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In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
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Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates. Fields et al., 2014). Details about the data used for the different species are provided in Table S1 . Sequence data were processed as follows: predicted CDS from the fully sequenced genomes of C. gigas (release 9) and P. fucata were retrieved from http://oysterdb.cn and http://marinegenomics.oist.jp/pinctada fucata, respectively. De novo transcriptome assemblies were performed for all the other 62 bivalve species with the CLC Genomics Workbench (v.7.5, CLC Bio, Aarhus, Denmark) using the de novo assembly tool with "automatic word size" and "automatic bubble size" parameters selected, and setting the minimum allowed contig length to 300 bp. In all transcriptomes, ORFs (Open Reading Frames) longer than 100 codons were predicted with TransDecoder (http://transdecoder.sourceforge.net). We selected the predicted CDS of C. gigas, and of one representative species for the Imparidentia (R. decussatus), Protobranchia (S. velum) and Palaeoheterodonta (P. grandis) lineages to identify a subset of evolutionarily conserved protein-coding genes with a 1:1 orthology ratio across Bivalvia. This was achieved by performing reciprocal tBLASTx searches (the e-value threshold was set a 1 × 10 −10 and only hits displaying sequence identity >50% were considered). This procedure resulted in a selection of 2,846 conserved protein-coding genes, whose orthologous sequences were retrieved in the remaining 60 species. Due to the heterogeneous tissue and developmental stage origin, the different sequencing platforms and depth applied, several of these evolutionarily conserved sequences could not be identified or were fragmented in some transcriptomes. In order to ensure a minimum quality criteria, all the selected species had to display at least 25% of the sequences included in the dataset of evolutionarily conserved genes, with an average length >500 nucleotides.
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Distributed under Creative Commons CC-BY 4.0 Analysis of synonymous codon usage patterns in sixty-four different bivalve species


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Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.
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molecules Recent Advances in Aptamer Discovery and Applications


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Background: Hepatitis C virus is a major cause of chronic liver diseases which can lead to permanent liver damage, hepatocellular carcinoma and death. The presently available treatment with interferon plus ribavirin, has limited benefits due to adverse side effects such as anemia, depression, fatigue, and "flu-like" symptoms. Herbal plants have been used for centuries against different diseases including viral diseases and have become a major source of new compounds to treat bacterial and viral diseases. Material: The present study was design to study the antiviral effect of Glycyrrhizin (GL) against HCV. For this purpose, HCV infected liver cells were treated with GL at non toxic doses and HCV titer was measured by Quantitative real time RT-PCR. Our results demonstrated that GL inhibit HCV titer in a dose dependent manner and resulted in 50% reduction of HCV at a concentration of 14 ± 2 μg. Comparative studies were made with interferon alpha to investigate synergistic effects, if any, between antiviral compound and interferon alpha 2a. Our data showed that GL exhibited synergistic effect when combined with interferon. Moreover, these results were verified by transiently transfecting the liver cells with HCV 3a core plasmid. The results proved that GL dose dependently inhibit the expression of HCV 3a core gene both at mRNA and protein levels while the GAPDH remained constant. Our results suggest that GL inhibit HCV full length viral particles and HCV core gene expression or function in a dose dependent manner and had synergistic effect with interferon. In future, GL along with interferon will be better option to treat HCV infection.
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Glycyrrhizin as antiviral agent against Hepatitis C Virus