron energy spectrum is obtained by diagonalization of the Hamiltonian including the exact Coulomb interaction. We find that the level-spacing fluctuations follow closely a Wigner-Dyson distribution, which indicates the emergence of quantum signatures of chaos due to the Coulomb interaction in an otherwise non-chaotic system. In general, the Poincar\'e maps of a classical analog of this quantum mechanical problem can exhibit a mixed classical dynamics. However, for the range of energies involved in the present system, the dynamics is strongly chaotic, aside from small regular regions. The system we study models a realistic semiconductor nanostructure, with electronic parameters typical of gallium arsenide.Comment: 4 pages, 3ps figure

Statistical Mechanics of Quantum Dots

Contains table of contents for Section 2, description of one research project and a list of publications.Joint Service Electronics Program Contract DAAL03-92-C-000

A Survey of Women in Academia and the role of a Multidisciplinary Professional Society

The Society of Women Engineers (SWE) is a global professional society of over 30,000 members with a mission to “Stimulate women to achieve full potential in careers as engineers and leaders, expand the image of the engineering profession as a positive force in improving the quality of life, and demonstrate the value of diversity”1. SWE is an organization that is deeply rooted in industry. The founding members were employed by firms that are a result of the industrial revolution, and thus the focus of its membership is on those that work for industry, consultants, and often themselves. This focus has unintentionally left a large population of its membership, the academic population, underrepresented and misunderstood. Early discussion at the board level in the mid 2000’s indicated a willingness for a paradigm shift. However, the representation of academics on the board and other leadership roles has been lacking. This can be attributed to the lower numbers of this group relative to the whole, as well as the requirements of tenure that do not support the time and dedication to such an endeavor. A small but influential group of members, including a former board member, and a few involved at various levels of the society have been working toward increasing opportunities for women in academia (WIA). Some of the initiatives have been the societal support of the WIA committee, the addition of professional development opportunities targeting women in academic careers, providing recognition and awards, and aiding in networking opportunities. These all lead toward career advancement, making SWE more attractive to women engineers in the academe. To further our understanding of available opportunities and those opportunities that will make membership and active participation more attractive to members in academia, a survey was developed. Information gathered by the survey include demographics, perceived needs, and potential contributions the individual could make in furthering the creation of professional development opportunities for this population. This work is intended to share the results of this survey, using descriptive statistics, further developing our understanding of this underserved population within SWE

Проблема правової культури в історії філософсько-педагогічної думки

(uk) Стаття присвячена проблемі правової культури в історії філософсько-педагогічної думки

Molecular sensing with hyperpolarized 129Xe using switchable chemical exchange relaxation transfer

A new approach for hyperpolarized 129Xe molecular sensors is explored using paramagnetic relaxation agents that can be deactivated upon chemical or enzymatic reaction with an analyte. Cryptophane encapsulated 129Xe within the vicinity of the paramagnetic center experiences fast relaxation that, through chemical exchange of xenon atoms between cage and solvent pool, causes accelerated hyperpolarized 129Xe signal decay in the dissolved phase. In this work, the relaxivity of GadoliniumIII-DOTA on 129Xe in the solvent was increased eightfold through tethering of the paramagnetic molecule to a cryptophane cage. This potent relaxation agent can be ‘turned off’ specifically for 129Xe through chemical reactions that spatially separate the GdIII centre from the attached cryptophane cage. Unlike 129Xe chemical shift based sensors, the new concept does not require high spectral resolution and may lead to a new generation of responsive contrast agents for molecular MRI

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment

Metabolism is at the heart of many biotechnologies from biofuels to medical diagnostics. Metabolomic methods that provide glimpses into cellular metabolism have rapidly developed into a critical component of the biotechnological development process. Most metabolomics methods have focused on what is happening inside the cell. Equally important are the biochemical transformations of the cell, and their effect on other cells and their environment; the exometabolome. Exometabolomics is therefore gaining popularity as a robust approach for obtaining rich phenotypic data, and being used in bioprocessing and biofuel development. Mass spectrometry imaging approaches, including several nanotechnologies, provide complimentary information by localizing metabolic processes within complex biological matrices. Together, the two technologies can provide new insights into the metabolism and interactions of cells