Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture,nitrate gradients

This study coupled a landscape-scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor, appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non-point source nitrogen pollution.     

Factors influencing the abundance of Japanese encephalitis vectors in ricefields in India – I. Abiotic

Mosquitoes of the Culex vishnui subgroup (Diptera: Culicidae) are the most important vectors of Japanese encephalitis (JE) and ricefields are their most productive breeding sites in south India, where predominant species of this subgroup are Culex tritaeniorhynchus Giles, Cx. pseudovishnui Colless and Cx. vishnui Theobald sensu stricto. The relationship of 13 abiotic variables with the abundance of Cx. vishnui subgroup immatures was investigated in transplanted rice fields for 3 years (1991-94) covering three different crop seasons. The results from the multiple regression model suggested paddy height (- ve), water temperature (+ ve), dissolved oxygen (- ve), ammonia nitrogen (- ve) and nitrate nitrogen (+ ve) to be the best predictor variables associated with the immature abundance, nearly always consistent in their effects within and between seasons. Application of synthetic nitrogenous fertilizers to the rice fields was followed by a rise in concentration of ammonia nitrogen and a subsequent increase in nitrate nitrogen level in the rice field water, during which an increase in the density of larval instars was observed.     

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Plant roots nurture a wide variety of microbes via exudation of metabolites, shaping the rhizosphere's microbial community. Despite the importance of plant specialized metabolites in the assemblage and function of microbial communities in the rhizosphere, little is known of how far the effects of these metabolites extend through the soil. We employed a fluid model to simulate the spatiotemporal distribution of daidzein, an isoflavone secreted from soybean roots, and validated using soybeans grown in a rhizobox. We then analysed how daidzein affects bacterial communities using soils artificially treated with daidzein. Simulation of daidzein distribution showed that it was only present within a few millimetres of root surfaces. After 14 days in a rhizobox, daidzein was only present within 2 mm of root surfaces. Soils with different concentrations of daidzein showed different community composition, with reduced α-diversity in daidzein-treated soils. Bacterial communities of daidzein-treated soils were closer to those of the soybean rhizosphere than those of bulk soils. This study highlighted the limited distribution of daidzein within a few millimetres of root surfaces and demonstrated a novel role of daidzein in assembling bacterial communities in the rhizosphere by acting as more of a repellant than an attractant.     

Thermostability of Japanese encephalitis vaccine produced in India.

Different batches of bulk vaccine, final bulk at in-process level, finished freeze-dried and reconstituted Japanese encephalitis vaccine were assayed for their stability at temperatures of 22, 37 and 40 degrees C. After ultrazonal purification of 50 times concentrated brain suspension, JE Bulk vaccine was found to be stable for up to 2 years at 4 degrees C, however, the percentage loss in potency (log 10 N antibody titre) after 2.5 years was 24%. Three-times concentrated final bulk showed rapid deterioration by the fourth week at 37 and 40 degrees C. Freeze-dried JE vaccine maintained at 22 degrees C for 28 weeks did not show perceptible deterioration. At 37 degrees C, the same vaccine started showing deterioration (14%) after 8 weeks whereas at 40 degrees C the loss of potency was 24% after 8 weeks. The freeze-dried vaccine was found to be stable for up to 2 weeks duration at 40 degrees C.     

Regular patterns for proteome-wide distribution of protein abundance across species

A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.     

Preventive strategies for frequent outbreaks of Japanese encephalitis in Northern India

Japanese encephalitis (JE) remains the most important cause of acute viral encephalitis and continues to spread to hitherto unaffected regions like Indonesia, Pakistan and Australia. Approximately 60% of the world population inhabits JE endemic areas. Despite its restricted range mostly in the developing countries, a high annual incidence of 50,000 cases and about 10,000 deaths has been reported. Disease can be fatal in 25% cases. Magnitude of the problem is even more alarming since the survivors are left with serious long-term neuropsychiatric sequelae. Almost every two years, epidemics of JE occur in Indian subcontinent with a high mortality. JE virus infection results in different disease manifestations in host from mild subclinical febrile illness to clinical infections leading to encephalitis. No antiviral treatment is so far available for JE. The prevention of JE can be achieved by controlling the vector or by immunization regime. The vector control in the rural areas, which are the worst affected ones, is practically almost impossible. Three vaccines that have been implicated against JE include inactivated mouse brain derived, inactivated cell culture derived and cell culture derived live attenuated JE vaccine. But each has its own limitation. Currently, attempts to synthesize recombinant DNA vaccine are being made. New therapeutics are on the way of development like use of minocycline, short interfering RNA, arctigenin, rosmarinic acid, DNAzymes etc. However, the immune mechanisms that lead to JE are complex and need to be elucidated further for the development of therapeutics as well as safe and efficacious JE vaccines.     

Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes

Through evolution, Hepatitis B Virus (HBV) developed highly intricate mechanisms exploiting host resources for its multiplication within a constrained genetic coding capacity. Yet a clear picture of viral hitchhiking of cellular processes with spatial resolution is still largely unsolved. Here, by leveraging bDNA-based fluorescence in situ hybridization (FISH) combined with immunofluorescence, we developed a microscopic approach for multiplex detection of viral nucleic acids and proteins, which enabled us to probe some of the key aspects of HBV life cycle. We confirmed the slow kinetics and revealed the high variability of viral replication at single-cell level. We directly visualized HBV minichromosome in contact with acetylated histone 3 and RNA polymerase II and observed HBV-induced degradation of Smc5/6 complex only in primary hepatocytes. We quantified the frequency of HBV pregenomic RNAs occupied by translating ribosome or capsids. Statistics at molecular level suggested a rapid translation phase followed by a slow encapsidation and maturation phase. Finally, the roles of microtubules (MTs) on nucleocapsid assembly and virion morphogenesis were analyzed. Disruption of MTs resulted in the perinuclear retention of nucleocapsid. Meanwhile, large multivesicular body (MVB) formation was significantly disturbed as evidenced by the increase in number and decrease in volume of CD63⁺ vesicles, thus inhibiting mature virion secretion. In conclusion, these data provided spatially resolved molecular snapshots in the context of specific subcellular activities. The heterogeneity observed at single-cell level afforded valuable molecular insights which are otherwise unavailable from bulk measurements.     

Factors influencing the abundance of Japanese encephalitis vectors in ricefields in India--II. Biotic

The relationship of insect predators and phytoplankton with the abundance of Culex tritaeniorhynchus Giles, Cx. vishnui Theobald and Cx. pseudovishnui Colless mosquito larvae and pupae (Diptera: Culicidae) in ricefields was investigated during three rice growing seasons. Notonectids were the most abundant insect predators, whereas diatoms dominated among phytoplankton. Multiple regression analysis showed that the occurrence of notonectids (both nymphs and adults) was negatively associated with larval abundance. Phytoplankton, especially diatoms and blue green algae (BGA), were found to favour abundance of culicine immatures during Navarai and Kuruvai crops, respectively. Larval gut analysis showed that the intake of algae by late instars was high, with 93%, 58% and 24% of diatoms, BGA and green algae, respectively. Filamentous algae may not necessarily be of nutritive value, but they are observed to form mats, which provide protection to the mosquito immatures from the predators.     

Aridity drives spatiotemporal patterns of masting across the latitudinal range of a dryland conifer

Masting, or the synchronous and irregular production of seed crops, is controlled by environmental conditions and resource budgets. Increasing temperatures and shifting precipitation regimes may alter the frequency and magnitude of masting, especially in species that experience chronic resource stress. Yet the effects of a changing climate on seed production are unlikely to be uniform across populations, particularly those that span broad abiotic gradients. In this study, we assessed the spatiotemporal patterns of masting across the latitudinal distribution of a widely distributed dryland conifer species, piñon pine Pinus edulis. We quantified seed cone production from 2004 to 2017 using cone abscission scars in 187 trees from 28 sites along an 1100 km latitudinal gradient to investigate the spatiotemporal drivers of seed cone production and synchrony across populations. Populations from chronically hot and dry areas (greater climatic water deficits and less monsoonal precipitation) tended to have greater interannual variability in seed cone production and smaller crop sizes. Mast years generally followed years with low vapor pressure deficits and high precipitation during key periods of the reproductive process, but the strength of these relationships varied across the region. Populations that received greater monsoonal precipitation were less sensitive to late summer vapor pressure deficits during seed cone initiation yet more sensitive to spring vapor pressure deficits during pollination. Spatially correlated patterns of vapor pressure deficit better predicted synchrony in seed cone production than geographic distance, and these patterns were conserved at distances up to 500 km. These results demonstrate that aridity drives spatiotemporal variability in seed cone production. As a result, projected increases in aridity are likely to decrease the frequency and magnitude of masting in these dry forests and woodlands. Declines in seed production may compound climatic limitations to recruitment and impede tree regeneration, with cascading effects for numerous wildlife species.     

