Factors affecting the initiation of mini-rhizomes from Trillium erectum and T. grandiflorum tissues in vitro

Leaf and stem explants of Trillium grandiflorum and T. erectum produced mini-rhizomes (MRs) in vitro which gave rise to shoots and roots. The apical portion of the stem and the basal portion of the leaves were the most effective explants from these tissues, while stem tissue was more responsive than leaf tissue. The best response with both species was observed on half-strength MS basal medium supplemented with cytokinin and auxin. T. erectum was more responsive than T. grandiflorum overall, and in some cases produced MRs in the absence of growth regulators. Culture at 21°C appeared to stimulate growth from T. grandiflorum tissues, compared with controls at 27°C, whereas the outgrowth of shoots from MRs was inhibited in both species at 21°C. In vitro production of MRs could provide a more rapid, alternative propagation method for these species than traditional methods.     

Development of immunohistochemical characteristics of intrafusal fibres in normal and de-efferented rat muscle spindles

Summary Intrafusal muscle fibres in adult muscle spindles differ in their myosin composition. After selective motor denervation intrafusal muscle fibres develop mature ultrastructural characteristics. In order to evaluate the role of fusimotor innervation on the maturation of the myosin composition of intrafusal muscle fibres we have examined with immunohistochemical techniques i) the postnatal development of muscle spindles in new-born rats and in 7–21 day old rats; ii) muscle spindles in the EDL of 21-day-old rats de-efferented at birth. For the characterization of myosins in intrafusal fibres we used three myosin antisera: antipectoral myosin, antiheart myosin and antiheart myosin adsorbed with muscle powder from the soleus muscle of guinea pig. We show in this study that during development intrafusal fibres change immunoreactivity and that in the absence of motor innervation bag fibres do not fully develop the myosin characteristics of control spindles. We conclude that the maturation of bag₁ and bag₂ fibres apparently requires next to the inductive influence of sensory axon terminals the presence and activity of fusimotor axons.     

Identification of the sex chromosomes in the bald eagle.

Karyotypes of five American bald eagles (Haliaeetus leucocephalus and H. alacanus) are compared. All had 2n=66 chromosomes which fell into 3 size groups: A, 20 pairs of biarmed chromosomes; B, 9 pairs of acrocentric chromosomes and C, 4 pairs of microchromosomes. C-banding was done in two eagles and a heterochromatic W chromosome was identified in a presumptive female. The ZZ and ZW chromosomes could be identified in the karyotypes.     

Lateral root development in the maize (Zea mays) lateral rootless1 mutant

Background and Aims

The maize lrt1 (lateral rootless1) mutant is impaired in its development of lateral roots during early post-embryonic development. The aim of this study was to characterize, in detail, the influences that the mutation exerts on lateral root initiation and the subsequent developments, as well as to describe the behaviour of the entire plant under variable environmental conditions.

Methods

Mutant lrt1 plants were cultivated under different conditions of hydroponics, and in between sheets of moist paper. Cleared whole mounts and anatomical sections were used in combination with both selected staining procedures and histochemical tests to follow root development. Root surface permeability tests and the biochemical quantification of lignin were performed to complement the structural data.

Key Results

The data presented suggest a redefinition of lrt1 function in lateral roots as a promoter of later development; however, neither the complete absence of lateral roots nor the frequency of their initiation is linked to lrt1 function. The developmental effects of lrt1 are under strong environmental influences. Mutant primordia are affected in structure, growth and emergence; and the majority of primordia terminate their growth during this last step, or shortly thereafter. The lateral roots are impaired in the maintenance of the root apical meristem. The primary root shows disturbances in the organization of both epidermal and subepidermal layers. The lrt1-related cell-wall modifications include: lignification in peripheral layers, the deposition of polyphenolic substances and a higher activity of peroxidase.

Conclusions

The present study provides novel insights into the function of the lrt1 gene in root system development. The lrt1 gene participates in the spatial distribution of initiation, but not in its frequency. Later, the development of lateral roots is strongly affected. The effect of the lrt1 mutation is not as obvious in the primary root, with no influences observed on the root apical meristem structure and maintenance; however, development of the epidermis and cortex are impaired.     

