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: Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone-and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts.

Answer: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study


Question: Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.

Answer: Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology


Question: Wenxiang diagram is a new two-dimensional representation that characterizes the disposition of hydrophobic and hydrophilic residues in a-helices. In this research, the hydrophobic and hydrophilic residues of two leucine zipper coiled-coil (LZCC) structural proteins, cGKIa 1 À 59 and MBS CT35 are dispositioned on the wenxiang diagrams according to heptad repeat pattern (abcdefg) n , respectively. Their wenxiang diagrams clearly demonstrate that the residues with same repeat letters are laid on same side of the spiral diagrams, where most hydrophobic residues are positioned at a and d, and most hydrophilic residues are localized on b, c, e, f and g polar position regions. The wenxiang diagrams of a dimetric LZCC can be represented by the combination of two monomeric wenxiang diagrams, and the wenxiang diagrams of the two LZCC (tetramer) complex structures can also be assembled by using two pairs of their wenxiang diagrams. Furthermore, by comparing the wenxiang diagrams of cGKIa 1 À 59 and MBS CT35 , the interaction between cGKIa 1 À 59 and MBS CT35 is suggested to be weaker. By analyzing the wenxiang diagram of the cGKIa 1 À 59. ÁMBS CT42 complex structure, most affected residues of cGKIa 1 À 59 by the interaction with MBS CT42 are proposed at positions d, a, e and g of the LZCC structure. These findings are consistent with our previous NMR results. Incorporating NMR spectroscopy, the wenxiang diagrams of LZCC structures may provide novel insights into the interaction mechanisms between dimeric, trimeric, tetrameric coiled-coil structures.

Answer:
The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism