niryuu/sni-each-converted huggingface dataset:
Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as 1 kb. The genomic signature is therefore proposed as a tool to detect HTs. Since DNA transfers originate from species with a signature different from those of the recipient species, the analysis of local variations of signature along recipient genome may allow for detecting exogenous DNA. The strategy consists in (i) scanning the genome with a sliding window, and calculating the corresponding local signature (ii) evaluating its deviation from the signature of the whole genome and (iii) looking for similar signatures in a database of genomic signatures. A total of 22 prokaryote genomes are analyzed in this way. It has been observed that atypical regions make up $6% of each genome on the average. Most of the claimed HTs as well as new ones are detected. The origin of putative DNA transfers is looked for among $12 000 species. Donor species are proposed and sometimes strongly suggested, considering similarity of signatures. Among the species studied, Bacillus subtilis, Haemophilus Influenzae and Escherichia coli are investigated by many authors and give the opportunity to perform a thorough comparison of most of the bioinformatics methods used to detect HTs. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org. ª 2005, the authors
Output: Detection and characterization of horizontal transfers in prokaryotes using genomic signature
This data article informs about Chiropteran diversity, new records, ecosystem services and possible pathogen carriers in fragmented forests (sub-divided by utility corridors, man-made structures, untouched and secondary plantations) within districts Setiu (Setiu Research Station), Hulu Terengganu (Saok and Lasir waterfalls) and Besut (Gunung Tebu Forest Reserve) of state Terengganu, Peninsular Malaysia. These bats were captured using harp traps and mist nets that were set 10 m apart across flyways, streams and less cluttered trees in the 50 m Â 50 m transect zones (identified at each site). All animals were distinguished by morphology and gender before their release at the site of capture. The data comprise of five bat family groups Hipposideridae, Megadermatidae, Pteropodidae, Rhinolophidae and Vespertilionidae. It is interesting to note that untouched Saok Waterfalls is home to wide variety of bats listed (68.8%), followed by secondary forests of Gunung Tebu Forest Reserve (24.8%), untouched Lasir Waterfalls (4.8%) and lastly, Setiu Research Station as least favored (1.6%). Chiroptera like Cynopterus brachyotis (n ¼ 23, 37.7%), Hipposideros bicolor (n ¼ 6, 9.8%) and Scotophilus kuhli (n ¼ 6, 9.8%) were most dominant in the checklist whereas Hipposideros armiger,
Output: Linkages between Chiropteran diversity and ecosystem services for sustainable fragmented forest conservation
Rapid urbanization combined with climate change necessitates new types of urban services that make best use of science and technology. The Integrated Urban Hydro-Meteorological, Climate and Environmental Services and systems are a new initiative from the World Meteorological Organization (WMO) that seeks to provide science-based integrated urban services supporting safe, healthy and resilient cities. Various cities have already started development and implementation of such Integrated Urban Services and successfully test and use them following specific requirements of local stakeholders. This paper demonstrates the novel concept and approach of Integrated Urban Hydro-Meteorological, Climate and Environmental Services (IUS) from a set of four case study cities: Hong Kong, Toronto, Mexico City and Paris, that use different IUS configurations with good existing practice. These cities represent a range of countries, climates and geophysical settings. The aggregate main joint similarities of the IUS in these cities and synergy of the cities' experience, achievements and research findings are presented, as well as identification of existing gaps in knowledge and further research needs. A list of potential criteria for identifying and classifying IUS demonstration cities is proposed. It will aid future, more detailed analysis of the IUS experience, and selection of additional demonstration cities. Urbanization is an ongoing phenomenon and a growing number of urban settings are particularly vulnerable to weather and climate events, including floods, storms, heat waves, sea-level rise and poor air quality. In addition, urban dwellers are the primary users of energy and resources, and contribute in a significant way to increasing atmospheric greenhouse gasses as well as air pollution. These alterations to the atmosphere from urban to global scales have consequent impacts on human health and the environment. But the urban setting also provides exciting opportunities for scientific advancement in the field of new observations, data assimilation, high resolution coupled modeling and user-specific systems and services for sustainable and climate smart cities. Most (90%) of the disasters affecting urban areas are of a hydro-meteorological nature and these have increased due to climate https://doi.
Output: Integrated urban services: Experience from four cities on different continents
Virus discovery based on cDNA-AFLP (amplified fragment length polymorphism) (VIDISCA) is a novel approach that provides a fast and effective tool for amplification of unknown genomes, e.g., of human pathogenic viruses. The VIDISCA method is based on double restriction enzyme processing of a target sequence and ligation of oligonucleotide adaptors that subsequently serve as priming sites for amplification. As the method is based on the common presence of restriction sites, it results in the generation of reproducible, species-specific amplification patterns. The method allows amplification and identification of viral RNA/DNA, with a lower cutoff value of 10 5 copies/ml for DNA viruses and 10 6 copies/ml for the RNA viruses. Previously, we described the identification of a novel human coronavirus, HCoV-NL63, with the use of the VIDISCA method.
