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Escherichia coli bacteriophage Gostya9, representing a new specieswithin the genus T5virus
No full textAbstractEscherichia coli bacteriophage Gostya9 (genus T5virus) was isolated from horse feces collected in Moscow, Russia, in 2013.This phage was associated in a single plaque with the previously reported phage 9g and was subsequently purified. Analysisof the complete genomic sequence of Gostya9 revealed that it is closely related to the T5-like bacteriophage DT57C, whichhad been isolated at the same location in 2007. These two viruses share 79.5% nucleotide sequence identity, which is belowthe 95% threshold applied currently to demarcate bacteriophage species. The most significant features distinguishing Gostya9from DT57C include 1) the presence of one long tail fiber protein gene, 122c (ltf), instead of the two genes, ltfA and ltfB,that are present in DT57C; 2) the absence of the gene for the receptor-blocking lytic conversion lipoprotein precursor llp;and 3) the divergence of the receptor-recognition protein, pb5, which is only distantly related at the amino acid sequencelevel. The observed features of the Gostya9 adsorption apparatus are suggestive of a possible novel specificity for the finalreceptor and make this phage interesting for possible direct application in phage therapy of E. coli infections or as a sourceof receptor-recognition protein for engineering new phage specificities
Genomic characterization, phylogenetic position and in situlocalization of a novel putative mononegavirus in Lepeophtheirussalmonis
No full textThe complete genome sequence of a novel mononegavirus, Lepeophtheirus salmonis negative-stranded RNA virus 1 (LsNSRV-1), obtained from a salmonid ectoparasite, Lepeophtheirus salmonis was determined. The viral genome contains fiveopen reading frames encoding three unknown proteins (ORF I, II and III), a putative glycoprotein (G), and a large (L) protein.Phylogenetic analysis placed LsNSRV-1 in the recently established mononegaviral family Artoviridae. LsNSRV-1 showeda prevalence of around 97% and was detected in all L. salmonis developmental stages. Viral genomic and antigenomic RNAwas localized to nerve tissue, connective tissue, epithelial cells of the gut, subepidermal tissue, exocrine and cement glands,as well as the testis, vas deferens and spermatophore sac of male L. salmonis and the ovaries and oocytes of females. ViralRNA was detected in both the cytoplasm and the nucleoli of infected cells, and putative nuclear export and localizationsignals were found within the ORF I, III and L proteins, suggesting nuclear replication of LsNSRV-1. RNA interference(RNAi) was induced twice during development by the introduction of a double-stranded RNA fragment of ORF I, resultingin a transient knockdown of viral RNA. A large variation in the knockdown level was seen in adult males and off springs ofknockdown animals, whereas the RNA level was more stable in adult females. Together with the localization of viral RNAwithin the male spermatophore and female oocytes and the amplification of viral RNA in developing embryos, this suggeststhat LsNSRV-1 is transmitted both maternally and paternally. Small amounts of viral RNA were detected at the site wherechalimi were attached to the skin of Atlantic salmon (Salmo salar). However, as the RNAi-mediated treatment did not resultin LsNSRV-1-negative offspring and the virus failed to replicate in the tested fish cell cultures, it is difficult to investigatethe influence of secreted LsNSRV-1 on the salmon immune response
Proteomic analysis of monkey kidney LLC?MK2 cells infectedwith a Thai strain Zika virus
No full textAbstractZika virus (ZIKV) has been endemic in Southeast Asian countries for several years, but the presence of the virus has notbeen associated with significant outbreaks of infection unlike other countries around the world where the Asian lineage ZIKVwas introduced recently. However, few studies have been undertaken using the endemic virus. The Thai isolate was shownto have a similar tissue tropism to an African isolate of ZIKV, albeit that the Thai isolate infected cells at a lower level ascompared to the African isolate. To further understand the pathogenesis of the Thai isolate, a 2D-gel proteomic analysis wasundertaken of ZIKV infected LLC-MK2 cells. Seven proteins (superoxide dismutase [Mn], peroxiredoxin 2, ATP synthasesubunit alpha, annexin A5 and annexin A1, carnitine o-palmitoyltransferase 2 and cytoskeleton-associated protein 2) wereidentified as differentially regulated. Of four proteins selected for validation, three (superoxide dismutase [Mn], peroxiredoxin2, ATP synthase subunit alpha, and annexin A1) were shown to be differentially regulated at both the transcriptional andtranslational levels. The proteins identified were primarily involved in energy production both directly, and indirectly throughmediation of autophagy, as well as in the response to oxidative stress, possibly occurring as a consequence of increasedenergy production. This study provides further new information on the pathogenesis of ZIKV
Identification and molecular characterization of Serratia marcescensphages vB_SmaA_2050H1 and vB_SmaM_2050HW
No full textAbstractSerratia marcescens is a rod-shaped, Gram-negative bacterium causing nosocomially acquired infections. Bacteriophagesare natural opponents of their pathogenic bacterial hosts and could be an alternative to traditional antibiotic treatments. Inthis study, two S. marcescens-specific bacteriophages, vB_SmaA_2050H1 and vB_SmaM_2050HW, were isolated fromtwo different waste samples in China. Phage plaque assays, transmission electron microscopy, host-range determination,and one-step growth curve analyses were performed for both phages. vB_SmaA_2050H1 was classified as belonging tothe family Ackermannviridae, and vB_SmaM_2050HW was classified as belonging to the family Myoviridae. One-stepgrowth curve analysis showed that the latent and rise period of vB_SmaA_2050H1 were 80 min and 50 min, respectively,with a burst size of approximately 103phage particles per infected cell. For vB_SmaM_2050HW, latent and rise periods of40 min and 60 min, respectively, were determined, with a burst size of approximately 110 phage particles per infected cell.vB_SmaA_2050H1 infected 10 of the 15 (66.67%) S. marcescens strains tested, while vB_SmaM_2050HW infected 12 (80%)of the strains. Whole-genome sequencing and annotation of each of the phage genomes revealed genome sizes of 159,631bp and 276,025 bp for vB_SmaA_2050H1 and vB_SmaM_2050HW, respectively, with the respective genomes containing213 and 363 putative open reading frames. Sequence analysis of the genomes revealed that vB_SmaA_2050H1 is a memberof the ViI-like family, while vB_SmaM_2050HW is a novel virulent bacteriophage. These findings provide further insightsinto the genomic structures of S. marcescens bacteriophages
An optimization model to determine appointment scheduling window for an outpatient clinic with patient no-shows
No full textAbstract Thispaper investigatesappointment schedulingfor anoutpatient department in West China Hospital (WCH),one ofthelargestsinglepointofaccesshospitalsintheworld.Our pilotdataanalysisshowsthattheappointmentsystematWCH can be improved through leveraging the scheduling window (i.e., the number of days in advance a patient makes an appointment for future services). To gain full insight into this strategy,ourstudyconsiderstwocases,basedonifpatientsare willing to wait for scheduled appointments or not. We developed a stylized single server queueing model to find optimal schedulingwindows.Resultsshowthat,whenpatientsareless sensitive to time delay (i.e., patients will wait for scheduled services),leveringschedulingwindowsisnoteffectivetominimize the total cost per day of the appointment system. In contrast, when patients are sensitive to time delay (i.e., patients may find services elsewhere), then our model considers the potential cost of physician idle time. The modeling resultsindicate that the total cost per day is relatively sensitive to the magnitude of scheduling window. Thus, adopting a proper scheduling window is very important. In addition, our study provesthatthecostfunctionsofbothcasesarequasi-concave, which are also validated by actual data drawn from the Healthcare Information System at WCH. A comparison of numerical results between two cases is made to draw further managerial insights into scheduling policies for WCH. Discussion of our findings and research limitations are also provided.Keywords Schedulingwindow .Outpatientappointment . Patientno-shows .Queueingtheory .Healthcaremanagemen
Classification of hospital admissions into emergency and elective care: a machine learning approach
No full textAn amino acid duplication/insertion in the Bm126 gene of Bombyxmori nucleopolyhedrovirus alters viral gene expression as shownby differential gene expression analysis
No full textAbstractOpen reading frame (ORF) 126 (Bm126) of Bombyx mori nucleopolyhedrovirus (BmNPV) is not essential for viral replication,and two subtypes of this gene have been identified in China. The Bm126-SX subtype encodes a protein with a simpleamino acid duplication/insertion relative to the Bm126-GD subtype; however, significant differences in the cytopathic effectand infectivity of viruses carrying these variant genes have been observed. To elucidate the cause of these differences, differentialgene expression analysis was performed at the early stage of infection with viruses harbouring variants of Bm126.Differential expression was observed for 103, 209, and 313 host genes and 9, 44, and 67 viral genes in vGD126 samples relativeto the control samples (vSX126) at 6, 12, and 24 h postinfection, respectively. These results indicated that the duplication/insertion in Bm126 altered the viral expression pattern. The differentially expressed host genes were found to be related toribosome, spliceosome, and proteasome pathways, and several factors involved in signal transduction were also identified.The differential expression of these viral and host genes was confirmed by qPCR. This study indicates that the amino acidduplication/insertion in the Bm126 gene has a biological function related to the regulation of viral gene expression and servesas a basis for further characterization of Bm126 gene function
High frequency and diversity of parechovirus A in a cohortof Malawian children
No full textAbstractParechoviruses (PeVs) are highly prevalent viruses worldwide. Over the last decades, several studies have been publishedon PeV epidemiology in Europe, Asia and North America, while information on other continents is lacking. The aim of thisstudy was to describe PeV circulation in a cohort of children in Malawi, Africa. A total of 749 stool samples obtained fromMalawian children aged 6 to 60 months were tested for the presence of PeV by real-time PCR. We performed typing byphylogenetic and Basic Local Alignment Search Tool (BLAST) analysis. PeV was found in 57% of stool samples. Age wassignificantly associated with PeV positivity (p = 0.01). Typing by phylogenetic analysis resulted in 15 different types, whileBLAST typing resulted in 14 different types and several indeterminate strains. In total, six strains showed inconsistenciesin typing between the two methods. One strain, P02-4058, remained untypable by all methods, but appeared to belong tothe recently reclassified PeV-A19 genotype. PeV-A1, -A2 and -A3 were the most prevalent types (26.8%, 13.8% and 9.8%,respectively). Both the prevalence and genetic diversity found in our study were remarkably high. Our data provide animportant contribution to the scarce data available on PeV epidemiology in Africa