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The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster , but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes ( e.g. , larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster , the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains., (Copyright © 2017 Leung et al.)

Objective: This study investigates possible advantages in pulsed over continuous 405-nm light-emitting diode (LED) light for bacterial inactivation and energy efficiency., Background: Alternative nonantibiotic methods of disinfection and infection control have become of significant interest. Recent studies have demonstrated the application of systems using 405-nm LEDs for continuous disinfection of the clinical environment, and also for potential treatment of contaminated wounds., Methods: Liquid suspensions of 10 3 colony-forming units/mL populations of Staphylococcus aureus were subject to pulsed 405-nm light of different frequencies, duty cycles, and intensities and for different lengths of time., Results: Pulsed exposures with the same average irradiance of 16 mW/cm 2 and varying duty cycle (25%, 50%, 75%) showed very similar performance compared with continuous exposures, with 95-98% reduction of S. aureus achieved for all duty cycles. The pulsing frequency was varied in intervals from 100 Hz to 10 kHz and appeared to have little effect on antimicrobial efficacy. However, when comparing pulsed with continuous exposure, an improvement in inactivation per unit optical energy was achieved, with results showing an increase of approximately 83% in optical efficiency., Conclusions: These results suggest that under pulsed conditions, a lower energy consumption and lower perceived brightness could be achieved, thus potentially providing improved operating conditions for medical/infection control applications without compromising antimicrobial efficacy.

A novel method is presented for calculating the information channel capacity of spike trains. This method works by fitting a χ-distribution to the distribution of distances between responses to the same stimulus: the χ-distribution is the length distribution for a vector of Gaussian variables. The dimension of this vector defines an effective dimension for the noise and by rephrasing the problem in terms of distance based quantities, this allows the channel capacity to be calculated. As an example, the capacity is calculated for a data set recorded from auditory neurons in zebra finch.

A novel methodology has been developed for the investigation of bacterial spores. Specifically, this method has been used to probe the spore coat composition of two different Bacillus stearothermophilus variants. This technique may be useful in many applications; most notably, development of novel detection schemes toward potentially harmful bacteria. This method would also be useful as an ancillary environmental monitoring system where sterility is of importance (i.e., food preparation areas as well as invasive and minimally invasive medical applications). This unique detection scheme is based on the near-infrared (NIR) surface-enhanced Raman scattering (SERS) from single, optically trapped, bacterial spores. The SERS spectra of bacterial spores in aqueous media have been measured using SERS substrates based on approximately 60-nm-diameter gold colloids bound to 3-aminopropyltriethoxysilane derivatized glass. The light from a 787-nm laser diode was used to trap and manipulate as well as simultaneously excite the SERS of an individual bacterial spore. The collected SERS spectra were examined for uniqueness and the applicability of this technique for the strain discrimination of Bacillus stearothermophilus spores. Comparison of normal Raman and SERS spectra reveals not only an enhancement of the normal Raman spectral features but also the appearance of spectral features absent in the normal Raman spectrum.

Chitosan, a naturally occurring biopolymer, was used as a scaffold for the covalent binding of single-stranded DNA oligonucleotide probes in a fluorescence-based nucleic acid hybridization assay. Chitosan's pH dependent chemical and electrostatic properties enable its deposition on electrodes and metal surfaces, as well as on the bottom of microtiter plates. A combinatorial 96-well microtiter plate format was used to optimize chemistries and reaction conditions leading to hybridization experiments. We found the coupling of oligonucleotides using relatively common glutaraldehyde chemistry was quite robust. Our hybridization results for complementary ssDNA oligonucleotides (E. coli dnaK sequences) demonstrated linear fluorescence intensity with concentration of E. coli dnaK-specific oligonucleotide from 0.73 microM to 6.6 microM. Moreover, hybridization assays were specific as there was minimal fluorescence associated with noncomplementary groEL oligonucleotide. Finally, these results demonstrate the portability of a DNA hybridization assay based on covalent coupling to chitosan, which, in turn, can be deposited onto various surfaces. More arduous surface preparation techniques involving silanizing agents and hazardous washing reagents are eliminated using this technique., (Copyright 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 646-652, 2003.)

