The contribution of viral and host cell factors to replication of the hepatitis C virus RNA genome

Studies on the hepatitis C virus (HCV) life cycle have been aided by the development of in vitro systems that permit replication of the viral RNA genome and virus particle production. However, the exact functions of the viral proteins, particularly those engaged in RNA synthesis, are poorly understood. It is thought that NS4B, one of the replicase components, induces the formation of replication complexes (RCs) derived from host cell membranes. These RCs appear as punctate foci at the endoplasmic reticulum (ER) membrane and incorporate the viral and cellular proteins necessary for HCV RNA synthesis. To gain insight into the nature of RCs, green fluorescent protein (GFP) was inserted into the coding region of NS5A, one of the HCV-encoded replicase components. The impact of the GFP insertion was examined in the context of a subgenomic replicon (SGR) based on JFH1, a genotype 2a HCV strain that exhibits efficient RNA replication in cell culture. The resulting construct was capable of robust replication and allowed characterisation of NS5A in live cells that synthesised viral RNA. NS5A displayed a diffuse, ER-like distribution and was also observed in foci. These foci are presumed to represent RCs and NS5A was relatively immobile at these sites. This result was confirmed using SGRs harbouring a photoactivatable derivative of GFP (PAGFP). Utilising plasmid-encoded HCV polyproteins, it was apparent that the targeting of NS5A to these structures was dependent on NS4B. Removal of the NS4B coding region resulted in a diffuse, ER-like distribution of NS5A, with little evidence of the protein within RCs. NS5A was mobile under these conditions, suggesting that the dynamics of NS5A are linked to focus formation by NS4B. To further investigate these findings, a panel of 15 alanine substitutions was constructed in the C-terminal region of NS4B. Transient replication assays revealed that five mutants were incapable of replication, two displayed an attenuated phenotype, and eight exhibited replication levels comparable to the wild-type (wt) genome. Of the five non-replicating mutants, two were defective in their ability to produce foci, while one failed to generate any foci. Thus, the C-terminus of NS4B is important for RC formation. Loss of NS4B foci correlated with decreased NS5A located in these structures. Furthermore, NS5A hyperphosphorylation was reduced for mutants compromised in foci production. This suggests that the membranous changes induced by NS4B provide a favourable environment for post-translational modifications of NS5A. Interestingly, the remaining two non-replicating mutants displayed no impairment in foci production and the characteristics of NS5A were also unaltered. Therefore, in addition to producing the cellular environment for HCV genome synthesis, NS4B is likely to play a more direct role in RNA replication. HCV RCs are believed to be relatively enclosed structures that permit limited exchange of materials with the cytoplasm. In support of this hypothesis, previous reports have shown that NS5A is the only replicase component capable of restoring replication to defective genomes when supplied in trans. In those studies, SGRs harbouring replication-lethal NS4B mutations could not be rescued by trans-complementation. Utilising the five novel non-replicating genomes described above, the potential to trans-complement NS4B in transient replication assays was re-examined. Wt protein produced from a functional HCV replicon could trans-complement defective NS4B expressed from two of the five mutants. Moreover, active replication could be reconstituted from two defective viral RNAs harbouring mutations within NS4B and NS5A. These findings have important implications for our understanding of RC formation. Genome-length JFH1 RNA produces infectious virus particles in Huh-7 cells. Using this system, it has become increasingly apparent that some HCV-encoded replication components are also involved in virus assembly and release. To determine whether NS4B had any influence on these latter stages of the virus life cycle, the NS4B mutations that did not block RNA replication were introduced into the full-length JFH1 genome. While the majority of mutants had no effect on virus production, one mutant consistently enhanced infectious virus titres by up to five-fold compared to wt JFH1. Interestingly, introduction of the same mutation into a chimeric J6-JFH1 genome resulted in repressed virion production. Together, these results suggest that NS4B contributes to virus assembly and release in a genotype-specific manner. In an attempt to identify novel cellular proteins involved in HCV genome replication, a siRNA library targeting 299 nucleotide-binding proteins was screened. For the screen, a robust system was established using two cell lines (derived from Huh-7 and U2OS cells) that replicated tri-cistronic SGRs. While the U2OS cell line supported HCV RNA replication less efficiently compared to Huh-7 cells, this cell type was efficiently transfected with siRNA. Consequently, increased gene-silencing and greater effects on HCV replication were observed in the U2OS cell line. Thus, U2OS cells may be a suitable alternative to Huh-7 cells for HCV-related siRNA studies. For the library screen, all siRNAs were tested in both cell lines, and cell viability measurements allowed specific effects on viral RNA synthesis to be characterised. The screen identified several cellular proteins that enhanced and suppressed HCV RNA replication. This study provides an important framework for more detailed analyses of these proteins in the future

Lipid content and biomass analysis in autotrophic and heterotrophic algal species

