Morphology-induced collective behaviors: dynamic pattern formation in water-floating elements

Complex systems involving many interacting elements often organize into patterns. Two types of pattern formation can be distinguished, static and dynamic. Static pattern formation means that the resulting structure constitutes a thermodynamic equilibrium whose pattern formation can be understood in terms of the minimization of free energy, while dynamic pattern formation indicates that the system is permanently dissipating energy and not in equilibrium. In this paper, we report experimental results showing that the morphology of elements plays a significant role in dynamic pattern formation. We prepared three different shapes of elements (circles, squares, and triangles) floating in a water-filled container, in which each of the shapes has two types: active elements that were capable of self-agitation with vibration motors, and passive elements that were mere floating tiles. The system was purely decentralized: that is, elements interacted locally, and subsequently elicited global patterns in a process called self-organized segregation. We showed that, according to the morphology of the selected elements, a different type of segregation occurs. Also, we quantitatively characterized both the local interaction regime and the resulting global behavior for each type of segregation by means of information theoretic quantities, and showed the difference for each case in detail, while offering speculation on the mechanism causing this phenomenon.     

Dual function of protein confinement in chaperonin-assisted protein folding.

The GroEL/GroES chaperonin system mediates the folding of a range of newly synthesized polypeptides in the bacterial cytosol. Using a rapid biotin-streptavidin-based inhibition of chaperonin function, we show that the cage formed by GroEL and its cofactor GroES can have a dual role in promoting folding. First, enclosure of nonnative protein in the GroEL:GroES complex is essential for folding to proceed unimpaired by aggregation. Second, folding inside the cage can be significantly faster than folding in free solution, independently of ATP-driven cycles of GroES binding and release. This suggests that confinement of unfolded protein in the narrow hydrophilic space of the chaperonin cage smoothes the energy landscape for the folding of some proteins, increasing the flux of folding intermediates toward the native state.     

Isolation of cadmium sensitive mutants in Chlamydomonas reinhardtii by transformation/insertional mutagenesis

Abstract An arg7, cw15, mt⁺ strain of Chlamydomonas reinhardtii (CC1618) was transformed with pARG7.8, a plasmid containing the wild-type ARG7 gene. Over 2300 arg⁺ transformants were selected on TAP media. Upon subsequent analysis on TAP plus cadmium plates, five of the transformants failed to grow at a level of 400 μM cadmium and were designated as cadmium sensitive (Cd^s) mutants. Hybridization data indicated that vector (pBR329) sequences were present in these five mutants, but not in the untransformed parental strain. Two of the mutants have been back crossed to an arg7, cw15, Cd⁺, mt⁻ strain (CC425) and found to have progeny which always cosegregate the arg⁺ and Cd^s phenotypesin these two mutants results from the insertion of the plasmid pARG7.8 into a gene involving cadmium detoxification, and it provides a method by which to clone the interrupted gene(s).     

Electron microscopy and image analysis of the multicatalytic proteinase

One electron micrographs, negatively stained multicatalytic proteinase molecules are viewed end-on (ring shaped) or side-on (rectangular shaped). For aurothioglucose, ammonium molybdate- and phosphotungstate-stained molecules, the dimensions measured are consistent. In contrast, uranyl acetate-staining reveals ring-shaped particles which vary in diameter between 12 and 16 nm. This is due to a partial collapse and substantial flattening of the structure. Digital image analysis of side-on views of the particles reveals a tripartite, reel-shaped structure. Within the ring-like, end-on projections of ammonium molybdate-stained molecules six local centres of mass can be discerned; their position appears to depart, however, from a true six-fold symmetry.     

Urinalysis of patients suffering from climatic heat stress (Sharav)

Hot dry winds (Sharav in Israel) are notorious for causing controversial symptoms such as depression, discomfort, headaches, irritability and exacerbation of respiratory ailments. Daily urinalysis combined with study of the complaints of two hundred weather-sensitive patients suffering from Sharav have shown that there exist at least three different patterns of reaction: serotonin hypersecretion causing a general "Irritation Syndrome", catecholamine deficiency resulting in the "Exhaustion Syndrome", histamine and creatinine overproduction combined with clinical "Hyperthyroidism - Forme Fruste" and typical thyroid complaints. These syndromes are amenable to appropriate treatment controlled by urinalysis.

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Zusammenfassung Trockene heisse Wüstenwinde (Sharav in Israel) rufen eine seltsame Mischung von Symptomen hervor wie Depression, Unwohlsein, Kopfschmerzen, Reizbarkeit und Verschlimmerung respiratorischer Beschwerden. Tägliche Urinuntersuchungen kombiniert mit dem Studium der verschiedenen Beschwerden von 200 Sharav-gefühligen Personen haben gezeigt, dass drei verschiedene Reaktionsformen vorliegen: Serotonin-Ausschüttung, die zu einem allgemeinen Irritationssyndrom führt; Katecholamin-Mangel, der zu einem typischen Erschöpfungssyndrom führt; Histamin- und Kreatinin-Ausschüttung, die mit leichtem Hyperthyreoidismus einhergehen. Letzteres Syndrom bereitet dem Patienten nur an Sharav-Tagen Beschwerden. Die Syndrome sind durch gezielte und Urin-kontrollierte Behandlung heilbar.

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Resume Des vents chauds et secs provenant du désert (le Charav en Israël par exemple) sont connus pour provoquer un ensemble de symptômes particuliers tels que dépression nerveuse, indisposition, céphalées, irritabilité et aggravation des troubles respiratoires. L'analyse journalière de l'urine et l'étude des divers symptômes que présentaient 200 personnes sensibles au Charav ont montré la présence de trois formes différentes de réactions: sécrétion accrue de sérotonine qui conduit à un syndrome d'irritabilité générale; une carence en catécholamine qui se traduit par un syndrome typique d'épuisement; une sécrétion d'histamine et de créatinine parallèle à un faible hyperthyréoïdisme. Ce dernier syndrome ne provoque des troubles aux patients que durant les jours où le Charav souffle. Ces trois syndromes sont guérissables par une médication appropriée et dont l'effet est contrôlé par des analyses d'urine.

     

Silencing of cryptic prophages in Corynebacterium glutamicum

DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.