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: Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify ''novel'' genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (,30%) were located in genomic region unique to strain 2336 (,18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations.

Answer: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen ''Histophilus somni 2336


Question: for detecting the gene encoding the σB major outer-capsid protein of novel duck reovirus (NDRV). A set of primers, composed of two outer primers, two inner primers and two loop primers, was designed based on the gene of interest. The LAMP reaction was conducted in a traditional laboratory water bath at 65 °C for 50 min. We compared the performance of calcein/Mn 2+ and SYBR Green I dyes, as well as electrophoresis on agarose gel stained with GoldView nucleic acid dye to detect the RT-LAMP-amplified products and all assays could be employed to discriminate between positive and negative specimens in visible or UV light. Our data showed that there is no cross-reaction with other viruses and the RT-LAMP technique displayed high sensitivity for detecting NDRV with a minimal detection limit of 200 fg RNA input. This assay was more sensitive than conventional PCR in detecting NDRV both in natural and experimental infection. In conclusion, the RT-LAMP technique was remarkably sensitive, specific, rapid, simple and profitable for the identification of NDRV.

Answer: Detection of Novel duck reovirus (NDRV) using visual reverse transcription loop-mediated isothermal amplification (RT-LAMP)


Question: Respiratory virus infections (RVIs) are increasingly recognized as a cause of significant morbidity and mortality in recipients of hematologic stem cell transplant (HCT) and patients with hematologic malignancy (HM). 1,2 With now widespread use of molecular diagnostics, the epidemiology and spectrum of clinical disease of these infections can be better characterized. Apart from influenza, the currently available antivirals are limited in efficacy and/or associated with potential for toxicity, thus emphasizing the importance of prevention strategies. This article provides a review of the epidemiology, clinical characteristics, management, and prevention of RVIs in HCT recipients and HM patients. No disclosures. KEYWORDS Respiratory virus infection Hematopoietic stem cell transplant RSV Influenza Parainfluenza Human metapneumovirus Rhinovirus Coronavirus The morbidity and associated complications of respiratory virus infections are greater in hematopoietic stem cell transplant recipients and patients with hematologic malignancy than in immunocompetent individuals, with severity of illness related to the degree of immunosuppression. Molecular microbiologic testing is the gold standard for diagnosis, allowing differentiation of what are largely overlapping clinical syndromes. Most of the respiratory viruses, apart from influenza and in some circumstances respiratory syncytial virus and adenovirus, are managed supportively. Prevention is key and should focus on vaccination for influenza, avoidance of ill contacts, and compliance with principles of infection control. Infect Dis Clin N Am 33 (2019) 523-544 a Studies are a combination of PCR and traditional laboratory methods (eg, culture, direct fluorescent antibody, and enzyme immunoassay). b PCR-based studies. c Includes all-cause and attributable mortality with variable timeframe to death. d One mortality in a coinfected patient attributed to enterovirus/rhinovirus infection.

Answer:
Respiratory Virus Infections of the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient