Antigen-driven selection in germinal centers as reflected by the shape characteristics of immunoglobulin gene lineage trees: a large-scale simulation study

During the immune response, the generation of memory B lymphocytes in germinal centers involves affinity maturation of the cells’ antigen receptors, based on somatic hypermutation of receptor genes and antigen-driven selection of the resulting mutants. Affinity maturation is vital for immune protection, and is the basis of humoral immune learning and memory. Lineage trees of somatically hypermutated immunoglobulin genes often serve to qualitatively illustrate claims concerning the dynamics of affinity maturation in germinal centers. Here, we derive the quantitative relationships between parameters characterizing affinity maturation dynamics (proliferation, differentiation and mutation rates, initial affinity of the Ig to the antigen, and selection thresholds) and the mathematical properties of lineage trees, using a computer simulation which combines mathematical models for all mature B cell populations, stochastic models of hypermutation and selection, lineage tree generation and measurement of graphical tree characteristics. We identified seven key lineage tree properties, and found correlations of these with initial clone affinity and with the selection threshold. These two parameters were found to be the main factors affecting lineage tree shapes in both primary and secondary response trees. The results also confirm that recycling from centrocytes back to centroblasts is highly likely.     

Identification of the endostyle as a stem cell niche in a colonial chordate

Stem cell populations exist in "niches" that hold them and regulate their fate decisions. Identification and characterization of these niches is essential for understanding stem cell maintenance and tissue regeneration. Here we report on the identification of a novel stem cell niche in Botryllus schlosseri, a colonial urochordate with high stem cell-mediated developmental activities. Using in vivo cell labeling, engraftment, confocal microscopy, and time-lapse imaging, we have identified cells with stemness capabilities in the anterior ventral region of the Botryllus' endostyle. These cells proliferate and migrate to regenerating organs in developing buds and buds of chimeric partners but do not contribute to the germ line. When cells are transplanted from the endostyle region, they contribute to tissue development and induce long-term chimerism in allogeneic tissues. In contrast, cells from other Botryllus' regions do not show comparable stemness capabilities. Cumulatively, these results define the Botryllus' endostyle region as an adult somatic stem cell niche.     

Slow oscillations in neural networks with facilitating synapses

The synchronous oscillatory activity characterizing many neurons in a network is often considered to be a mechanism for representing, binding, conveying, and organizing information. A number of models have been proposed to explain high-frequency oscillations, but the mechanisms that underlie slow oscillations are still unclear. Here, we show by means of analytical solutions and simulations that facilitating excitatory (E _f) synapses onto interneurons in a neural network play a fundamental role, not only in shaping the frequency of slow oscillations, but also in determining the form of the up and down states observed in electrophysiological measurements. Short time constants and strong E _f synapse-connectivity were found to induce rapid alternations between up and down states, whereas long time constants and weak E _f synapse connectivity prolonged the time between up states and increased the up state duration. These results suggest a novel role for facilitating excitatory synapses onto interneurons in controlling the form and frequency of slow oscillations in neuronal circuits.     

Chlorella sorokiniana UTEX 2805, a heat and intense, sunlight-tolerant microalga with potential for removing ammonium from wastewater

In the summer of 2003, a microalga strain was isolated from a massive green microalgae bloom in wastewater stabilization ponds at the treatment facility of La Paz, B.C.S., Mexico. Prevailing environmental conditions were air temperatures over 40 degrees C, water temperature of 37 degrees C, and insolation of up to 2400 micromol m2 s(-1) at midday for several hours at the water surface for four months. The microalga was identified as Chlorella sorokiniana Shih. et Krauss, based on sequencing its entire 18S rRNA gene. In a controlled photo-bioreactor, this strain can grow to high population densities in synthetic wastewater at temperatures of 40-42 degrees C and light intensity of 2500 micromol m2 s(-1) for 5h daily and efficiently remove ammonium from the wastewater under these conditions better than under normal lower temperature (28 degrees C) and lower light intensity (60 micromol m2 s(-1)). When co-immobilized with the bacterium Azospirillum brasilense that promotes growth of microalgae, the population of microalga grew faster and removed even more ammonium. Under exposure to extreme growth conditions, the quantity of four photosynthetic pigments increased in the co-immobilized cultures. This strain of microalga has potential as a wastewater treatment agent under extreme conditions of temperature and light intensity.     

The MOSIX Direct File System Access Method for Supporting Scalable Cluster File Systems

MOSIX is a cluster management system that supports preemptive process migration. This paper presents the MOSIX Direct File System Access (DFSA), a provision that can improve the performance of cluster file systems by allowing a migrated process to directly access files in its current location. This capability, when combined with an appropriate file system, could substantially increase the I/O performance and reduce the network congestion by migrating an I/O intensive process to a file server rather than the traditional way of bringing the file's data to the process. DFSA is suitable for clusters that manage a pool of shared disks among multiple machines. With DFSA, it is possible to migrate parallel processes from a client node to file servers for parallel access to different files. Any consistent file system can be adjusted to work with DFSA. To test its performance, we developed the MOSIX File-System (MFS) which allows consistent parallel operations on different files. The paper describes DFSA and presents the performance of MFS with and without DFSA.     

