Isolation of bovine coronavirus (BCoV) in monolayers of HmLu-1 cells Isolamento de coronavírus bovino (BCoV) em monocamada de cultura de células da linhagem HmLu-1
coronavírus bovino (BCoV), isolamento, células HmLu-1, bovine coronavirus (BCoV), isolation, HmLu-1 cells
Isolation of BCoV was performed in monolayers of HmLu-1 cells, using 20 fecal samples from clinical cases of diarrhea in calves. Samples were positive for BCoV by means of hemagglutination / hemagglutination inhibition (HA/HI). Up to the fifth serial passage, 13 of these isolates presented syncytial cytopathic effect, similar to Kakegawa standard strain. When isolates were submitted to seroneutralization with gammaglobulin anti-bovine coronavirus, 8 of them were considered to be positive, once cytopathic effect was neutralized. After titration and seroneutralization in microplates, only three of them were confirmed as positive. The lineage HmLu-1 showed higher permissivity to BCoV isolation, but the low intensity of viral replication demonstrated that new methodologies should be developed for this purpose and then submitted to confirmation of isolation by means of seroneutralization.A partir de 20 amostras fecais de bezerros, com quadro clínico de diarréia, positivas para BCoV por hemaglutinação/inibição da hemaglutinação (HA/HI), procedeu-se o isolamento viral em monocamadas de células da linhagem HmLu-1. Até a quinta passagem seriada, 13 apresentaram efeito citopático do tipo sincicial, semelhante à amostra padrão Kakegawa de BCoV. Ao serem submetidas a uma reação de soroneutralização com gamaglobulina anti-coronavírus bovino, 8 delas foram consideradas positivas, uma vez que o efeito citopático foi neutralizado. Ao serem tituladas e submetidas à reação de soroneutralização em microplacas, apenas 3 delas puderam ser confirmadas como positivas. As células da linhagem HmLu-1 mostraram-se permissivas para o isolamento de BCoV, todavia a baixa intensidade na replicação viral demonstrou ser necessário o desenvolvimento de novas metodologias para se poder alcançar esse intuito e a confirmação do isolamento por soroneutralização.
José Antonio Jerez, Fabio Gregori, Paulo Eduardo Brandão, Cesar Alejandro Rosales Rodriguez, Fumio Honma Ito, Maria da Glória Buzinaro, Takeo Sakai
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms
Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63). For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual k-mers (k-19 to k-63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities of unique contigs per single k-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-k assemblies with redundancy removal. The complete extraction of biological information in de novo transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual k-mer assemblies but not in the CA.
Haznedaroglu Berat Z, Reeves Darryl, Rismani-Yazdi Hamid, Peccia Jordan
Biology (General), Computer applications to medicine. Medical informatics
The role of infections and coinfections with newly identified and emerging respiratory viruses in children
Abstract Acute respiratory infections are a major cause of morbidity in children both in developed and developing countries. A wide range of respiratory viruses, including respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza viruses (PIVs), adenovirus, rhinovirus (HRV), have repeatedly been detected in acute lower respiratory tract infections (LRTI) in children in the past decades. However, in the last ten years thanks to progress in molecular technologies, newly discovered viruses have been identified including human Metapneumovirus (hMPV), coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus. These discoveries have heavily modified previous knowledge on respiratory infections mainly highlighting that pediatric population is exposed to a variety of viruses with similar seasonal patterns. In this context establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present an overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.
