Description: This article discusses interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. Abstract: Background: Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets. Methods: Pairwise alignment techniques are used here to calculate genetic distances between sequence pairs. These methods are pleasingly parallel and have been shown to more accurately reflect accurate genetic distances in highly variable regions of rRNA genes that do traditional multiple sequence alignment (MSA) approaches. By utilizing Needleman-Wunsch (NW) pairwise alignment in conjunction with novel implementations of interpolative multidimensional scaling (MDS), the authors have developed an effective method for visualizing massive biosequence data sets and quickly identifying potential gene clusters. Results: This study demonstrates the use of interpolative MDS to obtain clustering results that are qualitatively similar to those obtained through ...

Description: This article discusses LIN, a Medicago truncatula gene. Abstract: Ethyl methanesulfonate mutagenesis of the model legume Medicago truncatula has previously identified several genes required for early steps in nodulation. Here, the authors describe a new mutant that is defective in intermediate steps of nodule differentiation. The lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. Genetic analyses indicate that the symbiotic phenotype is conferred by a single gene that maps to the lower arm of linkage group 1. Transcriptional markers for early Nod factor responses (RIP1 and ENOD40) are induced in lin, as is another early nodulin, ENOD20, a gene expressed during the differentiation of nodule primordia. By contrast, other markers correlated with primordium differentiation (CCS52A), infection progression (MtN6), or nodule morphogenesis (ENOD2 and ENOD8) show reduced or no induction in homozygous lin individuals. Taken together, these results suggest that LIN functions in maintenance of rhizobial infections and differentiation of nodules from nodule primordia.

Description: This article discusses multiple domains in MtENOD8 protein. Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane (SymM), a single rhizobium, and the soluble space between them, called the symbiosome space (Syms). The SymS is enriched with plant-derived proteins, including the MtENOD8 protein. Here, the authors present evidence from GFP fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in non-nodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific re-direction MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with re-direction of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with Medicago mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for re-direction of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. The authors' evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome ...

Description: This article discusses the origin and composition of cucurbit phloem exudate. Cucurbits exude profusely when stems or petioles are cut. The authors conducted studies on pumpkin (Cucurbita maxima) and cucumber (Cucumis sativus) to determine the origin and composition of the exudate. Morphometric analysis indicated that the exudate is too voluminous to derive exclusively from the phloem. Cold, which inhibits phloem transport, did not interfere with exudation. However, ice water applied to the roots, which reduces root pressure, rapidly diminished exudation rate. Sap was seen by microscopic examination to flow primarily from the fascicular phloem in cucumber, and several other cucurbit species, but primarily from the extrafascicular phloem in pumpkin. Following exposure of leaves to 14CO2, radiolabeled stachyose and other sugars were detected in the exudate in proportions expected of authentic phloem sap. Most of this radiolabel was released during the first 20 s. Sugars in exudate were dilute. The sugar composition of exudate from extrafascicular phloem near the edge of the stem differed from that of other sources in that it was high in hexose and low in stachyose. The authors conclude that sap is released from cucurbit phloem upon wounding but contributes negligibly to total exudate volume. The sap ...

Description: This article accompanies a poster presentation on the quantification of emotional bias by an Emotional-Gain model. The authors have developed a computational model that quantifies emotion objectively based on neurobiological mechanisms that increases the chance of survival in the real world. This model is based on the EMOTION-I and EMOTION-II models with the extension of proportionality hypothesis added to the desirable gain signal to these models.