Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding

The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA binding and RNA-induced oligomerization of NP. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. Calculation of the root-mean-square fluctuations highlighted the presence of two flexible loops in NP trimer: loop 1 (73–90), loop 2 (200–214). In NP, loops 1 and 2 formed a 10–15 Å-wide pinch giving access to the RNA binding groove. Loop 1 was stabilized by interactions with K113 of the adjacent β-sheet 1 (91–112) that interacted with the RNA grove (linker 360–373) via multiple hydrophobic contacts. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. Our data suggest that the flexibility of loops 1 and 2 is required for RNA sampling and binding which likely involve conformational change(s) of the nucleoprotein.     

Retroviral recombination in vivo: viral replication patterns and genetic structure of simian immunodeficiency virus (SIV) populations in rhesus macaques after simultaneous or sequential intravaginal inoculation with SIVmac239Deltavpx/Deltavpr and SIVmac239Deltanef

To characterize the occurrence, frequency, and kinetics of retroviral recombination in vivo, we intravaginally inoculated rhesus macaques, either simultaneously or sequentially, with attenuated simian immunodeficiency virus (SIV) strains having complementary deletions in their accessory genes and various degrees of replication impairment. In monkeys inoculated simultaneously with SIVmac239Deltavpx/Deltavpr and SIVmac239Deltanef, recombinant wild-type (wt) virus and wild-type levels of plasma viral RNA (vRNA) were detected in blood by 2 weeks postinoculation. In monkeys inoculated first with SIVmac239Deltavpx/Deltavpr and then with SIVmac239Deltanef, recombination occurred but was associated with lower plasma vRNA levels than plasma vRNA levels seen for monkeys inoculated intravaginally with wt SIVmac239. In one monkey, recombination occurred 6 weeks after the challenge with SIVmac239Deltanef when plasma SIVmac239Deltavpx/Deltavpr RNA levels were undetectable. In monkeys inoculated first with the more highly replicating strain, SIVmac239Deltanef, and then with SIVmac239Deltavpx/Deltavpr, wild-type recombinant virus was not detected in blood or tissues. Instead, a virus that had repaired the deletion in the nef gene by a compensatory mutation was found in one animal. Overall, recombinant SIV was eventually found in four of six animals intravaginally inoculated with the two SIVmac239 deletion mutants. These findings show that recombination can occur readily in vivo after mucosal SIV exposure and thus contributes to the generation of viral genetic diversity and enhancement of viral fitness.     

Effect of shift work on the night-time secretory patterns of melatonin, prolactin, cortisol and testosterone

In a study of the internal desynchronization of circadian rhythms in 12 shift workers, 4 of them, aged 25-34 years, agreed to be sampled every 2 h during their night shift (0000 hours to 0800 hours). They were oil refinery operators with a fast rotating shift system (every 3-4 days). We found marked changes in the secretory profiles of melatonin, prolactin and testosterone. Melatonin had higher peak-values resulting in a four-times higher amplitude than in controls. With respect to prolactin and testosterone, peak and trough times were erratic and the serum concentrations were significantly decreased in shift workers. Serum cortisol presented a decreased rhythm amplitude together with higher concentrations at 0000 hours in shift workers. This study clearly shows that fast rotating shift-work modifies peak or trough values and rhythm amplitudes of melatonin, prolactin, testosterone and cortisol without any apparent phase shift of these hormones. Whether the large rhythm amplitude of melatonin may be considered as a marker of tolerance to shift work, as reported for body temperature and hand grip strength, since it would help the subjects to maintain their internal synchronization, needs further investigation.     

Accidental selenium poisoning of growing pigs

Chronic selenium (Se) toxicosis was diagnosed in two groups of growing pigs. Emaciation, loss of hair, necrotic areas in the skin, lesions of the coronary band and hooves, postnecrotic atrophic cirrhosis of liver, and lumbal poliomyelomalacia were the principal findings. High Se concentrations were detected in blood plasma. Addition of the calculated amounts of sodium selenite directly to the feedstuff instead to mineral premix was the cause of this intoxication.     

Dynamics of Salix caprea L. populations during forest regeneration after strong herbivore pressure

Abstract. Broadleaved forest communities degenerated through strong pressure from large herbivores. Relief of this pressure led to regeneration, in particular of Salix caprea and other light-seeded pioneer trees: Populus tremula, Betula pendula and B. pubescens. This regeneration proceeded following conservation protection of degenerate stands in a nature reserve and later in Biaowiéza National Park. The emergence and development of the Salix caprea population proceeded following the expansion of Picea abies, which coincided with the period of enhanced animal pressure on the broadleaved forest. Salix caprea filled all the gaps in the tree stand after the destruction of trees and undergrowth by herbivores (in the years 1892–1915). The species also appeared abundantly in old, at the time unforested, clearings and felled areas. Here, S. caprea developed large populations with certain trees in good condition, with a growth form typical of forest trees and attaining considerable heights. The majority of trees were 50 - 60 yr old at the time of death, although some individuals reached 74 yr of age. The process of extinction of the Salix population — observed over 19 yr on permanent plots with marked trees — proceeded very quickly, especially in the first decade of observation. It led to the almost complete disappearance of S. caprea from the forest communities of Biaowiéza National Park. The death of individual trees is preceded by impairment of their health and reduced annual increments in the last 4–9 years of their life. The development of populations of permanent constituents of the forest, notably Carpinus betulus, Tilia cordata, Acer platanoides and Ulmus glabra, under the canopy of light-seeded trees, and the absence of a new generation of pioneer trees points to the end of the process of regeneration in the forest communities of BiaHwiéza National Park.     

