Pressure Induced Topological Phase Transitions in Membranes

Some highly unusual features of a lipid-water liquid crystal are revealed by high pressure x-ray diffraction, light scattering and dilatometric studies of the lamellar (bilayer $L_{\alpha}$) to nonlamellar inverse hexagonal ($H_{II}$) phase transition. (i) The size of the unit cell of the $H_{II}$ phase increases with increasing pressure. (ii) The transition volume, $\Delta V_{bh}$, decreases and appears to vanish as the pressure is increased. (iii) The intensity of scattered light increases as $\Delta V_{bh}$ decreases. Data are presented which suggest that this increase is due to the formation of an intermediate cubic phase, as predicted by recent theoretical suggestions of the underlying universal phase sequence.Comment: 12 pages, typed using REVTEX 2.

Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas Genome Database (http://www.pseudomonas.com) integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions and manually curated annotation updates. The latest release implements an ability to view sequence polymorphisms in P. aeruginosa PAO1 versus other reference strains, incomplete genomes and single gene sequences. This aids analysis of phenotypic variation between closely related isolates and strains, as well as wider population genomics and evolutionary studies. The wide range of tools for comparing Pseudomonas annotations and sequences now includes a strain-specific access point for viewing high precision computational predictions including updated, more accurate, protein subcellular localization and genomic island predictions. Views link to genome-scale experimental data as well as comparative genomics analyses that incorporate robust genera-geared methods for predicting and clustering orthologs. These analyses can be exploited for identifying putative essential and core Pseudomonas genes or identifying large-scale evolutionary events. The Pseudomonas Genome Database aims to provide a continually updated, high quality source of genome annotations, specifically tailored for Pseudomonas researchers, but using an approach that may be implemented for other genera-level research communities

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license

The Wrangel Island Polynya in early summer : trends and relationships to other polynyas and the Beaufort Sea High

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 39 (2012): L05503, doi:10.1029/2011GL050691.Polynyas, regions of reduced sea ice concentration relative to their surroundings, are important features of the polar climate system in which enhanced fluxes of heat, moisture, and momentum can occur between the atmosphere and ocean. As such, they play a significant role in many atmospheric, oceanographic and biological processes. There are concerns that in a warming climate, in which there is a trend towards a reduction in sea ice cover, that the location, size and duration of many polynyas may change resulting in climatological and ecological impacts. In this paper, we identify an early summer manifestation of the Wrangel Island polynya that forms in the western Chuckchi Sea. We show that over the past 30 years there has been an increased frequency of occurrence as well as a doubling in the size of the polynya. The polynya is shown to form when there is an enhanced easterly flow over the Chukchi Sea that is associated with an anomalously intense Beaufort Sea High (BSH), a closed anti-cyclonic atmospheric circulation that forms over the Beaufort Sea. We also show that there has been a concomitant trend towards a more intense BSH over the same time period and we propose that this trend is responsible for the observed changes in the Wrangel Island polynya. Given its large and increasing size, the early summer polynya may also play an important and unaccounted role in the physical and biological oceanography of the western Chukchi Sea.GWKM was supported by the Natural Science and Engineering Research Council of Canada. RSP was supported by the NOAA project NA08-OAR4320895.2012-09-1

Взаємозв’язок великих кондратьєвських циклів розвитку економіки і системних світових конфліктів

Однією з найважливіших проблем, що постала перед сучасною наукою у зв’язку із стрімким розгортанням глобальної економічної кризи, загостренням світових конфліктів, є вироблення науково обґрунтованих «метричних» експрес прогнозів розвитку суспільства на ближчу і далеку перспективу

Mapping interactions with the chaperone network reveals factors that protect against tau aggregation.

A network of molecular chaperones is known to bind proteins ('clients') and balance their folding, function and turnover. However, it is often unclear which chaperones are critical for selective recognition of individual clients. It is also not clear why these key chaperones might fail in protein-aggregation diseases. Here, we utilized human microtubule-associated protein tau (MAPT or tau) as a model client to survey interactions between ~30 purified chaperones and ~20 disease-associated tau variants (~600 combinations). From this large-scale analysis, we identified human DnaJA2 as an unexpected, but potent, inhibitor of tau aggregation. DnaJA2 levels were correlated with tau pathology in human brains, supporting the idea that it is an important regulator of tau homeostasis. Of note, we found that some disease-associated tau variants were relatively immune to interactions with chaperones, suggesting a model in which avoiding physical recognition by chaperone networks may contribute to disease

