Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity

Background

Ebolaviruses cause a severe and often fatal haemorrhagic fever in humans, with some species such as Ebola virus having case fatality rates approaching 90%. Currently, the worst Ebola virus outbreak since the disease was discovered is occurring in West Africa. Although thought to be a zoonotic infection, a concern is that with increasing numbers of humans being infected, Ebola virus variants could be selected which are better adapted for human-to-human transmission.

Results

To investigate whether genetic changes in Ebola virus become established in response to adaptation in a different host, a guinea pig model of infection was used. In this experimental system, guinea pigs were infected with Ebola virus (EBOV), which initially did not cause disease. To simulate transmission to uninfected individuals, the virus was serially passaged five times in naïve animals. As the virus was passaged, virulence increased and clinical effects were observed in the guinea pig. An RNAseq and consensus mapping approach was then used to evaluate potential nucleotide changes in the Ebola virus genome at each passage.

Conclusions

Upon passage in the guinea pig model, EBOV become more virulent, RNA editing and also coding changes in key proteins become established. The data suggest that the initial evolutionary trajectory of EBOV in a new host can lead to a gain in virulence. Given the circumstances of the sustained transmission of EBOV in the current outbreak in West Africa, increases in virulence may be associated with prolonged and uncontrolled epidemics of EBOV.     

4-[(8-Alkyl-8-azabicyclo[3.2.1]octyl-3-yl)-3-arylanilino]-N,N-diethylbenzamides: high affinity, selective ligands for the delta opioid receptor illustrate factors important to antagonist activity

The tropane derived compounds, 4-[(8-alkyl-8-azabicyclo[3.2.1]octyl-3-yl)-3-arylanilino]-N,N-d iethylbenzamides (5a-d), were synthesized and found to have high affinity and selectivity for the delta receptor. Compounds 5a-d are structurally similar to the full agonist (-)-RTI-5989-54 (3); yet, efficacy studies for compounds in this series (5a-d) reveal greatly diminished agonist activity as well as antagonism not found in piperidine-based compounds like 3.     

Measurement of the molecular masses of hydrophilic and hydrophobic subunits of ATP synthase and complex I in a single experiment

The adenosine triphosphate (ATP) synthase and complex I in mitochondria are membrane-bound multisubunit assemblies of both hydrophilic and hydrophobic proteins. Hitherto, the mass spectrometric measurement of their molecular masses has required that many of the hydrophobic proteins be analyzed separately from the other components in two different experiments. Here we describe a procedure that allows the molecular masses of all, or nearly all, of the subunits of each complex to be measured in a single experiment. The key feature is a mobile phase, in which hydrophilic and hydrophobic components remain soluble, that is compatible with reverse phase chromatography. In this way, the masses of all 17 subunits of bovine ATP synthase, 14 of the 17 subunits of the enzyme from Saccharomyces cerevisiae, 42 of the 45 subunits of bovine complex I, and all 28 of the subunits of bovine subcomplex Iα were measured. The method was used to characterize the subunits of ATP synthases and complexes I from a variety of species and to follow the progress of mild trypsinolysis of ATP synthase. It could be applied to other respiratory and photosynthetic complexes and, in general, to any protein complex that contains both hydrophilic and hydrophobic subunits.     

Expression of active human sialyltransferase ST6GalNAcI in Escherichia coli

Background  

The presence of terminal, surface-exposed sialic acid moieties can greatly enhance the in vivo half-life of glycosylated biopharmaceuticals and improve their therapeutic efficacy. Complete and homogeneous sialylation of glycoproteins can be efficiently performed enzymically in vitro but this process requires large amounts of catalytically active sialyltransferases. Furthermore, standard microbial hosts used for large-scale production of recombinant enzymes can only produce small quantities of glycosyltransferases of animal origin, which lack catalytic activity.     

