Influence of the Escherichia coli oxyR gene function on λ prophage maintenance

In Escherichia coli hosts, hydrogen peroxide is one of the factors that may cause induction of λ prophage. Here, we demonstrate that H₂O₂-mediated λ prophage induction is significantly enhanced in the oxyR mutant host. The mRNA levels for cI gene expression were increased in a λ lysogen in the presence of H₂O₂. On the other hand, stimulation of the p _M promoter by cI857 overproduced from a multicopy plasmid was decreased in the ΔoxyR mutant in the presence of H₂O₂ but not under normal growth conditions. The purified OxyR protein did bind specifically to the p _M promoter region. This binding impaired efficiency of interaction of the cI protein with the OR3 site, while stimulating such a binding to OR2 and OR1 sites, in the regulatory region of the p _M promoter. We propose that changes in cI gene expression, perhaps in combination with moderately induced SOS response, may be responsible for enhanced λ prophage induction by hydrogen peroxide in the oxyR mutant. Therefore, OxyR seems to be a factor stimulating λ prophage maintenance under conditions of oxidative stress. This proposal is discussed in the light of efficiency of induction of lambdoid prophages bearing genes coding for Shiga toxins.     

Assessing the use of genomic DNA as a predictor of the maximum absorbance wavelength of avian SWS1 opsin visual pigments

Recently, in vitro mutation studies have made it possible to predict the wavelengths of maximum absorbance (λ_max) of avian UV/violet sensitive visual pigments (SWS1) from the identity of a few key amino acid residues in the opsin gene. Given that the absorbance spectrum of a cone’s visual pigment and of its pigmented oil droplet can be predicted from just the λ_max, it may become possible to predict the entire spectral sensitivity of a bird using genetic samples from live birds or museum specimens. However, whilst this concept is attractive, it must be validated to assess the reliability of the predictions of λ_max from opsin amino acid sequences. In this paper, we have obtained partial sequences covering three of the known spectral tuning sites in the SWS1 opsin and predicted λ_max of all bird species for which the spectral absorbance has been measured using microspectrophotometry. Our results validate the use of molecular data from genomic DNA to predict the gross differences in λ_max between the violet- and ultraviolet-sensitive subtypes of SWS1 opsin. Additionally, we demonstrate that a bird, the bobolink Dolichonyx oryzivorus L., can have more than one SWS1 visual pigment in its retina.     

Development of a colorimetric assay for rapid quantitative measurement of clavulanic acid in microbial samples

We developed a colorimetric assay to quantify clavulanic acid (CA) in culture broth of Streptomyces clavuligerus, to facilitate screening of a large number of S. clavuligerus mutants. The assay is based on a β-lactamase-catalyzed reaction, in which the yellow substrate nitrocefin (λ _max=390 nm) is converted to a red product (λ _max=486 nm). Since CA can irreversibly inhibit β-lactamase activity, the level of CA in a sample can be measured as a function of the A ₃₉₀/A ₄₈₆ ratio in the assay mixture. The sensitivity and detection window of the assay were determined to be 50 μg L⁻¹ and 50 μg L⁻¹ to 10 mg L⁻¹, respectively. The reliability of the assay was confirmed by comparing assay results with those obtained by HPLC. The assay was used to screen a pool of 65 S. clavuligerus mutants and was reliable for identifying CA over-producing mutants. Therefore, the assay saves time and labor in large-scale mutant screening and evaluation tasks. The detection window and the reliability of this assay are markedly better than those of previously reported CA assays. This assay method is suitable for high throughput screening of microbial samples and allows direct visual observation of CA levels on agar plates.     

HIV spread in the San Francisco cohort: Scaling of the effective logistic rate for seropositivity

A simple scaling (semigroup) property is manifest in the functional form of the effective logistic rate for the increase in the HIV seropositive fraction in the San Francisco (City Clinic) cohort. Witht _i=4.5 years, this scaling property—r→λ^-2r undert→[λt+(λ−1)t _i] for all parameter values λ≧1—encapsulates the effects of relevant biological and sociological changes in the key epidemiological variables during the 8-year seropositive rise period, 1978–1985 inclusive.     

Radial theory of the ion current onto a probe in a low-pressure plasma with allowance for volume ionization and collisions with neutrals

The ion current onto a spherical or cylindrical probe is analyzed in the cold-ion approximation with allowance for ionization and collisions with neutrals. An expression for the ion density that takes into account both ionization and collision in the finite-size perturbed region is derived. The current-voltage characteristics for the dimensionless parameters r _p/λ _D = 0.0001−10, λ _i /λ _D = 0.01 − ∞, and zλ _D/(kT _e /M)^1/2 = 0−5 are determined by numerically solving Poisson’s equation, and the corresponding approximate expressions are obtained.     

