Structure of a Plant-Specific Partitivirus Capsid Reveals a Novel Coat Protein Architecture with a Hypervariable Protrusion

SUMMARYPersistent plant viruses may be the most common viruses in wild plants. A growing body of evidence for mutualism between such viruses and their hosts, suggests that they play an important role in ecology and agriculture. Here we present the structure of a plant-specific partitivirus capsid at 2.9 Å resolution by Cryo-EM. Structural features, including the T=1 arrangement of 60 coat protein dimers, are shared with fungal partitiviruses and the picobirnavirus lineage of dsRNA viruses. However, the topology of the capsid is markedly different with protrusions emanating from, and partly comprising, the binding interface of coat protein dimers. We show that a disordered region at the apex of the protrusion is not required for capsid assembly and represents a hypervariable site characteristic of the plant-specific partitiviruses. These results suggest a structural basis for the acquisition of additional functions by partitivirus coat proteins that enables mutualistic relationships with diverse plant hosts.

Local industrial pollution induces astrocyte cytoskeleton rearrangement in the dice snake brain: GFAP as a biomarker

The present study was designed to evaluate the responsiveness of modulation of glial fibrillary acidic protein (GFAP) content and its fragmentation in the snake brain as a biomarker of local industrial pollution of aquatic ecosystems. Despite GFAP being a well known cytoskeleton marker of astrocytes’ reactivity in the brain of vertebrates, its expression in the snake brain remains insufficiently described. The GFAP expression and its fragmentation were detected using the immunoblot method in the snake brain. ROS level was determined with dichlorofluorescein diacetate fluorescence. The content of the glial fibrillary acidic protein (GFAP) of filament (cytoskeleton) and soluble (cytosol) fractions in the brain of dice snake Natrix tessellata from three ecosystems with different rates of industrial pollution were studied (two polluted and one clean control site). Characteristic increase in GFAP fragmentation was noted for the snakes from both the researched polluted sites. Significant increase in the content of the GFAP cleaved polypeptide fragments induced by industrial pollution exposure was confirmed in the snakes’ brains. Meaningful GFAP fragmentation was determined in snake brain astrocytes as an increase in cleaved fragments of 47–35 kDa molecular weight for both soluble and cytoskeletal GFAP fractions. We found significant abnormality in the ratio of the GFAP soluble fraction to the cytoskeletal one in contaminant-exposed dice snakes. It should testify to significant metabolic disturbance in nerve cells of the dice snakes. Furthermore, growth of reactive oxygen species level as the main cause of oxidative stress was determined in brains of the snakes exposed to environmental toxicity. Thus, astrocyte cytoskeleton disorders are associated with pollutant-induced redox imbalance in the snake brain. Despite the limited data on glial cell biology in the reptilian brain, the observed results prove that snake astrocytes can respond to the environmental toxicity using typical astroglial response. The presented results evidence that monitoring of molecular characteristics of glial cytoskeleton in dice snakes could be used as reliable biomarker of neurotoxicity and adverse effects of industrial pollution. Further studies are required to elucidate the role of astrocyte cytoskeleton in the response against neurotoxic contaminants.

TRANSFORMATION OF TRADITIONAL SETTLEMENTS AND DISASTER VULNERABILITY

As a setting of life and cultural products made by humans, settlements always undergo transformation along with the dynamics of their inhabitants’ lives. The dynamics of occupants, in addition to being impacted by the development of local knowledge, changes in the way humans respond to climate, and cultural transformation, are also influenced by external factors. External factors that influence settlement transformation can arise in the form of urbanisation, changes in social and political systems, economics, and technological development. In traditional societies, natural threats are predictable and conquerable. The transformation of settlements can take place in the same frame, promoting natural considerations, or in a different frame with the existence of new ideas and knowledge and technology coming from the outside. To be able to understand the transformation of traditional settlements and their transformations in relation to disaster vulnerability, this paper evaluated the causing factors, patterns, and consequences resulted from the transformation of settlements. For this reason, urban morphological studies are applied as an evaluation method. The results of the evaluation of settlement transformations reveal that traditional settlements are farther away leaving natural-harmony patterns at the root of their existence. Economic approach has replaced the cosmological-based settlement. It is recommended that natural site characteristic should be taken into consideration in order to avoid natural disaster in the future. This means that the traditional approach is still relevant in contemporary situation.Keywords: Traditional settlements; transformation; disaster vulnerablity

Characterizing Environmental Surveillance Sites in Nigeria and Their Sensitivity to Detect Poliovirus and Other Enteroviruses