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.Massively parallel sequencing has increased our ability to study microbial communities to a greater depth and at decreased sequencing costs to an extent that replication and gradient interrogation are now reasonably attainable. However, this massive throughput has mostly been used in exploratory studies, given the challenges to analysis of the big data sets generated and the relative novelty of the technique. To date, no report of a study that has used this method to describe the microbial community over a large area influenced by complicated hydrogeochemical factors during bioremediation has been published. Here, we used pyrosequencing technology complemented with a hypothesis-based approach to identify bacteria associated with biostimulation of U(VI) reduction at Area 3 of the U.S. Department of Energy''s (DOE''s) Oak Ridge Field Research Center (FRC) at Oak Ridge, TN.The Oak Ridge FRC is one of the most-studied sites for uranium bioremediation (2, 8, 19-22, 27, 37, 45-48). Previously used as a uranium enrichment plant, the site remains contaminated with depleted uranium, nitrate, and acidity. To deal with uranium contamination, dissimilatory metal reduction has been studied as an alternative that reduces risk by converting toxic soluble metals and radionuclides to insoluble, less toxic forms (2, 3, 16, 21, 26, 45). For example, some microbes can use metals such as Cr(VI), Se(VI), and the radionuclides U(VI) and Tc(VII) as final electron acceptors, producing a reduced insoluble species, thus blocking dispersal and reducing bioavailability.The ability to reduce U(VI) to U(IV) has been found in several unrelated phylogenetic groups, i.e., Delta-, Beta-, and Gammaproteobacteria, Firmicutes, Deinococci, and Actinobacteria, among others (42). Most previous studies have focused on the Fe(III)-reducing bacteria (FRB), especially Geobacter, and the sulfate-reducing bacteria (SRB), especially Desulfovibrio. Uranium(VI) reduction for bioremediation purposes has been tested and confirmed in laboratory-scale experiments using serum bottles (13, 18, 48), microcosms (23, 32), sediment columns (14, 43), and in situ field studies (3, 21, 41, 45), with the last one demonstrating the feasibility of U(VI) remediation and the correlation of U(VI) reduction with FRB (3, 6, 18, 31, 41) or SRB (40), or both (8, 19, 49).During field studies at Area 3 of the Oak Ridge site, a hydraulic control system together with ethanol injection successfully promoted U(VI) reduction from 5 μM to levels below U.S. Environmental Protection Agency (EPA) maximum contaminant levels (MCLs) for drinking water (0.126 μM) over a 2-year period (46). Reduction of U(VI) to U(IV) was confirmed by X-ray absorption near edge structure (XANES) (22, 46). Previous microbial surveys of sediments and groundwater from Area 3 wells by the use of 16S rRNA gene clone libraries detected genera known to harbor U(VI)-reducing members, such as Geobacter, Desulfovibrio, Anaeromyxobacter, Desulfosporosinus, and Acidovorax, after U(VI) reduction was established (8, 19). In one study, microbial counts from sediments were correlated with the hydraulic path, suggesting differences in organic carbon availability throughout Area 3 (8). The study that tracked the groundwater microbial communities of four locations of Area 3 over a 1.5-year period during ethanol stimulation found that nitrate, uranium, sulfide, and ethanol were correlated with particular bacterial populations and that the engineering control of dissolved oxygen and delivered nutrients was also significant in explaining the microbial community variability (19). However, the analysis of communities has been focused on limited wells and the community of the entire test area has not been characterized.On the basis of the previous results, we further hypothesized that the hydrological control strategy employed for the remediation of the site constrained the geochemistry of the site by controlling the distribution of organic carbon substrates and other nutrients and that this in turn selected a characteristic microbial community that was distinguishable from its surrounding community. We used massively parallel sequencing of 16S rRNA genes from sediments of 15 wells to characterize the microbial communities along hydrological gradients from the microbiologically active and hydraulically protected inner-loop zone to less active and still contaminated areas outside the treatment area and downgradient. Our sediment-sampling strategy allows a more precise spatial characterization than the use of groundwater samples, where filtering large volumes of water is often required, and also because samples of the attached communities can differ from the planktonic ones, as expected in oligotrophic aquifers (15), such as this site. The deeper sequencing allowed a more extensive survey of the communities, higher confidence in the detection of less dominant but significant members, and a more statistically robust indicator species assessment. We were able to detect groups significantly associated with U(VI) reduction and to explain differences in community structure with hydrogeochemical conditions.     

