Turnip mosaic potyvirus (TuMV) is probably the most widespread and damaging virus that infects cultivated brassicas worldwide. Previous work has indicated that the virus originated in western ...Eurasia, with all of its closest relatives being viruses of monocotyledonous plants. Here we report that we have identified a sister lineage of TuMV-like potyviruses (TuMV-OM) from European orchids. The isolates of TuMV-OM form a monophyletic sister lineage to the brassica-infecting TuMVs (TuMV-BIs), and are nested within a clade of monocotyledon-infecting viruses. Extensive host-range tests showed that all of the TuMV-OMs are biologically similar to, but distinct from, TuMV-BIs and do not readily infect brassicas. We conclude that it is more likely that TuMV evolved from a TuMV-OM-like ancestor than the reverse. We did Bayesian coalescent analyses using a combination of novel and published sequence data from four TuMV genes helper component-proteinase protein (HC-Pro), protein 3(P3), nuclear inclusion b protein (NIb), and coat protein (CP). Three genes (HC-Pro, P3, and NIb), but not the CP gene, gave results indicating that the TuMV-BI viruses diverged from TuMV-OMs around 1000 years ago. Only 150 years later, the four lineages of the present global population of TuMV-BIs diverged from one another. These dates are congruent with historical records of the spread of agriculture in Western Europe. From about 1200 years ago, there was a warming of the climate, and agriculture and the human population of the region greatly increased. Farming replaced woodlands, fostering viruses and aphid vectors that could invade the crops, which included several brassica cultivars and weeds. Later, starting 500 years ago, inter-continental maritime trade probably spread the TuMV-BIs to the remainder of the world.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Hymexazol is a volatile fungicide widely used in agriculture, causing its abundance in the atmosphere; thus, its atmospheric fate and conversion are of great importance when assessing its ...environmental impacts. Herein, we report a theoretical kinetic mechanism for the oxidation of hymexazol by OH radicals, as well as the subsequent reactions of its main products with O2 and then with NO by using the Rice–Ramsperger–Kassel–Marcus-based Master equation kinetic model on the potential energy surface explored at the ROCBS-QB3//M06-2X/aug-cc-pVTZ level. The predicted total rate constants k total(T, P) for the reaction between hymexazol and OH radicals show excellent agreement with scarcely available experimental values (e.g., 3.6 × 10–12 vs (4.4 ± 0.8) × 10–12 cm3/molecule/s at T = 300 K and P = 760 Torr); thus, the calculated kinetic parameters can be confidently used for modeling/simulation of N-heterocycle-related applications under atmospheric and even combustion conditions. The model shows that 3,4-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-5-yl (IM2), 3,5-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-4-yl (IM3), and (3-hydroxy-1,2-oxazol-5-yl)methyl (P8) are the main primary intermediates, which form the main secondary species of (3,4-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-5-yl)dioxidanyl (IM4), (3,5-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-4-yl)dioxidanyl (IM7), and ((3-hydroxy-1,2-oxazol-5-yl)methyldioxidanyl (IM11), respectively, through the reactions with O2. The main secondary species then can react with NO to form the main tertiary species, namely, (3,4-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-5-yl)oxidanyl (P19), (3,5-dihydroxy-5-methyl-4,5-dihydro-1,2-oxazol-4-yl)oxidanyl (P21), and (3-hydroxy-1,2-oxazol-5-yl)methyloxidanyl (P23), respectively, together with NO2. Besides, hymexazol could be a persistent organic pollutant in the troposphere due to its calculated half-life τ1/2 of 13.7–68.1 h, depending on the altitude.
Cauliflower mosaic virus (CaMV) is a plant pararetrovirus with a double-stranded DNA genome. It is the type member of the genus Caulimovirus in the family Caulimoviridae. CaMV is transmitted by sap ...inoculation and in nature by aphids in a semi-persistent manner. To investigate the patterns and timescale of CaMV migration and evolution, we sequenced and analyzed the genomes of 67 isolates of CaMV collected mostly in Greece, Iran, Turkey, and Japan together with nine published sequences. We identified the open-reading frames (ORFs) in the genomes and inferred their phylogeny. After removing recombinant sequences, we estimated the substitution rates, divergence times, and phylogeographic patterns of the virus populations. We found that recombination has been a common feature of CaMV evolution, and that ORFs I-V have a different evolutionary history from ORF VI. The ORFs have evolved at rates between 1.71 and 5.81×10(-4) substitutions/site/year, similar to those of viruses with RNA or ssDNA genomes. We found four geographically confined lineages. CaMV probably spread from a single population to other parts of the world around 400-500 years ago, and is now widely distributed among Eurasian countries. Our results revealed evidence of frequent gene flow between populations in Turkey and those of its neighboring countries, with similar patterns observed for Japan and the USA. Our study represents the first report on the spatial and temporal spread of a plant pararetrovirus.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Fibrinolytic enzymes, such as Nattokinases from Bacillus species are known to degrade the fibrin blood clots. They belong to serine protease group having commercial applications, such as therapeutic ...agents and functional food formulation.