Background Environmental surveillance (ES) for poliovirus is increasingly important for polio eradication, often detecting circulating virus before paralytic cases are reported. The sensitivity of ES depends on appropriate selection of sampling sites, which is difficult in low-income countries with informal sewage networks. Methods We measured ES site and sample characteristics in Nigeria during June 2018–May 2019, including sewage physicochemical properties, using a water-quality probe, flow volume, catchment population, and local facilities such as hospitals, schools, and transit hubs. We used mixed-effects logistic regression and machine learning (random forests) to investigate their association with enterovirus isolation (poliovirus and nonpolio enteroviruses) as an indicator of surveillance sensitivity. Results Four quarterly visits were made to 78 ES sites in 21 states of Nigeria, and ES site characteristic data were matched to 1345 samples with an average enterovirus prevalence among sites of 68% (range, 9%–100%). A larger estimated catchment population, high total dissolved solids, and higher pH were associated with enterovirus detection. A random forests model predicted “good” sites (enterovirus prevalence >70%) from measured site characteristics with out-of-sample sensitivity and specificity of 75%. Conclusions Simple measurement of sewage properties and catchment population estimation could improve ES site selection and increase surveillance sensitivity.

Pathological changes with the enteropathy caused by difillobotriosis in dogs

Pathomorphological research of dogs intes-tine allowed us to describe in more detail all encountered cases of pathological manifesta-tion and effect of broad tapeworm on differ-ent tissue structures and their frag-ments.Enteropathies are polymorphous and are introduced with different etiological fac-tors. Intestine helminthiases have heavy share of ethiofactors.Microscopic signs of intestinal lesion of dogs during diphylloboth-riasis were characterized with obvious changes in mucosa and submucosa and their damage pathological changes in a smooth muscle layer were rarely noted.Serous coat and all its structural fragments complied with the norm and didn't have pathological. Extensive zones of damage from mehanical injury were not noted,there were areas of gut wall changes with damage and intestinal villi destruction and epithelial membrane destruc-tion possibly caused by morphological and physiological structural features of the para-site. Characteristic pathological signs were symptomatic desquamation of tessellated epithelium.Extensive damage of serous coat tracedin all the microslides prepared for his-tologic study.All these changes can be a pos-sible reason of development of reduction of nutrient intake.Such kind of research as pathological process encourages more de-tailed identifying of clinical status during diphyllobothriasis and its not characteristic or specific manifestations and will be the additional criteria of high-impact therapeu-tics or its evidence.

Wildfire Alters Spatial Patterns of Available Soil Nitrogen and Understory Environments in a Valley Boreal Larch Forest

Wildfire, a primary natural disturbance in many forests, affects soil nutrient availability and spatial distributions of forest plants. However, post-fire changes in soil nutrients and spatial patterns of understory environments at fine scales are poorly understood. Here, we characterized spatial patterns of soil nitrogen availability and site characteristics at a 3-year-post-fire and an unburned site in a valley boreal larch forest. We also examined the relationship between soil nitrogen availability and site characteristics. The results showed that the burned site had higher NO3− and lower NH4+ than the control. The herb, litter and coarse wood debris cover was greater at the burned site than at the control site with higher soil pH, depth of the organic horizon (DOH) and shrub cover. Relative variability (coefficient of variation) in soil nitrogen and site characteristic variables at the control site was greater than at the burned site except for shrub and regeneration tree seedling cover. Spatial structure (quantified by semi-variograms) was lacking for soil nitrogen and site characteristic variables except for DOH, herb and shrub cover at the control site, but wildfire created a strong spatial structure for all variables. Shorter spatial autocorrelation ranges of soil nitrogen (1.6–3.5 m) and site characteristic variables (2.6–6.0 m) were detected at the burned site, indicating higher heterogeneity. The spatial scale of soil NH4+ was congruent with those of herb, shrub and regeneration tree seedling cover, indicating local coupling, while that of soil NO3− was not. The number of correlations between soil nitrogen and site characteristic variables in the burned site was greater than in the control. These results indicate that fire could not only create higher heterogeneity patches of soil resources, but also strengthen the local coupling between soil resources and understory vegetation, which may impact the establishment and growth of new individual plants.