Output: Detection of New Viruses by VIDISCA Virus Discovery Based on cDNA-Amplified Fragment Length Polymorphism
A sthma is the most common chronic respiratory disorder in childhood, affecting about 10% of local children. 1 Asthma exacerbation resulting in hospitalization accounts for a major fraction of the total cost of asthma care in society. 2 Prospective epidemio-logic studies show that up to 80% of childhood asthma exacerbations are associated with viral upper respiratory tract infections (RTIs). 3 Among respiratory viruses, human rhinovirus (HRV) infection preceded as many as 50% of asthma exacerbations in children. 4 Infl uenza viruses also accounted for substantial morbidity (eg, up to 200 annual outpatient visits per 1,000 children) in children with asthma and other chronic medical conditions. 5 Respiratory syncytial virus (RSV) is another major pathogen causing asthma exacerbation. 4 Background: Up to 80% of asthma exacerbations in white children are associated with viral upper respiratory infections. The relative importance of different respiratory pathogens and relevant microbiological data in Asian children are unclear. This study elucidated the epidemiology of respiratory infections in Hong Kong children with asthma exacerbation. Methods: A total of 209 children aged 3-18 years with asthma exacerbations and 77 controls with stable asthma were recruited. The severity of asthma exacerbations was assessed according to Global Initiative for Asthma guideline, and subjects aged 6 years or older performed exhaled nitric oxide and spirometric measurements. Nested multiplex polymerase chain reaction was used to detect 20 different respiratory pathogens. Results: Respiratory pathogens were detected in 105 (51.0%) subjects. The presence of any respiratory pathogen was associated with asthma exacerbation (odds ratio [OR], 2.77; 95% CI, 1.51-5.11; P , .001). Specifi cally, human rhinovirus (HRV) infection was more common among children with asthma exacerbation (OR, 2.38; 95% CI, 1.09-5.32; P 5 .018). All other pathogens or coinfections were not associated with asthmatic attacks. None of these respiratory infections was associated with the severity of asthma exacerbation ( P . .15 for all). During peak HRV season in the winter of 2007 to 2008, this virus was detected in 46.4% of children with asthma exacerbations. Conclusions: Respiratory viral infections are commonly found in children with asthma exacerbation, with HRV being the most important pathogen in our patients. Respiratory viral infection is a triggering factor for asthma exacerbation but does not correlate with its severity. Abbreviations: FeNO 5 fractional exhaled nitric oxide concentration; HBoV 5 human bocavirus; HCoV 5 human coronavirus; HMPV 5 human metapneumovirus; HRV 5 human rhinovirus; ICS 5 inhaled corticosteroid; NPA 5 nasopharyngeal aspirate; OR 5 odds ratio; PCR 5 polymerase chain reaction; RSV 5 respiratory syncytial virus; RTI 5 respiratory tract infection
Output: Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation
Recently a new monoterpene dial, dehydroiridodial, was isolated as a pungent principle of Actinidia polygama Miq., and it was synthesized by K. Yoshihara et ai (7). On the other hand, chrysomelidial (1), the stereoisomer of dehydroiridodial, was isolated from the larval defensive secretion of a chrysomelide beetle (Plagiodera versicolora) in 1977, and it was synthesized in 1978 by J. Meinwald et al. (8). Both syntheses were non-stereospecific involving tedious separation steps. We first attempted the stereocontrolled synthesis of chrysomelidial from 4-methyltricyclo[3,3,0,0^'^]octan-3-one (2) which was prepared from diethyl 2-cyclopentene-l-ylmalonate by the general method of Doering. Methylation of diethyl 2-cyclopentene-l-ylmalonate with metyl iodide followed by hydrolysis and decarboxylation afforded 2-(2-cyclopentene-lyl)propionic acid in
Output: Progress in the Synthesis of Iridoids and Related Natural Products Sachihiko Isoe 1. 2.1 Synthesis of ChrysomelidiaI(6) (Scheme 2)
We carried out a study, using a questionnaire, that indicated that persons with Parkinson's disease (PD) catch relatively fewer colds that are unusually mild. This tendency seems to have no clear relationship to the severity of the PD, the time after the onset of PD, or whether or not the patient is taking antiparkinsonian drugs either as mono therapy or in combination. The study found no similar phenomena among spouses of the PD patients or among patients with cerebrovascular disease. These results suggest that a low frequency of colds is a unique feature in persons with PD. ᭧
Output: Rare tendency of catching cold in Parkinson's disease
We screened 217 bats of at least 20 species from 17 locations in Kenya during July and August of 2006 for the presence of adenovirus, rhabdovirus, and paramyxovirus nucleic acids using generic reverse transcription polymerase chain reaction (RT-PCR) and PCR assays. Of 217 bat fecal swabs examined, 4 bats were adenovirus DNA-positive, 11 bats were paramyxovirus RNA-positive, and 2 bats were rhabdovirus RNA-positive. Three bats were coinfected by two different viruses. By sequence comparison and phylogenetic analysis, the Kenya bat paramyxoviruses and rhabdoviruses from this study may represent novel viral lineages within their respective families; the Kenya bat adenoviruses could not be confirmed as novel, because the same region sequences from other known bat adenovirus genomes for comparison were lacking. Our study adds to previous evidence that bats carry diverse, potentially zoonotic viruses and may be coinfected with more than one virus. for excellent technical and logistical assistance. The authors thank Krista Queen for her assistance with the manuscript preparation. The authors also thank Michael Lo for his assistance with cell culture isolation and Yan Li for her assistance with high-throughput sequencing by 454 GS-FLX.
