Sixty percent of emerging viruses have a zoonotic origin, making transmission from animals a major threat to public health. Prompt identification and analysis of these pathogens are indispensable to ...taking action toward prevention and protection of the affected population. We quantifiably compared classical and modern approaches of virus purification and enrichment in theory and experiments. Eventually, we established an unbiased protocol for detection of known and novel emerging viruses from organ tissues (tissue-based universal virus detection for viral metagenomics TUViD-VM). The final TUViD-VM protocol was extensively validated by using real-time PCR and next-generation sequencing. We could increase the amount of detectable virus nucleic acids and improved the detection of viruses <75,000-fold compared with other tested approaches. This TUViD-VM protocol can be used in metagenomic and virome studies to increase the likelihood of detecting viruses from any biological source.
The severe Ebola virus disease epidemic occurring in West Africa stems from a single zoonotic transmission event to a 2‐year‐old boy in Meliandou, Guinea. We investigated the zoonotic origins of the ...epidemic using wildlife surveys, interviews, and molecular analyses of bat and environmental samples. We found no evidence for a concurrent outbreak in larger wildlife. Exposure to fruit bats is common in the region, but the index case may have been infected by playing in a hollow tree housing a colony of insectivorous free‐tailed bats (Mops condylurus). Bats in this family have previously been discussed as potential sources for Ebola virus outbreaks, and experimental data have shown that this species can survive experimental infection. These analyses expand the range of possible Ebola virus sources to include insectivorous bats and reiterate the importance of broader sampling efforts for understanding Ebola virus ecology.
Synopsis
The severe Ebola virus disease epidemic occurring in West Africa likely stems from a single zoonotic transmission event involving a 2‐year‐old boy in Meliandou, Guinea, who might have been infected by hunting or playing with insectivorous free‐tailed bats living in a nearby hollow tree.
Monitoring data show that larger wildlife did not experience a recent decline and is therefore unlikely to have served as the source for the Ebola virus disease epidemic in West Africa.
Fruit bat hunting and butchering are common activities in southern Guinea, therefore facilitating direct human contact.
Children are also exposed to insectivorous bats through hunting in and around villages.
No large colony of fruit bats exists in or nearby the index village (Meliandou).
The 2‐year‐old index case may have been infected by playing in a hollow tree housing a colony of insectivorous free‐tailed bats (Mops condylurus).
The severe Ebola virus disease epidemic occurring in West Africa likely stems from a single zoonotic transmission event involving a 2‐year‐old boy in Meliandou, Guinea, who might have been infected by hunting or playing with insectivorous free‐tailed bats living in a nearby hollow tree.
The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related ...species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference. There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods. At the same time, this representation needs to be easily accessible and extendable to account for the constant change of available genomes.
We introduce seq-seq-pan, a framework that provides methods for adding or removing new genomes from a set of aligned genomes and uses these to construct a whole genome alignment. Throughout the sequential workflow the alignment is optimized for generating a representative linear presentation of the aligned set of genomes, that enables its usage for annotation and in downstream analyses.
By providing dynamic updates and optimized processing, our approach enables the usage of whole genome alignment in the field of pan-genomics. In addition, the sequential workflow can be used as a fast alternative to existing whole genome aligners for aligning closely related genomes. seq-seq-pan is freely available at https://gitlab.com/rki_bioinformatics.
Near Berlin, Germany, several juvenile red squirrels (Sciurus vulgaris) were found with moist, crusty skin lesions. Histology, electron microscopy, and cell culture isolation revealed an ...orthopoxvirus-like infection. Subsequent PCR and genome analysis identified a new poxvirus (Berlin squirrelpox virus) that could not be assigned to any known poxvirus genera.
We present design and test results of the front-end circuit developed in a 0.25 mum complementary metal-oxide semiconductor technology. The aim of this work is to study the performance of a deep ...submicron process in applications for fast binary front ends for silicon strip detectors. The channel comprises a fast transimpedance preamplifier working with an active feedback loop, two stages of the amplifier-integrator circuits providing 22 ns peaking time, and a two-stage differential discriminator. A particular effort has been made to minimize the current and the power consumption of the preamplifier, while keeping the required noise and timing performance. For a detector capacitance of 20 pF noise below 1500 e - equivalent noise charge (ENC) has been achieved for 300 muA bias current in the input transistor, which is comparable with the levels achieved in the past for the front end using a bipolar input transistor. The total supply current of the front end is 600 muA and the power dissipation is 1.5 mW per channel. The offset spread of the comparator is below 3 mV rms
The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain isolated from a Danish pig, suggests putative adaptation to the porcine host and absence of distinct ...virulence-associated traits.