We report the results of experiments designed to improve the efficacy of the solar disinfection of drinking water, inactivation process. The effects of periodic agitation, covering the rear surface of the container with aluminium foil, container volume and turbidity on the solar inactivation kinetics of Escherichia coli (starting population = 10(6) CFU ml(-1)) were investigated. It was shown that agitation promoted the release of dissolved oxygen from water with subsequent decrease in the inactivation rates of E. coli. In contrast, covering the rear surface of the solar disinfection container with aluminium foil improved the inactivation efficiency of the system. The mean decay constant for bacterial populations in foil-backed bottles was found to be a factor of 1.85 (std. dev. = 0.43) higher than that of non-foil-backed bottles. Inactivation rates decrease as turbidity increases. However, total inactivation was achievable in 300 NTU samples within 8 h exposure to strong sunshine. Inactivation kinetics was not dependent on the volume of the water container for volumes in the range 500-1500 ml.

Here we describe the detection of live Pseudomonas aeruginosa using a sensing film containing a fourth-generation hydroxy-terminated polyamidoamine (PAMAM) dendrimer (i.e., G4-OH) and SYTOX Green fluorescent nucleic acid stain. The films are configured on simple, disposable plastic coupons or optical fibers and are interrogated using a miniature fiber-optic spectrometer. SYTOX Green is generally considered a dead cell stain because it is not able to cross the membranes of live cells. In the presence of PAMAM-OH (G4-OH) in water, the bacterial cell becomes permeable to the SYTOX dye and the fluorescence is significantly enhanced. The fluorescence increases with the bacteria concentration, and the intensity at 5.4 x 10(7) cells mL(-1) is 350% higher than the liquid controls without PAMAM-OH. We also demonstrate that dendrimers stabilize the sensing film. After drying and desiccation, the SYTOX Green/PAMAM-OH films are still able to quantitatively detect P. aeruginosa in water. Incorporation of glucose into the SYTOX Green/ PAMAM-OH film may improve the homogeneity of the film and enhances the fluorescence signal an additional 11-25%.

The feasibility of using a generalized stochastic inversion methodology to estimate aerosol size distributions accurately by use of spectral extinction, backscatter data, or both is examined. The stochastic method used, inverse Monte Carlo (IMC), is verified with both simulated and experimental data from aerosols composed of spherical dielectrics with a known refractive index. Various levels of noise are superimposed on the data such that the effect of noise on the stability and results of inversion can be determined. Computational results show that the application of the IMC technique to inversion of spectral extinction or backscatter data or both can produce good estimates of aerosol size distributions. Specifically, for inversions for which both spectral extinction and backscatter data are used, the IMC technique was extremely accurate in determining particle size distributions well outside the wavelength range. Also, the IMC inversion results proved to be stable and accurate even when the data had significant noise, with a signal-to-noise ratio of 3.

A series of experiments is reported to identify and characterize the inactivation process in operation when drinking water, heavily contaminated with a Kenyan isolate of Escherichia coli, is stored in transparent plastic bottles that are then exposed to sunlight. The roles of optical and thermal inactivation mechanisms are studied in detail by simulating conditions of optical irradiance, water turbidity and temperature, which were recorded during a series of solar disinfection measurements carried out in the Kenyan Rift Valley. Optical inactivation effects are observed even in highly turbid water (200 ntu) and at low irradiances of only 10 mW cm-2. Thermal inactivation is found to be important only at water temperatures above 45 degrees C, at which point strong synergy between optical and thermal inactivation processes is observed. The results confirm that, where strong sunshine is available, solar disinfection of drinking water is an effective, low cost method for improving water quality and may be of particular use to refugee camps in disaster areas. Strategies for improving bacterial inactivation are discussed.

A determination of the viability of an endospore detection technique using terbium dipicolinate photoluminescence in the presence of other chemical and biological materials was performed. The compounds and organisms examined, possible environmental constituents, covered three broad categories:  organic compounds, inorganic compounds, and biological materials. Each substance was tested for a false positive, which occurs if the intrinsic terbium photoluminescence is enhanced in the absence of a bacterial endospore. The detection technique was also investigated for false negatives, which occur if a known positive endospore signal is inhibited significantly. Although several materials may give rise to false negative signals, none caused a false positive signal to be observed.

An inverse, Monte Carlo (IMC) technique is developed to solve the electromagnetic inverse-scattering problem from generally complex distributions of dielectric particles. One can verify the technique using simulated scattering data from aerosols composed of spherical dielectrics. The IMC method is found to give accurate inversion results even when the data have a signal-to-noise ratio to as low as 3:1.