Inhibition of inducible nitric oxide synthase exacerbates chronic cerebral toxoplasmosis in Toxoplasma gondii-susceptible C57BL/6 mice but does not reactivate the latent disease in T. gondii-resistant BALB/c mice

Infection of C57BL/6 mice with Toxoplasma gondii leads to progressive and ultimately fatal chronic Toxoplasma encephalitis (TE). Genetic deletion or inhibition of inducible nitric oxide synthase (iNOS) from the beginning of infection increased the number of T. gondii cysts in the brain and markedly reduced the time-to-death in this mouse strain. In the present study, we addressed whether iNOS also contributes to the control of intracerebral parasites in a clinically stable latent infection that develops in T. gondii-resistant BALB/c mice after resolution of the acute phase of TE. iNOS was expressed in the inflammatory cerebral infiltrates of latently infected BALB/c mice, but the number of iNOS+ cells was significantly lower than in the brains of chronically infected T. gondii-susceptible C57BL/6 mice. In BALB/c mice with latent TE (> 30 days of infection), treatment with the iNOS inhibitors L-N6-iminoethyl-lysine or L-nitroarginine-methylester for < or = 40 days did not result in an increase of the intracerebral parasitic load and a reactivation of the disease, despite the presence of iNOS-suppressive inhibitor levels in the brain. However, L-nitroarginine-methylester treatment had remarkably toxic effects and induced a severe wasting syndrome with high mortality. In contrast to BALB/c mice, L-N6-iminoethyl-lysine treatment rapidly exacerbated the already established chronic TE of C57BL/6 mice. Thus, the containment of latent toxoplasms in T. gondii-resistant BALB/c mice is independent of iNOS, whereas the temporary control of intracerebral parasites in T. gondii-susceptible C57BL/6 mice with chronic TE requires iNOS activity.     

Online Adaptation of a c-VEP Brain-Computer Interface(BCI) Based on Error-Related Potentials and Unsupervised Learning

The goal of a Brain-Computer Interface (BCI) is to control a computer by pure brain activity. Recently, BCIs based on code-modulated visual evoked potentials (c-VEPs) have shown great potential to establish high-performance communication. In this paper we present a c-VEP BCI that uses online adaptation of the classifier to reduce calibration time and increase performance. We compare two different approaches for online adaptation of the system: an unsupervised method and a method that uses the detection of error-related potentials. Both approaches were tested in an online study, in which an average accuracy of 96% was achieved with adaptation based on error-related potentials. This accuracy corresponds to an average information transfer rate of 144 bit/min, which is the highest bitrate reported so far for a non-invasive BCI. In a free-spelling mode, the subjects were able to write with an average of 21.3 error-free letters per minute, which shows the feasibility of the BCI system in a normal-use scenario. In addition we show that a calibration of the BCI system solely based on the detection of error-related potentials is possible, without knowing the true class labels.     

Temporal autocorrelation functions for movement rates from global positioning system radiotelemetry data

Autocorrelation has been viewed as a problem in telemetry studies because sequential observations are not independent in time or space, therefore violating assumptions for statistical inference. Yet nearly all ecological and behavioural data are autocorrelated in both space and time. We argue that there is much to learn about the structure of ecological and behavioural data from patterns of autocorrelation. Such patterns include periodicity in movement and patchiness in spatial data, which can be characterized by an autocorrelogram, semivariogram or spectrum. We illustrate the utility of temporal autocorrelation functions (ACFs) for analysing step-length data from GPS telemetry of wolves (Canis lupus), cougars (Puma concolor), grizzly bears (Ursus arctos) and elk (Cervus elaphus) in western Alberta. ACFs often differ by season, reflecting differences in foraging behaviour. In wilderness landscapes, step-length ACFs for predators decay slowly to apparently random patterns, but sometimes display strong daily rhythms in areas of human disturbance. In contrast, step lengths of elk are consistently periodic, reflecting crepuscular activity.     

Loss of collagen-receptor DDR1 delays renal fibrosis in hereditary type IV collagen disease

Alport syndrome is a hereditary type IV collagen disease leading to progressive renal fibrosis, hearing loss and ocular changes. End stage renal failure usually develops during adolescence. COL4A3?/? mice serve as an animal model for progressive renal scarring in Alport syndrome. The present study evaluates the role of Discoidin Domain Receptor 1 (DDR1) in cell–matrix interaction involved in pathogenesis of Alport syndrome including renal inflammation and fibrosis.DDR1/COL4A3 Double-knockouts were compared to COL4A3?/? mice with 50% or 100% expression of DDR1, wildtype controls and to DDR1?/? COL4A3+/+ controls for over 6 years. Double-knockouts lived 47% longer, mice with 50% DDR1 lived 29% longer and showed improved renal function (reduction in proteinuria and blood urea nitrogen) compared to animals with 100% DDR1 expression. Loss of DDR1 reduced proinflammtory, profibrotic cells via signaling of TGFβ, CTGF, NFκB and IL-6 and decreased deposition of extracellular matrix. Immunogold-staining and in-situ hybridisation identified podocytes as major players in DDR1-mediated fibrosis and inflammation within the kidney.In summary, glomerular epithelial cells (podocytes) express DDR1. Loss of DDR1-expression in the kidney delayed renal fibrosis and inflammation in hereditary type IV collagen disease. This supports our hypothesis that podocyte–matrix interaction via collagen receptors plays an important part in progression of renal fibrosis in Alport disease. The blockade of collagen-receptor DDR1 might serve as an important new therapeutic concept in progressive fibrotic and inflammatory diseases in the future.