The present study reports some characteristics and fibrinolytic activity of serine protease from B. subtilis C10 strain that was isolated from shrimp shell.
Extracellular enzyme from B. subtilis C10 culture was harvested and partially purified by ammonium sulphate precipitation. Fibrinolytic activity of the enzyme was determined by zymography and measured by spectrophotometry with fibrinogen and thrombin used as substrates. The optimal temperature and pH for fibrinolytic activity were studied in the range of 31-43ºC and 5-10, respectively. The thermal and pH stability of enzyme was studied by incubating enzyme for 30 min in the same range of temperature and pH as above. The effect of some metal ions and reagents on fibrinolytic activity of enzyme was evaluated by concentrations of 5 mM and 5%, respectively.
Zymogram analysis indicated the presence of four fibrinolytic enzymes with molecular weights of approximately 69, 67, 39 and 36 kDa. The optimal temperature and pH for enzyme activity were 37°C and 9, respectively. The thermal and pH stability ranged from 35-39°C and 8-10, respectively. Fibrinolytic activity reached a maximum value of about 400 U/mg protein after 16 h of C10 strain culture. Enzyme has been drastically inhibited by PMSF and SDS, and partially inhibited by EDTA, while Triton X-100 has significantly increased enzyme activity. Effects of ions such as Mg2+, Ca2+ and Mn2+ on enzyme were negligible, except Cu2+ and Zn2+ have strongly decreased its activity.
Results from the present study suggested that enzyme obtained from B. subtilis C10 could be serine protease that has a high fibrinolytic activity up to about 400 U/mg protein at the most appropriate temperature and pH of 37ºC and 9. This activity can be improved up to 142% by incubating enzyme with 5% Triton X-100 for 30 min.
This study provides a detailed understanding of how the reaction between CH3NH, one of the primary products of the CH3NH2 + OH/Cl reactions, and NOx occurs in the atmosphere since the reaction is ...expected to be a dominant sink for the tropospheric CH3NH radical. First, we focus on the reaction of the aminyl radical CH3NH with NO2, complementing the known reaction between CH3NH and NO, to provide the overall picture of the CH3NH + NOx system. The reaction was meticulously examined across the extended range of temperature (298–2000 K) and pressure (0.76–76 000 torr) using quantum chemistry calculations and kinetic modeling based on the framework of the Rice–Ramsperger–Kassel–Marcus (RRKM)-based master equation. Highly correlated electronic structure calculations unveil that the intricate reaction mechanism of the CH3NH + NO2 reaction, which can proceed through O-addition or N-addition to form NO2, encompasses numerous steps, channels, and various intermediates and products. The temperature-/pressure-dependent kinetic behaviors and product distribution of the CH3NH + NO2 reaction are revealed under atmospheric and combustion conditions. The main products under atmospheric conditions are found to be CH3NHO and NO, as well as CH3NHNO2, while under combustion conditions, the primary products are only CH3NHO and NO. Given its stability under ambient conditions, CH3NHNO2, a nitramine, is believed to have the potential to induce DNA damage, which can ultimately result in severe cancers. Secondly, by building upon prior research on the CH3NH + NO system, this study shows that the reaction of CH3NH with NOx holds greater importance in urban areas with elevated NOx emissions than other oxidants like O2. Furthermore, this reaction occurs swiftly and results in the creation of various compounds, such as the carcinogenic nitrosamine (CH3NHNO), carcinogenic nitramine (CH3NHNO2), CH3NNOH, (CH3NN + H2O) and (CH3NHO + NO).
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•Detailed kinetic mechanism of the OH-initiated oxidation of cyclopentadiene is computationally reported for T = 298 – 2000 K &P = 0.76 – 7600 Torr.•Kinetic discrepancies among ...literature data are resolved.•Reaction mechanism shift is observed with the dominance of OH-addition and H-abstraction channels at low and high temperatures, respectively.•U-shaped T-dependence and weakly positive P-dependence at low temperatures of the rate constants are observed.