Pulmonary hypertension (PHT) is associated with increased mortality in hemodialysis (HD) patients. The ventricular gradient optimized for right ventricular pressure overload (VG-RVPO) is sensitive to ...early changes in right ventricular overload. The study aimed to assess the ability of the VG-RVPO to detect PHT and predict all-cause and cardiac mortality in HD patients. 265 selected HD patients were enrolled. Clinical, biochemical, electrocardiographic, and echocardiographic parameters were evaluated. Patients were divided into normal and abnormal VG-RVPO groups, and were followed-up for 3 years. Abnormal VG-RVPO patients were more likely to be at high or intermediate risk for PHT, were older, had longer HD vintage, higher prevalence of myocardial infarction, higher parathormone levels, shorter pulmonary flow acceleration time, lower left ventricular ejection fraction, higher values of left atrial volume index, left ventricular mass index, and peak tricuspid regurgitant velocity. Both all-cause and CV mortality were higher in abnormal VG-RVPO group. In multivariate Cox analysis, VG-RVPO remained an independent and strong predictor of all-cause and CV mortality. In HD patients, abnormal VG-RVPO not only predicts PHT, but also all-cause and CV mortality.
The issue of reject water has to be considered in almost every biological municipal or industrial wastewater treatment plant (WWTP) that applies aerobic or anaerobic digestion of sewage sludge. ...Reject water is usually returned to the beginning of the treatment process, which results in periodical disturbances in stable and efficient sewage treatment. Due to planned modernization of one of the biggest dairy WWTPs in Poland, a laboratory scale research has been carried out to determine quality characteristics of reject water. Aerobic and anaerobic digestion was applied to a mixture of two kinds of sludge: excessive and flotation. According to research performed by the author results (range value) of reject water were: 7.3 to 12.9 mg N-NH4/L after aerobic and 460.0 to 574.0 mg N-NH4/L after anaerobic digestion. The study has confirmed a higher value of organic substances in reject water after anaerobic digestion in comparison with aerobic. Due to high concentration of ammonia nitrogen in reject water obtained during co-digestion of excessive and flotation sludge, a separated system for its treatment should be applied. The results of research work presented in this paper provided a base for the project of the pilot installation with constructed wetland.
A multielectrode array system has been developed to study how the retina processes and encodes visual images. This system can simultaneously record the extracellular electrical activity from hundreds ...of retinal output neurons as a dynamic visual image is focused on the input neurons. The retinal output signals detected can be correlated with the visual input to study the neural code used by the eye to send information about the visual world to the brain. The system consists of the following components: 1) a 32 /spl times/ 16 rectangular array of 512 planar microelectrodes with a sensitive area of 1.7 mm/sup 2/; the electrode spacing is 60 /spl mu/m and the electrode diameter is 5 /spl mu/m (hexagonal arrays with 519 electrodes are under development); 2) eight 64-channel custom-designed integrated circuits to platinize the electrodes and ac couple the signals; 3) eight 64-channel integrated circuits to amplify, band-pass filter, and analog multiplex the signals; 4) a data acquisition system; and 5) data processing software. This paper will describe the design of the system, the experimental and data analysis techniques, and some first results with live retina. The system is based on techniques and expertise acquired in the development of silicon microstrip detectors for high-energy physics experiments.
Abstract
Motivation
Next generation sequencing (NGS) has provided researchers with a powerful tool to characterize metagenomic and clinical samples in research and diagnostic settings. NGS allows an ...open view into samples useful for pathogen detection in an unbiased fashion and without prior hypothesis about possible causative agents. However, NGS datasets for pathogen detection come with different obstacles, such as a very unfavorable ratio of pathogen to host reads. Alongside often appearing false positives and irrelevant organisms, such as contaminants, tools are often challenged by samples with low pathogen loads and might not report organisms present below a certain threshold. Furthermore, some metagenomic profiling tools are only focused on one particular set of pathogens, for example bacteria.
Results
We present PAIPline, a bioinformatics pipeline specifically designed to address problems associated with detecting pathogens in diagnostic samples. PAIPline particularly focuses on userfriendliness and encapsulates all necessary steps from preprocessing to resolution of ambiguous reads and filtering up to visualization in a single tool. In contrast to existing tools, PAIPline is more specific while maintaining sensitivity. This is shown in a comparative evaluation where PAIPline was benchmarked along other well-known metagenomic profiling tools on previously published well-characterized datasets. Additionally, as part of an international cooperation project, PAIPline was applied to an outbreak sample of hemorrhagic fevers of then unknown etiology. The presented results show that PAIPline can serve as a robust, reliable, user-friendly, adaptable and generalizable stand-alone software for diagnostics from NGS samples and as a stepping stone for further downstream analyses.
Availability and implementation
PAIPline is freely available under https://gitlab.com/rki_bioinformatics/paipline.
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