Analysis of The Javan Green Peafowl (Pavo muticus muticus Linnaeus 1758) Habitat in Baluran and Alas Purwo National Park, East Java

Information of javan green peafowl habitat is commontly informate as general and only discribing typical habitat used. Details information and data of the componen habitat, availability and function such as (food resources, shelter, cover, drinking site, nesting site, etc), and characteristic function of habitat componen at every habitat type are very important to be known how habitat component support to the javan green peafowl live Baluran and Alas Purwo national park is one of distribution javan green peafowl and it was choosen to study on the habitat analysis. The research was aimed to is to analysis and synthesis of availability, fucntion and characteristic habitat of javan green peafowl and to descripbe of ideal habitat for javan green peafowl. Vegetation analysis was used as method approach to obtain composition, structure of vegetation and potential food, shelter, cover and nesting site. Base on activities of the bird and combaining with use of habitat component, analysis of habitat used was done. The result showed that javan green peafowl get food at open area and feed much on grasses and shrubs.Drinking site is areal where water available contiously. The characteristic of feeding site is open area which is growth by grasses and shrubs. The shelter sites were used by the birds such as trees or ground bellow trees where are closed to feeding site. Characteristic roosting site is tall trees (emergent trees), the leaves are not dense, rather open, the branches of the trees form a relatively upright angle to the stem, and not far from the trees present the open area. The green peafowl select nest places at open area which is grow by shrubs and put the eggs at the ground. The ideally habitat of the javan green peafowl composed by open area which is growing by grasses and shrubs as feeding site, places where water resources available as drinking site, tree or shaded places as sheltering and resting site, tree, forest or dense shrubs for covering/refuge site, dust places for dusting activities, open area for dancing and open area which is growing by shrubs for nested places were compound closed each other.

Ideas and perspectives: how coupled is the vegetation to the boundary layer?

Understanding the sensitivity of transpiration to stomatal conductance is critical to simulating the water cycle. This sensitivity is a function of the degree of coupling between the vegetation and the atmosphere and is commonly expressed by the decoupling factor. The degree of coupling assumed by models varies considerably and has previously been shown to be a major cause of model disagreement when simulating changes in transpiration in response to elevated CO2. The degree of coupling also offers us insight into how different vegetation types control transpiration fluxes, which is fundamental to our understanding of land–atmosphere interactions. To explore this issue, we combined an extensive literature summary from 41 studies with estimates of the decoupling coefficient estimated from FLUXNET data. We found some notable departures from the values previously reported in single-site studies. There was large variability in estimated decoupling coefficients (range 0.05–0.51) for evergreen needleleaf forests. This is a result that was broadly supported by our literature review but contrasts with the early literature which suggests that evergreen needleleaf forests are generally well coupled. Estimates from FLUXNET indicated that evergreen broadleaved forests were the most tightly coupled, differing from our literature review and instead suggesting that it was evergreen needleleaf forests. We also found that the assumption that grasses would be strongly decoupled (due to vegetation stature) was only true for high precipitation sites. These results were robust to assumptions about aerodynamic conductance and, to a lesser extent, energy balance closure. Thus, these data form a benchmarking metric against which to test model assumptions about coupling. Our results identify a clear need to improve the quantification of the processes involved in scaling from the leaf to the whole ecosystem. Progress could be made with targeted measurement campaigns at flux sites and greater site characteristic information across the FLUXNET network.

Ideas and perspectives: How coupled is the vegetation to the boundary layer?

Understanding the sensitivity of transpiration to stomatal conductance is critical to simulating the water cycle. This sensitivity is a function of the degree of coupling between the vegetation and the atmosphere, and is commonly expressed by the decoupling factor. The level of decoupling assumed by models varies considerably and has previously been shown to be a major cause for model disagreement when simulating changes in transpiration in response to elevated CO2. The degree of coupling also offers us insight into how different vegetation types control transpiration fluxes, fundamental to our understanding of land–atmosphere interactions. To explore this issue, we estimated the decoupling factor from FLUXNET data, finding notable departures from values previously reported in single site studies. Evergreen needleleaf forests appear to be on the whole more decoupled than the literature suggests, whilst evergreen broadleaved forests and shrubs were considerably more coupled than is suggested in the literature or than would be predicted based on leaf size and plant stature. We found that the assumption that grasses would be strongly decoupled (due to vegetation stature) was only true for high precipitation sites. These results were robust to assumptions about aerodynamic conductance and energy balance closure. Thus, these data form a benchmarking metric against which to test model assumptions about coupling. Our results identify a clear need to improve the quantification of the processes involved in scaling from the leaf to the whole ecosystem. Progress could be made with targeted measurement campaigns at flux sites, as well as more site characteristic information across the FLUXNET network.