The Feasibility of Using High Resolution Genome Sequencing of Influenza A Viruses to Detect Mixed Infections and Quasispecies

Background

The rapidly expanding availability of de novo sequencing technologies can greatly facilitate efforts to monitor the relatively high mutation rates of influenza A viruses and the detection of quasispecies. Both the mutation rates and the lineages of influenza A viruses are likely to play an important role in the natural history of these viruses and the emergence of phenotypically and antigenically distinct strains.

Methodology and Principal Findings

We evaluated quasispecies and mixed infections by de novo sequencing the whole genomes of 10 virus isolates, including eight avian influenza viruses grown in embryonated chicken eggs (six waterfowl isolates - five H3N2 and one H4N6; an H7N3 turkey isolate; and a bald eagle isolate with H1N1/H2N1 mixed infection), and two tissue cultured H3N2 swine influenza viruses. Two waterfowl cloacal swabs were included in the analysis. Full-length sequences of all segments were obtained with 20 to 787-X coverage for the ten viruses and one cloacal swab. The second cloacal swab yielded 15 influenza reads of ∼230 bases, sufficient for bioinformatic inference of mixed infections or quasispecies. Genomic subpopulations or quasispecies of viruses were identified in four egg grown avian influenza isolates and one cell cultured swine virus. A bald eagle isolate and the second cloacal swab showed evidence of mixed infections with two (H1 and H2) and three (H1, H3, and H4) HA subtypes, respectively. Multiple sequence differences were identified between cloacal swab and the virus recovered using embryonated chicken eggs.

Conclusions

We describe a new approach to comprehensively identify mixed infections and quasispecies in low passage influenza A isolates and cloacal swabs and add to the understanding of the ecology of influenza A virus populations.     

Efficient detection of viral transmissions with Next-Generation Sequencing data

Background

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis has been frequently used in the study of HCV outbreaks and transmission chains; helping identify a cluster of sequences as linked by transmission if their genetic distances are below a previously defined threshold. However, HCV exists as a population of numerous variants in each infected individual and it has been observed that minority variants in the source are often the ones responsible for transmission, a situation that precludes the use of a single sequence per individual because many such transmissions would be missed.The use of Next-Generation Sequencing immensely increases the sensitivity of transmission detection but brings a considerable computational challenge because all sequences need to be compared among all pairs of samples.

Methods

We developed a three-step strategy that filters pairs of samples according to different criteria: (i) a k-mer bloom filter, (ii) a Levenhstein filter and (iii) a filter of identical sequences. We applied these three filters on a set of samples that cover the spectrum of genetic relationships among HCV cases, from being part of the same transmission cluster, to belonging to different subtypes.

Results

Our three-step filtering strategy rapidly removes 85.1% of all the pairwise sample comparisons and 91.0% of all pairwise sequence comparisons, accurately establishing which pairs of HCV samples are below the relatedness threshold.

Conclusions

We present a fast and efficient three-step filtering strategy that removes most sequence comparisons and accurately establishes transmission links of any threshold-based method. This highly efficient workflow will allow a faster response and molecular detection capacity, improving the rate of detection of viral transmissions with molecular data.

     

5-Fluorouracil-induced cardiotoxicity mimicking myocardial infarction: a case report

Background  

Severe cardiotoxicity is a documented, but very unusual side-effect of intravenous 5-fluorouracil therapy. The mechanism producing cardiotoxicity is poorly understood.     

Dystrophin-glycoprotein complex and Ras and Rho GTPase signaling are altered in muscle atrophy

The dystrophin-glycoprotein complex (DGC)is a sarcolemmal complex whose defects cause muscular dystrophies. Thenormal function of this complex is not clear. We have proposed thatthis is a signal transduction complex, signaling normal interactionswith matrix laminin, and that the response is normal growth andhomeostasis. If so, the complex and its signaling should be altered inother physiological states such as atrophy. The amount of some of the DGC proteins, including dystrophin, -dystroglycan, and-sarcoglycan, is reduced significantly in rat skeletal muscleatrophy induced by tenotomy. Furthermore, H-Ras, RhoA, and Cdc42decrease in expression levels and activities in muscle atrophy. Whenthe small GTPases were assayed after laminin or -dystroglycandepletion, H-Ras, Rac1, and Cdc42 activities were reduced, suggesting aphysical linkage between the DGC and the GTPases. Dominant-negativeCdc42, introduced with a retroviral vector, resulted in fibers thatappeared atrophic. These data support a putative role for the DGC intransduction of mechanical signals in muscle.

