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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Question: 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.

Answer: Distributed under Creative Commons CC-BY 4.0 Analysis of synonymous codon usage patterns in sixty-four different bivalve species


Question: Understanding viral transmission dynamics within populations of reservoir hosts can facilitate greater knowledge of the spillover of emerging infectious diseases. While bat-borne viruses are of concern to public health, investigations into their dynamics have been limited by a lack of longitudinal data from individual bats. Here, we examine capture-mark-recapture (CMR) data from a species of Australian bat (Myotis macropus) infected with a putative novel Alphacoronavirus within a Bayesian framework. Then, we developed epidemic models to estimate the effect of persistently infectious individuals (which shed viruses for extensive periods) on the probability of viral maintenance within the study population. We found that the CMR data analysis supported grouping of infectious bats into persistently and transiently infectious bats. Maintenance of coronavirus within the study population was more likely in an epidemic model that included both persistently and transiently infectious bats, compared with the epidemic model with non-grouping of bats. These findings, using rare CMR data from longitudinal samples of individual bats, increase our understanding of transmission dynamics of bat viral infectious diseases.

Answer: Persistent infections support maintenance of a coronavirus in a population of Australian bats (Myotis macropus)


Question: between the virion and the host cell. We focused on using synthetic peptides for developing antibodies against SARS-CoV, which aimed to block viral invasion by eliciting an immune response specific to the native SARS-CoV S protein. Methods: Six peptide sequences corresponding to the surface regions of SARS-CoV S protein were designed and investigated by use of combined bioinformatics and structural analysis. These synthetic peptides were used to immunize both rabbits and monkeys. Antisera collected 1 week after the second immunization were analyzed by ELISA and tested for antibody specificity against SARS-CoV by immunofluorescent confocal microscopy. Conclusions: Synthetic peptides can elicit specific antibodies to SARS-CoV. The study provides insights for the future development of SARS vaccine via the synthetic-peptide-based approach.

Answer:
Synthetic Peptide Studies on the Severe Acute Respiratory Syndrome (SARS) Coronavirus Spike Glycoprotein: Perspective for SARS Vaccine Development