Decrease in cytosine methylation at CpG island shores and increase in DNA fragmentation during zebrafish aging.

Age-related changes in DNA methylation have been demonstrated in mammals, but it remains unclear as to the generality of this phenomenon in vertebrates, which is a criterion for the fundamental cause of senescence. Here we showed that the zebrafish genome gradually and clearly lost methylcytosine in somatic cells, but not in male germ cells during aging, and that age-dependent hypomethylation preferentially occurred at a particular domain called the CpG island shore, which is associated with vertebrates' genes and has been shown to be hypomethylated in humans with age. We also found that two CpG island shores hypomethylated in zebrafish oocytes were de novo methylated in fertilized eggs, which suggests that the zebrafish epigenome is reset upon fertilization, enabling new generations to restart with a heavily methylated genome. Furthermore, we observed an increase in cleavage of the zebrafish genome to an oligonucleosome length in somatic cells from the age of 12 months, which is suggestive of an elevated rate of apoptosis in the senescent stage.

Exome sequencing reveals a novel MRE11 mutation in a patient with progressive myoclonic ataxia.

Progressive myoclonic ataxia (PMA) is a clinical syndrome defined as progressive ataxia and myoclonus and infrequent seizures in the absence of progressive dementia. Due to the extremely heterogeneous nature of PMA, a large proportion of PMA cases remain molecularly undiagnosed. The aim of this study was to clarify the molecular etiology of PMA. The patient was a 52-year-old female from consanguineous parents. She developed a jerking neck movement at age 9, which gradually expanded to her entire body. On physical examination at age 47, she exhibited generalized, spontaneous myoclonus that occurred continuously. She also presented with mild limb and truncal ataxia. An electroencephalogram revealed no abnormalities. A brain MRI displayed no atrophy of the cerebellum. Electrophysiological studies suggested myoclonus of a subcortical origin. For further evaluation, we performed exome sequencing, and we identified a novel homozygous missense mutation in the MRE11 gene (NM_005590:c.140C>T:p.A47V). Subsequently, we analyzed the expression of MRE11 and related proteins (RAD50 and NBS1) via Western blot, and they were markedly decreased compared to a healthy control. Mutations in the MRE11 gene have been known to cause an ataxia-telangiectasia-like (ATLD) disorder. Accumulating evidence has indicated that its wide phenotypic variations in ATLD correspond to genotypic differences. Interestingly, our case exhibited a relatively mild decrease in NBS1 compared to previously reported cases of a homozygous missense mutation, which may account for the milder phenotype in this patient. Moreover, together with a recently reported case of an MRE11 mutation, it is suggested that MRE11 mutations can present as PMA.

DEAD-box protein Ddx46 is required for the development of the digestive organs and brain in zebrafish.

Spatially and temporally controlled gene expression, including transcription, several mRNA processing steps, and the export of mature mRNA to the cytoplasm, is essential for developmental processes. It is well known that RNA helicases of the DExD/H-box protein family are involved in these gene expression processes, including transcription, pre-mRNA splicing, and rRNA biogenesis. Although one DExD/H-box protein, Prp5, a homologue of vertebrate Ddx46, has been shown to play important roles in pre-mRNA splicing in yeast, the in vivo function of Ddx46 remains to be fully elucidated in metazoans. In this study, we isolated zebrafish morendo (mor), a mutant that shows developmental defects in the digestive organs and brain, and found that it encodes Ddx46. The Ddx46 transcript is maternally supplied, and as development proceeds in zebrafish larvae, its ubiquitous expression gradually becomes restricted to those organs. The results of whole-mount in situ hybridization showed that the expression of various molecular markers in these organs is considerably reduced in the Ddx46 mutant. Furthermore, splicing status analysis with RT-PCR revealed unspliced forms of mRNAs in the digestive organ and brain tissues of the Ddx46 mutant, suggesting that Ddx46 may be required for pre-mRNA splicing during zebrafish development. Therefore, our results suggest a model in which zebrafish Ddx46 is required for the development of the digestive organs and brain, possibly through the control of pre-mRNA splicing.

Zebrafish Dmrta2 regulates neurogenesis in the telencephalon.

Although recent findings showed that some Drosophila doublesex and Caenorhabditis elegans mab-3 related genes are expressed in neural tissues during development, their functions have not been fully elucidated. Here, we isolated a zebrafish mutant, ha2, that shows defects in telencephalic neurogenesis and found that ha2 encodes Doublesex and MAB-3 related transcription factor like family A2 (Dmrta2). dmrta2 expression is restricted to the telencephalon, diencephalon and olfactory placode during somitogenesis. We found that the expression of the proneural gene, neurogenin1, in the posterior and dorsal region of telencephalon (posterior-dorsal telencephalon) is markedly reduced in this mutant at the 14-somite stage without any defects in cell proliferation or cell death. In contrast, the telencephalic expression of her6, a Hes-related gene that is known to encode a negative regulator of neurogenin1, expands dramatically in the ha2 mutant. Based on over-expression experiments and epistatic analyses, we propose that zebrafish Dmrta2 controls neurogenin1 expression by repressing her6 in the posterior-dorsal telencephalon. Furthermore, the expression domains of the telencephalic marker genes, foxg1 and emx3, and the neuronal differentiation gene, neurod, are downregulated in the ha2 posterior-dorsal telencephalon during somitogenesis. These results suggest that Dmrta2 plays important roles in the specification of the posterior-dorsal telencephalic cell fate during somitogenesis.

