Two types of recombination hotspots in bacteriophage T4: one requires DNA damage and a replication origin and the other does not

Recombination hotspots have previously been discovered in bacteriophage T4 by two different approaches, marker rescue recombination from heavily damaged phage genomes and recombination during co-infection by two undamaged phage genomes. The phage replication origin ori(34) is located in a region that has a hotspot in both assays. To determine the relationship between the origin and the two kinds of hotspots, we generated phage carrying point mutations that should inactivate ori(34) but not affect the gene 34 reading frame (within which ori(34) is located). The mutations eliminated the function of the origin, as judged by both autonomous replication of plasmids during T4 infection and two-dimensional gel analysis of phage genomic replication intermediates. As expected from past studies, the ori(34) mutations also eliminated the hotspot for marker rescue recombination from UV-irradiated genomes. However, the origin mutations had no effect on the recombination hotspot that is observed with co-infecting undamaged phage genomes, demonstrating that some DNA sequence other than the origin is responsible for inflated recombination between undamaged genomes. The hotspots for marker rescue recombination may result from a replication fork restart process that acts upon origin-initiated replication forks that become blocked at nearby DNA damage. The two-dimensional gel analysis also revealed phage T4 replication intermediates not previously detected by this method, including origin theta forms.     

PARASITISM VERSUS COMMENSALISM: THE CASE OF TABULATE ENDOBIONTS

Abstract:  Tube-like traces of organisms belonging to the ichnogenus Chaetosalpinx Sokolov have been considered in the literature as commensal endobiontic organisms of tabulate corals. Their position between the corallites (or sometimes within the septa), perforation of the host's skeleton and soft tissue, modification of its phenotype and a possible inhibition of its growth show that the relationship between these organisms and tabulate corals can best be interpreted as parasitism rather than commensalism, as previously suggested. Such an interpretation may be extended to the ichnogenera Helicosalpinx Oekentorp and Actinosalpinx Sokolov, which show identical placement within the host colony and similar features, such as the absence of their own wall.     

Automated determination of bone age and bone mineral density in patients with juvenile idiopathic arthritis: a feasibility study

Introduction

Chronic inflammation combined with glucocorticoid treatment and immobilization puts juvenile idiopathic arthritis (JIA) patients at risk of impaired growth and reduced bone mineral density (BMD). Conventional methods for evaluating bone age and BMD are time-consuming or come with additional costs and radiation exposure. In addition, an automated measurement of bone age and BMD is likely to be more consistent than visual evaluation. In this study, we aimed to evaluate the feasibility of an automated method for determination of bone age and (cortical) bone mineral density (cBMD) in severely affected JIA patients. A secondary objective was to describe bone age and cBMD in this specific JIA population eligible for biologic treatment.

Methods

In total, 69 patients with standard hand radiographs at the start of etanercept treatment and of calendar age within the reliability ranges (2.5 to 17 years for boys and 2 to 15 years for girls) were extracted from the Dutch Arthritis and Biologicals in Children register. Radiographs were analyzed using the BoneXpert method, thus automatically determining bone age and cBMD expressed as bone health index (BHI). Agreement between measurements of the left- and right-hand radiographs and a repeated measurement of the left hand were assessed with the intraclass correlation coefficient (ICC). Regression analysis was used to identify variables associated with Z-scores of bone age and BHI.

Results

The BoneXpert method was reliable in the evaluation of radiographs of 67 patients (radiographs of 2 patients were rejected because of poor image quality). Agreement between left- and right-hand radiographs (ICC = 0.838 to 0.996) and repeated measurements (ICC = 0.999 to 1.000) was good. Mean Z-scores of bone age (−0.36, P = 0.051) and BHI (−0.85, P < 0.001) were lower compared to the healthy population. Glucocorticoid use was associated with delayed bone age (0.79 standard deviation (SD), P = 0.028), and male gender was associated with a lower Z-score of BHI (0.65 SD, P = 0.021).

Conclusions

BoneXpert is an easy-to-use method for assessing bone age and cBMD in patients with JIA, provided that radiographs are of reasonable quality and patients’ bone age lies within the age ranges of the program. The population investigated had delayed bone maturation and lower cBMD than healthy children.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0424-1) contains supplementary material, which is available to authorized users.     