This work computationally reports a detailed kinetic mechanism of the OH-initiated reaction of 1,3-cyclopentadiene (CPDN), a key intermediate during the oxidation processes of aromatic and acyclic compounds, in the wide range of T = 298 – 2000 K and P = 0.76 – 7600 Torr. The temperature- and pressure-dependent behaviors of the title reaction were simulated using the RRKM-based Master Equation rate model on the potential energy profile explored at M06-2X/aug-cc-pVTZ level. The model reveals that the OH-addition on Cα of CPDN to form adduct 5-hydroxycyclopent-2-en-1-yl dominates at low temperatures (e.g., T ≤ 1000 K at 760 Torr), while the direct H-abstraction channels from Cα and Cβ of CPDN become predominant at high temperatures (e.g., T > 1000 K at 760 Torr). The observed U-shaped temperature-dependent behaviors and slightly positive pressure dependence at low temperatures (e.g., T ≤ 1000 K &P = 760 Torr) of the total rate constants are described by a double modified Arrhenius expression as ktot(T) = 1.61 × 109 × T−6.67 × exp-1627.6 K/T + 3.87 × 10-17 × T2.08 × exp-2519.9 K/T (cm3/molecule/s) for T = 298 – 2000 K &P = 760 Torr. Discrepancies in ktotal(T, P) between the early calculations and measurements in low- and high-temperature regimes are also resolved. Also, the thermodynamically consistent mechanism is provided to advance modeling and simulation of any CPDN-related applications.
A major obstacle in prioritizing species or habitats for conservation is the degree of unrecognized diversity hidden within complexes of morphologically similar, "cryptic" species. Given that ...amphibians are one of the most threatened groups of organisms on the planet, our inability to diagnose their true diversity is likely to have significant conservation consequences. This is particularly true in areas undergoing rapid deforestation, such as Southeast Asia. The Southeast Asian genus Leptolalax is a group of small-bodied, morphologically conserved frogs that inhabit the forest-floor. We examined a particularly small-bodied and morphologically conserved subset, the Leptolalax applebyi group, using a combination of molecular, morphometric, and acoustic data to identify previously unknown diversity within. In order to predict the geographic distribution of the group, estimate the effects of habitat loss and assess the degree of habitat protection, we used our locality data to perform ecological niche modelling using MaxEnt. Molecular (mtDNA and nuDNA), acoustic and subtle morphometric differences revealed a significant underestimation of diversity in the L. applebyi group; at least two-thirds of the diversity may be unrecognised. Patterns of diversification and microendemism in the group appear driven by limited dispersal, likely due to their small body size, with several lineages restricted to watershed basins. The L. applebyi group is predicted to have historically occurred over a large area of the Central Highlands of Vietnam, a considerable portion of which has already been deforested. Less than a quarter of the remaining forest predicted to be suitable for the group falls within current protected areas. The predicted distribution of the L. applebyi group extends into unsurveyed watershed basins, each potentially containing unsampled diversity, some of which may have already been lost due to deforestation. Current estimates of amphibian diversity based on morphology alone are misleading, and accurate alpha taxonomy is essential to accurately prioritize conservation efforts.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Leptolalax applebyi group of Asian leaf-litter frogs currently comprises four species of particularly small-bodied (<40 mm SVL) species distributed in the Central Highlands of Vietnam and ...northeastern Cambodia. In addition to their small size, the group is characterized by their morphological and genetic similarities, as well as their breeding habitat at headwaters of small mountain streams and seeps. A recent study suggested that at least two-thirds of the diversity of the group remained hidden within morphologically cryptic lineages. We expand upon the molecular, morphometric, and acoustic data and formally delineate and describe five of these lineages as distinct species: Leptolalax ardens sp. nov., Leptolalax kalonensis sp. nov., Leptolalax pallidus sp. nov., Leptolalax maculosus sp. nov., and Leptolalax tadungensis sp. nov. Due to habitat loss, the current ranges of these species are likely to be a fraction of their historical extent and under continued threat from deforestation.
The global trade in amphibians is widespread, involves hundreds of species, and has been implicated in amphibian population declines. The pet trade is the primary driver for population declines in ...one Southeast Asian newt species (Laotriton laoensis), and is a known threat to most of the 13 other known species from the region. Despite this, there has been little attempt to assess the impact of collection for the pet trade on Southeast Asian newts. We examined available import data from the US, Europe and Hong Kong, assessed current online trade and surveyed local pet traders within Southeast Asia. Large numbers of Southeast Asian newts are harvested from the wild to meet the demands of the international pet trade, with more than 7500 individual newts imported into the US alone during 2005–2014. Internet trade surveys revealed the global extent of the trade, with Southeast Asian newts for sale as pets in 15 countries throughout Europe, Asia and North America, at between~USD30–260 each. The trade in newts within Southeast Asia appears negligible in comparison. Urgent measures are required in order to conserve Southeast Asian newts but the lack of data on the species and number of individuals impacted by the pet trade makes it difficult to monitor and accurately assess its threat. We strongly recommend that all Southeast Asian newts be listed on CITES. This measure should improve monitoring of trade and provides importing countries opportunity to curb trade in species that were illegally harvested, thus helping to safeguard wild populations.
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•The pet trade is a threat to Southeast Asian newt species, but is poorly understood.•The limited import data available revealed substantial trade in Southeast Asian newts.•Internet surveys revealed Southeast Asian newts for sale as pets in 15 countries.•We recommend that all Southeast Asian newts should be listed in CITES.
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