Debiaggi Maurizia, Canducci Filippo, Ceresola Elisa Rita, Clementi Massimo
Proteomic analysis of chicken embryonic trachea and kidney tissues after infection in ovo by avian infectious bronchitis coronavirus
Abstract Background Avian infectious bronchitis (IB) is one of the most serious diseases of economic importance in chickens; it is caused by the avian infectious coronavirus (IBV). Information remains limited about the comparative protein expression profiles of chicken embryonic tissues in response to IBV infection in ovo. In this study, we analyzed the changes of protein expression in trachea and kidney tissues from chicken embryos, following IBV infection in ovo, using two-dimensional gel electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS). Results 17 differentially expressed proteins from tracheal tissues and 19 differentially expressed proteins from kidney tissues were identified. These proteins mostly related to the cytoskeleton, binding of calcium ions, the stress response, anti-oxidative, and macromolecular metabolism. Some of these altered proteins were confirmed further at the mRNA level using real-time RT-PCR. Moreover, western blotting analysis further confirmed the changes of annexin A5 and HSPB1 during IBV infection. Conclusions To the best of our knowledge, we have performed the first analysis of the proteomic changes in chicken embryonic trachea and kidney tissues during IBV infection in ovo. The data obtained should facilitate a better understanding of the pathogenesis of IBV infection.
Kong Xiangang, Geng Heyuan, Shao Yuhao, Han Zongxi, Cao Zhongzan, Liu-Sheng Wang
Epidemiological factors and worldwide pattern of Middle East respiratory syndrome coronavirus from 2013 to 2016
Disease Outbreaks, global health, MERS-CoV, Risk factors, World Health Organization
Javad Aghazadeh-Attari,1 Iraj Mohebbi,2 Behnam Mansorian,2 Jamal Ahmadzadeh,1 Mohammad Mirza-Aghazadeh-Attari,3 Kazhal Mobaraki,1 Sima Oshnouei1 1Social Determinants of Health Research Center, Urmia University of Medical Sciences, Urmia, Iran; 2Social Determinants of Health Research Center, Occupational Medicine Center, Urmia University of Medical Sciences, Urmia, Iran; 3Medical Philosophy and History Research Center, Tabriz University of Medical Sciences, Tabriz, Iran Background: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging threat to global health security with high intensity and lethality. This study was conducted to investigate epidemiological factors and patterns related to this disease.Methods: Full details of MERS-CoV cases available on the disease outbreak news section of the World Health Organization official website from January 2013 to November 2016 were retrieved; demographic and clinical information, global distribution status, potential contacts, and probable risk factors for the mortality of laboratory-confirmed MERS-CoV cases were extracted and analyzed by following standard statistical methods.Results: Details of 1,094 laboratory-confirmed cases were recorded, including 421 related deaths. Significant differences were observed in the presentation of the disease from year to year, and all studied parameters differed during the years under study (all P-values <0.05). Evaluation of the effects of various potential risk factors of the final outcome (dead/survived) revealed that two factors, namely, the morbid case being native and travel history, are significant based on a unifactorial analysis (P <0.05). From 2013 to 2016, these factors remained important. However, factors that were significant in predicting mortality varied in different years.Conclusion: These findings point to interesting potential dimensions in the dynamic of this disease. Furthermore, effective national and international preparedness plans and actions are essential to prevent, control, and predict such viral outbreaks; improve patient management; and ensure global health security. Keywords: disease outbreaks, global health, MERS-CoV, risk factors, World Health Organization
Aghazadeh-Attari J, Mohebbi I, Mansorian B, Ahmadzadeh J, Mirza-Aghazadeh-Attari M, Mobaraki K, Oshnouei S
International Journal of General Medicine
Free-Form Deformation Approach for Registration of Visible and Infrared Facial Images in Fever Screening
thermal imaging, Fever screening, temperature measurement, canthi detection, multi-modality image registration, Free-form deformation, Demons algorithm, cubic B-spline algorithm
Fever screening based on infrared (IR) thermographs (IRTs) is an approach that has been implemented during infectious disease pandemics, such as Ebola and Severe Acute Respiratory Syndrome. A recently published international standard indicates that regions medially adjacent to the inner canthi provide accurate estimates of core body temperature and are preferred sites for fever screening. Therefore, rapid, automated identification of the canthi regions within facial IR images may greatly facilitate rapid fever screening of asymptomatic travelers. However, it is more difficult to accurately identify the canthi regions from IR images than from visible images that are rich with exploitable features. In this study, we developed and evaluated techniques for multi-modality image registration (MMIR) of simultaneously captured visible and IR facial images for fever screening. We used free form deformation (FFD) models based on edge maps to improve registration accuracy after an affine transformation. Two widely used FFD models in medical image registration based on the Demons and cubic B-spline algorithms were qualitatively compared. The results showed that the Demons algorithm outperformed the cubic B-spline algorithm, likely due to overfitting of outliers by the latter method. The quantitative measure of registration accuracy, obtained through selected control point correspondence, was within 2.8 ± 1.2 mm, which enables accurate and automatic localization of canthi regions in the IR images for temperature measurement.
