Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA

An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization

Intrinsic Doping in Electrodeposited ZnS Thin Films for Application in Large-Area Optoelectronic Devices

Zinc sulphide (ZnS) thin films with both n- and p-type electrical conductivity were grown on glass/fluorine-doped tin oxide-conducting substrates from acidic and aqueous solution containing ZnSO4 and (NH4)2S2O3 by simply changing the deposition potential in a two-electrode cell configuration. After deposition, the films were characterised using various analytical techniques. X-ray diffraction analysis reveals that the materials are amorphous even after heat treatment. Optical properties (transmittance, absorbance and optical bandgap) of the films were studied. The bandgaps of the films were found to be in the range (3.68–3.86) eV depending on the growth voltage. Photoelectrochemical cell measurements show both n- and p-type electrical conductivity for the films depending on the growth voltage. Scanning electron microscopy shows material clusters on the surface with no significant change after heat treatment at different temperatures. Atomic force microscopy shows that the surface roughness of these materials remain fairly constant reducing only from 18 nm to 17 nm after heat treatment. Thickness estimation of the films was also carried out using theoretical and experimental methods. Direct current conductivity measurements on both as-deposited and annealed films show that resistivity increased after heat treatment

A Differential Drug Screen for Compounds That Select Against Antibiotic Resistance

Antibiotics increase the frequency of resistant bacteria by providing them a competitive advantage over sensitive strains. Here, we develop a versatile assay for differential chemical inhibition of competing microbial strains, and use it to identify compounds that preferentially inhibit tetracycline-resistant relative to sensitive bacteria, thus “inverting” selection for resistance. Our assay distinguishes compounds selecting directly against specific resistance mechanisms and compounds whose selection against resistance is based on their physiological interaction with tetracycline and is more general with respect to resistance mechanism. A pilot screen indicates that both types of selection-inverting compounds are secreted by soil microbes, suggesting that nature has evolved a repertoire of chemicals that counteracts antibiotic resistance. Finally, we show that our assay can more generally permit simple, direct screening for drugs based on their differential activity against different strains or targets

The distribution and transitions of physicians in Japan: a 1974–2004 retrospective cohort study

<p>Abstract</p> <p>Background</p> <p>In Japan, physicians freely choose their specialty and workplace, because to date there is no management system to ensure a balanced distribution of physicians. Physicians in Japan start their careers in hospitals, then become specialists, and then gradually leave hospitals to work in private clinics and take on primary care roles in their specialty fields. The present study aimed to analyse national trends in the distribution and career transitions of physicians among types of facilities and specialties over a 30-year period.</p> <p>Methods</p> <p>We obtained an electronic file containing physician registration data from the Survey of Physicians, Dentists and Pharmacists. Descriptive statistics and data on movement between facilities (hospitals and clinics) for all physicians from 1974, 1984, 1994 and 2004 were analysed. Descriptive statistics for the groups of physicians who graduated in 1970, 1980 and 1990 were also analysed, and we examined these groups over time to evaluate their changes of occupation and specialty.</p> <p>Results</p> <p>The number of physicians per 100 000 population was 113 in 1974, and rose to 212 by 2004. The number of physicians working in hospitals increased more than threefold. In Japan, while almost all physicians choose hospital-based positions at the beginning of their career, around 20% of physicians withdrew from hospitals within 10 years, and this trend of leaving hospitals was similar among generations. Physicians who graduated in 1980 and registered in general surgery, cardiovascular surgery or paediatric surgery were 10 times more likely to change their specialty, compared with those who registered in internal medicine. More than half of the physicians who registered in 1970 had changed their specialties within a period of 30 years.</p> <p>Conclusion</p> <p>The government should focus primarily on changing the physician fee schedule, with careful consideration of the balance between office-based physicians and hospital-based physicians and among specialties. To implement effective policies in managing health care human resources, policy-makers should also pay attention to continuously monitoring physicians' practising status and career motivations; and national consensus is needed regarding the number of physicians required in each type of facility and specialty as well as region.</p

Predicting survival of de novo metastatic breast cancer in Asian women: Systematic review and validation study

10.1371/journal.pone.0093755PLoS ONE94-POLN

Genomic features and computational identification of human microRNAs under long-range developmental regulation

<p>Abstract</p> <p>Background</p> <p>Recent functional studies have demonstrated that many microRNAs (miRNAs) are expressed by RNA polymerase II in a specific spatiotemporal manner during the development of organisms and play a key role in cell-lineage decisions and morphogenesis. They are therefore functionally related to a number of key protein coding developmental genes, that form genomic regulatory blocks (GRBs) with arrays of highly conserved non-coding elements (HCNEs) functioning as long-range enhancers that collaboratively regulate the expression of their target genes. Given this functional similarity as well as recent zebrafish transgenesis assays showing that the miR-9 family is indeed regulated by HCNEs with enhancer activity, we hypothesized that this type of miRNA regulation is prevalent. In this paper, we therefore systematically investigate the regulatory landscape around conserved self-transcribed miRNAs (ST miRNAs), with their own known or computationally inferred promoters, by analyzing the hallmarks of GRB target genes. These include not only the density of HCNEs in their vicinity but also the presence of large CpG islands (CGIs) and distinct patterns of histone modification marks associated with developmental genes.</p> <p>Results</p> <p>Our results show that a subset of the conserved ST miRNAs we studied shares properties similar to those of protein-coding GRB target genes: they are located in regions of significantly higher HCNE/enhancer binding density and are more likely to be associated with CGIs. Furthermore, their putative promoters have both activating as well as silencing histone modification marks during development and differentiation. Based on these results we used both an elevated HCNE density in the genomic vicinity as well as the presence of a bivalent promoter to identify 29 putative GRB target miRNAs/miRNA clusters, over two-thirds of which are known to play a role during development and differentiation. Furthermore these predictions include miRNAs of the miR-9 family, which are the only experimentally verified GRB target miRNAs.</p> <p>Conclusions</p> <p>A subset of the conserved miRNA loci we investigated exhibits typical characteristics of GRB target genes, which may partially explain their complex expression profiles during development.</p

An experimental study of low-level laser therapy in rat Achilles tendon injury

The aim of this controlled animal study was to investigate the effect of low-level laser therapy (LLLT) administered 30 min after injury to the Achilles tendon. The study animals comprised 16 Sprague Dawley male rats divided in two groups. The right Achilles tendons were injured by blunt trauma using a mini guillotine, and were treated with LLLT or placebo LLLT 30 min later. The injury and LLLT procedures were then repeated 15 hours later on the same tendon. One group received active LLLT (λ = 904 nm, 60 mW mean output power, 0.158 W/cm2 for 50 s, energy 3 J) and the other group received placebo LLLT 23 hours after LLLT. Ultrasonographic images were taken to measure the thickness of the right and left Achilles tendons. Animals were then killed, and all Achilles tendons were tested for ultimate tensile strength (UTS). All analyses were performed by blinded observers. There was a significant increase in tendon thickness in the active LLLT group when compared with the placebo group (p < 0.05) and there were no significant differences between the placebo and uninjured left tendons. There were no significant differences in UTS between laser-treated, placebo-treated and uninjured tendons. Laser irradiation of the Achilles tendon at 0.158 W/cm2 for 50 s (3 J) administered within the first 30 min after blunt trauma, and repeated after 15 h, appears to lead to edema of the tendon measured 23 hours after LLLT. The guillotine blunt trauma model seems suitable for inflicting tendon injury and measuring the effects of treatment on edema by ultrasonography and UTS. More studies are needed to further refine this model