Biofuels are a form of renewable energy derived from living matter, typically plants. The push for biofuels began in order to decrease the amount of carbon dioxide (CO2) released into the atmosphere, as biofuels are essentially carbon neutral. The idea is the same amount of CO2 the plants took in to perform photosynthesis will then be released in the burning of the biofuels. Algae is an excellent source of biofuels because it grows quickly and is versatile in terms of the type of fuel it can produce. The two most common mechanisms for algae growth are heterotrophic or photoautotrophic. Heterotrophically grown algae uses an exogenous energy source, such as glucose, and uses the energy stored in it to perform cellular functions. Glucose also serves as a source of carbon and hydrogen, which are the primary elements found in lipids. In addition heterotrophic algae requires other nutrients for survival, such as water, vitamins, and inorganic ions. Algae grown photoautotrophically uses pigments in cellular photoreceptors to convert energy from light into adenosine triphosphate (ATP), an energy source, and to produce glucose. It also requires water, vitamins, and inorganic ions like the heterotrophic algae does. Some algal species, such as Chlorella zofingiensis, can be grown both photoautotrophically and heterotrophically. This algae species will be the subject of our experiment. Our experiment seeks to discover the most efficient way of growing algae to produce the highest amount of lipids. In addition to serving as a key component of cell and organelle membranes, lipids are a common form of high efficiency, long-term energy storage for living organisms, which is why lipids are extracted and processed to form biofuels. We propose growing one species of algae photoautotrophically by providing it with proper amounts of light but eliminating any glucose available. We will also grow the same species heterotrophically, with exogenous access to glucose, but eliminating all exposure to light sources. Finally, we will grow the same species mixotrophically with access to both glucose and light. Once the algae is grown, it will be harvested and analyzed for its lipid profile to determine which algae sample has the highest percent lipid content. We will also measure the percent biomass of each sample to determine which primary energy source leads to the greatest amount of total algal growth, percent organic material, and percent lipid content. We predict the algae grown with access to both sunlight and exogenous glucose will produce both the highest lipid content and the highest percent of biomass

The Economics of Selling Crop Residue Biomass for Cellulosic Ethanol Production at the Farm Level

A partial budget decision making framework has been developed to assist crop producers in analyzing the profitability of selling cellulosic biomass from their fields for ethanol production. A multidisciplinary approach is taken in assessing the agronomic and economic factors relevant to biomass contract sales decisions – with direct application made to western Great Plains cropping systems and enterprises. Within this framework the benefits of increased revenue from cellulosic biomass contract sales and potential government assistance payments are considered against possible decreased revenue from diminished crop yields resulting from less crop residue cover and subsequent soil moisture evaporation. Increased biomass harvesting and handling are also considered, as is the cost of replacing crop nutrients removed as part of biomass harvest operations. Examples of the profitability of cellulosic biomass contract sales in center pivot irrigated corn and non-irrigated wheat enterprises are shown.Resource /Energy Economics and Policy,

A randomised controlled study of high intensity exercise as a dishabituating stimulus to improve hypoglycaemia awareness in people with type 1 diabetes:a proof of concept study

Aims/hypothesis Approximately 25% of people with type 1 diabetes have suppressed counterregulatory hormonal and symptomatic responses to insulin-induced hypoglycaemia, which renders them at increased risk of severe, disabling hypoglycaemia. This is called impaired awareness of hypoglycaemia (IAH), the cause of which is unknown. We recently proposed that IAH develops through habituation, a form of adaptive memory to preceding hypoglycaemia. Consistent with this hypothesis, we demonstrated restoration of defective counterregulatory hormonal responses to hypoglycaemia (referred to as dishabituation) in a rodent model of IAH following introduction of a novel stress stimulus (high intensity training [HIT]). In this proof-of-concept study we sought to further test this hypothesis by examining whether a single episode of HIT would amplify counterregulatory responses to subsequent hypoglycaemia in people with type 1 diabetes who had IAH (assessed by Gold score ≥4, modified Clarke score ≥4 or Dose Adjustment For Normal Eating (DAFNE) hypoglycaemia awareness rating 2 or 3). The primary outcome was the difference in adrenaline response to hypoglycaemia following both a single episode of HIT and rest. Methods In this randomised, crossover study 12 participants aged between 18 and 55 years with type 1 diabetes for ≥5 years and an HbA1c < 75 mmol/mol (9%) were recruited. Individuals were randomised using computer generated block randomisation to start with one episode of HIT (4 × 30 s cycle sprints [2 min recovery] at 150% of maximum wattage achieved during V˙O2peak assessment) or rest (control). The following day they underwent a 90 min hyperinsulinaemic–hypoglycaemic clamp study at 2.5 mmol/l with measurement of hormonal counterregulatory response, symptom scores and cognitive testing (four-choice reaction time and digit symbol substitution test). Each intervention and subsequent clamp study was separated by at least 2 weeks. The participants and investigators were not blinded to the intervention or measurements during the study. The investigators were blinded to the primary outcome and blood analysis results. Results All participants (six male and six female, age 19–54 years, median [IQR] duration of type 1 diabetes 24.5 [17.3–29.0] years, mean [SEM] HbA1c 56 [3.67] mmol/mol; 7.3% [0.34%]) completed the study (both interventions and two clamps). In comparison with the rest study, a single episode of HIT led to a 29% increase in the adrenaline (epinephrine) response (mean [SEM]) (2286.5 [343.1] vs 2953.8 [384.9] pmol/l); a significant increase in total symptom scores (Edinburgh Hypoglycaemia Symptom Scale: 24.25 [2.960 vs 27.5 [3.9]; p < 0.05), and a significant prolongation of four-choice reaction time (591.8 [22.5] vs 659.9 [39.86] ms; p < 0.01] during equivalent hypoglycaemia induced the following day. Conclusions/interpretation These findings are consistent with the hypothesis that IAH develops in people with type 1 diabetes as a habituated response and that introduction of a novel stressor can restore, at least partially, the adapted counterregulatory hormonal, symptomatic and cognitive responses to hypoglycaemia.Output Status: Forthcoming/Available Onlin

