Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif

The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs.     

Tuberculosis Treatment in HIV Infected Ugandans with CD4 Counts >350 Cells/mm3 Reduces Immune Activation with No Effect on HIV Load or CD4 Count

Background

Both HIV and TB cause a state of heightened immune activation. Immune activation in HIV is associated with progression to AIDS. Prior studies, focusing on persons with advanced HIV, have shown no decline in markers of cellular activation in response to TB therapy alone.

Methodology

This prospective cohort study, composed of participants within a larger phase 3 open-label randomized controlled clinical trial, measured the impact of TB treatment on immune activation in persons with non-advanced HIV infection (CD4>350 cells/mm³) and pulmonary TB. HIV load, CD4 count, and markers of immune activation (CD38 and HLA-DR on CD4 and CD8 T cells) were measured prior to starting, during, and for 6 months after completion of standard 6 month anti-tuberculosis (TB) therapy in 38 HIV infected Ugandans with smear and culture confirmed pulmonary TB.

Results

Expression of CD38, and co-expression of CD38 and HLA-DR, on CD8 cells declined significantly within 3 months of starting standard TB therapy in the absence of anti-retroviral therapy, and remained suppressed for 6 months after completion of therapy. In contrast, HIV load and CD4 count remained unchanged throughout the study period.

Conclusion

TB therapy leads to measurable decreases in immune activation in persons with HIV/TB co-infection and CD4 counts >350 cells/mm³.     

Collagen and mature elastic fibre organisation as a function of depth in the human cornea and limbus

A network of circumferentially oriented collagen fibrils exists in the periphery of the human cornea, and is thought to be pivotal in maintaining corneal biomechanical stability and curvature. However, it is unknown whether or not this key structural arrangement predominates throughout the entire corneal thickness or exists as a discrete feature at a particular tissue depth; or if it incorporates any elastic fibres and how, with respect to tissue depth, the circumcorneal annulus integrates with the orthogonally arranged collagen of the central cornea. To address these issues we performed a three-dimensional investigation of fibrous collagen and elastin architecture in the peripheral and central human cornea using synchrotron X-ray scattering and non-linear microscopy. This showed that the network of collagen fibrils circumscribing the human cornea is located in the posterior one-third of the tissue and is interlaced with significant numbers of mature elastic fibres which mirror the alignment of the collagen. The orthogonal arrangement of collagen in the central cornea is also mainly restricted to the posterior stromal layers. This information will aid the development of corneal biomechanical models aimed at explaining how normal corneal curvature is sustained and further predicting the outcome of surgical procedures.     

Role of host GTPases in infection by Listeria monocytogenes

The bacterial pathogen Listeria monocytogenes induces internalization into mammalian cells and uses actin‐based motility to spread within tissues. Listeria accomplishes this intracellular life cycle by exploiting or antagonizing several host GTPases. Internalization into human cells is mediated by the bacterial surface proteins InlA or InlB. These two modes of uptake each require a host actin polymerization pathway comprised of the GTPase Rac1, nucleation promotion factors, and the Arp2/3 complex. In addition to Rac1, InlB‐mediated internalization involves inhibition of the GTPase Arf6 and participation of Dynamin and septin family GTPases. After uptake, Listeria is encased in host phagosomes. The bacterial protein GAPDH inactivates the human GTPase Rab5, thereby delaying phagosomal acquisition of antimicrobial properties. After bacterial‐induced destruction of the phagosome, cytosolic Listeria uses the surface protein ActA to stimulate actin‐based motility. The GTPase Dynamin 2 reduces the density of microtubules that would otherwise limit bacterial movement. Cell‐to‐cell spread results when motile Listeria remodel the host plasma membrane into protrusions that are engulfed by neighbouring cells. The human GTPase Cdc42, its activator Tuba, and its effector N‐WASP form a complex with the potential to restrict Listeria protrusions. Bacteria overcome this restriction through two microbial factors that inhibit Cdc42‐GTP or Tuba/N‐WASP interaction.     

Modeling changes in soil organic matter in Amazon forest to pasture conversion with the Century model

Land use and land cover changes in the Brazilian Amazon region have major implications for regional and even global carbon cycling. We analyzed the effects of the predominant land use change, conversion of tropical forest to pasture, on total soil C and N, using the Century ecosystem model and data collected from the Nova Vida ranch, Western Brazilian Amazon. We estimated equilibrium organic matter levels, plant productivity and residue carbon inputs under native forest conditions, then simulated deforestation following the slash and burn procedure. Soil organic matter dynamics were simulated for pastures established in 1989, 1987, 1983, 1979, 1972, 1951, and 1911. Using input data from the Nova Vida ranch, the Century model predicted that forest clearance and conversion to pasture would cause an initial decline in soil C and N stocks, followed by a slow rise to levels exceeding those under native forest. Simulated soil total C and N levels (2500 g C m^?2 and 245 g N m^?2 in the 0–20 cm layer) prior to conversion to pasture were close to those measured in the native forest. Simulated above‐ and below‐ground biomass for the forest and pasture were comparable with literature values from this region. The model predicted the long‐term changes in soil C and N under pasture inferred from the pasture chronosequence, but there was considerable variation in soil C stocks for pastures <20 years in age. Differences in soil texture between pastures were relatively small and could not account for much of the variability between different pastures of similar ages, in either the measured or simulated data. It is likely that much of the variability in C stocks between pastures of similar ages is related to initial C stocks immediately following deforestation and that this was the largest source of variability in the chronosequence. Internal C cycling processes in Century were evaluated using measurements of microbial biomass and soil δ¹³C. The relative magnitude and long‐term trend in microbial biomass simulated by the model were consistent with measurements. The close fit of simulated to measured values of δ¹³C over time suggests that the relative loss of forest‐derived C and its replacement by pasture‐derived C was accurately predicted by the model. After 80 years, almost 90% of the organic matter in the top 20 cm was pasture derived. While our analysis represents a single ‘case study’ of pasture conversion, our results suggest that modeling studies in these pasture systems can help to evaluate the magnitude of impacts on C and N cycling, and determine the effect of management strategies on pasture sustainability.     

