Permutation pattern discovery in biosequences.

Functionally related genes often appear in each other's neighborhood on the genome; however, the order of the genes may not be the same. These groups or clusters of genes may have an ancient evolutionary origin or may signify some other critical phenomenon and may also aid in function prediction of genes. Such gene clusters also aid toward solving the problem of local alignment of genes. Similarly, clusters of protein domains, albeit appearing in different orders in the protein sequence, suggest common functionality in spite of being nonhomologous. In the paper, we address the problem of automatically discovering clusters of entities, be they genes or domains: we formalize the abstract problem as a discovery problem called the (pi)pattern problem and give an algorithm that automatically discovers the clusters of patterns in multiple data sequences. We take a model-less approach and introduce a notation for maximal patterns that drastically reduces the number of valid cluster patterns, without any loss of information, We demonstrate the automatic pattern discovery tool on motifs on E. Coli protein sequences.     

The GPSM2/LGN GoLoco motifs are essential for hearing

The planar cell polarity (PCP) pathway is responsible for polarizing and orienting cochlear hair cells during development through movement of a primary cilium, the kinocilium. GPSM2/LGN, a mitotic spindle-orienting protein associated with deafness in humans, is a PCP effector involved in kinocilium migration. Here, we link human and mouse truncating mutations in the GPSM2/LGN gene, both leading to hearing loss. The human variant, p.(Trp326*), was identified by targeted genomic enrichment of genes associated with deafness, followed by massively parallel sequencing. Lgn ^ΔC mice, with a targeted deletion truncating the C-terminal GoLoco motifs, are profoundly deaf and show misorientation of the hair bundle and severe malformations in stereocilia shape that deteriorates over time. Full-length protein levels are greatly reduced in mutant mice, with upregulated mRNA levels. The truncated Lgn ^ΔC allele is translated in vitro, suggesting that mutant mice may have partially functioning Lgn. Gαi and aPKC, known to function in the same pathway as Lgn, are dependent on Lgn for proper localization. The polarization of core PCP proteins is not affected in Lgn mutants; however, Lgn and Gαi are misoriented in a PCP mutant, supporting the role of Lgn as a PCP effector. The kinocilium, previously shown to be dependent on Lgn for robust localization, is essential for proper localization of Lgn, as well as Gαi and aPKC, suggesting that cilium function plays a role in positioning of apical proteins. Taken together, our data provide a mechanism for the loss of hearing found in human patients with GPSM2/LGN variants.     

Intraspecific variation in defense against a generalist lepidopteran herbivore in populations of Eruca sativa (Mill.)

Populations of Eruca sativa (Brassicaceae) from desert and Mediterranean (Med) habitats in Israel differ in their defense against larvae of the generalist Spodoptera littoralis but not the specialist Pieris brassicae. Larvae of the generalist insect feeding on plants of the Med population gained significantly less weight than those feeding on the desert plants, and exogenous application of methyl jasmonate (MJ) on leaves of the Med plants significantly reduced the level of damage created by the generalist larvae. However, MJ treatment significantly induced resistance in plants of the desert population, whereas the generalist larvae caused similar damage to MJ‐induced and noninduced plants. Analyses of glucosinolates and expression of genes in their synthesis pathway indicated that defense in plants of the Med population against the generalist insect is governed by the accumulation of glucosinolates. In plants of the desert population, trypsin proteinase inhibitor activity was highly induced in response to herbivory by S. littoralis. Analysis of genes in the defense‐regulating signaling pathways suggested that in response to herbivory, differences between populations in the induced levels of jasmonic acid, ethylene, and salicylic acid mediate the differential defenses against the insect. In addition, expression analysis of myrosinase‐associated protein NSP2 suggested that in plants of the desert population, glucosinolates breakdown products were primarily directed to nitrile production. We suggest that proteinase inhibitors provide an effective defense in the desert plants, in which glucosinolate production is directed to the less toxic nitriles. The ecological role of nitrile production in preventing infestation by specialists is discussed.     

Intraspecific variation in seed dispersal of a Neotropical tree and its relationship to fruit and tree traits