A Systematic Review of Argumentation Related to the Engineering-Designed World

Background Across academic disciplines, researchers have found that argumentation‐based pedagogies increase learners\u27 achievement and engagement. Engineering educational researchers and teachers of engineering may benefit from knowledge regarding how argumentation related to engineering has been practiced and studied. Purpose/Hypothesis Drawing from terms and concepts used in national standards for K‐12 education and accreditation requirements for undergraduate engineering education, this study was designed to identify how arguments and argumentation related to the engineering‐designed world were operationalized in relevant literature. Methodology Specified search terms and inclusion criteria were used to identify 117 empirical studies related to engineering argumentation and educational research. A qualitative content analysis was used to identify trends across these studies. Findings Overall, engineering‐related argumentation was associated with a variety of positive learner outcomes. Across many studies, arguments were operationalized in practice as statements regarding whether an existing technology should be adopted in a given context, usually with a limited number of supports (e.g., costs and ethics) provided for each claim. Relatively few studies mentioned empirical practices, such as tests. Most studies did not name the race/ethnicity of participants nor report engineering‐specific outcomes. Conclusions Engineering educators in K‐12 and undergraduate settings can create learning environments in which learners use a range of epistemic practices, including empirical practices, to support a range of claims. Researchers can study engineering‐specific outcomes while specifying relevant demographics of their research participants

Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa

Once the genome sequence of an organism is obtained, attention turns from identifying genes to understanding their function, their organization and control of metabolic pathways and networks that determine its physiology. Recent technical advances in acquiring genome-wide data have led to substantial progress in identifying gene functions. However, we still do not know the function of a large number of genes and, even when a gene product has been assigned to a functional class, we cannot normally predict its contribution to the phenotypic behaviour of the cell or organism - the phenome. In this study, we assessed bacterial growth parameters of 4030 non-redundant PA14 transposon mutants in the pathogenic bacterium Pseudomonas aeruginosa. The genome-wide simultaneous analysis of 119 distinct growth-related phenotypes uncovered a comprehensive phenome and provided evidence that most genotypes are not phenotypically isolated but rather define specific complex phenotypic clusters of genotypes. Since phenotypic overlap was demonstrated to reflect the relatedness of genotypes on a global scale, knowledge of an organism's phenome might significantly contribute to the advancement of functional genomics

Quantitative Interpretation of a Genetic Model of Carcinogenesis Using Computer Simulations

The genetic model of tumorigenesis by Vogelstein et al. (V theory) and the molecular definition of cancer hallmarks by Hanahan and Weinberg (W theory) represent two of the most comprehensive and systemic understandings of cancer. Here, we develop a mathematical model that quantitatively interprets these seminal cancer theories, starting from a set of equations describing the short life cycle of an individual cell in uterine epithelium during tissue regeneration. The process of malignant transformation of an individual cell is followed and the tissue (or tumor) is described as a composite of individual cells in order to quantitatively account for intra-tumor heterogeneity. Our model describes normal tissue regeneration, malignant transformation, cancer incidence including dormant/transient tumors, and tumor evolution. Further, a novel mechanism for the initiation of metastasis resulting from substantial cell death is proposed. Finally, model simulations suggest two different mechanisms of metastatic inefficiency for aggressive and less aggressive cancer cells. Our work suggests that cellular de-differentiation is one major oncogenic pathway, a hypothesis based on a numerical description of a cell's differentiation status that can effectively and mathematically interpret some major concepts in V/W theories such as progressive transformation of normal cells, tumor evolution, and cancer hallmarks. Our model is a mathematical interpretation of cancer phenotypes that complements the well developed V/W theories based upon description of causal biological and molecular events. It is possible that further developments incorporating patient- and tissue-specific variables may build an even more comprehensive model to explain clinical observations and provide some novel insights for understanding cancer

Ventilation of the Arctic Ocean: Mean ages and inventories of anthropogenic CO2 and CFC-11

The Arctic Ocean constitutes a large body of water that is still relatively poorly surveyed because of logistical difficulties, although the importance of the Arctic Ocean for global circulation and climate is widely recognized. For instance, the concentration and inventory of anthropogenic CO2 (C ant) in the Arctic Ocean are not properly known despite its relatively large volume of well-ventilated waters. In this work, we have synthesized available transient tracer measurements (e.g., CFCs and SF6) made during more than two decades by the authors. The tracer data are used to estimate the ventilation of the Arctic Ocean, to infer deep-water pathways, and to estimate the Arctic Ocean inventory of C ant. For these calculations, we used the transit time distribution (TTD) concept that makes tracer measurements collected over several decades comparable with each other. The bottom water in the Arctic Ocean has CFC values close to the detection limit, with somewhat higher values in the Eurasian Basin. The ventilation time for the intermediate water column is shorter in the Eurasian Basin (∼200 years) than in the Canadian Basin (∼300 years). We calculate the Arctic Ocean C ant inventory range to be 2.5 to 3.3 Pg-C, normalized to 2005, i.e., ∼2% of the global ocean C ant inventory despite being composed of only ∼1% of the global ocean volume. In a similar fashion, we use the TTD field to calculate the Arctic Ocean inventory of CFC-11 to be 26.2 ± 2.6 × 106 moles for year 1994, which is ∼5% of the global ocean CFC-11 inventor