The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins

A novel method of rapid and specific detection of polymerase chain reaction (PCR) products from bacterial genomes using Zn finger proteins was developed. Zn finger proteins are DNA-binding proteins that can sequence specifically recognize PCR products. Since Zn finger proteins can directly detect PCR products without undergoing dehybridization, unlike probe DNA, and can double check the specific PCR amplification and sequence specificity of the PCR products, this novel method would be quick and highly accurate. In this study, we tried to detect Legionella pneumophila using Sp1. It was found that a 49 bp L. pneumophila-specific region containing the Sp1 recognition site is located on the flhA gene of the L. pneumophila genome. We succeeded in specifically detecting PCR products amplified from L. pneumophila in the presence of other bacterial genomes by ELISA, and demonstrated that Sp1 enables the discrimination of L. pneumophila-specific PCR products from others. By fluorescence depolarization measurement, these specific PCR products could be detected within 1 min. These results indicate that the rapid and simple detection of PCR products specific to L. pneumophila using a Zn finger protein was achieved. This methodology can be applied to the detection of other bacteria using various Zn finger proteins that have already been reported.     

Reinstatement of Grateloupia subpectinata (Rhodophyta, Halymeniaceae) based on morphology and rbcL sequences

Morphological observations and molecular analyses of the north‐western Pacific species of the red algal genus Grateloupia (Halymeniaceae) indicate the presence of an entity, which is somewhat similar in gross morphology to G. asiatica Kawaguchi et Wang but is distinguished from the latter species by some morphological features. These include: (i) a somewhat fleshy texture; (ii) wider and much thicker (4.5–10 mm wide and up to 1300 μm thick) axes, of which an inner cortex consists of more (6–9) cells; (iii) generally longer (up to 17 cm), marginal and surface proliferations that are clearly constricted (terete) at bases; and (iv) much elongated, oblong auxiliary cells. Phylogenetic analysis using the ribulose‐l,5‐bisphosphate carboxylase/ oxygenase (rbcL) gene of G. asiatica and the alga in question shows them to be distantly related and strongly supports the differentiation of these two entities at the species level. Judging from the literature, this entity is actually Grateloupia subpectinata Holmes, which has been placed into synonymy under G. asiatica [as G. filicina (Lamouroux) C. Agardh] or G. prolongata J. Agardh in previous reports, and therefore the Holmes name is reinstated.     

Nematocyst composition of the cubomedusan Chiropsalmus quadrigatuschanges with growth

The nematocysts of Chiropsalmus quadrigatus (Cubozoa; Cubomedusa; Chirodropidae) were examined to determine if their composition changes with an increase in body size. Fixed tentacles of specimens collected in Okinawa, Japan, were homogenized and their nematocysts were observed under a differential interference contrast microscope. Six nematocyst types were observed in medusae of all sizes microbasic mastigophores (MM), large and small trirhopaloids (lTR and sTR), holotrichous isorhizas (HI), ellipsoidal isorhizas (eI), and ovoid isorhizas (oI). Two other nematocysts, large ovoid isorhizas (loI) and microbasic euryteles (ME), were observed only in small individuals. There was also marked difference in proportion of tentacular nematocysts between small and large individuals. HI was the dominant type in small specimens, while MM and eI were predominant in large specimens. Nematocyst composition in the bell and pedalia also differed between small and large individuals. Bells of small medusae contained oI and sTR, while only oI were observed in most large individuals. The pedalia of small medusae had clusters of MM, ME, sTR, and oI. Such single clusters on pedalium bases were characteristic of small individuals. The pedalia of large individuals contained scattered oI. Tentacles of medusae are used for prey capture, so the changes in the major type of nematocysts in tentacles may reflect changes in prey type.     