Output: Short Report: Molecular Detection of Adenoviruses, Rhabdoviruses, and Paramyxoviruses in Bats from Kenya
: Alcohol dependence; alcoholism; chronic alcohol exposure; alcohol and other drug effects and consequences; genetic factors; environmental factors; brain; neurobiology; translational studies; human studies; animal studies; animal models Vol. 31, No. 3, 2008 215 SOURCE: A and B from Koob, G.F., and Le Moal, M. Drug Addiction, Dysregulation of Reward, and Allostasis. Neuropsychopharmacology 24:97-129, 2001.; C from Koob G.F., Alcoholism: Allostasis and Beyond. Alcoholism: Clinical and Experimental Research 27(2):232-243, 2003. NOTES: ACTH = adrenocorticotrophin; AMYG = amygdala; BNST = bed nucleus of the stria terminalis; CRF = corticotropin-releasing factor; HPC = hippocampus; NE = nore pinephine; PFC, prefrontal cortex; PIT = pituitary gland; PVN = paraventricular nucleus. JOHNSON, R.; PFEFFERBAUM, A.; HART, T.; AND KOPELL, B.S. P300 latency in chronic alcoholics and depressed patients: A preliminary report. In Karrer, R.; Cohen, J.; Tueting, P. Eds. Brain and
Output: Translational Studies of Alcoholism Bridging the Gap
Infectious bronchitis virus (IBV) causes highly contagious respiratory or urogenital tract diseases in chickens. The Maryland 27(Md27) strain was first isolated in 1976 from diseased chicken flocks in the Delmarva Peninsula region. To understand the genetic diversity and phylogenetic relationship of existing strains with Md27, the complete nucleotide sequence of the 3'end coding region (~7.2 kb) of Md27 was determined and compared with other IBV strains and coronaviruses. It has the same S-3-M-5-N-3' gene order, as is the case of other IBV strains. The spike gene of Md27 exhibits 97% identity with the SE17 strain. There are deletions at the spike gene, non-coding region between M and 5 genes, and at the 3'untranslated region (UTR), which is different from Ark-like strains. Phylogenetic analysis and sequence alignments demonstrate that Md27 is a chimera containing different gene segments that are most closely related to the SE17, Conn and JMK strains. This current study provides evidence for genomic mutations and intergenic recombination that have taken place in the evolution of IBV strain Md27.
Output: Complete Nucleotide Analysis of the Structural Genome of the Infectious Bronchitis Virus Strain Md27 Reveals its Mosaic Nature
Cystic fibrosis (CF) is a hereditary disease that is characterized by defective mucociliary clearance, airway obstruction, chronic infection, and persistent inflammation. Cystic fibrosis pulmonary exacerbation (CFPE) majorly causes the morbidity of CF patients. Although CF has been demonstrated to change the composition of lung microbial community, previous studies have not made efforts to study the differences in the mechanism of assembly and diversity maintenance of lung microbial community in CF patients. In this study, we applied the neutral theory of biodiversity to comparatively investigate the assembly and diversity maintenance of the lung microbial community before and after the antibiotic treatment by reanalyzing the dataset from Fodor et al's study. We found that no one sample in the lung microbial communities of the sputum samples of Exacerbation group, nor those of End-of-treatment group satisfied the predictions of neutral model, suggesting that the neutral-process does not dominate in CF patients before and after antibiotic treatments. By comparing the biodiversity parameter between Exacerbation and End-of-treatment group, we found that the former had the significantly higher biodiversity, but the change in diversity parameter is slight and the P value is close to.05 (P value = .41). Therefore, our second finding is that although CFPE may increase the biodiversity of lung microbial community, the change is not essential. Abbreviations: CF = cystic fibrosis, CFPE = cystic fibrosis pulmonary exacerbation, CFTR = cystic fibrosis transmembrane conductance regulator, MLE = the maximum likelihood estimation, NGS = the next generation DNA sequencing, OTU = operational taxonomic unit, SAD = the species abundance distributions.
Output: Testing the neutral theory of biodiversity with the microbiome dataset from cystic fibrosis patients
Pneumococcal infections are the leading cause of community-acquired pneumonia. Although the type 1 interferon-α (IFN-α) is a well-known antiviral cytokine, the role of IFN-α in antipneumococcal host defense and its therapeutic potential remain poorly understood. We have investigated these issues by using a murine transgene expression model. We found that in control animals, Streptococcus pneumoniae infection caused severe weight loss and excessive lung inflammation, associated with rapid bacterial outgrowth. In contrast, the animals that received a single dose of an adenoviral vector expressing IFN-α prior to pneumococcal infection demonstrated rapid and effective control of bacterial replication and lung inflammation and improved clinical outcome. Enhanced protection by IFN-α was due to increased activation of neutrophils and macrophages with increased release of reactive oxygen and nitrogen species and bacterial killing. Furthermore, we found that raised levels of IFN-α in the lung remained immune protective even when the gene transfer vector was given at a time postpneumococcal infection. Our study thus shows that the classically antiviral type 1 IFN can be exploited for enhancing immunity against pneumococcal infection via its activating effects on innate immune cells. Our findings hold implications for the therapeutic use of IFN-α gene transfer strategies to combat pneumococcal infections.
