Selective accumulation of a novel antimalarial rhodacyanine derivative, SSJ-127, in an organelle of Plasmodium berghei

SSJ-127, a novel antimalarial rhodacyanine derivative, has shown potent antimalarial activity against chloroquine-resistant Plasmodium strains in vitro and subcutaneous administration of SSJ-127 results in a complete cure of a mouse malaria model. SSJ-127 was detected by fluorescence microscopy in the mouse malaria parasites Plasmodium berghei after exposure of infected red blood cells to the compound in vitro and in vivo. Selective accumulation of SSJ-127 in an organelle is observed in all blood stages of live malaria parasites. The organelle is clearly different from the mitochondrion and the nucleus in terms of morphology. The shape of the organelle changed during the asexual blood stages of the parasite. There was always a close association between the organelle and the mitochondrion. These results raised the possibility that SSJ-127 accumulates in an apicoplast of the malaria parasite and affects protozoan parasite-specific pathways.     

Optical Diffraction Studies of Muscle Fibers

A new technique to monitor light diffraction patterns electrically is applied to frog semitendinosus muscle fibers at various levels of stretch. The intensity of the diffraction lines, sarcomere length change, and the length-dispersion (line width) were calculated by fast analogue circuits and displayed in real time. A heliumneon laser (wavelength 6328 Å) was used as a light source. It was found that the intensity of the first-order diffraction line drops significantly (30-50%) at an optimal sarcomere length of 2.8 μm on isometric tetanic stimulation. Such stimulation produced contraction of half-sarcomeres by about 22 nm presumably by stretching inactive elements such as tendons. The dispersion of the sarcomere lengths is extremely small, and it is proportional to the sarcomere length (less than 4%). The dispersion increases on stimulation. These changes on isometric tetanic stimulation were dependent on sarcomere length. No vibration or oscillation in the averaged length of the sarcomeres was found during isometric tetanus within a resolution of 3 nm; however, our observation of increased length dispersion of the sarcomeres together with detection of the averaged shortening of the sarcomere lengths suggests the presence of asynchronous cyclic motions between thick and thin filaments. An alternative explanation is simply an increase of the length dispersion of sarcomeres without cyclic motions.     

Gene structure and functional properties of mouse CRTH2, a prostaglandin D2 receptor

CRTH2, the second receptor for prostaglandin D(2) (PGD(2)), is thought to play a role in allergic inflammations through the induction of chemotactic migration and/or the activation of Th2, eosinophils, and basophils, in humans. We previously identified the mouse CRTH2 homolog of human CRTH2 and suggest that animal models would provide a clear understanding on the precise function of CRTH2 in allergic disorders. To this end we have confirmed that mouse CRTH2 is similar in gene structure to human CRTH2 and revealed that mouse CRTH2 is predominantly expressed in the eosinophils derived from IL-5-transgenic mice. Moreover, mouse CRTH2 harbors the ability to bind PGD(2) with high affinity and intracellular Ca(2+) mobilization in a Gi-dependent manner and chemotactic responses in several transfected cell lines. The results demonstrated here indicate that mouse CRTH2 is the functional ortholog of human CRTH2 and paves the way for future analysis of the in vivo functions of CRTH2.     

Triplet fraction buildup effect of the DNA-YOYO complex studied with fluorescence correlation spectroscopy

DNA fragments of various lengths and YOYO-1 iodide (YOYO) were mixed at various ratios, and fluorescence was measured using fluorescence correlation spectroscopy. The number of substantially emitting YOYO molecules binding to the DNA and the binding intervals between the YOYO molecules were estimated for DNA-YOYO complexes of various lengths. In the present study, we found an interesting phenomenon: triplet buildup. Because fluorophores that fall into the triplet state do not emit fluorescence, a part of the dark period can be recovered by emitting photons from other excited YOYO molecules in the same DNA strings in the confocal elements. The remaining dark period can be considered to be the total miss-emission rate. Estimates of the total miss-emission rate are important for calculation of the length and amount of DNA.     

Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC 17616

The Burkholderia multivorans strain ATCC 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 Mb. To determine the distribution and organization of the amino acid biosynthetic genes on the genome of this beta-proteobacterium, various auxotrophic mutations were isolated using a Tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. Analysis by pulsed-field gel electrophoresis revealed that 20 out of 23 insertion mutations were distributed on the 3.4-Mb chromosome. More detailed analysis of the his, trp, arg, and lys mutations and their flanking regions revealed the following properties of these auxotrophic genes: (i) all nine his genes were clustered on the 3.4-Mb chromosome; (ii) seven trp genes were organized within two distinct regions, i.e., a trpEGDC cluster on the 3.4-Mb chromosome and a trpFBA cluster on the 2.5-Mb chromosome; (iii) the leu gene cluster, leuCDB, was also located close to the trpFBA cluster; and (iv) lysA and argG genes were located on the 2.5-Mb chromosome, in contrast to the argH gene, which was located on the 3.4-Mb chromosome. Southern hybridization analysis, allelic exchange mutagenesis of ATCC 17616, and complementation tests demonstrated that all of the genes examined were functional and existed as a single copy within the genome. The present findings also indicated that the 2.5-Mb chromosome carried various auxotrophic genes with no structural or functional counterparts on the remaining two chromosomes.     

Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205

The technical formulation of hexachlorocyclohexane (HCH) mainly consists of the insecticidal γ-isomer and noninsecticidal α-, β-, and δ-isomers, among which β-HCH is the most recalcitrant and has caused serious environmental problems. A γ-HCH-utilizing bacterial strain, Sphingobium sp. MI1205, was isolated from soil which had been contaminated with HCH isomers. This strain degraded β-HCH more rapidly than the well-characterized γ-HCH-utilizing strain Sphingobium japonicum UT26. In MI1205, β-HCH was converted to 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL) via 2,3,4,5,6-pentachlorocyclohexanol (PCHL). A haloalkane dehalogenase LinB (LinB_MI) that is 98% identical (seven amino-acid differences among 296 amino acids) to LinB from UT26 (LinB_UT) was identified as an enzyme responsible for the two-step conversion of β-HCH to TCDL. This property of LinB_MI contrasted with that of LinB_UT, which catalyzed only the first step conversion of β-HCH to PCHL. Site-directed mutagenesis and computer modeling suggested that two of the seven different amino acid residues (V134 and H247) forming a catalytic pocket of LinB are important for the binding of PCHL in an orientation suitable for the reaction in LinB_MI. However, mutagenesis also indicated the involvement of other residues for the activity unique to LinB_MI. Sequence analysis revealed that MI1205 possesses the IS6100-flanked cluster that contains two copies of the linB _MI gene. This cluster is identical to the one located on the exogenously isolated plasmid pLB1, suggesting that MI1205 had recruited the linB genes by a horizontal transfer event.     

Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides

PrimPol is a DNA damage tolerance enzyme possessing both translesion synthesis (TLS) and primase activities. To uncover its potential role in TLS-mediated IgV_λ hypermutation and define its interplay with other TLS polymerases, PrimPol^?/? and PrimPol^?/?/Polη^?/?/Polζ ^?/? gene knockouts were generated in avian cells. Loss of PrimPol had no significant impact on the rate of hypermutation or the mutation spectrum of IgV_λ. However, PrimPol^?/? cells were sensitive to methylmethane sulfonate, suggesting that it may bypass abasic sites at the IgV_λ segment by repriming DNA synthesis downstream of these sites. PrimPol^?/? cells were also sensitive to cisplatin and hydroxyurea, indicating that it assists in maintaining / restarting replication at a variety of lesions. To accurately measure the relative contribution of the TLS and primase activities, we examined DNA damage sensitivity in PrimPol^?/? cells complemented with polymerase or primase-deficient PrimPol. Polymerase-defective, but not primase-deficient, PrimPol suppresses the hypersensitivity of PrimPol^?/? cells. This indicates that its primase, rather than TLS activity, is pivotal for DNA damage tolerance. Loss of TLS polymerases, Polη and Polζ has an additive effect on the sensitivity of PrimPol^?/? cells. Moreover, we found that PrimPol and Polη-Polζ redundantly prevented cell death and facilitated unperturbed cell cycle progression. PrimPol^?/? cells also exhibited increased sensitivity to a wide variety of chain-terminating nucleoside analogs (CTNAs). PrimPol could perform close-coupled repriming downstream of CTNAs and oxidative damage in vitro. Together, these results indicate that PrimPol's repriming activity plays a central role in reinitiating replication downstream from CTNAs and other specific DNA lesions.     

Automatically detecting and tracking free‐ranging Japanese macaques in video recordings with deep learning and particle filters

Recently, automated observation systems for animals using artificial intelligence have been proposed. In the wild, animals are difficult to detect and track automatically because of lamination and occlusions. Our study proposes a new approach to automatically detect and track wild Japanese macaques (Macaca fuscata) using deep learning and a particle filter algorithm. Macaque likelihood is derived through deep learning and used as an observation model in a particle filter to predict the macaques’ position and size in an image. By using deep learning as an observation model, it is possible to simplify the observation model and improve the accuracy of the classifier. We investigated whether the algorithm could find body regions of macaques in video recordings of free‐ranging groups at Katsuyama, Japan to evaluate our model. Experimental results showed that our method with deep learning as an observation model had higher tracking accuracy than a method that uses a support vector machine. More generally, our study will help researchers to develop automatic observation systems for animals in the wild.