Species abundance distributions in neutral models with immigration or mutation and general lifetimes

We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate λ. Thus, the population size is a homogeneous, binary Crump–Mode–Jagers process (which is not necessarily a Markov process). We assume that types are clonally inherited. We consider two classes of speciation models in this setting. In the immigration model, new individuals of an entirely new species singly enter the population at constant rate μ (e.g., from the mainland into the island). In the mutation model, each individual independently experiences point mutations in its germ line, at constant rate θ. We are interested in the species abundance distribution, i.e., in the numbers, denoted I _n (k) in the immigration model and A _n (k) in the mutation model, of species represented by k individuals, k = 1, 2, . . . , n, when there are n individuals in the total population. In the immigration model, we prove that the numbers (I _t (k); k ≥ 1) of species represented by k individuals at time t, are independent Poisson variables with parameters as in Fisher’s log-series. When conditioning on the total size of the population to equal n, this results in species abundance distributions given by Ewens’ sampling formula. In particular, I _n (k) converges as n → ∞ to a Poisson r.v. with mean γ/k, where γ : = μ/λ. In the mutation model, as n → ∞, we obtain the almost sure convergence of n ⁻¹ A _n (k) to a nonrandom explicit constant. In the case of a critical, linear birth–death process, this constant is given by Fisher’s log-series, namely n ⁻¹ A _n (k) converges to α ^k /k, where α : = λ/(λ + θ). In both models, the abundances of the most abundant species are briefly discussed.     

The gas washout determination under a symmetry assumption

In an open circuit gas washout determination the output of test substance is shown to be of the form ∑ _i=0 ^∞ A _i λ _i ^k on thekth expiration whereA _i >0,i=1,2,... and 1 > λ₁ ≥ λ₂...≥ 0 provided the transition from inspiration to expiration has certain symmetry properties with the transition from expiration to inspiration. In general, no direct physical interpretation such as volume for theA _t ’s or fraction of retained gas on expiration for the λ _i is justified.     

An Annular Plasmonic Lens Under Illumination of Circularly Polarized Light

In this paper, we consider a circular central aperture surrounded with annular depth-tuned grooves and investigate the beaming effect of the structure under illumination of a circularly polarized (CP) plane wave. As a CP plane wave is equivalent to the superposition of two linearly polarized plane waves (TM and TE) with a phase difference of π/2, the superposition of the electric field intensity, ( | E_x |² + | E_y |² ) \left( {{{\left| {E_x} \right|}^2} + {{\left| {E_y} \right|}^2}} \right) , is observed in the transmission field. In addition, two plasmonic modes are found at the resonant wavelengths λ ₁ and λ ₂ with each consisting of multiple wavelengths. At the wavelength λ ₁ = 420 nm, the significant near-field collimation is formed along the direction z, having a long propagation distance up to 1.75 μm (≈4λ) away from the exit plane of the new plasmonic lens.     

An urn model study of variability within a compartment

Formulas are derived for the mean and variance of the number of radioactive atoms present in a compartment (or urn). Initally,n ₁ radioactive atoms andb stable atoms are placed in the urn; and subsequently,r stable atoms are added and an equal number,r, of a random mixture of stable and radioactive atoms is removed per unit time. The expected number of radioactive atoms,E(t), present at timet is, as expected,n ₁ e^−λt where λ=(r/Δt)/(b+r+n ₁). The relative variance, σ²(t)/n ₁ ² , vanishes to zero forr=1, atoms per unit time and for a large number ofn ₁ radioactive atoms; but for a large number of bothr andn ₁ atoms the relative variance is ∼e ^−λt , equal to the fractional retention, fort>1/λ. Thus in studies where radionuclides are injected into animals and a single compartment represents the data, if a large variance is observed it might be due to the fact that large numbers of atoms are transferred out in unit time. When a small variance is observed, this is probably due to the fact that few atoms are transferred in smaller units of time (such that λ is the same in both cases). Research sponsored by the Energy Research and Development Administration under contract with Union Carbide Corporation.     

Two-stage continuous operation of recombinant Escherichia coli using the bacteriophage λ Q − vector

A two-stage continuous culture of Escherichia coli in combination with a bacteriophage λ system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. A phage λ vector with a Q ⁻ mutation was used to enhance the expression of the λ system. The optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned gene were determined in both batch and continuous cultures. For all culturing modes, the full induction of the cloned gene was observed 4 h after the temperature shift. In the two stage continuous culture, the overproduction reached their maxima at D=0.25 h⁻¹ with 1.5 S ₀ of the medium supply. The maximum productivity of the total β-galactosidase was 16.3×10⁶ U l⁻¹ h⁻¹, which was approximately seven times higher than that in the single-copy lysogenic stage. The recombinant cells were stable in the lysogenic state for more than 260 h, while they were stable for 40 h in the lytic state. The instability that developed rapidly in the second tank is believed to be due to the accumulation of lysis proteins as a result of vector leakage during the operation.     

