The greenhouse effect: the impacts of carbon dioxide (CO2), ultraviolet-B (UV-B) radiation and ozone (O3) on vegetation (crops)

Man's influence on the greenhouse effect, the heating of the atmosphere due to increasing concentrations of tropospheric trace gases, is of much international concern. Among the climatic variables, elevated levels of carbon dioxide (CO₂), ultraviolet-B (UV-B) radiation and ozone (O₃) are known to have a direct effect on vegetation. Our current knowledge of these effects is mainly based on studies involving single stress mode. Thus, the joint effects of CO₂, UV-B and O₃ on vegetation are poorly understood. Nevertheless, based on the literature analysis of plant response to individual stress factors, it can be concluded that sorghum, pea, bean, potato, oat, lettuce, cucumber, rice and tomato are among the crop species potentially sensitive to the joint effects of the aforementioned three variables. Similar information for tree species is essentially lacking.At least with some climatic variables such as O₃, present modeling efforts of cause-effect relationships have proven to be controversial. While at a regional geographic scale ambient CO₂ concentrations appear to be relatively homogeneous, ambient concentrations of O₃ exhibit significant temporal and spatial variability. Because of the protective action of O₃ against UV-B, similar but inverse temporal and spatial variability is expected in the surface levels of UV-B. Thus, future experimental designs should consider these exposure dynamics and modeling cuase-effect relationships should be directed to stochastic processes.     

Transmembrane signal transduction of the alpha(IIb)beta(3) integrin

Integrins are composed of noncovalently bound dimers of an alpha- and a beta-subunit. They play an important role in cell-matrix adhesion and signal transduction through the cell membrane. Signal transduction can be initiated by the binding of intracellular proteins to the integrin. Binding leads to a major conformational change. The change is passed on to the extracellular domain through the membrane. The affinity of the extracellular domain to certain ligands increases; thus at least two states exist, a low-affinity and a high-affinity state. The conformations and conformational changes of the transmembrane (TM) domain are the focus of our interest. We show by a global search of helix-helix interactions that the TM section of the family of integrins are capable of adopting a structure similar to the structure of the homodimeric TM protein Glycophorin A. For the alpha(IIb)beta(3) integrin, this structural motif represents the high-affinity state. A second conformation of the TM domain of alpha(IIb)beta(3) is identified as the low-affinity state by known mutational and nuclear magnetic resonance (NMR) studies. A transition between these two states was determined by molecular dynamics (MD) calculations. On the basis of these calculations, we propose a three-state mechanism.     

耐热碱性磷酸酶(FD-TAP)的结构模型研究

 以大肠杆菌碱性磷酸酶 (BAP)为主要结构模板 ,用计算机同源结构模拟方法构建了耐热碱性磷酸酶 (FD TAP)的三维结构 ,对它们的结构特征进行了分析比较 ,并用Profile 3D和Ramachand ran图等方法分析了结构的合理性 .在此基础上 ,又构建了FD TAP 3个突变体的结构 ,用CHARMM能量计算法研究了FD TAP及其 3个突变体的能量与酶蛋白热稳定性之间的关系 ,得到了与实验完全一致的结果 .结果说明 ,如果氨基酸残基置换使蛋白质分子的总能量降低 ,疏水性增高和柔韧性减小 ,往往使蛋白质的耐热性增加     

Diaminopimelic acid (DAP) analogs bearing isoxazoline moiety as selective inhibitors against meso-diaminopimelate dehydrogenase (m-Ddh) from Porphyromonas gingivalis

Two diastereomeric analogs (1 and 2) of diaminopimelic acid (DAP) bearing an isoxazoline moiety were synthesized and evaluated for their inhibitory activities against meso-diaminopimelate dehydrogenase (m-Ddh) from the periodontal pathogen, Porphyromonas gingivalis. Compound 2 showed promising inhibitory activity against m-Ddh with an IC₅₀ value of 14.9 µM at pH 7.8. The two compounds were further tested for their antibacterial activities against a panel of periodontal pathogens, and compound 2 was shown to be selectively potent to P. gingivalis strains W83 and ATCC 33277 with minimum inhibitory concentration (MIC) values of 773 µM and 1.875 mM, respectively. Molecular modeling studies revealed that the inversion of chirality at the C-5 position of these compounds was the primary reason for their different biological profiles. Based on these preliminary results, we believe that compound 2 has properties consistent with it being a lead compound for developing novel pathogen selective antibiotics to treat periodontal diseases.     