Titanium-based transition-edge photon number resolving detector with 98% detection efficiency with index-matched small-gap fiber coupling.

We have realized a high-detection-efficiency photon number resolving detector at an operating wavelength of about 850 nm. The detector consists of a titanium superconducting transition edge sensor in an optical cavity, which is directly coupled to an optical fiber using an approximately 300-nm gap. The gap reduces the sensitive area and heat capacity of the device, leading to high photon number resolution of 0.42 eV without sacrificing detection efficiency or signal response speed. Wavelength dependent efficiency in fiber-coupled devices, which is due to optical interference between the fiber and the device, is also decreased to less than 1% in this configuration. The overall system detection efficiency is 98%±1% at wavelengths of around 850 nm, which is the highest value ever reported in this wavelength range.

Hong-Ou-Mandel dip measurements of polarization-entangled photon pairs at 1550 nm.

We performed a quantum interference experiment using two polarization-entangled photon pairs at 1550 nm, created in periodically poled lithium niobate waveguides. Using four-fold coincidences, a Hong-Ou-Mandel dip at diagonal polarization was observed with a visibility of 74.5% before subtracting accidental coincidences. This experiment lays a foundation for demonstrating polarization-based entanglement swapping and for realizing a quantum relay.

Wavelength-multiplexed distribution of highly entangled photon-pairs over optical fiber.

We report the first experimental demonstration of wavelength-multiplexed entanglement distribution over optical fiber. Forty-four channels of polarization-entangled photon-pairs were produced from a single pulse-pumped, short periodically-poled lithium niobate waveguide and distributed over 10 km of dispersion-shifted optical fiber. Entanglement fidelities of the distributed photon-pairs exceeded 0.86 for all selected channels.

Broadband source of telecom-band polarization-entangled photon-pairs for wavelength-multiplexed entanglement distribution.

Studies on telecom-band entangled photon-pair sources for entanglement distribution have so far focused on their narrowband operations. Fiber-based sources are seriously limited by spontaneous Raman scattering while sources based on quasi-phase-matched crystals or waveguides are usually narrowband because of long device lengths and/or operations far from degeneracy. An entanglement distributor would have to multiplex many such narrowband sources before entanglement distribution to fully utilize the available fiber transmission bandwidth. In this work, we demonstrate a broadband source of polarization-entangled photon-pairs suitable for wavelength-multiplexed entanglement distribution over optical fiber. We show that our source is potentially capable of simultaneously supporting up to forty-four independent wavelength channels.

Distribution of polarization-entangled photonpairs produced via spontaneous parametric down-conversion within a local-area fiber network: theoretical model and experiment.

We present a theoretical model for the distribution of polarization-entangled photon-pairs produced via spontaneous parametric down-conversion within a local-area fiber network. This model allows an entanglement distributor who plays the role of a service provider to determine the photon-pair generation rate giving highest two-photon interference fringe visibility for any pair of users, when given user-specific parameters. Usefulness of this model is illustrated in an example and confirmed in an experiment, where polarization-entangled photon-pairs are distributed over 82 km and 132 km of dispersion-managed optical fiber. Experimentally observed visibilities and entanglement fidelities are in good agreement with theoretically predicted values.

Stable source of high quality telecom-band polarization-entangled photon-pairs based on a single, pulse-pumped, short PPLN waveguide.

We demonstrate a stable source of high quality telecom-band polarization-entangled photon-pairs based on a single, pulse-pumped, short periodically-poled lithium niobate (PPLN) waveguide. Full quantum state tomographic measurement performed on the photon-pairs has revealed a very high state purity of 0.94, and an entanglement fidelity exceeding 0.96 at the low-rate-regime. At higher rates, entanglement quality degrades due to emission of multiple-pairs. Using a new model, we have confirmed that the observed degradation is largely due to double- and triple-pair emissions.

Extensive expansion and diversification of the chemokine gene family in zebrafish: identification of a novel chemokine subfamily CX.

BACKGROUND: The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported. RESULTS: We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development. CONCLUSION: The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.

Quantum efficiency measurements by bidirectional coincidence counting of correlated photon pairs.

We propose and demonstrate a procedure for characterizing the quantum efficiency of a single-photon detector in the telecommunication wavelength band. Our procedure employs a bidirectional coincidence counting technique to distinguish optical component losses from the detection efficiency. The standard deviations of the measured quantum efficiencies were nearly identical to the standard deviations derived from a detection probability having a Poisson distribution.

After-pulse-discarding in single-photon detection to reduce bit errors in quantum key distribution.

We demonstrate fiber-optic quantum key distribution (QKD) at 1550 nm using single-photon detectors operating at 5 MHz. Such high speed single-photon detectors are essential to the realization of efficient QKD. However, after-pulses increase bit errors. In the demonstration, we discard after-pulses by measuring time intervals of detection events. For a fiber length of 10.5 km, we have achieved a key rate of 17 kHz with an error of 2%.