Phenyl-terminated fatty acids in seeds of various aroids

A series of homologous omega-phenylalkanoic acids and omega-phenylalkenoic acids were isolated from seed lipids of various genera of the subfamily Aroideae of Araceae (the Jack-in-the-Pulpit family) and characterized. Besides the major acids, 11-phenylundecanoic acid, 13-phenyltridecanoic acid and 15-phenylpentadecanoic acid, all other homologous odd carbon number omega-phenylalkanoic acids from C7 to C23 were detected in trace amounts. Additionally, one even carbon number acid, 12-phenyldodecanoic acid was found in several specimens in trace amounts. Similarly, two series of homologous odd carbon number monounsaturated omega-phenylalkenoic acids were found and characterized using dimethyl disulfide derivatization to locate the positions of their double bonds. In five acids from C11 to C19, the double bond is located at the same distance, A7, from the phenyl ring. In the other two acids of C13 and C15 chain length, the double bond is located at delta5 from the phenyl ring.     

Developing optimal prediction models for cancer classification using gene expression data

Microarrays can provide genome-wide expression patterns for various cancers, especially for tumor sub-types that may exhibit substantially different patient prognosis. Using such gene expression data, several approaches have been proposed to classify tumor sub-types accurately. These classification methods are not robust, and often dependent on a particular training sample for modelling, which raises issues in utilizing these methods to administer proper treatment for a future patient. We propose to construct an optimal, robust prediction model for classifying cancer sub-types using gene expression data. Our model is constructed in a step-wise fashion implementing cross-validated quadratic discriminant analysis. At each step, all identified models are validated by an independent sample of patients to develop a robust model for future data. We apply the proposed methods to two microarray data sets of cancer: the acute leukemia data by Golub et al. and the colon cancer data by Alon et al. We have found that the dimensionality of our optimal prediction models is relatively small for these cases and that our prediction models with one or two gene factors outperforms or has competing performance, especially for independent samples, to other methods based on 50 or more predictive gene factors. The methodology is implemented and developed by the procedures in R and Splus. The source code can be obtained at http://hesweb1.med.virginia.edu/bioinformatics.     

A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits

The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a 'fragment assay' that depends on high concentrations of methanol or ethanol. Here we describe a version of this assay that does not require alcohol and use it to show, both crystallographically and biochemically, that crystals of the large ribosomal subunits from Haloarcula marismortui are enzymatically active. Addition of these crystals to solutions containing substrates results in formation of products, which ceases when crystals are removed. When substrates are diffused into large subunit crystals, the subsequent structure shows that products have formed. The CC-puromycin-peptide product is found bound to the A-site and the deacylated CCA is bound to the P-site, with its 3prime prime or minute OH near N3 A2486 (Escherichia coli A2451). Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis.     

Altering molecular recognition of RNA aptamers by allosteric selection

In a continuing effort to explore structural and functional dynamics in RNA catalysis, we have created a series of allosteric hammerhead ribozymes that are activated by theophylline. Representative ribozymes exhibit greater than 3000-fold activation upon effector-binding and cleave with maximum rate constants that are equivalent to the unmodified hammerhead ribozyme. In addition, we have evolved a variant allosteric ribozyme that exhibits an effector specificity change from theophylline to 3-methylxanthine. Molecular discrimination between the two effectors appears to be mediated by subtle conformational differences that originate from displacement of the phosphodiester backbone near the effector binding pocket. These findings reveal the importance of abstruse aspects of molecular recognition by nucleic acids that are likely to be unapproachable by current methods of rational design.     

Altered HLA Class I Profile Associated with Type A/D Nucleophosmin Mutation Points to Possible Anti-Nucleophosmin Immune Response in Acute Myeloid Leukemia

Nucleophosmin 1 (NPM1) mutations are frequently found in patients with acute myeloid leukemia (AML) and the newly generated sequences were suggested to induce immune response contributing to the relatively favorable outcome of patients in this AML subset. We hypothesized that if an efficient immune response against mutated nucleophosmin can be induced in vivo, the individuals expressing HLA alleles suitable for presenting NPM-derived peptides should be less prone to developing AML associated with NPM1 mutation. We thus compared HLA class I frequencies in a cohort of patients with mutated NPM1 (63 patients, NPMc+), a cohort of patients with wild-type NPM1 (94 patients, NPMwt) and in normal individuals (large datasets available from Allele Frequency Net Database). Several HLA allelic groups were found to be depleted in NPMc+ patients, but not in NPMwt compared to the normal distribution. The decrease was statistically significant for HLA B*07, B*18, and B*40. Furthermore, statistically significant advantage in the overall survival was found for patients with mutated NPM1 expressing at least one of the depleted allelic groups. The majority of the depleted alleles were predicted to bind potent NPM-derived immunopeptides and, importantly, these peptides were often located in the unmutated part of the protein. Our analysis suggests that individuals expressing specific HLA allelic groups are disposed to develop an efficient anti-AML immune response thanks to aberrant cytoplasmic localization of the mutated NPM protein.