Metabolic Quotient Measured by Free-Water Method in Six Enclosures with Different Silver Carp Densities

Quasi-continuous DO and pH measurements (total 47 days) were conducted during enclosure experiments (6 enclosures; 5 × 5 × 2.5 m), in which a biomass gradient of silver carp was created. After subtracting the air–water exchanges of O₂ and CO₂, the chemical and biochemical changes in DO (dissolved oxygen) and DIC (dissolved inorganic carbon) were estimated in order to evaluate MQ (metabolic quotient: DO change divided by DIC change) at intervals of 1 hour. By removing small absolute changes below the threshold value (0.01 mM h^?1), the averaged values of the 24 MQ means for the respective 1-hour periods ranged from 0.96 to 1.20 in the six enclosures. Because the MQs in the daytime inversely correlated well with the ratio of NH⁺ ₄–N to (NH⁺ ₄–N + NO^? ₃–N), not the ecosystems, i.e., density of fish, community structure of zooplankton and phytoplankton, but the form of nitrogen uptaken for primary production principally determined the MQs. The higher MQs observed in the daytime compared with the nighttime (from 14% to 21% except 3% for one enclosure) could not be explained by the denitrification and/or dissolution of CaCO₃ in the sediments, therefore suggesting the selectively faster decomposition of part of the organic matter provided through primary production, in other words, an accumulation of another part of the organic matter in the diurnal and/or daily time scale.     

Mutation in keratin 18 induces mitochondrial fragmentation in liver-derived epithelial cells

Microtubules (MTs) and microfilaments (MFs) are known to modulate mitochondrial morphology, distribution and function. However, little is known evidence about the role of intermediate filaments (IFs) in modulating mitochondria except desmin. To investigate whether or not the IFs regulate mitochondrial morphology, distribution, and function, we manipulated the IFs of cultured epithelial cells to express a mutant keratin 18 (K18). In contrast to the filamentous expression of wild K18, mutant K18 induced aggregation of K8/18, showing no fine IF network in the cells. In mutant K18-transfected cells, the mitochondria were fragmented into small spheroids, although they were observed as mitochondrial fibers in un-transfected or wild K18-transfected cells. Fluorescence recovery after photobleaching of fluorescence-labeled mitochondria was markedly less in the mutant K18-transfected cells, although a significant recovery was confirmed in wild K18-transfected cells. These findings suggest that the IFs are important for the maintenance of normal mitochondrial structures.     

Steric constraint in the primary photoproduct of sensory rhodopsin II is a prerequisite for light-signal transfer to HtrII

Sensory rhodopsin II (SRII, also called pharaonis phoborhodopsin, ppR) is responsible for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all- trans to 13- cis initiates conformational changes in the protein, leading to activation of the cognate transducer protein (HtrII). We previously observed enhancement of the C 14-D stretching vibration of the retinal chromophore at 2244 cm (-1) upon formation of the K state and interpreted that a steric constraint occurs at the C 14D group in SRII K. Here, we identify the counterpart of the C 14D group as Thr204, because the C 14-D stretching signal disappeared in T204A, T204S, and T204C mutants as well as a C 14-HOOP (hydrogen out-of-plane) vibration at 864 cm (-1). Although the K state of the wild-type bacteriorhodopsin (BR), a light-driven proton pump, possesses neither 2244 nor 864 cm (-1) bands, both signals appeared for the K state of a triple mutant of BR that functions as a light sensor (P200T/V210Y/A215T). We found a positive correlation between these vibrational amplitudes of the C 14 atom at 77 K and the physiological phototaxis response. These observations strongly suggest that the steric constraint between the C 14 group of retinal and Thr204 of the protein is a prerequisite for light-signal transduction by SRII.     