     

The Fragilis interferon-inducible gene family of transmembrane proteins is associated with germ cell specification in mice

Background  

Specification of primordial germ cells in mice depends on instructive signalling events, which act first to confer germ cell competence on epiblast cells, and second, to impose a germ cell fate upon competent precursors. fragilis, an interferon-inducible gene coding for a transmembrane protein, is the first gene to be implicated in the acquisition of germ cell competence.     

Biogenesis,characterization, and the effect of vicenin‐gold nanoparticles on glucose utilization in 3T3‐L1 adipocytes: A bioinformatic approach to illuminate its interaction with PTP 1B and AMPK

This study reported the synthesis of Vicenin‐2 gold nanoparticles (VN‐AuNPs) and evaluated their effect on the glucose utilization efficiency of 3T3‐L1 adipocytes. The VN‐AuNPs were characterized by microscopic, DLS and spectral analysis. The bio‐reducing efficiency of Vicenin‐2 (VN) was computed and confirmed by HPLC analysis. The stability of VN‐AuNPs in various physiological media was explored. The cytotoxicity and glucose uptake assays were performed in 3T3‐L1 adipocytes. The docking of VN with PTP1B and AMPK was also performed. The color change and UV absorption at 537 nm preliminarily confirmed the VN reduced gold nanoparticles. The VN‐AuNPs appeared as spherical particles (57 nm) and face centered cubic crystals under TEM and XRD analysis, respectively. Its zeta potential was found to be ?6.53 mV. The FT‐IR spectra of VN and its AuNPs confirmed its stability. The computed reducing potential of VN was similar to the extent of VN utilized during the synthesis of VN‐AuNPs. The VN‐AuNPs showed a remarkable stability in different physiological media. At 100 µM concentration, VN‐AuNPs displayed 78.21% cell viability. A concentration dependent increase in glucose uptake was noted in 3T3‐L1 adipocytes when incubated with VN‐AuNPs. The docking data revealed a strong interaction of VN with the binding pockets of PTP1B and AMPK. This demonstrates that the fabricated VN‐AuNPs might enhance the intracellular VN availability mediated cellular glucose utilization and this would serve as a novel nanodrug for the management of diabetes. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1096–1106, 2015     

Creating new specific ligand-receptor pairs for transgene regulation

The creation of specifically matched ligand-receptor pairs that are orthogonal to naturally present interacting pairs is essential for the development of small molecule-regulated gene expression systems for biotechnological applications. However, for many years this task has represented a significant challenge for synthetic chemists and protein engineers. Recently, Doyle and colleagues demonstrated that highly specific ligand-receptor pairs can be engineered in a rapid fashion by creating large libraries of protein variants and applying a selection scheme to identify variants with improved activation by the target synthetic ligand.     

Rice husk filtrate as a nutrient medium for the growth of Desulfotomaculum nigrificans: characterisation and sulfate reduction studies

The filtrate obtained by interacting a known amount of rice husk with deionised, Milli-Q water was assessed as a carbon source and nutrient medium for the growth of Desulfotomaculum nigrificans, a typical sulfate-reducing bacterium. The filtrate contained essential growth constituents such as magnesium, potassium, phosphorous apart from calcium, sodium, chloride and sulfate ions. Based on the 1H and 13C NMR characterization studies, the organic composition of the components dissolved from the rice husk, was found to be: (i) 66% lignocellulosic material, (ii) 24% xylose+arabinose and (iii) 10% galactose. The growth studies indicated a 15-fold increase in the bacterial cell number in about 20 days. Nearly 81% and 66% reduction in sulfate concentration could be achieved in about 28 days, from the solutions containing initial sulfate concentrations of 550 mg/l and 1200 mg/l respectively. In both the cases studied, the iron concentration could be reduced by over 85%.