Effects of Acute Lorazepam Administration on Aminergic Activity in Normal Elderly Subjects: Relationship to Performance Effects and Apolipoprotein Genotype

The effects of acute lorazepam challenges on plasma (p) HVA, MHPG, and 5-HIAA, and their relationship to drug-induced cognitive and motor deficits and the apolipoprotein (APOE)-epsilon4 allele were examined. Eighteen healthy elderly (8 epsilon4 carriers) received placebo or acute oral lorazepam doses (0.5 mg or 1 mg) in random sequence, 1-week apart. Cognitive assessment and plasma levels of pHVA, pMHPG, and p5-HIAA were determined at baseline and at 1, 2.5, and 5 h postchallenge. There was no drug-to-placebo difference in monoamine levels and no consistent relationship between changes in monoamine levels and cognitive performance, regardless of epsilon4 status. However, the 1.0 mg dose increased p5-HIAA in epsilon4 carriers, whereas it caused a reduction in noncarriers. Higher baseline pMHPG and p5-HIAA levels were associated with better baseline memory. The epsilon4 allele may modulate the effect of lorazepam on p5-HIAA, but further studies are needed to confirm this finding and elucidate its possible significance.     

Remotely Monitoring Change in Vegetation Cover on the Montebello Islands,Western Australia,in Response to Introduced Rodent Eradication

The Montebello archipelago consists of 218 islands; 80 km from the north-west coast of Western Australia. Before 1912 the islands had a diverse terrestrial fauna. By 1952 several species were locally extinct. Between 1996 and 2011 rodents and cats were eradicated, and 5 mammal and 2 bird species were translocated to the islands. Monitoring of the broader terrestrial ecosystem over time has been limited. We used 20 dry-season Landsat images from 1988 to 2013 and estimation of green fraction cover in nadir photographs taken at 27 sites within the Montebello islands and six sites on Thevenard Island to assess change in vegetation density over time. Analysis of data averaged across the 26-year period suggests that 719 ha out of 2169 ha have increased in vegetation cover by up to 32%, 955 ha have remained stable and 0.6 ha have declined in vegetation cover. Over 492 ha (22%) had no vegetation cover at any time during the period analysed. Chronological clustering analysis identified two breakpoints in the average vegetation cover data occurring in 1997 and 2003, near the beginning and end of the rodent eradication activities. On many islands vegetation cover was declining prior to 1996 but increased after rodents were eradicated from the islands. Data for North West and Trimouille islands were analysed independently because of the potential confounding effect of native fauna being introduced to these islands. Mala (Lagorchestes hirsutus) and Shark Bay mice (Pseudomys fieldi) both appear to suppress native plant recruitment but not to the same degree as introduced rodents. Future research should assess whether the increase in vegetation cover on the Montebello islands is due to an increase in native or introduced plants.     

Genome size in Dahlia Cav. (Asteraceae–Coreopsideae)

The genus Dahlia (Asteraceae–Coreopsideae) is monophyletic according to a recent DNA phylogeny (ETS and ITS of rDNA). Traditionally, the genus has been divided into sections, but these have been shown not to be monophyletic. We have studied variation in genome size (DNA C-values) in a sample of species to investigate the possible effects of secondary metabolites on flow cytometry and Feulgen densitometry, and to see whether genome size variation has any systematic or phylogenetic significance. Using a range of cultivars, secondary compounds from corollas were shown to have only minor effects on the Feulgen method; the floral pigments were found to be relatively inert and seemed to have been extracted on fixation with acetic methanol. Freshly expanded corollas showed apparent apoptotic DNA decay in epidermal cells, so need to be used with caution. Flow cytometric measurements with propidium iodide in some cultivars resulted in a very similar average genome size (2C = 8.62 pg) as compared with Feulgen densitometry (2C = 8.84 pg). Leaf cytosol of D. variabilis has a demonstrable inhibitory effect on propidium iodide fluorescence, which may explain some of the intraspecific variation of C-values observed. DNA 2C-values ranged from 3.30 pg in D. dissecta (2n = 34) to 9.62 pg in a D. variabilis cultivar (2n = 64). The D. variabilis cultivars had broadly similar C-values showing a 1.16-fold range between cultivars. Some of this variation probably results from technical variables and the extent of genuine variation is uncertain. The highest 2Cx-value occurred in one D. coccinea accession (2.47 pg, 2n = 32; x = 8). D. coccinea with 2n = 64 showed slightly reduced Cx-values compared to D. coccinea with 2n = 32. Artificially produced interspecific hybrids had C-values that corresponded closely with expectations from the measured values obtained from their parents.