Output: Type 1 interferon gene transfer enhances host defense against pulmonary Streptococcus pneumoniae infection via activating innate leukocytes
Y.-J. Jeong). † These two authors contributed equally to this work. The outbreak of severe acute respiratory syndrome (SARS) in 2002 affected thousands of people and an efficient diagnostic system is needed for accurate detection of SARS coronavirus (SARS CoV) to prevent or limit future outbreaks. Of the several SARS CoV structural proteins, the nucleocapsid protein has been shown to be a good diagnostic marker. In this study, an ssDNA aptamer that specifically binds to SARS CoV nucleocapsid protein was isolated from a DNA library containing 45-nuceotide random sequences in the middle of an 88mer single-stranded DNA. After twelve cycles of systematic evolution of ligands by exponential enrichment (SELEX) procedure, 15 ssDNA aptamers were identified. Enzyme-linked immunosorbent assay (ELISA) analysis was then used to identify the aptamer with the highest binding affinity to the SARS CoV nucleocapsid protein. Using this approach, an ssDNA aptamer that binds to the nucleocapsid protein with a K d of 4.93 ± 0.30 nM was identified. Western blot analysis further demonstrated that this ssDNA aptamer could be used to efficiently detect the SARS CoV nucleocapsid protein when compared with a nucleocapsid antibody. Therefore, we believe that the selected ssDNA aptamer may be a good alternative detection probe for the rapid and sensitive detection of SARS.
Output: Novel system for detecting SARS coronavirus nucleocapsid protein using an ssDNA aptamer
Mapuera virus (MPRV) was isolated from a fruit bat in Brazil in 1979, but its host range and diseasecausing potential are unknown. Porcine rubulavirus (PoRV) was identified as the aetiological agent of disease outbreaks in pigs in Mexico during early 1980s, but the origin of PoRV remains elusive. In this study, the completed genome sequence of MPRV was determined, and the complete genome sequence of PoRV was assembled from previously published protein-coding genes and the noncoding genome regions determined from this study. Comparison of sequence and genome organization indicated that PoRV is more closely related to MPRV than to any other members of the genus Rubulavirus. In the P gene coding region of both viruses, there is an ORF located at the 5 0 end of the P gene overlapping with the P protein coding region, similar to the C protein ORF present in most viruses of the subfamily Paramyxovirinae, but ab-sent in other known rubulaviruses. Based on these findings, we hypothesise that PoRV may also originate from bats, and spillover events from bats to pigs, either directly or via an intermediate host, were responsible for the sporadic disease outbreaks observed in Mexico.
Output: Full-length genome sequence and genetic relationship of two paramyxoviruses isolated from bat and pigs in the Americas
Porcine deltacoronavirus (PDCoV) is a recently identified coronavirus in the genus Deltacoronavirus that can cause enteric disease including diarrhea, vomiting, dehydration and mortality in neonatal piglets. Serological assays to detect anti-PDCoV antibodies are presently limited to certain laboratories and geographic regions. In this study, a recombinant M protein-based indirect enzyme-linked immunosorbent assay (PDCoV-rM ELISA) was developed and utilized to determine the prevalence of anti-PDCoV IgG in Hebei province. The PDCoV-rM ELISA showed no cross-reaction with antisera against transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine rotavirus (PRV), porcine circovirus 2 (PCV2), classical swine fever virus (CSFV) or porcine reproductive and respiratory syndrome virus (PRRSV). The diagnostic sensitivity was 90.6% and the diagnostic specificity was 93.3%. A total of 871 serum samples collected in Hebei from January 2015 to October 2016 were checked for presence of antibodies against PDCoV using the novel PDCoV-rM ELISA. Anti-PDCoV IgG antibodies were detected in 11% (96/871) of the samples and in 25% (10/40) of the investigated farms. The data suggest that PDCoV has a low seroprevalence in pig population in Hebei province, China.
