Positive and negative selection of Tcrb-V6+ T cells

Tcrb-V6⁺ T cells are deleted by an endogenous superantigen probably encoded by a mouse mammary tumor provirus (Mtv), Mtv-7, in association with major histocompatibility complex (MHC) class II molecules. In contrast, Tcrb-V6⁺CD4⁺ T cells are positively selected by MHC class II E molecules in Mtv-7 ^– mice. We have examined the levels of Tcrb-V6⁺CD4⁺ and Tcrb-V6⁺CD8⁺ T cells from six combinations of backcross mice. In this paper we show that: 1) Tcrb-V6⁺CD8⁺ T cells can be positively selected by MHC class I molecules; 2) MHC class II A molecules can also influence the levels of Tcrb-V6⁺CD4⁺ T cells; 3) Mtv-7 ^– NZW mice have a new Mtv, Mtv-44, which co-segregates with a gene encoding the partial deletion ligand for Tcrb-V6⁺ T cells; 4) the remaining Tcrb-V6⁺ T cells from mice with partial deletion of these T cells appear not to be anergized in the periphery. Address correspondence and offprint requests to: K. Tomonari.     

Correlation between the Vß4+CD8+ T-cell population and theH-2 d haplotype

The Vß4 ⁺ T-cell population was examined with a newly established antibody, KT4, specific for Vß4. Between 4.8% and 19.4% of CD3⁺ peripheral T cells from various inbred strains of mice or Fl hybrids expressed Vß4. The CD4 T-cell population had higher numbers of V4⁺ T cells (5.5%–20.6%) than the CD8 T-cell population (2.5%–10.7%). Deletion of certain Vexpressing T cells due to the presence of the Mls^a antigen and/or the absence of certainTcrb-V genes increased relative numbers of Vß4⁺ T cells. The data suggest that V4⁺ CD8⁺ T cells might be positively selected by H-2^d molecules.     

Transcriptomic analysis of epigenetic modification genes in the termite Reticulitermes speratus

Eusocial insects display a caste system in which different castes are morpho-logically and physiologically specialized for different tasks.Recent studies have revealed that epigenetic modifications,including DNA methylation and histone modification,me-diate caste determination and differentiation,longevity,and polyethism in eusocial insects.Although there has been a growing interest in the relationship between epigenetic mech-anisms and phenotypic plasticity in termites,there is ltte information about differential expression levels among castes and expression sites for these genes in termites.Here we show royaltissuc-specific expression of epigenetic modification genes in the termite Reticulitermes speratus.Using RNA-seq,we identified 74 genes,including three DNA methyltransferases,seven sirtuins,48 Trithorax group proteins,and 16 Polycomb group proteins.Among these genes,15 showed king-specific expression,and 52 showed age-dependent differential expression in kings and queens.Quantitative real-time PCR revealed that DNA methyltransferase 3 is expressed specifically in the king's testis and fat body,whereas some histone modification genes are remarkably expressed in the king's testis and queen's ovary.These findings imply that epigenetic modification plays important roles in the gamete production process in termite kings and queens.     

Evolution of Mammalian Opn5 as a Specialized UV-absorbing Pigment by a Single Amino Acid Mutation

Opn5 is one of the recently identified opsin groups that is responsible for nonvisual photoreception in animals. We previously showed that a chicken homolog of mammalian Opn5 (Opn5m) is a G_i-coupled UV sensor having molecular properties typical of bistable pigments. Here we demonstrated that mammalian Opn5m evolved to be a more specialized photosensor by losing one of the characteristics of bistable pigments, direct binding of all-trans-retinal. We first confirmed that Opn5m proteins in zebrafish, Xenopus tropicalis, mouse, and human are also UV-sensitive pigments. Then we found that only mammalian Opn5m proteins lack the ability to directly bind all-trans-retinal. Mutational analysis showed that these characteristics were acquired by a single amino acid replacement at position 168. By comparing the expression patterns of Opn5m between mammals and chicken, we found that, like chicken Opn5m, mammalian Opn5m was localized in the ganglion cell layer and inner nuclear layer of the retina. However, the mouse and primate (common marmoset) opsins were distributed not in the posterior hypothalamus (including the region along the third ventricle) where chicken Opn5m is localized, but in the preoptic hypothalamus. Interestingly, RPE65, an essential enzyme for forming 11-cis-retinal in the visual cycle is expressed near the preoptic hypothalamus of the mouse and common marmoset brain but not near the region of the chicken brain where chicken Opn5m is expressed. Therefore, mammalian Opn5m may work exclusively as a short wavelength sensor in the brain as well as in the retina with the assistance of an 11-cis-retinal-supplying system.     