The distribution of wind‐dispersed seeds around a parent tree depends on diaspore and tree traits, as well as wind conditions and surrounding vegetation. This study of a neotropical canopy tree, Platypodium elegans, explored the extent to which parental variation in diaspore and tree traits explained (1) rate of diaspore descent in still air, (2) distributions of diaspores dispersed from a 40‐m tower in the forest, and (3) natural diaspore distributions around the parent tree. The geometric mean rate of descent in still air among 20 parents was highly correlated with geometric mean wing loading^1/2 (r = 0.84). However, diaspore traits and rate of descent predicted less variation in dispersal distance from the tower, although descent rate⁻¹ consistently correlated with dispersal distance. Measured seed shadows, particularly their distribution edges, differed significantly among six parents (DBH range 62–181 cm) and were best fit by six separate anisotropic dispersal kernels and surveyed fecundities. Measured rate of descent and tree traits, combined in a mechanistic seed dispersal model, did not significantly explain variation among parents in natural seed dispersal distances, perhaps due to the limited power to detect effects with only six trees. Seedling and sapling distributions were at a greater mean distance from the parents than seed distributions; saplings were heavily concentrated at far distances. Variation among parents in the distribution tails so critical for recruitment could not be explained by measured diaspore or tree traits with this sample size, and may be determined more by wind patterns and the timing of abscission in relation to wind conditions. Studies of wind dispersal need to devote greater field efforts at recording the “rare” dispersal events that contribute to far dispersal distances, following their consequences, and in understanding the mechanisms that generate them.     

Preliminary characterization of the hemolysin of Rhizopus nigricans

A hemolysin was extracted from fungous mats ofRhizopus nigricans cultured for two weeks in modified Sabouraud broth. Preliminary characterization indicated that the active substance is water soluble, stable after heating to 100°C, not destroyed by proteolytic enzymes, not dialyzable, and not precipitable with ethanol. It is however precipitable with ammonium sulfate and extractable with lipid solvents. Lipid fractionation revealed activity in the non-acidic phospholipid fraction. The cumulative findings suggest that the active hemolytic substance is a lipid perhaps attached to a protein.

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Zusammenfassung Das Hämolysin war vom Pilzmyzelium vonRhizopus nigricans extrahiert worden, das in Sabouraud's Brühe für zwei Wochen gezüchtet worden ist. Vorläufige Charakteristik zeigte, daß die aktive Substanz wasserlöslich, hitzeresistent ist und sie durch proteolytische Fermente nicht zerstört wird. Sie ist dialysierbar, und wird durch Ethanol nicht prezipitiert. Jedoch ist sie durch Ammoniumsulfate prezipitiert und durch Fettlösungsmittel extrahierbar Lipoidfraktionierung zeigte eine Aktivität in der nich-saueren Phospholipoidfraktion. Kumulative Befunde legen es nahe, daß die aktive, hämolytische Substanz ein an Protein gebundenes Lipoid ist.

     

Pathways of acetone's metabolism in the rat

Distributions of 14C were different from those of 13C in glucoses formed by livers of rats in diabetic ketosis and perfused with [2-14C]acetone and [2-13C]lactate. There was 32-73% of the 14C and 8-12% of the 13C in carbons 3 and 4 of the glucoses with the remaining 14C and 13C distributed about equally in the other carbons. Incorporations of 14C from [2-14C]acetone (14-39%) also exceeded those from [2-14C]pyruvate (8-10%) into carbons 3 and 4 of glucoses formed by hepatocytes from rats fed acetone or fasted. [2-14C]Acetone and [2-14C]pyruvate were infused into rats that were fed, fasted, given acetone in their drinking water, or in diabetic ketosis. Thirty-seven to 52% of the 14C in the glucoses formed was in their carbons 3 and 4 when the acetone was infused and 8 to 14% when the pyruvate was infused. [1,3-14C]Hydroxybutyrate was formed by the rats in diabetic ketosis given [2-14C]acetone. It is concluded that acetone is metabolized in rats to a large extent by a pathway in which lactate or its metabolic equivalent is not an intermediate and that pathway is via acetyl-CoA. via acetyl-CoA.     

Types of muscarinic response in xenopus oocytes

Four distinct types of membrane response of $\text{Xenopus laevis}$ oocytes to the application of acetylcholine (ACh) are described. The responses of single oocytes in summer are different from those in winter. The four response types differ in their dependence on the dose of acetylcholine and on the presence of calcium ions, and may appear solely or in various combinations in single oocytes. All response types can be elicited by oxotremorine and blocked by atropine.     

Divalent cations and transmitter release at low concentration of tetrodotoxin

Transmitter release from frog motor terminals was studied in the presence of very low concentrations of tetrodotoxin (TTX, 4.10(-10)--6.10(-9) g/ml). TTX reversibly reduced the amplitude of the end-plate potential (epp), while leaving the amplitude distribution to follow Poisson's law. The effects of a number of divalent cations were studied in the presence of TTX. It was found that after the addition of TTX there was an increase in the constant of dissociation of calcium and strontium from a hypothetical membrane "release site," while the dissociation constants of magnesium and manganese remained unaltered. It is concluded that the release site is probably intracellular and that a reduced presynaptic spike amplitude, as well as magnesium and manganese ions, decrease the access of calcium and strontium to the site.     

Nonspecific photophysiological immunization]

A hypothesis is suggested on the positive effect of light radiation on the formation of protective immune mechanism related to the photophysiological destruction of porphyrins. References to experimental data are given which illustrate the possibility for existence of such a mechanism.