A proposal for universal formulas for estimating leaf water status of herbaceous and woody plants based on spectral reflectance properties

The present study deals with the relationships between water status parameters of plant leaves and reflectances (R_λ) at characteristic wavelengths, between 522 and 2450 nm, as well as reflectance ratios, R_λ/R₁₄₃₀, R_λ/R₁₆₅₀, R_λ/R₁₈₅₀, R_λ/R₁₉₂₀, and R_λ/R₁₉₅₀, based on the air-drying experimental results of soybean (Glycine max Merr.), maize (Zea mays L.), tuliptree (Liriodendron tulipifera L.) and viburnum (Viburnum awabuki K. Koch.) plants. The water status parameters include leaf water content per unit leaf area (LWC), specific leaf water content (SWC), leaf moisture percentage of fresh weight (LMP), relative leaf water content (RWC) and relative leaf moisture percentage on fresh weight basis (RMP). Effective spectral reflectances and reflectance ratios for estimating the LWC, SWC, LMP, RWC and RMP were identified. With these spectral indices, approaches to estimating LWC, RWC and RMP were discussed. Eventually, an attempt on universal formulas was made for estimating the leaf moisture conditions of both herbaceous and woody plants as mentioned above. Moreover, applicability of these formulas was checked with the field experimental results of soybean and maize grown under water and nutrient stresses. This revised version was published online in June 2006 with corrections to the Cover Date.     

Scattering spectrum properties and their relationship to biogeochemical parameters: a case study in Taihu Lake

The scattering spectrum properties of highly turbid and eutrophic inland case 2 water from Taihu Lake were studied during three cruises from 2006 to 2007. The scattering [b _p(λ)] and backscattering [b _bp(λ)] coefficients and the backscattering probability (B) for Taihu Lake were found to show a clear spectral dependence, and this dependence was well simulated by a power-law function. This dependence, however, became weak when algae dominated the sample points. The mean values of the power-law index for b _p(λ), v, in Oct 2006, Mar 2007 and Nov 2007 were −0.6712, −0.8129 and −0.7600, respectively. To interpret the spectral characteristics and mechanisms of b _p(λ) and b _bp(λ), water samples were collected simultaneously for the biogeochemical characterization of suspended particles. The average values of the specific scattering coefficients for total suspended matter, inorganic suspended matter (ISPM) and organic suspended matter (OSPM) were 0.634 (550 nm), 1.057 (532 nm), and 0.396 g m⁻² (532 nm), respectively. The power-law index of b _bp(λ) (Y) was significantly related to ISPM/OSPM and b _bp(532 nm), but only weakly related to the particle size distribution index. The mean (spatial and wavelength) values of B in Oct 2006, Mar 2007, and Nov 2007 were 0.0108, 0.0138, and 0.0125, respectively. B decreases with increasing ISPM concentration because of the large contribution of ISPM to b _b(λ) and the strong restraint on b _bp(λ) caused by the multi-scattering effect under high-turbidity conditions.     

Retroviral-mediated gene transfer of CSF-1 into op/op stromal cells to correct defective in vitro osteoclastogenesis

Colony-stimulating factor-1 (CSF-1) released by stromal cells in the bone microenvironment is essential for the proliferation of osteoclast progenitors. In op/op mutant mice, a thymidine insertion in the coding sequence of the CSF-1 gene results in CSF-1 deficiency that in turn leads to decreased osteoclast production and osteopetrosis. Because the osteopetrotic defect is due to the failure of stromal cells to produce CSF-1, we determined if retroviral-mediated gene transfer of the wild-type CSF-1 cDNA into op/op stromal cells would restore their ability to support osteoclast formation in vitro. A retroviral vector, L-CSF-1-SN, was constructed by inserting 1,867 bp of the wild-type CSF-1 cDNA into pLXSN. After transduction with L-CSF-1-SN or LXSN constructs, a stable PA317 packaging cell line that produced a high viral titre was isolated. Viral supernatant from this line was used to infect op/op bone marrow stromal cells. Stable L-CSF-1-SN op/op stromal clones overexpressed CSF-1 mRNA and released CSF-1 into conditioned medium, compared with no CSF-1 released by LXSN op/op stroma. The amount of CSF-1 produced by two clones was similar to the physiologic level released by normal littermate stroma. Southern blot analysis confirmed the presence of intact proviral sequences in transduced cells. In coculture assays, L-CSF-1-SN, but not LXSN, op/op stromal cells supported the formation of TRAP-positive multinucleated cells in the absence of exogenous CSF-1. These findings indicate that genetically engineered stromal cells may be used to improve defective osteoclastogenesis and suggest that targeting stromal cells to bone is a potentially useful therapeutic modality for treating bone disorders. J. Cell. Physiol. 176:323–331, 1998. © 1998 Wiley-Liss, Inc.     