Insecticide resistance status of three vectors of Japanese encephalitis in east central India

Japanese encephalitis (JE) has been reported in different districts of Odisha state (east central India) since 1992. During 2016, a major outbreak of JE and acute encephalitis syndrome (AES) occurred in the Malkangiri district of Odisha, causing 103 deaths in children, of which 37 were caused by JE and 66 by AES. Information on insecticide resistance in JE vectors is important for the selection of appropriate insecticides for use in vector control. The present study was designed to determine the resistance status of three important vectors of JE, Culex vishnui, Culex tritaeniorhynchus and Culex bitaeniorhynchus (Diptera: Culicidae), against dichlorodiphenyltrichloroethane (DDT), malathion and deltamethrin in three districts of Odisha state affected by JE. Female adult mosquitoes were collected using mouth aspirators both indoors and outdoors in JE‐affected villages and used in susceptibility bioassays following World Health Organization guidelines. Knock‐downs were recorded every 10 min up to 1 h and mortality rates were recorded at 24 h post‐exposure. Culex vishnui and Cx. tritaeniorhynchus showed resistance to DDT, malathion and deltamethrin, whereas Cx. bitaeniorhynchus was susceptible in all study districts. The information generated by this study will be highly useful in the planning and implementing of appropriate vector control operations for the prevention and control of JE in east central India.     

Comparing growth patterns among field populations of cereal aphids reveals factors limiting their maximum abundance

Cereal stands in central Europe are commonly infested with three species of aphids that may become serious pests. With increasing abundance, the proportion of a particular species in the total aphid population may remain constant, suggesting a density-independent exponential growth, or the proportion can change, suggesting density-dependent constraints on growth. The constraints that affect particular species, and thus their relative abundance, were studied. The proportionality between maximum abundances of the cereal aphids was studied using a 10-year census of the numbers of aphids infesting 268 winter wheat plots. For two species their abundance on leaves and ears was compared. With increasing aphid density the maximum abundance of Rhopalosiphum padi (Linnaeus) remained proportional, but not that of Sitobion avenae (Fabricius), which was constrained by the smaller surface area of ears compared to leaves. There was no evidence of inter-specific competition. Maximum abundance of R. padi and Metopolophium dirhodum (Walker) on leaves did not change proportionally as the proportion of M. dirhodum decreased with increasing overall aphid density. This decrease was probably caused by the restricted distribution of M. dirhodum, which is confined to leaves, where space is limiting. No change in proportion between populations was detected when the average densities were below 0.54 aphids per leaf or ear. Non-proportional relationships between aphid populations appeared to be due to spatial constraints, acting upon the more abundant population. Detecting the limitation of population growth can help with the assessment of when density-independent exponential growth is limited by density-dependent factors. This information may help in the development of models of cereal aphid population dynamics.     

Coherent patterns of abundance and size of a tropical snapper in dynamic estuary systems

Although tropical estuaries are important juvenile habitats for the snapper, Lutjanus russelli, the extent of this utilisation, and relationships to physical variation are unknown. We used fish trapsto investigate spatial and temporal patterns of distribution, abundance and size of L. russelli within and between three tropical estuaries (Cattle, Barramundi and Alligator Creeks) over a two year period. L. russelli showed no indication of spatial segregation by size along the lengths of the estauries. The probability of capturing L. russelli was similar throughout Barramundi Creek and the seaward parts of Cattle Creek. However, the probability of capture fell markedly in upstream regions of Cattle Creek. These areas where characterised by depressed salinity levels due to seasonal flooding. High probabilities of capture of L. russelli during the wet and post-wet seasons in the whole of Barramundi Creek correlated with the time of smallest modal sizes. Thisreflected the entry of large numbers of small recruits into the trappable population. Temporal patterns in mean length were consistent for both years. The major feature of the size data was a clear pattern of seasonal change in the mean fork length of L. russelli, with largest mean sizes occurring in the pre-wet and the smallest mean sizes in the wet and post-wet seasons. This pattern probably reflected the interaction of four processes; the entry of new recruits into the trappable population, growth and mortality during residence in the estuarine nursery habitats, and migration of large fish away from the estuaries. The three creeks studied provided L. russelli with a harsh and extremely variable environment. Over the three creeks, salinities ranged from extremely hyposaline (0) to very hypersaline (55.5) and varied up to 39 within a location. However, despite the substantial physical differences and the spatial separation of the three estuaries, the patterns of temporal change were clear and consistent. Overall, the annual pattern of change insize seemed to relate more to biological processes of recruitment, mortality and migration than to responses to physical variability.     