Constitutive activation of G-proteins by polycystin-1 is antagonized by polycystin-2.

Polycystin-1 (PC1), a 4,303-amino acid integral membrane protein of unknown function, interacts with polycystin-2 (PC2), a 968-amino acid alpha-type channel subunit. Mutations in their respective genes cause autosomal dominant polycystic kidney disease. Using a novel heterologous expression system and Ca(2+) and K(+) channels as functional biosensors, we found that full-length PC1 functioned as a constitutive activator of G(i/o)-type but not G(q)-type G-proteins and modulated the activity of Ca(2+) and K(+) channels via the release of Gbetagamma subunits. PC1 lacking the N-terminal 1811 residues replicated the effects of full-length PC1. These effects were independent of regulators of G-protein signaling proteins and were lost in PC1 mutants lacking a putative G-protein binding site. Co-expression with full-length PC2, but not a C-terminal truncation mutant, abrogated the effects of PC1. Our data provide the first experimental evidence that full-length PC1 acts as an untraditional G-protein-coupled receptor, activity of which is physically regulated by PC2. Thus, our study strongly suggests that mutations in PC1 or PC2 that distort the polycystin complex would initiate abnormal G-protein signaling in autosomal dominant polycystic kidney disease.     

Monitoring of black mangrove restoration with nursery-reared seedlings on an arid coastal lagoon

Black mangrove (Avicennia germinans) seedlings (n=555) were grown from field-collected propagules for 3 months in a new type of terrestrial nursery. They were grown in clusters of five plants, and then they were transplanted to a clear-cut zone in a lagoon fringed by a mangrove forest at Laguna de Balandra, Baja California Sur, Mexico. Survival and plant development of transplants were monitored at 6-monthly intervals for 2 years. After 1 month, the survival of seedlings was 96%, later stabilizing at approximately 77%. After 24 months, 74% of the plants were still alive. The best cluster, showing maximum growth under mangrove swamp conditions in this arid zone, was a two-plant cluster. The lagoon has a low natural regeneration rate of 48 plants per 350 m² per 6 years of monitoring. This study shows the feasibility of restoring destroyed arid-coast lagoons with black mangroves.     

Effect of Accessory Proteins P19 and P20 on Cytolytic Activity of Cyt1Aa from Bacillus thuringiensis subsp. israelensis in Escherichia coli

The gene coding for the accessory protein P19 of Bacillus thuringiensis subsp. israelensis was expressed in Escherichia coli and its product was characterized. To investigate its putative role in δ-endotoxin crystallization as a P20-like polypeptide, each of the two encoding genes, p20 and p19, was cloned for inducible expression coordinatively with cyt1Aa. The latter is known to kill its transgenic host. P20 but not P19 stabilized Cyt1Aa and protected the host cells from its lethal effect. Neither GroEL nor GroES, expressed in trans, affected Cyt1Aa as did P20. The function of P20 is thus more specific than that of the chaperones, but that of P19 remains enigmatic. The correct sequence of p19, confirmed in all five isolates of B. thuringiensis subsp. israelensis, does not explain the slow electrophoretic mobility of its 179 amino acids product. Received: 5 March 2001 / Accepted: 3 April 2001     

H-Ras Nanocluster Stability Regulates the Magnitude of MAPK Signal Output

H-Ras is a binary switch that is activated by multiple co-factors and triggers several key cellular pathways one of which is MAPK. The specificity and magnitude of downstream activation is achieved by the spatio-temporal organization of the active H-Ras in the plasma membrane. Upon activation, the GTP bound H-Ras binds to Galectin-1 (Gal-1) and becomes transiently immobilized in short-lived nanoclusters on the plasma membrane from which the signal is propagated to Raf. In the current study we show that stabilizing the H-Ras-Gal-1 interaction, using bimolecular fluorescence complementation (BiFC), leads to prolonged immobilization of H-Ras.GTP in the plasma membrane which was measured by fluorescence recovery after photobleaching (FRAP), and increased signal out-put to the MAPK module. EM measurements of Raf recruitment to the H-Ras.GTP nanoclusters demonstrated that the enhanced signaling observed in the BiFC stabilized H-Ras.GTP nanocluster was attributed to increased H-Ras immobilization rather than to an increase in Raf recruitment. Taken together these data demonstrate that the magnitude of the signal output from a GTP-bound H-Ras nanocluster is proportional to its stability.