Three <Emphasis Type="Italic">nth</Emphasis> homologs are all required for efficient repair of spontaneous DNA damage in <Emphasis Type="Italic">Deinococcus radiodurans</Emphasis>

Deinococcus radiodurans is a bacterium that can survive extreme DNA damage. To understand the role of endonuclease III (Nth) in oxidative repair and mutagenesis, we constructed nth single, double and triple mutants. The nth mutants showed no significant difference with wild type in both IR resistance and H₂O₂ resistance. We characterized these strains with regard to mutation rates and mutation spectrum using the rpoB/Rif^r system. The Rif^r frequency of mutant MK1 (△dr0289) was twofold higher than that of wild type. The triple mutant of nth (ME3)generated a mutation frequency 34.4-fold, and a mutation rate 13.8-fold higher than the wild type. All strains demonstrated specific mutational hotspots. Each single mutant had higher spontaneous mutation frequency than wild type at base substitution (G:C → A:T). The mutational response was further increased in the double and triple mutants. The higher mutation rate and mutational response in ME3 suggested that the three nth homologs had non-overlapped and overlapped substrate spectrum in endogenous oxidative DNA repair.     

Genetic analysis of an essential cytoplasmic domain of Escherichia coli SecY based on resistance to Syd, a SecY-interacting protein

We previously described a dominant negative secY ^-d 1 allele in Escherichia coli, whose product interferes with protein export, presumably by sequestering SecE, the stabilizing partner of SecY. Syd is the product of a multicopy suppressor of the secY ^-d 1 phenotype, and its overproduction preferentially stabilizes the wild-type SecY protein. In contrast, overproduction of Syd is toxic to the secY24 mutant, which shows a partial defect in SecY-SecE interaction. We isolated Syd-resistant revertants from the secY24 mutant. Pseudo-reversions mapped to sites at or near the secY24 mutation site (Gly240→Asp). The secY249 mutation (Ala249→Val) intragenically suppressed Syd sensitivity, but not the temperature-sensitive Sec phenotype of the secY24 mutation. The SecY249 mutant protein shows a reduced capacity to be stabilized by Syd, suggesting that the mutation weakens the SecY-Syd interaction. The other two mutations changed residue 240 (the site of the secY24 alteration) to Asn (secY245) or Ala (secY241) and restored the ability of the cell to export protein. Although the secY245 mutant retained some sensitivity␣to Syd overproduction, the secY241 mutant was completely Syd-resistant. Furthermore, the secY241 mutation seemed to represent a “hyper reversion” with respect to the SecY-SecE interaction. Protein export in this mutant was no longer sensitive to SecY^-d1. When the secY ^-d 1 mutation was combined intragenically with secY241, the resulting double mutant gene (secY ^-d 1–241) showed an increased ability to interfere with protein export. On the basis of our model for SecY^-d1, these results suggest that the secY241 alteration enhances SecY-SecE interaction. These results indicate that residue 240 of SecY is crucial for the interaction between the cytosolic domains of SecY and SecE required for the establishment of the translocase complex. Received: 20 October 1997 / Accepted: 1 December 1997     

The abc1-/coq8- respiratory-deficient mutant of Schizosaccharomyces pombe suffers from glutathione underproduction and hyperaccumulates Cd2+

The abc1 ⁻ /coq8 ⁻ gene deletion respiratory-deficient mutant NBp17 of fission yeast Schizosaccharomyces pombe displayed a phenotypic fermentation pattern with enhanced production of glycerol and acetate, and also possessed oxidative stress-sensitive phenotypes to H₂O₂, menadione, tBuOOH, Cd²⁺, and chromate in comparison with its parental respiratory-competent strain HNT. As a consequence of internal stress-inducing mutation, adaptation processes to restore the redox homeostasis of mutant NBp17 cells were detected in minimal glucose medium. Mutant NBp17 produced significantly increased amounts of O₂^•− and H₂O₂ as a result of the decreased internal glutathione concentration and the only slightly increased glutathione reductase activity. The Cr(VI) reduction capacity and hence the ^•OH production ability were decreased. The mutant cells demonstrated increased specific activities of superoxide dismutases and glutathione reductase (but not catalase) to detoxify at least partially the overproduction of reactive oxygen species. All these features may be explained by the decreased redox capacity of the mutant cells. Most notably, mutant NBp17 hyperaccumulated yellow CdS.