Real-Time Imaging of Cellulose Reorientation during Cell Wall Expansion in Arabidopsis Roots

Cellulose forms the major load-bearing network of the plant cell wall, which simultaneously protects the cell and directs its growth. Although the process of cellulose synthesis has been observed, little is known about the behavior of cellulose in the wall after synthesis. Using Pontamine Fast Scarlet 4B, a dye that fluoresces preferentially in the presence of cellulose and has excitation and emission wavelengths suitable for confocal microscopy, we imaged the architecture and dynamics of cellulose in the cell walls of expanding root cells. We found that cellulose exists in Arabidopsis (Arabidopsis thaliana) cell walls in large fibrillar bundles that vary in orientation. During anisotropic wall expansion in wild-type plants, we observed that these cellulose bundles rotate in a transverse to longitudinal direction. We also found that cellulose organization is significantly altered in mutants lacking either a cellulose synthase subunit or two xyloglucan xylosyltransferase isoforms. Our results support a model in which cellulose is deposited transversely to accommodate longitudinal cell expansion and reoriented during expansion to generate a cell wall that is fortified against strain from any direction.The walls of growing plant cells must fulfill two simultaneous and seemingly contradictory requirements. First, they must expand to accommodate cell growth, which is anisotropic in many tissues and determines organ morphology. Second, they must maintain their structural integrity, both to constrain the turgor pressure that drives cell growth and to provide structural rigidity to the plant. These requirements are met by constructing primary cell walls that can expand along with growing cells, whereas secondary cell walls are deposited after cell growth has ceased and serve the latter function.One of the major constituents of both types of cell walls is cellulose, which exists as microfibrils composed of parallel β-1,4-linked glucan chains that are held together laterally by hydrogen bonds (Somerville, 2006). Microfibrils are 2 to 5 nm in diameter, can extend to several micrometers in length, and exhibit high tensile strength that allows cell walls to withstand turgor pressures of up to 1 MPa (Franks, 2003). In vascular plants, cellulose is synthesized by a multimeric cellulose synthase (CESA) complex composed of at least three types of glycosyl transferases arranged into a hexameric rosette (Somerville, 2006). After delivery to the plasma membrane, CESA initially moves in alignment with cortical microtubules (Paredez et al., 2006), but its trajectory can be maintained independently of microtubule orientation. For example, in older epidermal cells of the root elongation zone in Arabidopsis (Arabidopsis thaliana), cellulose microfibrils at the inner wall face are oriented transversely despite the fact that microtubules reorient from transverse to longitudinal along the elongation zone (Sugimoto et al., 2000), suggesting that microtubule orientation and cellulose deposition are independent in at least some cases.Depending on species, cell type, and developmental stage, cellulose microfibrils may be surrounded by additional networks of polymers, including hemicelluloses, pectins, lignin, and arabinogalactan proteins (Somerville et al., 2004). Hemicelluloses are composed of β-1,4-linked carbohydrate backbones with side branches and include xyloglucans, mannans, and arabinoxylans. Xyloglucan is thought to interact with the surface of cellulose and form cross-links between adjacent microfibrils (Vissenberg et al., 2005). In some cell types, pectin or lignin may also participate in cross-linking or entrapment of other cell wall polymers. It is unclear how the associations between networks of different cell wall components are relaxed to allow for cell wall expansion during growth.Several models have been proposed for the behavior of cell wall components during wall expansion. The passive reorientation hypothesis (also called the multinet growth hypothesis; Preston, 1982) postulates that in longitudinally expanding cells, cellulose microfibrils are synthesized in a transverse pattern and are then reoriented toward the longitudinal axis due to the strain generated by turgor pressure (Green, 1960). This phenomenon has been observed in the multicellular alga Nitella (Taiz, 1984). In higher plants, there is less direct evidence for passive reorientation, and another hypothesis holds that wall expansion involves active, local, and controlled remodeling of cellulose microfibrils along a diversity of orientations (Baskin, 2005). Such remodeling could be achieved by proteins such as xyloglucan endotransglycosylases (XETs), which break and rejoin xyloglucan chains, and expansins, which loosen cell walls in vitro in a pH-dependent manner (Cosgrove, 2005). Marga et al. measured cellulose microfibril orientation at the innermost layer of the cell wall before and after in vitro extension and did not observe reorientation (Marga et al., 2005). This suggests that processes other than microfibril reorientation might be involved in wall expansion, at least under certain circumstances or in some wall layers. Thus, the degree to which cellulose microfibrils are reoriented after their synthesis during wall expansion has remained unclear.One difficulty in resolving this problem has been the inability to directly image cellulose microfibrils in the growing cell wall. Existing methods to assess cellulose structure and orientation in plant cell walls are limited by the low contrast of cellulose in transmission electron microscopy, the ability to image only the surface of the wall using field emission scanning electron microscopy, and the use of polarized light microscopy in combination with dyes such as Congo red to measure only the bulk orientation of cellulose microfibrils (Baskin et al., 1999; Sugimoto et al., 2000; Verbelen and Kerstens, 2000; MacKinnon et al., 2006). In addition, the sample manipulation required for the former two methods has the potential to introduce artifacts (Marga et al., 2005). Although cellulose microfibril orientation differs at the inner and outer surfaces of the cell wall (Sugimoto et al., 2000) and presumably changes over time, the dynamics of cellulose reorientation during cell wall expansion have not been observed to date.In this study, we tested fluorescent dyes for their potential to allow imaging of cellulose distribution in the walls of Arabidopsis seedlings by confocal microscopy. We used one of these dyes to characterize the distribution of cellulose in wild-type root cells and in mutants with reduced cellulose or xyloglucan. By directly observing the fine structure of cellulose over time in growing wild-type root cells, we concluded that cellulose microfibrils in these cells reorient in a transverse to longitudinal direction as predicted by the passive reorientation hypothesis.     

Adaptive immunity to rhinoviruses: sex and age matter

Background

Rhinoviruses (RV) are key triggers in acute asthma exacerbations. Previous studies suggest that men suffer from infectious diseases more frequently and with greater severity than women. Additionally, the immune response to most infections and vaccinations decreases with age. Most immune function studies do not account for such differences, therefore the aim of this study was to determine if the immune response to rhinovirus varies with sex or age.

Methods

Blood mononuclear cells were isolated from 63 healthy individuals and grouped by sex and age (≤50 years old and ≥52 years old). Cells were cultured with rhinovirus 16 at a multiplicity of infection of 1. The chemokine IP-10 was measured at 24 h as an index of innate immunity while IFNγ and IL-13 were measured at 5 days as an index of adaptive immunity.

Results

Rhinovirus induced IFNγ and IL-13 was significantly higher in ≤50 year old women than in age matched men (p < 0.02 and p < 0.05) and ≥52 year old women (p < 0.02 and p > 0.005). There was no sex or age based difference in rhinovirus induced IP-10 expression. Both IFNγ and IL-13 were negatively correlated with age in women but not in men.

Conclusions

This study suggests that pre-menopausal women have a stronger adaptive immune response to rhinovirus infection than men and older people, though the mechanisms responsible for these differences remain to be determined. Our findings highlight the importance of gender and age balance in clinical studies and in the development of new treatments and vaccines.     

Optimal long-term humoral responses to replication-defective herpes simplex virus require CD21/CD35 complement receptor expression on stromal cells

Replication-defective herpes simplex virus (HSV) strains elicit durable immune responses and protect against virulent HSV challenge in mice, despite being unable to establish latent infection in neuronal cells. Mechanisms for generating long-lived immunity in the absence of viral persistence remain uncertain. In animals immunized with replication-defective HSV, durable serum immunoglobulin G (IgG) responses were elicited. Surprisingly, Western blot analyses revealed that the specificities of antiviral IgG changed over time, and antibody reactivity to some viral proteins was detected only very late. Thus, some of the durable IgG activity appeared to be contributed by either new or significantly enhanced antibody responses at late times. Following immunization, radiation bone marrow-chimeric mice lacking complement receptors CD21 and CD35 on stromal cells elicited only short-lived serum IgG and failed to mount recall responses to subsequent HSV exposure. Our results suggest that complement-mediated retention of viral antigens by stromal cells, such as follicular dendritic cells, is critical for optimal maintenance of antibody responses and B-cell memory following vaccination with replication-defective HSV.