With addition of an absorber to dye-doped microdroplets, an absorption-dependent blue shift in the lasing spectra has been observed. The better the spectral overlap between the absorption and the fluorescence spectra of the dye, the larger the blue shift. The experimental observations are explained by a simple model of dye lasing in an optical cavity that includes losses because of the absorber and radiation leakage.

We report the first observations, to our knowledge, of lasing emission from a single, evaporating, layered, micrometer-sized droplet. The droplet consists of an ~7.9-microm-radius glass core covered by a liquid shell of an initial 3 x 10(-4) M Rhodamine 6G dye-doped glycerin/water solution. After pumping by a doubled (532 nm) Nd:YAG pulsed laser, droplet lasing occurs over a range of shell thicknesses from ~14.5 to ~0.4 microm. At the smallest shell thickness, a dramatic increase in both the number and intensity of the lasing peaks occurs, in addition to a large (>40-nm) blue shift in the spectral bandwidth of lasing emission. A discussion of possible enhancement mechanisms responsible for these novel findings is given.

Rank annihilation-factor analysis is potentially the best method of analyzing fluorescence lidar returns because of the following capability. Rank annihilation can recognize a fluorescence signal of a component that is hidden by a large fluorescence background without a spectrum of that background. Theoretical models were developed to analyze the effectiveness of rank annihilation-factor analysis in the interpretation of lidar returns. Interferents such as background fluorescence, photon-counting noise, sky radiance, and atmospheric extinction degraded the lidar-return spectra in numerical simulations. The rank annihilation-factor analysis detection algorithm was most severely biased by the combination of photon-counting noise and sky radiance. Rank annihilation calculations were also compared with calculations done by two other detection algorithms: finding peak wavelengths and the least-squares technique. Rank annihilation is better than both techniques.

Suppression of morphology-dependent resonances of the light elastically scattered by a laser-illuminated, micrometer-sized droplet is reported. A single nonabsorbing droplet is levitated by using an electrodynamic quadrupole trap, and the scattered light is monitored as the droplet slowly evaporates. The size of the droplet is approximated by using the instability characteristics of the electrodynamic trap. To determine the refractive index and droplet radius precisely, the experimental scattering curve is fitted to a scattering curve that is generated from Mie theoretical calculations. The procedure is then repeated for absorbing droplets. The quality factor Q of each experimental resonance is determined and used to quantify the suppression effect. A dramatic suppression of narrow resonances occurs with increased absorption, whereas little or no effect is seen in moderate to broad resonances.

Samples of atmospheric particulate matter were collected on cellulose membrane filters at selected locations in Europe during 1976 and 1977 as part of an international cooperative atmospheric characterization program. These samples are analyzed for imaginary refractive index in the 0.3-1.7-microm spectral region. These data are used to determine the range of variability of the imaginary refractive index and are examined for seasonal variations. These data are discussed in the light of results of analysis of samples collected from other parts of the world and samples that were analyzed as a function of particle size.

Determinations of the imaginary refractive index in the ultraviolet and visible spectral regions as determined from diffuse reflectance measurements are presented. Materials examined are carbon black and oxides of iron, lead, mercury, copper, manganese, and vanadium along with lead iodide and iron sulfide.

Bacillus medusa was found to carry three phages or phagelike structures named phi med-1, phi med-2, and phi med-3. phi med-1 is a minute, 25-nm-diameter particle without a tail. It was extracted from the sporulation lysate of a phi med-2-minus strain of B. medusa and purified by differential centrifugation. The nucleic acid from this structure was shown to be orcinol positive, alkali sensitive, RNase sensitive, and DNase resistant. An RNase-resistant core of nucleic acid was not found, indicating that it was single-stranded RNA. A host strain has not yet been found for phi med-1. Phage phi med-3 was induced with mitomycin C or UV light and consisted of empty heads of 57 nm in diameter, whereas phi med-2 induced with mitomycin was a phage of 60-nm head diameter and 220-nm tail length. The sporulation sequence proceeded faster in those mutants lacking phi med-2, and when the phage was reintroduced to B. medusa the extended wild-type sporulation sequence was observed. B. thuringiensis var. schwetzova was sensitive to phi med-2 and yielded small turbid plaques. B. medusa produced small numbers of phi med-2 during growth. The other phage may be produced at the same time but were not detected. Phi med-1 was found in sporulating cells by electron microscopy techniques. Its release from these was demonstrated by both electron microscopy techniques and a radioactive assay. It appears to participate in the formation of a surface layer on the parasporal inclusion of B. medusa.