Complex formation of amphotericin B in sterol-containing membranes as evidenced by surface plasmon resonance

Amphotericin B (AmB) is a membrane-active antibiotic that increases the permeability of fungal membranes. Thus, the dynamic process of its interaction with membranes poses intriguing questions, which prompted us to elaborate a quick and reliable method for real-time observation of the drug's binding to phospholipid liposomes. We focused on surface plasmon resonance (SPR) and devised a new modification method of sensor chips, which led to a significant reduction in the level of nonspecific binding of the drug in a control lane. With this method in hand, we examined the affinity of AmB for various membrane preparations. As expected, AmB exhibited much higher affinity for sterol-containing palmitoyloleoylphosphatidylcholine membranes than those without sterol. The sensorgrams recorded under various conditions partly fitted theoretical curves, which were based on three interaction models. Among those, a two-state reaction model reproduced well the sensorgram of AmB binding to an ergosterol-containing membrane; in this model, two states of membrane-bound complexes, AB and AB*, are assumed, which correspond to a simple binding to the surface of the membrane (AB) and formation of another assembly in the membrane (AB*) such as an ion channel complex. Kinetic analysis demonstrated that the association constant in ergosterol-containing POPC liposomes is larger by 1 order of magnitude than that in the cholesterol-containing counterpart. These findings support the previous notion that ergosterol stabilizes the membrane-bound assembly of AmB.     

Lecithin: cholesterol acyltransferase is insufficient to prevent oxidative modification of low-density lipoprotein.

We tried to confirm the antioxidative capability of lecithin:cholesterol acyltransferase (LCAT) reported by Vohl et al. [Biochemistry (1999) 38, 5976-5981]. The enzyme solution protected LDL against oxidation. However, this protection was not due to LCAT enzyme, but to some unknown low-molecular-weight substance(s) in the solution; LCAT itself exerted little protective effect against LDL oxidation.     

Sensing of cytoplasmic pH by bacterial chemoreceptors involves the linker region that connects the membrane-spanning and the signal-modulating helices.

The two major chemoreceptors of Escherichia coli, Tsr and Tar, mediate opposite responses to the same changes in cytoplasmic pH (pH(i)). We set out to identify residues involved in pH(i) sensing to gain insight into the general mechanisms of signaling employed by the chemoreceptors. Characterization of various chimeras of Tsr and Tar localized the pH(i)-sensing region to Arg(259)-His(267) of Tar and Gly(261)-Asp(269) of Tsr. This region of Tar contains three charged residues (Arg(259)-Ser(261), Asp(263), and His(267)) that have counterparts of opposite charge in Tsr (Gly(261)-Glu(262), Arg(265), and Asp(269)). The replacement of all of the three charged residues in Tar or Arg(259)-Ser(260) alone by the corresponding residues of Tsr reversed the polarity of pH(i) response, whereas the replacement of Asp(263) or His(267) did not change the polarity but altered the time course of pH(i) response. These results suggest that the electrostatic properties of a short cytoplasmic region within the linker region that connects the second transmembrane helix to the first methylation helix is critical for switching the signaling state of the chemoreceptors during pH sensing. Similar conformational changes of this region in response to external ligands may be critical components of transmembrane signaling.     

Effects of activated charcoal, explant size, explant position and sucrose concentration on plant and shoot regeneration of Lilium longiflorum via young stem culture

An efficient system for the in vitro plant and shootregeneration of Lilium longiflorum was developed andaccomplished using transverse thin cell layers (tTCL) of young stems.tTCLs were cut transversely along young stems from which the shoot-tipshad been removed. Sections were measured accurately using a graded gridand were cut in 4 mm × 4 mm × 1 mm cubes, eliminatingepidermal tissue, and were cultured on one-half MS medium containing 8 gl^–1 agar, different sucrose concentrations (10, 20, 30 or 40g l^–1), and with or without 1 mg l^–1 activatedcharcoal (AC). Plants formed on the surface of tTCLs within 60 days onone-half MS medium containing 8 g l^–1 agar and 20 gl^–1 sucrose. Sections of 1 mm taken just below the apicalarea developed buds within 15 days, whereas the sections closer to thebase required about 45 days. Shoot regeneration was enhanced whensucrose concentration was used at 30 or 40 g l^–1 after 60days of culture. No root formation occurred. Both shooting and rootingoccurred when sucrose was used at 20 g l^–1. The plantletswere transferred to soil and grew well under greenhouseconditions.