Storage of Sperm in the Reptilian Oviduct

Female reptiles have the ability to store sperm within their reproductive tracts for extended periods of time. Sites of sperm storage in lizards and snakes include both the anterior vagina and the infundibulum. Vaginal receptacles are found in between longitudinal folds (snakes) and in tubules formed by invaginations of the epithelium (lizards). Infundibular receptacles are alveolar or tubular in structure and are formed from invaginations into the lamina propria of the oviduct wall. In turtles, sperm are stored in the posterior portion of the tuba, in tubular albumen-secreting glands. Sperm may be embedded within the cells of the receptacles, but the membranes of each remain intact. The morphology of the receptacles is characteristic of the normal glands of the area

Multisensory Integration Sites Identified by Perception of Spatial Wavelet Filtered Visual Speech Gesture Information

Perception of speech is improved when presentation of the audio signal is accompanied by concordant visual speech gesture information. This enhancement is most prevalent when the audio signal is degraded. One potential means by which the brain affords perceptual enhancement is thought to be through the integration of concordant information from multiple sensory channels in a common site of convergence, multisensory integration (MSI) sites. Some studies have identified potential sites in the superior temporal gyrus/sulcus (STG/S) that are responsive to multisensory information from the auditory speech signal and visual speech movement. One limitation of these studies is that they do not control for activity resulting from attentional modulation cued by such things as visual information signaling the onsets and offsets of the acoustic speech signal, as well as activity resulting from MSI of properties of the auditory speech signal with aspects of gross visual motion that are not specific to place of articulation information. This fMRI experiment uses spatial wavelet bandpass filtered Japanese sentences presented with background multispeaker audio noise to discern brain activity reflecting MSI induced by auditory and visual correspondence of place of articulation information that controls for activity resulting from the above-mentioned factors. The experiment consists of a low-frequency (LF) filtered condition containing gross visual motion of the lips, jaw, and head without specific place of articulation information, a midfrequency (MF) filtered condition containing place of articulation information, and an unfiltered (UF) condition. Sites of MSI selectively induced by auditory and visual correspondence of place of articulation information were determined by the presence of activity for both the MF and UF conditions relative to the LF condition. Based on these criteria, sites of MSI were found predominantly in the left middle temporal gyrus (MTG), and the left STG/S (including the auditory cortex). By controlling for additional factors that could also induce greater activity resulting from visual motion information, this study identifies potential MSI sites that we believe are involved with improved speech perception intelligibility

Fundamental Limitations of Cavity-assisted Atom Interferometry

Atom interferometers employing optical cavities to enhance the beam splitter pulses promise significant advances in science and technology, notably for future gravitational wave detectors. Long cavities, on the scale of hundreds of meters, have been proposed in experiments aiming to observe gravitational waves with frequencies below 1 Hz, where laser interferometers, such as LIGO, have poor sensitivity. Alternatively, short cavities have also been proposed for enhancing the sensitivity of more portable atom interferometers. We explore the fundamental limitations of two-mirror cavities for atomic beam splitting, and establish upper bounds on the temperature of the atomic ensemble as a function of cavity length and three design parameters: the cavity g-factor, the bandwidth, and the optical suppression factor of the first and second order spatial modes. A lower bound to the cavity bandwidth is found which avoids elongation of the interaction time and maximizes power enhancement. An upper limit to cavity length is found for symmetric two-mirror cavities, restricting the practicality of long baseline detectors. For shorter cavities, an upper limit on the beam size was derived from the geometrical stability of the cavity. These findings aim to aid the design of current and future cavity-assisted atom interferometers.Comment: 11 pages, 12 figure