The behavioural response of adult Petromyzon marinus to damage‐released alarm and predator cues

Using semi‐natural enclosures, this study investigated (1) whether adult sea lamprey Petromyzon marinus show avoidance of damage‐released conspecific cues, damage‐released heterospecific cues and predator cues and (2) whether this is a general response to injured heterospecific fishes or a specific response to injured P. marinus. Ten replicate groups of 10 adult P. marinus, separated by sex, were exposed to one of the following nine stimuli: deionized water (control), extracts prepared from adult P. marinus, decayed adult P. marinus (conspecific stimuli), sympatric white sucker Catostomus commersonii, Amazon sailfin catfish Pterygoplichthys pardalis (heterospecific stimuli), 2‐phenylethylamine (PEA HCl) solution, northern water snake Nerodia sipedon washing, human saliva (predator cues) and an adult P. marinus extract and human saliva combination (a damage‐released conspecific cue and a predator cue). Adult P. marinus showed a significant avoidance response to the adult P. marinus extract as well as to C. commersonii, human saliva, PEA and the adult P. marinus extract and human saliva combination. For mobile P. marinus, the N. sipedon washing induced behaviour consistent with predator inspection. Exposure to the P. pardalis extract did not induce a significant avoidance response during the stimulus release period. Mobile adult female P. marinus showed a stronger avoidance behaviour than mobile adult male P. marinus in response to the adult P. marinus extract and the adult P. marinus extract and human saliva combination. The findings support the continued investigation of natural damage‐released alarm cue and predator‐based repellents for the behavioural manipulation of P. marinus populations in the Laurentian Great Lakes.     

Discovery of orally bioavailable imidazo[1,2-a]pyrazine-based Aurora kinase inhibitors

We report a series of potent imidazo[1,2-a]pyrazine-based Aurora kinase inhibitors. Optimization of the solvent accessible 8-position led to improvements in both oral bioavailability and off-target kinase inhibition. Compound 25 demonstrates anti-tumor activity in an A2780 ovarian tumor xenograft model.     

Influence of high-density lipoprotein on estradiol stimulation of luteal steroidogenesis

The aim of this investigation was to determine whether luteal cells utilize cholesterol derived from high-density lipoprotein (HDL) for steroidogenesis and whether estrogen enhances luteal utilization of exogenous sterol. Incubation of Day 15 corpora lutea (CL) with different doses of human HDL resulted in a dose-dependent increase in progesterone production. HDL in vitro enhanced the overall steroidogenic capacity. However, the percentage of increases in 17 alpha-hydroxyprogesterone, testosterone and estradiol were significantly less than that of progesterone. Day 12 hypophysectomized and hysterectomized pregnant rats were treated with either estradiol, testosterone or vehicle for 72 h. Serum pregnenolone and progesterone were markedly increased by the steroid treatment, yet in vitro production of progesterone by CL in all the groups was similar. However, in the presence of HDL in the media, only luteal tissues from steroid-treated rats increased their progesterone output. The reduced production of progesterone by luteal cells of vehicle-treated rats was not due to an accumulation of pregnenolone but to an overall reduction in exogenous sterol utilization. In summary, results of this investigation suggest 1) luteal cells of pregnant rats effectively utilize cholesterol from HDL for maximal steroidogenesis, and 2) estradiol may stimulate luteal steroidogenesis, at least in part, by affecting the incorporation or utilization of cholesterol from HDL into the cell.     

Human exposure to magnetic fields: A comparative assessment of two dosimeters

Two types of dosimeters for measuring human exposure to 60 Hz magnetic fields were compared. Fifty adults wore the single-axis, wrist model AMEX (average magnetic field exposure system) and the triple axis, hip-pocket or pouch model AMEX-3D meters for 2 days. Ninety-six percent of the tests were accomplished without apparent dosimeter failure. The average root mean square magnetic flux density measurements with the AMEX3D (mean = 0.10 μT, S.D. = 0.07, range = 0.03 ? 0.31) were significantly higher than with the AMEX meter (mean = 0.07 μT, S.D. 0.05, range = 0.02 ? 0.27 μT) (t test, P < 0.01). There was substantial correlation between the AMEX and the AMEX-3D measurements (Pearson's correlation coefficient = 0.65, P < 0.01) but poor concordance (Intraclass correlation coefficient = ? 0.25). These results suggest that there is a wide variation in exposure to extremely low frequency magnetic fields in the population. Magnetic field measurements with the AMEX-3D are nearly always higher than with the AMEX dosimeters. Caution is advised when comparing magnetic field measurements made with different types of dosimeters. © 1994 Wiley-Liss, Inc.     

Examination of endopelic and epilithic algal community structure employing scanning electron microscopy

1. Biological community structure within a stream periphyton mat and sediment core was examined using scanning electron microscopy. Samples were fixed, freeze-fractured and viewed under normal conditions with a scanning electron microscope.
2. This technique enabled the analysis of orientation and spatial distribution of algal cells within the three-dimensional algal communities.
3. Fractured samples from a periphyton mat and sediment core at the Procter & Gamble Experimental Stream Facility showed layering of some dominant diatom species, such as Nitzschia dissipata , Melosira varians and Gyrosigma attenuatum . The spatial relationship of nematodes as potential algal predators was also revealed.
4. Advantages, disadvantages and potential future applications of this freeze fracture technique are discussed.