Output: Development and application of a recombinant M protein-based indirect ELISA for the detection of porcine deltacoronavirus IgG antibodies
Neurocysticercosis (NC) is a serious public health problem in Taenia solium endemic areas and in some immigrants and international travelers. A key intervention in preventing NC is elimination of taeniasis by chemotherapy. Currently, two safe and effective taenicides, namely niclosamide and praziquantel, are available. Both are on WHO Essential Drug list, but are often inaccessible in T. solium endemic areas. Natural remedies, still widely used in some endemic areas, are frequently carcinogenic or highly toxic and as such should be discontinued. Chemotherapeutic intervention to control T. solium taeniasis/cysticercosis, whilst theoretically feasible, has several practical obstacles. These include poor public awareness, problems with diagnosing Taenia carriers, poor availability of taenicides where needed and low priority afforded to the control of NC. These can be overcome, respectively, by effective health education, wider use of newly developed coproantigen tests, strengthening of health services infrastructure and essential drugs distribution, and increasing the priority given to prevention of NC, as a leading cause of epilepsy in T. solium endemic areas. Information is accumulating on rational approaches to population-based short-term chemotherapeutic control measures. These are: widely available modern diagnostic tools and taenicides, treatment of any case of taeniasis, confirmed or probable, focus-oriented chemotherapy, irrespective of Taenia species implicated, improved sanitation, cooperation of veterinary and medical services, linkage with programs against epilepsy and cooperation of better educated communities. Now, it remains to take an advantage of existing tools and experience. D
Output: Role of chemotherapy of taeniasis in prevention of neurocysticercosis
Given the manifold ways that depression impairs Darwinian fitness, the persistence in the human genome of risk alleles for the disorder remains a much debated mystery. Evolutionary theories that view depressive symptoms as adaptive fail to provide parsimonious explanations for why even mild depressive symptoms impair fitness-relevant social functioning, whereas theories that suggest that depression is maladaptive fail to account for the high prevalence of depression risk alleles in human populations. These limitations warrant novel explanations for the origin and persistence of depression risk alleles. Accordingly, studies on risk alleles for depression were identified using PubMed and Ovid MEDLINE to examine data supporting the hypothesis that risk alleles for depression originated and have been retained in the human genome because these alleles promote pathogen host defense, which includes an integrated suite of immunological and behavioral responses to infection. Depression risk alleles identified by both candidate gene and genome-wide association study (GWAS) methodologies were found to be regularly associated with immune responses to infection that were likely to enhance survival in the ancestral environment. Moreover, data support the role of specific depressive symptoms in pathogen host defense including hyperthermia, reduced bodily iron stores, conservation/withdrawal behavior, hypervigilance and anorexia. By shifting the adaptive context of depression risk alleles from relations with conspecifics to relations with the microbial world, the Pathogen Host Defense (PATHOS-D) hypothesis provides a novel explanation for how depression can be nonadaptive in the social realm, whereas its risk alleles are nonetheless represented at prevalence rates that bespeak an adaptive function.
Output: The evolutionary significance of depression in Pathogen Host Defense (PATHOS-D)
The 90 kDa ribosomal s6 kinases (RSKs) are a group of serine/threonine kinases consisting of 4 RSK isoforms (RSK1-4), of which RSK1 is also designated as p90RSK. p90RSK plays an important role in the Ras-mitogen-activated protein kinase (MAPK) signalling cascade and is the direct downstream effector of Ras-extracellular signal-regulated kinase (ERK1/2) signalling. ERK1/2 activation directly phosphorylates and activates p90RSK, which, in turn, activates various signalling events through selection of different phosphorylation substrates. Upregulation of p90RSK has been reported in numerous human diseases. p90RSK plays an important role in the regulation of diverse cellular processes. Thus, aberrant activation of p90RSK plays a critical role in the pathogenesis of organ dysfunction and damage. In this review, we focus on the current understanding of p90RSK functions and roles in the development and progression of kidney diseases. Roles of p90RSK, as well as other RSKs, in cardiovascular disorders and cancers are also discussed.
Output: Molecular Sciences Role of p90RSK in Kidney and Other Diseases
Bovine herpesvirus-1 (BHV-1) can replicate well in bovine-derived cell lines such as Madin Darby bovine kidney (MDBK) but grows poorly in hamster lung (HmLu-1). Virus replication, DNA synthesis, and immediate-early gene expression are severely restricted in HmLu-1. We compared adsorption and penetration of BHV-1 in permissive MDBK and semi-permissive HmLu-1 cells. At a low multiplicity of infection, BHV-1 attached to permissive MDBK cells twice as much as to HmLu-1. The presence of heparin inhibited the attachment of BHV-1 to MDBK cells by about 60%, but over 90% of the attachment was inhibited in HmLu-1. To investigate the penetration of BHV-1, we performed the quantitative measurement of viral DNA by quantitative competitive (QC)PCR in infected cells. In MDBK cells, virions attached to the cell surface, penetrated into the cells and were transported to the nucleus. However in HmLu-1, only a small fraction of the virions attached to the cell surface were allowed to penetrate. Our results indicated that the replication of BHV-1 in semi-permissive HmLu-1 was not dramatically restricted at one certain point but at some various stages including adsorption and penetration.
Output: Growth behavior of bovine herpesvirus-1 in permissive and semi-permissive cells
Antisense oligonucleotides and short interfering RNAs (siR-NAs) are nucleic acids-targeting reagents for gene expression modulation that are being developed as drugs for many applications. A number of useful synthetic nucleic acids analogues have been introduced recently to greatly improve their properties for use as therapeutics. However, their full effectiveness in cells and in vivo has often only been realized through development of suitable nonviral delivery systems. Among these, a range of natural and synthetic peptides have been found useful for enhancing cellular uptake and/or cell targeting of oligonucleotide analogues and siRNA. Such peptides are synthetically conjugated, used as noncovalent complexes, or used in combination with polymer, liposomal or exosome formulation techniques. This review begins by describing the modes of action of antisense reagents and siRNA and goes on to focus on recent advances in their peptide-mediated cell and in vivo delivery and how peptide use has influenced drug development. The review discusses the challenges associated with understanding the physiological and toxicological aspects of peptide-mediated delivery. Developments towards clinical use are also highlighted, with particular emphasis on peptide conjugates of oligonucleotide analogues used for treatment of neuromuscular diseases.