Mutant induction in gametophytes of Undaria pinnatifida (Phaeophyceae) by heavy ion beam irradiation

Undaria pinnatifida, the brown macroalga, is a major commercial edible seaweed, and there is increasing interest in breeding new, improved cultivars for market expansion. In this study, we attempted to establish mutagenesis in U. pinnatifida using Ar and C ion beams as mutagens to meet future demands. To screen irradiated generations for mutants, U. pinnatifida zoospores irradiated with Ar and C ion beams were cultivated in plastic Petri dishes. Some gametophytes derived from the irradiated zoospores showed growth arrest or cell death at the initial developmental stage. Although the growth inhibition and lethal effects were observed at high doses of each ion irradiation, the Ar ion irradiation had high biological effects on cell division and growth. The gametophytes that showed a reduction in cell elongation were designated as an inhibited cell elongation mutant. A comparison of the mutant induction frequencies revealed that the C ion beam showed a higher frequency than the Ar ion beam. The highest frequency was 0.83% at 12.5 Gy of the C ion beam. We determined the total number of sporophytes and embryos per female gametophyte after sporophyte induction. High‐dose irradiation with the Ar ion beam decreased the embryo and sporophyte formation, suggesting that the Ar ion beam also has exhibited high biological effects on the fertilization or embryogenesis processes or both. The developed heavy ion mutagenesis and mutant screening methods would be useful for mutation breeding and constructing specific mutant libraries in brown algae, and not only in U. pinnatifida.     

NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes

ABSTRACT

Hammerhead ribozymes are a model system for studying molecular mechanism of RNA catalysis. Physicochemical data-driven mechanistic studies are an indispensable step towards understanding the catalysis of hammerhead ribozymes. Here we characterized a model RNA duplex with catalytically important sheared-type G12-A9 base pair and A9-G10.1 metal ion-binding motif in hammerhead ribozymes. By using high magnetic field NMR, all base proton signals, including catalytic residues, were unambiguously assigned. We further characterized structural features of this RNA molecule and found that it reflects the structural features of the A9-G10.1 motif of hammerhead ribozymes. Therefore, this RNA molecule is suitable for extracting an intrinsic physicochemical properties of catalytically important residues.     

On Hepatitis C Virus Evolution: The Interaction between Virus and Host towards Treatment Outcome

Background

Hepatitis C is a disease spread throughout the world. Hepatitis C virus (HCV), the etiological agent of this disease, is a single-stranded positive RNA virus. Its genome encodes a single precursor protein that yields ten proteins after processing. NS5A, one of the non-structural viral proteins, is most associated with interferon-based therapy response, the approved treatment for hepatitis C in Brazil. HCV has a high mutation rate and therefore high variability, which may be important for evading the immune system and response to therapy. The aim of this study was to analyze the evolution of NS5A quasispecies before, during, and after treatment in patients infected with HCV genotype 3a who presented different therapy responses.

Methods

Viral RNA was extracted, cDNA was synthesized, the NS5A region was amplified and cloned, and 15 clones from each time-point were sequenced. The sequences were analyzed for evolutionary history, genetic diversity and selection.

Results

This analysis shows that the viral population that persists after treatment for most non-responder patients is present in before-treatment samples, suggesting it is adapted to evade treatment. In contrast, the population found in before treatment samples from most end-of-treatment responder patients either are selected out or appears in low frequency after relapse, therefore changing the population structure. The exceptions illustrate the uniqueness of the evolutionary process, and therefore the treatment resistance process, in each patient.

Conclusion

Although evolutionary behavior throughout treatment showed that each patient presented different population dynamics unrelated to therapy outcome, it seems that the viral population from non-responders that resists the treatment already had strains that could evade therapy before it started.     

Diel changes in the movement patterns of Ganges River dolphins monitored using stationed stereo acoustic data loggers

We monitored the underwater movements of Ganges River dolphins using stationed stereo acoustic data loggers. We estimated these movements using changes in the relative angle of the sound source direction (trajectory). Of the total acoustic recordings (66 h), 26.2% contained trajectories of dolphins, and 78.6% of these trajectories involved single animals, suggesting that dolphins tended to swim alone and were localized near the monitoring station. The observed trajectories were categorized as follows: staying type characterized by small changes in the sound source direction, moving type A (moving in the same direction), and moving type B (moving up and down the stream during recording). The average interpulse intervals of sounds in moving types A and B were significantly shorter than that of the staying type, suggesting that dolphins produce the former types of trajectories to echolocate across shorter distances during movement. The frequency of occurrence of moving type A increased during the night, whereas that of type B increased in the late afternoon and that of the staying type increased during the daytime. These results indicate that dolphins moving at night tended to use short‐range echolocation, whereas during the day, they remained in relatively small areas and used long‐range sonar.