Evolution of conserved secondary structures and their function in transcriptional regulation networks

<p>Abstract</p> <p>Background</p> <p>Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functions have not been fully studied.</p> <p>Results</p> <p>We searched for polymorphisms within conserved secondary structures and identified a number of SNPs within these elements even though they are highly conserved among species. The density of SNPs in conserved secondary structures is about 65% of that of their flanking, non-conserved, sequences. Classification of sites as stems or as loops/bulges revealed that the density of SNPs in stems is about 62% of that found in loops/bulges. Analysis of derived allele frequency data indicates that sites in stems are under stronger evolutionary constraint than sites in loops/bulges. Intergenic conserved secondary structures tend to associate with transcription factor-encoding genes with genetic distance being the measure of regulator-gene associations. A substantial fraction of intergenic conserved secondary structures overlap characterized binding sites for multiple transcription factors.</p> <p>Conclusion</p> <p>Strong purifying selection implies that secondary structures are probably important carriers of biological functions for conserved sequences. The overlap between intergenic conserved secondary structures and transcription factor binding sites further suggests that intergenic conserved secondary structures have essential roles in directing gene expression in transcriptional regulation networks.</p

Treatment of infants with congenital nasolacrimal duct obstruction

AIM: To explore the different ages of congenital nasolacrimal duct obstruction in infants, take different treatment methods at different times. <p>METHODS:The 87 cases of 102 children were divided into three different age groups: the first group of 25d-3mo of age 21 cases 26 eyes; The second group >3mo-7mo 31 cases 36 eyes; The third group >7-24mo of age 35 cases 40 eyes. For the first group of infants, the implementation of the lacrimal sac nasolacrimal duct massage + eye drops; for the second group of infants, carry lacrimal pressure washing treatment; for the third group of infants, the implementation of the nasolacrimal duct probing treatment. <p>RESULTS:The first group of children through the nasolacrimal duct sac massage + drops tobramycin eye drops treatment unobstructed 12, the cure rate was 46.2%; The second group of children through pressurized irrigation treatment lacrimal patency by 33, the cure rate was 91.7%; The third group of children through the nasolacrimal duct probing unobstructed 36 treatment, the cure rate was 90.0%. The second and third group were better than the first group(<i>χ</i>²=15.71, <i>P</i><0.01; <i>χ</i>²=15.27, <i>P</i><0.01); the treatment effect of the second and third groups was no significant difference(<i>χ</i>²=0.02, <i>P</i>>0.05).<p>CONCLUSION:Infants with congenital nasolacrimal duct obstruction should distinguish between ages, taking different treatments, in order to obtain a better therapeutic effect, and lacrimal pressure washing is the preferred way of treating infants with congenital nasolacrimal duct obstruction

Chemical bath deposition route for the synthesis of ultra-thin CuIn(S,Se)2 based solar cells.

CuIn(S,Se)2 (CISSe) photovoltaic grade thin films are usually grown by expensive vacuum based methods or chemical routes that require highly toxic precursors. In this work, we present the synthesis of CISSe absorbers by a simple chemical bath deposition (CBD) route. In the first step, In2S3/Cu2 − xS stack was deposited as a precursor by CBD on Mo-coated soda lime glass substrates, using respectively thioacetamide and N,N′ dimethylthiourea as S source. Then the CISSe thin films were synthesized by the precursor's selenization at 450 °C. The obtained films were characterized by X-ray diffraction (XRD), Raman spectroscopy and scanning electron microscopy (SEM). The tetragonal chalcopyrite structure of CISSe was identified by XRD and Raman, confirming that the major part of S was replaced by Se. SEM images show a compact and homogeneous film and by cross-section the thickness was estimated to be around 700 nm. Solar cells prepared with these absorbers exhibit an open circuit voltage of 369 mV, a short circuit current density of 13.7 mA/cm2 , a fill factor of 45% and an efficiency of 2.3%

A synchronous program algebra: a basis for reasoning about shared-memory and event-based concurrency

This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave) when composed in parallel. The algebra of rely/guarantee concurrency then becomes an instantiation of the more abstract algebra. Many of the core properties needed for rely/guarantee reasoning can be shown to hold in the abstract algebra where their proofs are simpler and hence allow a higher degree of automation. The algebra has been encoded in Isabelle/HOL to provide a basis for tool support for program verification. In rely/guarantee concurrency, programs are specified to guarantee certain behaviours until assumptions about the behaviour of their environment are violated. When assumptions are violated, program behaviour is unconstrained (aborting), and guarantees need no longer hold. To support these guarantees a second synchronous operator, weak conjunction, was introduced: both processes in a weak conjunction must agree to take each atomic step, unless one aborts in which case the whole aborts. In developing the laws for parallel and weak conjunction we found many properties were shared by the operators and that the proofs of many laws were essentially the same. This insight led to the idea of generalising synchronisation to an abstract operator with only the axioms that are shared by the parallel and weak conjunction operator, so that those two operators can be viewed as instantiations of the abstract synchronisation operator. The main differences between parallel and weak conjunction are how they combine individual atomic steps; that is left open in the axioms for the abstract operator.Comment: Extended version of a Formal Methods 2016 paper, "An algebra of synchronous atomic steps

Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genomescale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.Fil: Hughes, Lily C.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Ortí, Guillermo. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Huang, Yu. Beijing Genomics Institute; China. Chinese Academy of Sciences; República de ChinaFil: Sun, Ying. China National Genebank; China. Beijing Genomics Institute; ChinaFil: Baldwin, Carole C.. National Museum of Natural History; Estados UnidosFil: Thompson, Andrew W.. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Arcila, Dahiana. National Museum of Natural History; Estados Unidos. The George Washington University; Estados UnidosFil: Betancur, Ricardo. National Museum of Natural History; Estados Unidos. Universidad de Puerto Rico, Recinto de Rio Piedras; Puerto RicoFil: Li, Chenhong. Shanghai Ocean University; ChinaFil: Becker, Leandro Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Zhao, Xiaomeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Li, Xiaofeng. Chinese Academy of Sciences; República de China. Beijing Genomics Institute; ChinaFil: Wang, Min. Beijing Genomics Institute; ChinaFil: Fang, Chao. Chinese Academy of Sciences; República de ChinaFil: Xie, Bing. Bgi-shenzhen; ChinaFil: Zhoui, Zhuocheng. China Fisheries Association; ChinaFil: Huang, Hai. Hainan Tropical Ocean University; ChinaFil: Chen, Songlin. Yellow Sea Fisheries Research Institute Chinese Academy Of Fishery Science; ChinaFil: Venkatesh, Byrappa. A-star, Institute Of Molecular And Cell Biology;Fil: Shi, Qiong. Chinese Academy of Sciences; República de Chin

Genetic Variants in MARCO Are Associated with the Susceptibility to Pulmonary Tuberculosis in Chinese Han Population

BACKGROUND: Susceptibility to tuberculosis is not only determined by Mycobacterium tuberculosis infection, but also by the genetic component of the host. Macrophage receptor with a collagenous structure (MARCO) is essential components required for toll like receptor-signaling in macrophage response to Mycobacterium tuberculosis, which may contribute to tuberculosis risk. PRINCIPAL FINDINGS: To specifically investigated whether single nucleotide polymorphisms (SNPs) in MARCO gene are associated with pulmonary tuberculosis in Chinese Han population. By selecting tagging SNPs in MARCO gene, 17 tag SNPs were identified and genotyped in 923 pulmonary tuberculosis patients and 1033 healthy control subjects using a hospital based case-control association study. Single-point and haplotype analysis revealed an association in intron and exon region of MARCO gene. One SNP (rs17009726) was associated with susceptibility to pulmonary tuberculosis, where the carriers of the G allele had a 1.65 fold (95% CI = 1.32-2.05, p(corrected) = 9.27E-5) increased risk of pulmonary tuberculosis. Haplotype analysis revealed that haplotype GC containing G allele of 17009726 and haplotype TGCC (rs17795618T/A, rs1371562G/T, rs6761637T/C, rs2011839C/T) were also associated with susceptibility to pulmonary tuberculosis (p(corrected) = 0.0001 and 0.029, respectively). CONCLUSIONS: Our study suggested that genetic variants in MARCO gene were associated with pulmonary tuberculosis susceptibility in Chinese Han population, and the findings emphasize the importance of MARCO mediated immune responses in the pathogenesis of tuberculosis

Hepatoprotective and Antioxidant Effects of Licorice Extract against CCl4-Induced Oxidative Damage in Rats

Licorice has been used in Chinese folk medicine for the treatment of various disorders. Licorice has the biological capabilities of detoxication, antioxidation, and antiinfection. In this study, we evaluated the antihepatotoxic effect of licorice aqueous extract (LE) on the carbon tetrachloride (CCl4)-induced liver injury in a rat model. Hepatic damage, as reveled by histology and the increased activities of serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP) activities, and decreased levels of serum total protein (TP), albumin (Alb) and globulin (G) were induced in rats by an administration of CCl4 at 3 mL/kg b.w. (1:1 in groundnut oil). Licorice extract significantly inhibited the elevated AST, ALP and ALT activities and the decreased TP, Alb and G levels caused by CCl4 intoxication. It also enhanced liver super oxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), glutathione reductase (GR), Glutathione S-transferase (GST) activities and glutathione (GSH) level, reduced malondialdehyde (MDA) level. Licorice extract still markedly reverses the increased liver hydroxyproline and serum TNF-α levels induced by CCl4 intoxication. The data of this study support a chemopreventive potential of licorice extract against liver oxidative injury