Output: Citation: Molecular Therapy-Nucleic Acids (2011) 1, e27; Molecular Therapy-Nucleic Acids (2012) 1, e27
Severe acute respiratory syndrome (SARS) has become a global public health emergency. p38 mitogen-activated protein kinase (MAPK) and its downstream targets are activated in SARS coronavirus (SARS-CoV)-infected Vero E6 cells and activation of p38 MAPK enhances the cytopathic effects of SARS-CoV infection. In addition, weak activation of Akt cannot prevent SARS-CoV infection-induced apoptosis in Vero E6 cells. In the present study, we demonstrated that signal transducer and activator of transcription (STAT) 3, which is constitutively phosphorylated at tyrosine (Tyr)-705 and slightly phosphorylated at serine (Ser)-727 in Vero E6 cells, was dephosphorylated at Tyr-705 on SARS-CoV infection. In addition to phosphorylation of p38 MAPK in virus-infected cells, other MAPKs, i.e., extracellular signal-regulated kinase (ERK) 1/2 and c-Jun Nterminal kinase (JNK), were phosphorylated. Although inhibitors of ERK1/2 and JNK (PD98059 and SP600125) had no effect on phosphorylation status of STAT3, inhibitors of p38 MAPK (SB203580 and SB202190) partially inhibited dephosphorylation of STAT3 at Tyr-705. Tyr-705-phosphorylated STAT3 was localized mainly in the nucleus in mock infected cells, whereas STAT3 disappeared from the nucleus in virusinfected cells. As STAT3 acts as an activator of transcription in the nucleus, these results suggest that STAT3 lacks its activity on transcription in SARS-CoV-infected Vero E6 cells.
Output: Tyrosine dephosphorylation of STAT3 in SARS coronavirus-infected Vero E6 cells
A novel acetone extract from cottonseed oil sludge was firstly discovered against plant viruses including Tobacco mosaic virus (TMV), Rice stripe virus (RSV) and Southern rice black streaked dwarf virus (SRBSDV). Gossypol and β-sitosterol separated from the acetone extract were tested for their effects on anti-TMV and analysed by nuclear magnetic resonance (NMR) assay. In vivo and field trials in different geographic distributions and different host varieties declared that this extract mixture was more efficient than the commercial agent Ningnanmycin with a broad spectrum of anti-plant-viruses activity. No phytotoxic activity was observed in the treated plants and environmental toxicology showed that this new acetone extract was environmentally friendly, indicating that this acetone extract has potential application in the control of plant virus in the future.
Output: First Discovery of Acetone Extract from Cottonseed Oil Sludge as a Novel Antiviral Agent against Plant Viruses
Correspondence: Mingyue Zhu (mingyuezhu2002@163.com) or Mengsen Li (mengsenli@163.com) α-fetoprotein (AFP) is an early serum growth factor in foetal embryonic development and hepatic oncogenesis. A growing number of investigations of AFP as a tumour-specific biomarker have concluded that AFP is an important target for cancer treatment. AFP also plays an immunomodulatory role in the treatment of several autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, myasthenia gravis and thyroiditis. In an effort to support biochemical screening and drug design and discovery, we attempted to express and purify human AFP in a Bac-to-Bac system. Two key factors affecting the expression of recombinant human AFP (R-AFP), namely the infectious baculovirus inoculum volume and the culturing time post-infection, were optimized to maximize the yield. We achieved a high yield of approximately 1.5 mg/l of harvested medium with a 72-96 h incubation period after infection and an inoculum volume ratio of 1:100. We also assessed the role of R-AFP in the proliferation of the human liver cancer cell line Bel 7402, and the results indicated that R-AFP promoted the growth of hepatoma cells. We concluded that this method can produce high yields of R-AFP, which can be used for studies related to AFP.
Output: Expression and bioactivity of human α-fetoprotein in a Bac-to-Bac system
Introduction: Allergic reaction to dust mites is a relatively common condition among children, triggering cutaneous and respiratory responses that have a great impact on the health of this population. Anaphylactic hypersensitivity is characterized by an exacerbated response involving the production of regulatory cytokines responsible for stimulating the production of IgE antibodies. Objective: To investigate an association of variants in cytokine genes (IL1A 2889 , IL1B ) between patients sensitive to dust mites and a control group. Methods: A total of 254 patients were grouped as atopic and non-atopic according to sensitivity as evaluated by the Prick Test and to cytokine genotyping by the polymerase chain reaction-sequence specific primers (PCR-SSP) method using the Cytokine Genotyping Kit. Blomia tropicalis and a non-atopic control group showed significant differences between allele and genotype frequencies in the regulatory regions of cytokine genes, with important evidence for IL4 2590 in T/C (10.2% vs. 43.1%, odd ratio [OR] = 0.15, p = 5.2 10 28 , pc = 0.0000011, and 95% confidence interval [95%CI] = 0.07-0.32) and T/T genotypes (42.9% vs. 13.8%, OR = 4.69, p = 2.5 10 26 , pc = 0.000055, and 95%CI = 2.42-9.09). Other associations were observed in the pro-inflammatory cytokines IL1A 2889 Conclusion: Our results suggest a possible association between single nucleotide polymorphisms (SNPs) in cytokine genes and hypersensitivity to dust mites.
