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: The presentation of viral peptide epitopes to host cytotoxic T lymphocytes (CTLs) is crucial for adaptive cellular immunity to clear the virus infection, especially for some chronic viral infections. Indeed, hosts have developed effective strategies to achieve this goal. The ideal scenario would be that the peptide epitopes stimulate a broad spectrum of CTL responses with diversified T-cell receptor (TCR) usage (the TCR repertoire). It is believed that a diversified TCR repertoire requires a "featured" peptide to be presented by the host major histocompatibility complex (MHC). A featured peptide can be processed and presented in a number of ways. Here, using the X-ray diffraction method, the crystal structures of an antigenic peptide derived from rinderpest virus presented by bovine MHC class I N*01801 (BoLA-A11) have been solved, and two distinct conformations of the presented peptide are clearly displayed. A detailed analysis of the structure and comparative sequences revealed that the polymorphic amino acid isoleucine 73 (Ile73) is extremely flexible, allowing the MHC groove to adopt different conformations to accommodate the rinderpest virus peptide. This makes the peptide more featured by exposing different amino acids for T-cell recognition. The crystal structures also demonstrated that the N*01801 molecule has an unusually large A pocket, resulting in the special conformation of the P1 residue at the N terminus of the peptide. We propose that this strategy of host peptide presentation might be beneficial for creating a diversified TCR repertoire, which is important for a moreeffective CTL response. Viral diseases and other infections caused by intracellular pathogens of cattle result in large global economic losses every year. In the past several decades, rinderpest virus (RPV) (23, 40), foot-and-mouth disease virus (FMDV) (7), and bovine tuberculosis infection (62) have brought disastrous consequences, including social panic and even a threat to human health. Nearly 6 decades ago, most countries were committed to developing more-effective vaccines (46), and remarkable achievements were made in controlling threatening bovine viral infectious diseases and other zoonoses (23, 46). In the 1960s, British virologist Walter Plowright developed a live attenuated vaccine against rinderpest virus, which was widely used in rinderpest eradication efforts (40). However, it still remains extremely challenging for humans to completely eradicate a virus. The questions of how the bovine attenuated vaccine induces immune responses and how the viral peptides are presented and recognized by host immune molecules are still largely unanswered. Therefore, studies on bovine immunity against the rinderpest virus may provide clues for our battle against other viral infections. Generally speaking, effective vaccines have common characteristics: they are rich in T-cell and B-cell epitopes and can induce the immune system to generate protective immune responses (3, 36, 54) . During this process, major histocompatibility complex (MHC) molecules play a pivotal role in the host. MHC class I (MHC I) molecules form a heterotrimer complex composed of the heavy chain of MHC, the antigenic peptide, and ␤ 2 -microglobulin (␤ 2 m). Generally, MHC I loads endogenous peptides, including the virus-derived peptides. Briefly, at the initial stage of virus infection, antigenic proteins are processed in a proteasome-dependent or -independent manner. The resultant short peptides are then transported to the endoplasmic reticulum and are loaded onto the peptidebinding grooves of MHC I molecules. Consequently, the peptide-loading MHC I complexes are translocated to the cell surface and are recognized by cytotoxic T lymphocytes (CTLs) with specific T-cell receptors (TCRs) (49, 63). This immune recognition induces an MHC-restricted CD8 ϩ T-cell response that is characterized by the killing and elimination of the infected cells by effector T cells. The majority of virus-derived peptides are processed and presented through this pathway

Answer: Two Distinct Conformations of a Rinderpest Virus Epitope Presented by Bovine Major Histocompatibility Complex Class I N*01801: a Host Strategy To Present Featured Peptides ᰔ †


Question: With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules. In this study, we propose a novel numerical vector based on only primary sequences of organism to build their phylogeny. Three chemical and physical properties of primary sequences: purine, pyrimidine and keto are also incorporated to the vector. Using each property, we convert the nucleotide sequence into a new sequence consisting of only two kinds of letters. Therefore, three sequences are constructed according to the three properties. For each letter of each sequence we calculate the number of the letter, the average position of the letter and the variation of the position of the letter appearing in the sequence. Tested on several datasets related to mammals, viruses and bacteria, this new tool is fast in speed and accurate for inferring the phylogeny of organisms. Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 12226 |

Answer: A novel fast vector method for genetic sequence comparison OPEN


Question: A wide range of RNA viruses use programmed À1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed À1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics. Citation: Plant EP, Pérez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, et al. (2005) A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal. PLoS Biol 3(6): e172.

Answer:
A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal