OH detection by absorption of frequency-doubled diode laser radiation at 308nm

Radiation at 308 nm has been obtained by frequency doubling the output of a commercial diode laser cooled to 165 K. A single pass through a crystal of LiIO3 converted 1 mW of 616 nm radiation to 50 pW of UV, and this was used to detect the OH radical in absorption in a flow tube. Possible extensions of the method for detection of OH in the atmosphere are discussed

A review of structural brain abnormalities in Pallister-Killian syndrome

Background Pallister-Killian syndrome (PKS) is a rare multisystem developmental syndrome usually caused by mosaic tetrasomy of chromosome 12p that is known to be associated with neurological defects. Methods We describe two patients with PKS, one of whom has bilateral perisylvian polymicrogyria (PMG), the other with macrocephaly, enlarged lateral ventricles and hypogenesis of the corpus callosum. We have also summarized the current literature describing brain abnormalities in PKS. Results We reviewed available cases with intracranial scans (n = 93) and found a strong association between PKS and structural brain abnormalities (77.41%; 72/93). Notably, ventricular abnormalities (45.83%; 33/72), abnormalities of the corpus callosum (25.00%; 18/72) and cerebral atrophy (29.17%; 21/72) were the most frequently reported, while macrocephaly (12.5%; 9/72) and PMG (4.17%; 3/72) were less frequent. To further understand how 12p genes might be relevant to brain development, we identified 63 genes which are enriched in the nervous system. These genes display distinct temporal as well as region-specific expression in the brain, suggesting specific roles in neurodevelopment and disease. Finally, we utilized these data to define minimal critical regions on 12p and their constituent genes associated with atrophy, abnormalities of the corpus callosum, and macrocephaly in PKS. Conclusion Our study reinforces the association between brain abnormalities and PKS, and documents a diverse neurogenetic basis for structural brain abnormalities and impaired function in children diagnosed with this rare disorder

Cavity ringdown studies of the E–H transition in an inductively coupled oxygen plasma: comparison of spectroscopic measurements and modelling

The absolute number density of ground state oxygen atoms, O(3P), present in a 100 mTorr oxygen plasma has been determined as a function of operating power using cavity ringdown spectroscopy (CRDS). The dissociation fraction increases by an order of magnitude from ∼0.8% at 50 W to 8% at 250 W and reflects a similar increase in the electron density over this power range. Emission spectra show that the E–H switchover is accompanied by increased rotational heating of O2 and this behaviour is also observed in the translational temperatures determined by fitting the Doppler limited O(3P) CRDS data. The measurements are contextualised via a volume averaged kinetic model that uses the measured absolute densities of O(3P) and O2(a1Δg, v = 0) as a function of power as its benchmarks. Despite the inherent spatial inhomogeneity of the plasma, the volume averaged model, which uses a minimal set of reactions, is able to both reproduce previous measurements on the absolute density of O− and to infer physically reasonable values for both the electron temperature and number density as the E–H switch over is traversed. Time-resolved emission measurements return a value of 0.2 for the wall loss coefficient for O2(b1Σg+); as a consequence, the number density of O2(b1Σg+) is (at least) one order of magnitude less than O2(a1Δg)

The spatial distribution of HO2in an atmospheric pressure plasma jet investigated by cavity ring-down spectroscopy

Cold atmospheric pressure plasma jets make important contributions to a range of fields, such as materials processing and plasma medicine. In order to optimise the effect of those plasma sources, a detailed understanding of the chemical reaction networks is pivotal. However, the small diameter of plasma jets makes diagnostics challenging. A promising approach to obtain absolute number densities is the utilisation of cavity-enhanced absorption spectroscopy methods, by which line-of-sight averaged densities are determined. Here, we present first measurements on how the spatial distribution of HO2 in the effluent of a cold atmospheric pressure plasma jet can be obtained by cavity ring-down spectroscopy in an efficient way. Instead of recording fully wavelength resolved spectra, we will demonstrate that it is sufficient to measure the absorption coefficient at two wavelengths, corresponding to the laser being on and off the molecular resonance. By sampling the effluent from the 1.6 mm diameter nozzle in the radial direction at various axial positions, we determined that the distances over which the HO2 density was distributed were (3.9 ± 0.5) mm and (6.7 ± 0.1) mm at a distance of 2 mm and 10 mm below the nozzle of the plasma jet, respectively. We performed an Abel inversion in order to obtain the spatial distribution of HO2 that is presented along the symmetry axis of the effluent. Based on that localised density, which was (4.8 ± 0.6) ⋅ 1014 cm-3 at the maximum, we will discuss the importance of the plasma zone for the production of HO2

Chemical kinetics in an atmospheric pressure helium plasma containing humidity

Atmospheric pressure plasmas are sources of biologically active oxygen and nitrogen species, which makes them potentially suitable for the use as biomedical devices. Here, experiments and simulations are combined to investigate the formation of the key reactive oxygen species, atomic oxygen (O) and hydroxyl radicals (OH), in a radio-frequency driven atmospheric pressure plasma jet operated in humidified helium. Vacuum ultra-violet high-resolution Fourier-transform absorption spectroscopy and ultra-violet broad-band absorption spectroscopy are used to measure absolute densities of O and OH. These densities increase with increasing H 2 O content in the feed gas, and approach saturation values at higher admixtures on the order of 3 × 10 14 cm −3 for OH and 3 × 10 13 cm −3 for O. Experimental results are used to benchmark densities obtained from zero-dimensional plasma chemical kinetics simulations, which reveal the dominant formation pathways. At low humidity content, O is formed from OH + by proton transfer to H 2 O, which also initiates the formation of large cluster ions. At higher humidity content, O is created by reactions between OH radicals, and lost by recombination with OH. OH is produced mainly from H 2 O + by proton transfer to H 2 O and by electron impact dissociation of H 2 O. It is lost by reactions with other OH molecules to form either H 2 O + O or H 2 O 2 . Formation pathways change as a function of humidity content and position in the plasma channel. The understanding of the chemical kinetics of O and OH gained in this work will help in the development of plasma tailoring strategies to optimise their densities in applications

Genome organization and the role of centromeres in evolution of the erythroleukaemia cell line HEL.

BACKGROUND AND OBJECTIVES: The human erythroleukaemia (HEL) cell line has a highly rearranged genome. We matched whole chromosome analysis with cytogenomic microarray data to build a detailed description of these rearrangements. METHODOLOGY: We used a combination of single nucleotide polymorphism array and multiple fluorescence in situ hybridization approaches, and compared our array data with publicly available data for different sublines of HEL. B allele frequencies revealed the fate of each homologue for most chromosomes. RESULTS: At least two instances of the breakage-fusion-bridge cycle appear to have facilitated amplification of oncogenes and deletion of tumour suppressor genes. Because our study included centromere identification, we found that some abnormal chromosomes had centromeres that did not match the identity of the rest of the chromosome. CONCLUSIONS AND IMPLICATIONS: This study highlights the variety of complementary methods required to understand remodelling of the genome in cancer and uncover some of the mechanisms involved. We present evidence of centromere capture as a means of preserving broken chromosome segments. Testing for another highly repetitive DNA region, the nucleolus organizer region, helped identify the steps involved in chromosome 9 copy number aberrations. Increased use of techniques for identifying centromeres and other repetitive DNA regions will add to our understanding of genome remodelling and evolution. The pattern of chromosome 20 aberration in HEL supports an association of 20q11.21 amplification with erythroleukaemia (acute myeloid leukaemia subtype M6) in the context of 20q12 deletion. The differences between the karyotypes in different HEL sublines highlight the constantly evolving genomes of cultured cell lines

Detailed molecular cytogenetic characterisation of the myeloid cell line U937 reveals the fate of homologous chromosomes and shows that centromere capture is a feature of genome instability

BACKGROUND: The U937 cell line is widely employed as a research tool. It has a complex karyotype. A PICALM-MLLT10 fusion gene formed by the recurrent t(10;11) translocation is present, and the myeloid common deleted region at 20q12 has been lost from its near-triploid karyotype. We carried out a detailed investigation of U937 genome reorganisation including the chromosome 20 rearrangements and other complex rearrangements. RESULTS: SNP array, G-banding and Multicolour FISH identified chromosome segments resulting from unbalanced and balanced rearrangements. The organisation of the abnormal chromosomes containing these segments was then reconstructed with the strategic use of targeted metaphase FISH. This provided more accurate karyotype information for the evolving karyotype. Rearrangements involving the homologues of a chromosome pair could be differentiated in most instances. Centromere capture was demonstrated in an abnormal chromosome containing parts of chromosomes 16 and 20 which were stabilised by joining to a short section of chromosome containing an 11 centromere. This adds to the growing number of examples of centromere capture, which to date have a high incidence in complex karyotypes where the centromeres of the rearranged chromosomes are identified. There were two normal copies of one chromosome 20 homologue, and complex rearrangement of the other homologue including loss of the 20q12 common deleted region. This confirmed the previously reported loss of heterozygosity of this region in U937, and defined the rearrangements giving rise to this loss. CONCLUSIONS: Centromere capture, stabilising chromosomes pieced together from multiple segments, may be a common feature of complex karyotypes. However, it has only recently been recognised, as this requires deliberate identification of the centromeres of abnormal chromosomes. The approach presented here is invaluable for studying complex reorganised genomes such as those produced by chromothripsis, and provides a more complete picture than can be obtained by microarray, karyotyping or FISH studies alone. One major advantage of SNP arrays for this process is that the two homologues can usually be distinguished when there is more than one rearrangement of a chromosome pair. Tracking the fate of each homologue and of highly repetitive DNA regions such as centromeres helps build a picture of genome evolution. Centromere- and telomere-containing elements are important to deducing chromosome structure. This study confirms and highlights ongoing evolution in cultured cell lines

The ratio of X- and Y-Bearing sperm in ejaculates of men with three or more children of the same sex

Purpose: The present study evaluated the proportions of X-bearing and Y-bearing sperm within the semen of donors who were the declared fathers of three or more sons or daughters. Methods: The proportions of sperm were determined using dual-color fluorescence in situ hybridization to identify the X and Y chromosomes. Results: The only difference observed was in semen volume. There was no increase in the proportion of Y-bearing sperm for men with only sons (49.