Yedukondala Narendra Dwith Chenna, Pejhman Ghassemi, T. Joshua Pfefer, Jon Casamento, Quanzeng Wang
MERS may not be SARS; but India is still vulnerable
Plants as Factories for Human Pharmaceuticals: Applications and Challenges
plant molecular farming, edible vaccine, humanized glycan, Transient Expression, seed platform
Plant molecular farming (PMF), defined as the practice of using plants to produce human therapeutic proteins, has received worldwide interest. PMF has grown and advanced considerably over the past two decades. A number of therapeutic proteins have been produced in plants, some of which have been through pre-clinical or clinical trials and are close to commercialization. Plants have the potential to mass-produce pharmaceutical products with less cost than traditional methods. Tobacco-derived antibodies have been tested and used to combat the Ebola outbreak in Africa. Genetically engineered immunoadhesin (DPP4-Fc) produced in green plants has been shown to be able to bind to MERS-CoV (Middle East Respiratory Syndrome), preventing the virus from infecting lung cells. Biosafety concerns (such as pollen contamination and immunogenicity of plant-specific glycans) and costly downstream extraction and purification requirements, however, have hampered PMF production from moving from the laboratory to industrial application. In this review, the challenges and opportunities of PMF are discussed. Topics addressed include; transformation and expression systems, plant bioreactors, safety concerns, and various opportunities to produce topical applications and health supplements.
Jian YAO, Yunqi Weng, Alexia Dickey, Kevin Yueju Wang
International Journal of Molecular Sciences
Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae)
meiof auna, Direct development, Brain, nervous system, Annelida, Larva
Abstract Background Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain). Despite this heterogeneity of neural arrangements, the molecular profiles related to central nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy. Results We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct-developing meiofaunal annelid Dinophilus gyrociliatus. The small, compact brain shows expression of dimmed, foxg, goosecoid, homeobrain, nk2.1, orthodenticle, orthopedia, pax6, six3/6 and synaptotagmin-1. Although most of the studied markers localize to specific brain areas, the genes six3/6 and synaptotagmin-1 are expressed in nearly all perikarya of the brain. All genes except for goosecoid, pax6 and nk2.2 overlap in the anterior brain region, while the respective expression domains are more separated in the posterior brain. Conclusions Our findings reveal that the expression patterns of the genes foxg, orthodenticle, orthopedia and six3/6 correlate with those described in Platynereis dumerilii larvae, and homeobrain, nk2.1, orthodenticle and synaptotagmin-1 resemble the pattern of late larvae of Capitella teleta. Although data on other annelids are limited, molecular similarities between adult Dinophilus and larval Platynereis and Capitella suggest an overall conservation of molecular mechanisms patterning the anterior neural regions, independent from developmental and ecological strategies, or of the size and configuration of the nervous system.
Alexandra Kerbl, José M. Martín-Durán, Katrine Worsaae, Andreas Hejnol
Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions
virus-host interactions, coronavirus, arterivirus
Animal coronaviruses, such as infectious bronchitis virus (IBV), and arteriviruses, such as porcine reproductive and respiratory syndrome virus (PRRSV), are able to manifest highly contagious infections in their specific native hosts, thereby arising in critical economic damage to animal industries. This review discusses recent progress in studies of virus-host interactions during animal and human coronavirus and arterivirus infections, with emphasis on IBV-host cell interactions. These interactions may be directly involved in viral replication or lead to the alteration of certain signaling pathways, such as cell stress response and innate immunity, to facilitate viral replication and pathogenesis.
Ding Xiang Liu, Yanxin Zhong, Yong Wah Tan