Output: Association of Cytokines in Individuals Sensitive and Insensitive to Dust Mites in a Brazilian Population
Neuromodulation plays a critical role in brain function in both health and disease. New optical tools, and their validation in biological tissues, are needed that can image neuromodulation with high spatial and temporal resolution, which will add an important new dimension of information to neuroscience research. Here, we demonstrate the use of a catecholamine nanosensor with fluorescent emission in the 1000-1300 nm near-infrared window to measure dopamine transmission in ex vivo brain slices. These near-infrared catecholamine nanosensors (nIRCats) represent a broader class of nanosensors that can be synthesized from non-covalent conjugation of single wall carbon nanotubes (SWNT) with single strand oligonucleotides. We show that nIRCats can be used to detect catecholamine efflux in brain tissue driven by both electrical stimulation or optogenetic stimulation. Spatial analysis of electrically-evoked signals revealed dynamic regions of interest approximately 2 microns in size in which transients scaled with simulation intensity. Optogenetic stimulation of dopaminergic terminals produced similar transients, whereas optogenetic stimulation of glutamatergic terminals showed no effect on nIRCat signal. Bath application of nomifensine prolonged nIRCat fluorescence signal, consistent with reuptake blockade of dopamine. We further show that the chemically synthetic molecular recognition elements of nIRCats permit measurement of dopamine dynamics in the presence of dopamine receptor agonists and antagonists. These nIRCat nanosensors may be advantageous for future use because i) they do not require virus delivery, gene delivery, or protein expression, ii) their near-infrared fluorescence facilitates imaging in optically scattering brain tissue and is compatible for use in conjunction with other optical neuroscience tool sets, iii) the broad availability of unique near-infrared colors have the potential for simultaneous detection of multiple neurochemical signals, and iv) they are compatible with pharmacology.
Output: Imaging Striatal Dopamine Release Using a Non-Genetically Encoded Near-Infrared Fluorescent Catecholamine Nanosensor
The potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine. Word count: Main:
Output: Estimating the Asymptomatic Proportion of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020
are lacking, the present study investigated these missing links during experimental infection of three SPF cats with FECV strain UCD. Two cats showed mild clinical signs, faecal shedding of infectious virus from 4 dpi, a cell-associated viraemia at inconsistent time points from 5 dpi, a highly neutralising antibody response from 9 dpi, and no major abnormalities in leukocyte numbers. Faecal shedding lasted for 28-56 days, but virus shed during this stage was less infectious in enterocyte cultures and affected by mutations. Remarkably, in the other cat neither clinical signs nor acute shedding were seen, but virus was detected in blood cells from 3 dpi, and shedding of non-enterotropic, mutated viruses suddenly occurred from 14 dpi onwards. Neutralising antibodies arose from 21 dpi. Leukocyte numbers were not different compared to the other cats, except for the CD8 + regulatory T cells. These data indicate that FECV can infect immune cells even in the absence of intestinal replication and raise the hypothesis that the gradual adaptation to these cells can allow non-enterotropic mutants to arise. Feline coronaviruses (FCoVs) occur as two pathotypes, associated with either enteric or systemic diseases in cats. Feline enteric coronavirus (FECV) is an enterotropic virus, ubiquitously present in the cat population 1,2 . The enteritis caused by the intestinal replication can manifest as a transient anorexia, weight loss and/or diarrhoea, but clinical signs are often too mild to be noticed 1,3,4 . Feline infectious peritonitis virus (FIPV) most likely arises from FECV by accumulation of mutations in individually infected cats [5] [6] [7] [8] [9] [10] [11] . These yet not fully characterized mutations abrogate the enterocyte tropism but provide the virus with tools to productively replicate in monocytes/macrophages, causing a highly fatal systemic disease, feline infectious peritonitis (FIP), which is characterised by a diffuse vasculitis, polyserositis and severe lymphopaenia 12-17 . To date, it remains unknown where, when, and how this pathotype switch is induced in FECV-infected cats. Due to its pathogenic behaviour, FIPV has received considerable attention, and clinical, virological, and immunological parameters during both natural and experimental FIPV infections have frequently been studied 14-16 . The last decade, comprehensive studies on the FIPV parent virus, FECV, have extensively contributed to our current understanding of the epizootiology and pathogenesis 4,18-20 , but many crucial virological and immunological data on the FECV-cat interactions are missing to fully understand the behaviour of this FIPV parent virus. Due to the lack of an FECV-susceptible cell line, there is so far no information on the infectivity (and its
Output: Experimental feline enteric coronavirus infection reveals an aberrant infection pattern and shedding of mutants with impaired infectivity in enterocyte cultures OPEN
OBJECTIVE-To determine the incidence of transmission of MDR Acinetobacter baumannii and Pseudomonas aeruginosa from patients to healthcare workers (HCWs) during routine patient care. SETTING-Medical and surgical intensive care units. HCWs who entered the rooms of patients colonized with MDR A. baumannii or colonized with both MDR A. baumannii and MDR P. aeruginosa. We examined their hands before room entry, their disposable gloves and/or gowns upon completion of patient care, and their hands after removal of gloves and/or gowns and before hand hygiene. A. baumannii and 134 with patients colonized with both MDR A. baumannii and MDR P. aeruginosa. Of 199 interactions between HCWs and patients colonized with MDR A. baumannii, 77 (38.7% [95% confidence interval {CI}, 31.9%-45.5%]) resulted in HCW contamination of gloves and/or gowns, and 9 (4.5% [95% CI, 1.6%-7.4%]) resulted in contamination of HCW hands after glove removal before hand hygiene. Of 134 interactions with patients colonized with MDR P. aeruginosa, 11 (8.2% [95% CI, 3.6%-12.9%]) resulted in HCW contamination of gloves and/or gowns, and 1 resulted in HCW contamination of hands. Independent risk factors for contamination with MDR A. baumannii were manipulation of wound dressing (adjusted odds ratio [aOR], 25.9 [95% CI, 3.1-208.8]), manipulation of artificial airway (aOR, 2.1 [95% CI, 1.1-4.0]), time in room longer than 5 minutes (aOR, 4.3 [95% CI, 2.0-9.1]), being a physician or nurse practitioner (aOR, 7.4 [95% CI, 1.6-35.2]), and being a nurse (aOR, 2.3 [95% CI, 1.1-4.8]).