Precise localization and dynamic distribution of Japanese encephalitis virus in the rain nuclei of infected mice

Japanese encephalitis virus (JEV) is a pathogen that causes severe vector-borne zoonotic diseases, thereby posing a serious threat to human health. Although JEV is potentially neurotropic, its pathogenesis and distribution in the host have not been fully elucidated. In this study, an infected mouse model was established using a highly virulent P3 strain of JEV. Immunohistochemistry and in situ hybridization, combined with anatomical imaging of the mouse brain, were used to dynamically localize the virus and construct three-dimensional (3D) images. Consequently, onset of mild clinical signs occurred in some mice at 3.5 d post JEV infection, while most mice displayed typical neurological signs at 6 d post-infection (dpi). Moreover, brain pathology revealed typical changes associated with non-suppurative encephalitis, which lasted up to 8 d. The earliest detection of viral antigen was achieved at 3 dpi in the thalamus and medulla oblongata. At 6 dpi, the positive viral antigen signals were mainly distributed in the cerebral cortex, olfactory area, basal ganglia, thalamus, and brainstem regions in mice. At 8 dpi, the antigen signals gradually decreased, and the localization of JEV tended to concentrate in the cerebrum and thalamus, while no viral antigen was detected in the brain at 21 dpi. In this model, the viral antigen was first expressed in the reticular thalamic nucleus (Rt), and the virus content is relatively stable. The expression of the viral antigen in the hippocampal CA2 region, the anterior olfactory nucleus, and the deep mesencephalic nucleus was high and persistent. The 3D images showed that viral signals were mostly concentrated in the parietal cortex, occipital lobe, and hippocampus, near the mid-sagittal plane. In the early stages of infection in mice, a large number of viral antigens were detected in denatured and necrotic neurons, suggesting that JEV directly causes neuronal damage. From the time of its entry, JEV is widely distributed in the central nervous system thereby causing extensive damage.     

长江三角洲四城市城镇化过程景观动态变化格局比较

以1990、1995和2000年三期Landsat-TM/ETM⁺遥感影像解译的江苏省土地利用图为数据源,运用GIS的缓冲区分析和景观格局指数等方法,对南京、苏州、无锡和常州4市10年来的城市扩张规律和动态格局变化模式进行了定量研究,并在时间和空间维度上进行比较。结果表明：4市在1990—2000年的快速城市化过程中既有相似的发展规律又各自表现出不同的特点。10年间,4市城市用地面积都不断增加,但前5年增长规模和速度远大于后5年;1990—1995年,4市城市扩张以城市中心建成区不断外扩,摊大饼发展模式为主,而1996—2000年城市扩张则以城乡交错带新增城市用地斑块为主。南京最活跃的地带是距城市中心3～6 km地区;无锡的活跃带从距城市中心9～12 km处内移到6～9 km处;常州城市形态结构简单化最为明显;苏州景观破碎化趋势在1996—2000年间加剧。     

The role of urea in the oviposition behaviour of Japanese encephalitis vectors in rice fields of South India

The effect of urea on the oviposition behaviour of culicine vectors of Japanese encephalitis was studied in rice fields. Gravid females had a strong preference for oviposition in urea treated areas in rice fields, while no such preference was exhibited in untreated areas. The egg laying declined in the area where urea treated water surface had a mechanical barrier, which allowed volatile fractions to escape, but prevented contact with the water. Urea was shown to act as an oviposition attractant/stimulant for Culex tritaeniorhynchus, but its role was not clear for Cx. vishnui, as the number of egg rafts obtained for the latter species was low.