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Motivation: Recovering the gene structures is one of the important goals of genome assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene regions are still incomplete; thus, novel scaffolding approaches are required to complete gene regions. Results: We developed an efficient and fast genome scaffolding method called PEP_scaffolder, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human contigs; using human UniProt proteins as guides, the improvement on N50 size was 17% increase with an accuracy of ∼97%. PEP_scaffolder improved the proportion of fully covered proteins among all proteins, which was close to the proportion in the finished genome. The method provided a high accuracy of 91% using orthologs of distant species. Tested on simulated fly contigs, PEP_scaffolder outperformed other scaffolders, with the shortest running time and the highest accuracy. [ABSTRACT FROM AUTHOR]

Ten tri- and tetranucleotide microsatellite DNA markers were isolated and characterized from common carp ( Cyprinus carpio L.) to estimate genetic potential. These markers were tested in the samples from two closely related carp populations ( Cyprinus carpio var. xingguonensis and Cyprinus carpio var. wananensis). The number of the alleles ranged from three to nine, and observed and expected hererozygosities varied from 0.207 to 1.000 and from 0.499 to 0.900 in each population, respectively. No evidence for linkage disequilibrium was found, indicating that these markers will be useful for population studies. [ABSTRACT FROM AUTHOR]

Fifteen microsatellite loci were developed to examine the population structure of Japanese scallop, Patinopecten yessoensis. These markers were tested in samples from two geographically distant populations: the Sakhalin Island (Russia) and Dalian City (China). The mean numbers of alleles, observed and expected heterozygosities between the two populations were summarized by locus, but none of them show significant divergence between the two populations. Most loci conformed to Hardy–Weinberg expectation with the exception of loci HLJX-06, HLJX-12, HLJX-13 and HLJX-28, which had heterozygote deficits. [ABSTRACT FROM AUTHOR]

We report the development of 20 microsatellite markers for Fangzheng silver crucian carp, Carassius auratus gibelio (Bloch). Nineteen out of 20 showed polymorphism with alleles ranging from two to 14. These loci were screened to amplify the closely related species crucian carp, Carassius auratus auratus (Linnaeus) and all of them can amplify DNA with the size similar to the former. The origin of silver crucian carp is in issue and the population genetic structure is still unclear. Microsatellite markers isolated from the silver crucian carp and their utility in the crucian carp will be useful for these researches. [ABSTRACT FROM AUTHOR]

Eriocheir sinensis has higher commercial value as food source than any other species of Eriocheir in China. To protect its germplasm resources and evaluate impact on local ecology, molecular tools to characterize the population structure and identify kinships from different water systems are highly needed. We have newly identified a set of 18 microsatellite markers with the observed number of alleles at each locus ranges from 8 to 30, the observed heterozygosity ranges from 0.140 to 0.900. These newly isolated markers increase the available molecular resources that can be used to analyse population structure of Chinese mitten crab. [ABSTRACT FROM AUTHOR]

Two distinct myoglobin (mb) transcripts have been reported in common carp, Cyprinus carpio, which is a hypoxia-tolerant fish living in habitats with greatly fluctuant dissolved oxygen levels. Recombinant protein analysis has shown functional specialization of the two mb transcripts. In this work, analysis for mb-containing bacterial artificial chromosome (BAC) clones indicated different genome loci for common carp myoglobin-1 (mb-1) and myoglobin-2 (mb-2) genes. Fluorescence in situ hybridization (FISH) revealed that mb-1 and mb-2 are located on separate chromosomes. In both of the mb-1 and mb-2 containing BAC clones, gene synteny was well conserved with the homologous region on zebrafish chromosome 1, supporting that the common carp specific mb-2 gene originated from the recent whole genome duplication event in cyprinid lineage. Transcription factor binding sites search indicated that both common carp mb genes lacked specificity Protein 1 (Sp1) and myocyte enhancer factor-2 (MEF2) binding sites, which mediated muscle-specific and calcium-dependent expression in the well-studied mb promoters. Potential hypoxia response elements (HREs) were predicted in the regulatory region of common carp mb genes. These characteristics of common carp mb gene regulatory region well interpreted the hypoxia-inducible, non-muscle expression pattern of mb-1. In the case of mb-2, a 10 bp insertion to the binding site of upstream stimulatory factor (USF), which was a co-factor of hypoxia inducible factor (HIF), might cause the non-response to hypoxia treatment of mb-2. The case of common carp mb gene duplication and subsequent differentiation in expression pattern and protein function provided an example for adaptive evolution toward aquatic hypoxia tolerance. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the effect of health education on schistosomiasis in Kunshan City, so as to provide the evidence for making the consolidating strategy in the late stage of interruption of schistosomiasis transmission., Methods: The residents, middle school students and elementary school students were randomly sampled from one community, one middle school and one elementary school of each of two towns and they were investigated with interviews and questionnaires for the implementation of health education on schistosomiasis prevention and control., Results: A total of 452 middle school students (232 cases) and primary school students (220 cases) were surveyed. The awareness rate of total schistosomiasis knowledge was 98.21% among the students (the awareness rate of basic schistosomiasis knowledge was 98.42% and the awareness rate of preventive schistosomiasis knowledge was 98.01%). Among the 220 elementary school students, the awareness rate of total schistosomiasis knowledge was 97.21% (the awareness rate of basic schistosomiasis knowledge was 97.60% and the awareness rate of preventive schistosomiasis knowledge was 96.82%). Among the 232 middle school students, the awareness rate of total schistosomiasis knowledge was 99.17% ( χ 2 = 34.661, compared with the rate of the elementary school students) [the awareness rate of basic schistosomiasis knowledge was 99.20% ( χ 2 = 13.045, compared with the rate of the elementary school students) and the awareness rate of preventive schistosomiasis knowledge was 99.14% ( χ 2 = 21.796, compared with the rate of the elementary school students)]. There were significant differences between the elementary school students and middle school students in above-mentioned awareness rates (all P < 0.001). There were schistosomiasis health education materials or teaching plans in all the four schools. Among the 402 residents surveyed, the awareness rate of total schistosomiasis knowledge was 98.87%., Conclusions: The effect of health education on schistosomiasis prevention and control is very well, and the total awareness rate of schistosomiasis prevention and control knowledge among the population has reached the goal (more than 95%) of the medium- and long-term planning of schistosomiasis prevention and control in Kunshan City.