The fourfold way of the genetic code

We describe a compact representation of the genetic code that factorizes the table in quartets. It represents a “least grammar” for the genetic language. It is justified by the Klein-4 group structure of RNA bases and codon doublets. The matrix of the outer product between the column-vector of bases and the corresponding row-vector V^T = (C G U A), considered as signal vectors, has a block structure consisting of the four cosets of the K × K group of base transformations acting on doublet AA. This matrix, translated into weak/strong (W/S) and purine/pyrimidine (R/Y) nucleotide classes, leads to a code table with mixed and unmixed families in separate regions. A basic difference between them is the non-commuting (R/Y) doublets: AC/CA, GU/UG. We describe the degeneracy in the canonical code and the systematic changes in deviant codes in terms of the divisors of 24, employing modulo multiplication groups. We illustrate binary sub-codes characterizing mutations in the quartets. We introduce a decision-tree to predict the mode of tRNA recognition corresponding to each codon, and compare our result with related findings by Jestin and Soulé [Jestin, J.-L., Soulé, C., 2007. Symmetries by base substitutions in the genetic code predict 2′ or 3′ aminoacylation of tRNAs. J. Theor. Biol. 247, 391–394], and the rearrangements of the table by Delarue [Delarue, M., 2007. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13, 161–169] and Rodin and Rodin [Rodin, S.N., Rodin, A.S., 2008. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100, 341–355], respectively.     

Weakly nonlinear analysis of a hyperbolic model for animal group formation

We consider an one-dimensional nonlocal hyperbolic model for group formation with application to self-organizing collectives of animals in homogeneous environments. Previous studies have shown that this model displays at least four complex spatial and spatiotemporal group patterns. Here, we use weakly nonlinear analysis to better understand the mechanisms involved in the formation of two of these patterns, namely stationary pulses and traveling trains. We show that both patterns arise through subcritical bifurcations from spatially homogeneous steady states. We then use these results to investigate the effect of two social interactions (attraction and alignment) on the structure of stationary and moving animal groups. While attraction makes the groups more compact, alignment has a dual effect, depending on whether the groups are stationary or moving. More precisely, increasing alignment makes the stationary groups compact, and the moving groups more elongated. Also, the results show the existence of a threshold for the total group density, above which, coordinated behaviors described by stationary and moving groups persist for a long time.      

Growing with siblings: a common ground for cooperation or for fiercer competition among plants?

Recent work has shown that certain plants can identify their kin in competitive settings through root recognition, and react by decreasing root growth when competing with relatives. Although this may be a necessary step in kin selection, no clear associated improvement in individual or group fitness has been reported to qualify as such. We designed an experiment to address whether genetic relatedness between neighbouring plants affects individual or group fitness in artificial populations. Seeds of Lupinus angustifolius were sown in groups of siblings, groups of different genotypes from the same population and groups of genotypes from different populations. Both plants surrounded by siblings and by genotypes from the same population had lower individual fitness and produced fewer flowers and less vegetative biomass as a group. We conclude that genetic relatedness entails decreased individual and group fitness in L. angustifolius. This, together with earlier work, precludes the generalization that kin recognition may act as a widespread, major microevolutionary mechanism in plants.     

Distribution and molecular characterization of distinct Asian populations of Bemisia tabaci (Hemiptera: Aleyrodidae) in Japan

Bemisia tabaci (Gennadius) is considered to be the most economically important pest insect worldwide. The invasive variant, the Q biotype of B. tabaci was first identified in 2004, and has caused significant crop yield losses in Japan. The distribution and molecular characterization of the different biotypes of B. tabaci in Japan have been little investigated. In this study, B. tabaci populations were sampled from the Japanese Archipelago, the Amami Archipelago and the Ryukyu Islands between 2004 and 2008, and the nucleotide sequences of their mitochondrial cytochrome oxidase I genes were determined. Bayesian phylogenetic relationship analysis provided the first molecular evidence that the indigenous Japanese populations could be separated into four distinct genetic groups. One major native population from the Japanese Archipelago, given the genetic group name Lonicera japonica, was separated into an independent group, distinct from the other genetic groups. The second major population, the Nauru biotype in the Asia II genetic group, was identified in the Amami Archipelago and the Ryukyu Islands. Two distinct minor genetic groups, the Asia I and the China, were also identified. One invasive B‐related population belonging to the Mediterranean/Asia Minor/Africa genetic group has been identified in Honshu. All lineages generated by the phylogenetic analyses were supported by high posterior probabilities. These distinct indigenous B. tabaci populations developed in Japan under geographical and/or biological isolation, prior to recent invasions of the B and Q biotypes.     