Output: Frequent Multidrug-Resistant Acinetobacter baumannii Contamination of Gloves, Gowns, and Hands of Healthcare Workers
The ubiquitin-proteasome system (UPS) serves as the major intracellular pathway for protein degradation and plays crucial roles in several cellular processes. However, little is known about the potential actions of the UPS during fish virus infection. In this study, we elucidated the possible roles of UPS in the life cycle of Singapore grouper iridovirus (SGIV); a large DNA virus that usually causes serious systemic diseases with high mortality in groupers. Data from transcriptomic analysis of differentially expressed genes illustrated that expression of 65 genes within the UPS pathway, including ubiquitin encoding, ubiquitination, deubiquitination, and proteasome, were up-or down-regulated during SGIV infection. Using different proteasome inhibitors, inhibition of the proteasome decreased SGIV replication in vitro, accompanied by inhibition of virus assembly site formation, and viral gene transcription and protein transportation. Over-expression of ubiquitin partly rescued the inhibitory effect of ubiquitin inhibitor on SGIV replication, suggesting that UPS was required for fish iridovirus infection in vitro. Viral or host proteins regulated by proteasome inhibition during SGIV infection were investigated with two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sixty-two differentially expressed proteins, including 15 viral and 47 host proteins, were identified after SGIV infection. The host proteins were involved in ubiquitin-mediated protein degradation, metabolism, cytoskeleton, macromolecular biosynthesis, and signal transduction. Among them, 11 proteins were negatively regulated upon MG132 treatment during SGIV infection. This is believed to be the first study to provide evidence that UPS was essential for fish virus infection and replication.
Output: Ubiquitin-Proteasome System Is Required for Efficient Replication of Singapore Grouper Iridovirus
We study the number and date of structural breaks in international tourism demand. We use Bai and Perron (1998) structural break test for 25 countries and Madeira. We fill a gap in the literature regarding the ex-post detection of tourism crisis. We compare the date of tourism crises to the dating of these structural breaks. We observe those tourism crises are largely consistent with the dates of breaks. It is recognised that the tourism industry is vulnerable to some form of crises or disaster. However, despite the attention given to the nature and consequences of tourism crises and disasters, there is a gap in the literature regarding the ex-post detection of these events. In this article, we estimate both the number and date of structural breaks in international tourism arrival series for 25 countries and Madeira Island using the Bai and Perron (1998) structural break test. We compare the date of tourism crises and disasters to the dating of these structural breaks. We observe that tourism crises and disasters are largely consistent with the dates of breaks. Therefore, this method allows us to solve a gap in the tourism industry related to the correct allocation of negative shocks in international tourism arrival demand to crisis or disaster phenomena.
Output: Structural breaks in international tourism demand: Are they caused by crises or disasters?
During the replication cycle of Sindbis virus minus-strand synthesis stops normally at the time that plus-strand synthesis reaches a maximum rate. We have isolated and characterized revertants of ts24, a member of the A complementation group of Sindbis HR mutants, that we had demonstrated previously to have a temperature-sensitive defect in the regulation of minus-strand synthesis. These revertants of t&4 replicated efficiently at 40' but nevertheless retained the temperature sensitive defect in the regulation of minus-strand synthesis: they continued to synthesize minus strands late in the replication cycle at 40" but not at 30" and in the presence or absence of protein synthesis. Although failure to regulate the synthesis of minus strands resulted in continuous minus-strand synthesis and in the accumulation of minus strands, the rate of plus-strand synthesis was not increased concertedly. Minus strands synthesized after the rate of plus-strand synthesis had become constant were demonstrated to be utilized as templates for 26 S mRNA synthesis. Thus, the change from an increasing to a constant rate of plus-strand synthesis during the alphavirus replication cycle cannot be governed solely by the number of minus strands that accumulate in infected cells. We present a model for the preferential utilization of minus strands as a mechanism for the cessation of minus-strand synthesis that occurs normally during alphavirus replication.
Output: The Effect of Loss of Regulation of Minus-Strand RNA Synthesis on Sindbis Virus Replication