Descriptive review of geographic mapping of severe acute respiratory syndrome (SARS) on the Internet
Abstract From geographic mapping at different scales to location-based alerting services, geoinformatics plays an important role in the study and control of global outbreaks like severe acute respiratory syndrome (SARS). This paper reviews several geographic mapping efforts of SARS on the Internet that employ a variety of techniques like choropleth rendering, graduated circles, graduated pie charts, buffering, overlay analysis and animation. The aim of these mapping services is to educate the public (especially travellers to potentially at-risk areas) and assist public health authorities in analysing the spatial and temporal trends and patterns of SARS and in assessing/revising current control measures.
International Journal of Health Geographics
Computer applications to medicine. Medical informatics
Predicting the invasive potential of the cladoceran Daphnia lumholtzi Sars, 1885 (Crustacea: Cladocera: Daphniidae) in the Neotropics: are generalists threatened and relicts protected by their life-history traits?
biodiversity conservation, dispersión, Invasive species, reservoirs, Paraná River Basin, species distribution model
Invasive species are one of the major threats to biodiversity, which is aggravated in poorly known groups, such as cladocerans. Daphnia lumholtzi Sars (Cladocera: Anomopoda: Daphniidae) is currently invading the Neotropical region, and there are few records of this process. Our goal was to predict the invasive scenario for D. lumholtzi in the Neotropics using species distribution modelling and to assess the climatic overlap of the invader with the native species. We trained our MaxEnt model using occurrence records from native and invaded areas and projected it in the Neotropics. Additionally, we compared the climatic niche of some native species with the invader’s niche. Our model showed high environmental suitability in areas connected by the lowland Paraná River Basin (southwestern Brazil, eastern Argentina and Uruguay), in south-central Chile and Atlantic coastal areas. Widely distributed native species showed climatic overlap with the invader, while relict species did not. Daphnia lumholtzi thrives in warm and stable environments (e.g. the Paraná River basin), which of concern because the invader could already be spreading in that area. Native species could suffer due to climatic niche similarity, while natural barriers and local environmental conditions may protect relict species. We urge the need for further studies to understand this invasion process more fully.
Francisco Diogo R. Sousa, Alexandre V. Palaoro, Lourdes M. A. Elmoor-Loureiro, Alexey A. Kotov
Environmental sciences, Geography. Anthropology. Recreation, Physical geography
Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays
Abstract Background Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation. Results A method and SPR Opt (SNP and PCR-RFLP Optimization) software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed) are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes. Conclusion This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As more sequence data becomes available for multiple strains and isolates of a species, automated, computational approaches such as those described here will be essential to make sense of large amounts of information, and to guide and optimize efforts in the laboratory. The software and source code for SPR Opt is publicly available and free for non-profit use at http://www.llnl.gov/IPandC/technology/software/softwaretitles/spropt.php.
Membranous Replication Factories Induced by Plus-Strand RNA Viruses
membrane rearrangements, electron microscopy, electron tomography, Ultrastructure, double membrane vesicles, membranous replication factories, hepatitis C virus, flaviviruses, picornaviruses, coronaviruses
In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.
Detection of human coronavirus strain HKU1 in a 2 years old girl with asthma exacerbation caused by acute pharyngitis
respiratory viral infection, Asthma, coronavirus
Abstract Respiratory viral infections can trigger asthma attack which may lead to sever morbidity. In this report, using molecular methods, we show the chronological association between human coronavirus - HKU1 infection and asthma exacerbation in a two years and seven months old asthmatic girl who was not under treatment and was otherwise healthy.
Amini Razieh, Jahanshiri Fatemeh, Amini Yasaman, Sekawi Zamberi, Jalilian Farid
Indices of zooplankton community as valuable tools in assessing the trophic state and water quality of eutrophic lakes: long term study of Lake Võrtsjärv
zooplankton, biological indicators, Eutrophication, ecological state of lake
On the basis of long-term (1964-2011) research, we tested the hypothesis that the zooplankton community has a highly indicative value in assessing the ecosystem and trophic state of water bodies. Basing on the results of our study and taking into account relevant data from numerous zooplankton studies, we can conclude that the zooplankton measures deserving to be used as indicators in the monitoring of Lake Võrtsjärv (and other similar eutrophic water bodies) could be the following: i) indicatory species of eutrophic waters [Anuraeopsis fissa (Gosse), Keratella tecta (Gosse), Trichocerca rousseleti (Voigt), Chydorus sphaericus (O. F. Müller), Bosmina longirostris (O. F. Müller)]; ii) indicatory species of oligo-mesotrophic waters [Conochilus unicornis Rousselet, Kellicottia longispina (Kellicott), Ploesoma hudsoni (Imhof), Bosmina berolinensis Imhof, Eudiaptomus gracilis (Sars)]; iii) number and diversity of species; iv) mean zooplankter weight, mean cladoceran weight, mean rotifer weight and mean copepod weight; v) rotifer abundance; vi) the share (%) of rotifers in total zooplankton abundance; vii) the ratio of abundance of large cladocerans to abundance of all cladocerans (NLargeClad/NClad); viii) the ratio of calanoid copepod abundance to cyclopoid copepod abundance (NCal/NCycl); ix) the ratio of crustacean abundance to rotifer abundance (NCrust/NRot ). The results of our study show that several zooplankton parameters are among the biological quality elements (BQE) deserving to be included in the Water Frame Directive system.
SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform
Kmers, wavelet transform, complex numbers, sequence similarity, frequency domain
Abstract Background Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. Results A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Conclusions Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.
Jie Lin, Jing Wei, Donald Adjeroh, Bing-Hua Jiang, Yue Jiang
Biology (General), Computer applications to medicine. Medical informatics
A Novel Range Compression Algorithm for Resolution Enhancement in GNSS-SARs
GNSS-SAR, Global Navigation Satellite System, synthetic aperture radar, range compression, range resolution
In this paper, a novel range compression algorithm for enhancing range resolutions of a passive Global Navigation Satellite System-based Synthetic Aperture Radar (GNSS-SAR) is proposed. In the proposed algorithm, within each azimuth bin, firstly range compression is carried out by correlating a reflected GNSS intermediate frequency (IF) signal with a synchronized direct GNSS base-band signal in the range domain. Thereafter, spectrum equalization is applied to the compressed results for suppressing side lobes to obtain a final range-compressed signal. Both theoretical analysis and simulation results have demonstrated that significant range resolution improvement in GNSS-SAR images can be achieved by the proposed range compression algorithm, compared to the conventional range compression algorithm.
The invasive appearance of Eudiaptomus gracilis (G.O. Sars 1863) in Lago Maggiore
invasion, body size, zooplankton, copepods
Large, deep, subalpine Lago Maggiore has been regarded as an example of stability and resilience: while changes in zooplankton taxa composition were mainly recorded with introduction of allochthonous fish in the 1950s, eutrophication and reoligotrophication mainly affected abundance and biomass. As part of a monitoring project on pelagic zooplankton, samples were routinely collected in the open-water at least monthly over a 30 year period. During this time, copepods' numerical dominance resulted from the same species assemblage, including large Mixodiaptomus laciniatus (W. Lilljeborg 1889) and Cyclops abyssorum (G. O. Sars 1863), and smaller Eudiaptomus padanus (G. Burckhardt 1900) and Mesocyclops leuckarti (C. Claus 1857); large Megacyclops viridis (L. Jurine 1820) were recorded only occasionally in the open-water. Eudiaptomus gracilis (G.O. Sars 1863) invaded the lake in October 2006. Adult body length was typical of oligotrophic freshwater environments, and largely overlapped that of M. laciniatus, a species rarer than con-generic and numerically-dominant E. padanus. In the two years following E. gracilis invasion, M. laciniatus was not found in Lago Maggiore, suggesting that it disappeared from the lake. This is the second important change in Lago Maggiore copepod community, following the disappearance of Heterocope saliens (W. Lilljeborg 1863), which was recorded in the 1950s attendant with the introduction of fishes to the lake. The replacement of M. laciniatus by E. gracilis in Lago Maggiore is regarded as an opportunity for discussing the importance of size-mediated, rather than taxonomic-based, interactions between invasive and indigenous species, given the species' overlapping body size and similar level of abundance.
Glucose-6-Phosphate Dehydrogenase Enhances Antiviral Response through Downregulation of NADPH Sensor HSCARG and Upregulation of NF-κB Signaling
G6PD, NAD(P)H, coronavirus, Enterovirus, antiviral response, HSCARG
Glucose-6-phosphate dehydrogenase (G6PD)-deficient cells are highly susceptible to viral infection. This study examined the mechanism underlying this phenomenon by measuring the expression of antiviral genes—tumor necrosis factor alpha (TNF-α) and GTPase myxovirus resistance 1 (MX1)—in G6PD-knockdown cells upon human coronavirus 229E (HCoV-229E) and enterovirus 71 (EV71) infection. Molecular analysis revealed that the promoter activities of TNF-α and MX1 were downregulated in G6PD-knockdown cells, and that the IκB degradation and DNA binding activity of NF-κB were decreased. The HSCARG protein, a nicotinamide adenine dinucleotide phosphate (NADPH) sensor and negative regulator of NF-κB, was upregulated in G6PD-knockdown cells with decreased NADPH/NADP+ ratio. Treatment of G6PD-knockdown cells with siRNA against HSCARG enhanced the DNA binding activity of NF-κB and the expression of TNF-α and MX1, but suppressed the expression of viral genes; however, the overexpression of HSCARG inhibited the antiviral response. Exogenous G6PD or IDH1 expression inhibited the expression of HSCARG, resulting in increased expression of TNF-α and MX1 and reduced viral gene expression upon virus infection. Our findings suggest that the increased susceptibility of the G6PD-knockdown cells to viral infection was due to impaired NF-κB signaling and antiviral response mediated by HSCARG.
Yi-Hsuan Wu, Daniel Tsun-Yee Chiu, Hsin-Ru Lin, Hsiang-Yu Tang, Mei-Ling Cheng, Hung-Yao Ho