Boys will be boys: social affinity among males drives social segregation in western grey kangaroos

In many sexually dimorphic and polygynous species, individuals exhibit social segregation by grouping with others of their own sex. Several proximate mechanisms have been proposed to explain social segregation: female avoidance of males, male avoidance of females, avoidance of harassment, male social affinity, female social affinity and activity budget asynchrony. Some of these have been tested in ungulate species, but few previous studies have been able to rigorously test, or distinguish between, these mechanisms because they have failed to examine the fission/fusion dynamics of groups. We tested these proximate mechanisms simultaneously in western grey kangaroos Macropus fuliginosus , by examining whether females, small males or large males instigated segregation by leaving mixed-sex groups or joining individuals of their own sex or size class. Females, small males and large males left mixed-sex groups as if leaving were independent of sex–size class. In contrast, large males joined male-only groups more frequently than expected. These results suggest that the need for males to maintain contact with other males can contribute to the cohesion of male-only groups and promote segregation. As male–male competition occurs in many polygynous species that sexually segregate, a comparable mechanism might be operating in other taxa, and should be examined further.     

Induction of HIV-1 resistance: cell susceptibility to infection is an inverse function of globotriaosyl ceramide levels

To examine the role of the glycosphingolipid (GSL), globotriaosylceramide(Gb₃, CD77, p^k blood group antigen) in HIV-1 infection, we havepharmacologically modulated Gb₃ metabolism in an X4 HIV-1 infectablemonocytic cell line (THP-1) that naturally expresses Gb₃ andin a Gb₃-expressing glioblastoma cell line (U87) transfectedto express both CD4 and CCR5 to permit R5 HIV-1 infection. THP-1and U87 cells were treated with either a competitive inhibitorof -galactosidase A, 1-deoxygalactonojirimycin (DGJ) to induceGb₃ accumulation, or a glucosylceramide synthase inhibitor,phenyl-2-palmitylamino-3-pyrrolidino-1-propanol (P4) to depletecells of Gb₃. HIV susceptibility was determined via measurementof p24^gag antigen production by ELISA. In addition, total cellularGb₃ content was determined using thin layer chromatography followedby Verotoxin1 overlay binding. The cell surface expression ofGb₃ was verified by FACS analysis. We found that DGJ significantlydecreased THP-1 and U87 cell susceptibility to HIV-1_IIIB andHIV-1_BaL infection, respectively, at a concentration of approximately100 µM. In contrast, P4 (2 µM) substantiallyincreased cellular susceptibility to HIV-1 infection. Totalcellular GSL analysis verified increased Gb₃ expression in cellstreated with DGJ and considerable reduction of Gb₃ in P4-treatedcells as compared to controls. These results show a reciprocalrelationship between Gb₃ expression and infection with eitherX4 HIV-1_IIIB or R5 HIV-1_Ba-L. These results support previousstudies that Gb₃ provides resistance to HIV infection. VariableGb₃ expression may provide a natural HIV resistance factor inthe general population, and pharmacological manipulation ofGb₃ levels may provide an approach to induction of HIV resistance.     

Synthesis of monodeoxy and mono-O-methyl congeners of methyl β-d-mannopyranosyl-(1→2)-β-d-mannopyranoside for epitope mapping of anti-Candida albicans antibodies

A panel of six complementary monodeoxy and mono-O-methyl congeners of methyl β-d-mannopyranosyl-(1→2)-β-d-mannopyranoside (1) were synthesized by stereoselective glycosylation of monodeoxy and mono-O-methyl monosaccharide acceptors with a 2-O-acetyl-glucosyl trichloroacetimidate donor, followed by a two-step oxidation–reduction sequence at C-2′. The β-manno configurations of the final deprotected congeners 2–7 were confirmed by measurement of ¹J_C1,H1 heteronuclear and ³J_1′,2′ homonuclear coupling constants. These disaccharide derivatives will be used to map the protective epitope recognized by a protective anti-Candida albicans monoclonal antibody C3.1 (IgG3) and to determine its key polar contacts with the binding site.     

Adaptive weighted learning for unbalanced multicategory classification

Summary .  In multicategory classification, standard techniques typically treat all classes equally. This treatment can be problematic when the dataset is unbalanced in the sense that certain classes have very small class proportions compared to others. The minority classes may be ignored or discounted during the classification process due to their small proportions. This can be a serious problem if those minority classes are important. In this article, we study the problem of unbalanced classification and propose new criteria to measure classification accuracy. Moreover, we propose three different weighted learning procedures, two one-step weighted procedures, as well as one adaptive weighted procedure. We demonstrate the advantages of the new procedures, using multicategory support vector machines, through simulated and real datasets. Our results indicate that the proposed methodology can handle unbalanced classification problems effectively.