Physiologic third spacing can cause an increase in the volume of distribution of certain drugs, such as aminoglycosides, which results in a decrease in the serum concentration. The case reported here, that of a child with a large cavernous hemangioma, demonstrated this phenomenon. To obtain adequate serum and tissue concentrations, alteration of antimicrobial dosing may be needed in similar cases.

The attenuated total reflectance spectroscopy method of determining the complex refractive indices of materials which occur only as small particles was applied at a 10.6-microm wavelength to numerous pressed powder samples. Fresnel relations were used to obtain best fit values for the complex refractive indices of the samples. Good fits were obtained only when the particles were small compared to the wavelength. For such samples, several effective medium theories were used to predict values of bulk material refractive indices from those of samples with different volume packing fractions. Only the Bruggeman theory produced consistent results.

The absorption coefficient per unit mass alpha(cm(2)g(-l)) for aerosols in the wavelength range lambda = 1.06-10.6 microm is shown to be a sensitive function of particle size distribution and of both imaginary and real indexes of refraction. Hence the imaginary index of refraction cannot be accurately determined from absorption measurements on an aerosol sample as attempted by S. A. Schleusener et al., Appl. Opt. 15, 2546 (1976), unless the size distribution and real index of the aerosol material are known. Similar difficulties arise in attempts to infer imaginary index from transmission measurements through aerosol samples as done by F. E. Volz, Appl. Opt. 11, 755 (1972); 12, 564 (1973) and K. Fischer, Beitr. Phys. Atmos. 43, 244 (1970). In addition, scattering losses can further complicate the determination of imaginary index from transmission measurements.

We have developed a program to model atmospheric propagation and lidar return at visible and UV wavelengths. This model combines a transmission code suitable for use in the visible and UV regions with a backscatter code for Mie and fluorescence lidar return calculations and a sky background radiance code into a modular menu-driven user friendly FORTRAN program for an IBM PC or PC compatible system. This propagation model includes attenuation due to molecular scattering, molecular absorption, and particulate attenuation. The wavelength dependence of our aerosol attenuation is parametrized in terms of the visual range to provide an approximate match for UV and visible horizontal attenuation data. This aerosol model is compared with the AFGL standard aerosol models and experimental data on atmospheric attenuation as a function of the visual range.

Inhibition of angiotensin I-converting enzyme (ACE) (kininase II) provides a powerful new method for evaluating the role of the renin-angiotensin-aldosterone and kallikrein-kinin systems in the control of aldosterone secretion, renal function, and arterial blood pressure. This study compares the effects of long-term administration of a sulfhydryl inhibitor, captopril, with a nonsulfhydryl inhibitor, enalapril (1-[N-[1-(ethoxycarbonyl-3-phenylpropyl]-L-alanyl]-L-proline), in conscious sodium-deficient dogs. Plasma aldosterone concentration (PAC), plasma renin activity (PRA), urinary sodium excretion (UNaV), arterial pressure (AP), blood kinins (BK), urinary kinins (UK), and urinary kallikrein activity (UKA) were determined during long-term inhibition of ACE in sodium-deficient dogs. In response to captopril administration (20 mg/(kg . day], PAC decreased from 38.9 +/- 6.7 to 14.3 +/- 2.3 ng/dl, PRA increased from 3.58 +/- 0.53 to 13.7 +/- 1.6 ng/(ml . h), UNaV increased from 0.65 +/- 0.27 to 6.4 +/- 1.2 meq/day, AP decreased from 102 +/- 3 to 65 +/- 2 mm Hg, BK increased from 0.17 +/- 0.02 to 0.41 +/- 0.04 ng/ml, UK increased from 7.2 +/- 1.5 to 31.4 +/- 3.2 micrograms/day, and UKA decreased from 23.6 +/- 3.1 to 5.3 +/- 1.2 EU/day. Quantitatively similar changes in AP, UNaV, and PAC were observed in sodium-deficient dogs in response to long-term enalapril administration (4 mg/(kg X day]. In sodium-deficient dogs maintained on captopril or enalapril for several days, angiotensin II (AngII) infusion (3 ng/(kg X min] restored PAC, UNaV, and AP to levels observed in untreated sodium-deficient dogs. These data indicate that the long-term hypotensive and natriuretic actions of inhibitors of ACE are mediated by inhibition of AngII formation and that the renin-angiotensin system plays an essential role in regulating aldosterone secretion, renal function, and AP during sodium deficiency.