Structural study of copper(I)-bleomycin

Previous NMR studies on Cu(I)-bleomycin have suggested that this adduct has a geometry distinct from Fe(II)BLM. The coordination chemistry of this bleomycin derivative has been investigated through the extension of the NMR data reported previously, and the use of molecular dynamics calculations. The data collected from the NMR experiments support the coordination to the metal center of the primary and secondary amines in beta-aminoalanine and the pyrimidine ring. The detection in the NMR spectra of the signal derived from the amide hydrogen in beta-hydroxyhistidine indicates that this amide is protonated in Cu(I)-bleomycin, precluding participation of the pyrimidinyl carboxamide nitrogen in the coordination of Cu(I), as previously reported. Three-dimensional solution structures compatible with the NMR data have been assayed for Cu(I)-bleomycin for the first time by way of molecular dynamics calculations, and two models showing four and five coordination have been found to be those that better fit the experimental data. In both models the primary amine in beta-aminoalanine is coordinated such that it is located on the same side, with respect to the coordination cage, as the peptide linker fragment. This result seems important for the favored models to be compatible with either their possible oxidation to become one of the reported structures for Cu(II)BLM, or their transformation into Fe(II) adducts able to cause DNA damage.     

Reduction of Np(V) and precipitation of Np(IV) by an anaerobic microbial consortium

A combination of experimental, analytical, and modeling investigations shows that an anaerobic, sulfate-reducing consortium reduced Np(V) to Np(IV), with subsequent precipitation of a Np(IV) solid. Precipitation of Np(IV) during growth on pyruvate occurred before sulfate reduction began. H₂ stimulated precipitation of Np(IV) when added alone to growing cells, but it slowed precipitation when added along with pyruvate. Increasing concentrations of pyruvate also retarded precipitation. Accumulation of an intermediate pyruvate-fermentation product – probably succinate – played a key role in retarding Np(IV) precipitation by complexing the Np(IV). Hydrogen appears to have two roles in controlling Np precipitation: donating electrons for Np(V) reduction and modulating intermediate levels. That Np(V) is microbially reduced and subsequently precipitated under anaerobic conditions has likely beneficial implications for the containment of Np on lands contaminated by radionuclides, but complexation by fermentation intermediates can prevent immobilization by precipitation.     

Computer modeling of a potential agent against SARS-Cov-2 (COVID-19) protease

We have modeled modifications of a known ligand to the SARS-CoV-2 (COVID-19) protease, that can form a covalent adduct, plus additional ligand-protein hydrogen bonds.     

Molecular modeling of cobalt(II) hyaluronate

Structural data for complexes of hyaluronic acid and 3d metals(II) of the fourth group of the periodic table are lacking. A combined QM/MM method was used to solve the structure of the first coordination sphere around the cobalt(II) ion. Some available experimental data were compared with the results obtained via computation and were found to be in good agreement. Our results open the way for using molecular modeling to solve the structure of other metal(II) hyaluronates.     

Le Osservazioni Fitofenologiche Della Rete Italiana Nel 1929 (Annata VIII)

Abstract

Correlative techniques for estimating environmental requirements of species – variably termed ecological niche modeling or species distribution modeling – are becoming very popular tools for ecologists and biogeographers in understanding diverse aspects of biodiversity. These tools, however, are frequently applied in ways that do not fit well into knowledge frameworks in population ecology and biogeography, or into the realities of sampling biodiversity over real-world landscapes. We offer 10 “fixes” – adjustments to typical methodologies that will take into account population ecological and biogeographic frameworks to produce better models.     

Modeling the spread of invasive nutrias (Myocastor coypus) over Iran

Nutria (Myocastor coypus) is a native aquatic rodent to South America, and was introduced to Europe, Asia, Africa and North America for fur farming. The South American nutria or coypu is now considered a pest in the area of introduction, because of its negative impact on biological diversity and ecological relationships. Having information on the invasion range of exotic species is crucial for understanding the ecology of invasive spread and for making good conservation and management planning to address this problem. At the beginning of the 20th century, nutria was introduced into Asia. Nutria was recorded for the first time in Iran in 1995. In the present study we proposed a multiple spatial scale approach to predict the invasion trends of the nutria in Iran, and to define up the “suitable scale” for predicting the invasion trends of this species. Our results highlighted the importance of environmental variables including vegetation density (for food and nesting) and water resource (streams, rivers, and lakes) in distribution of the nutria. Potential areas for the presence of the nutria are located near the Caspian Sea, west and central Iran which receive more precipitation than other parts of the country. Therefore, these parts of Iran may face a much greater risk of invasion risk in the future. Moreover, these results can show the possible risk of nutria invasion to the northern and western neighbors of Iran.     

Influence of a nonaqueous phase liquid (NAPL) on biodegradation of phenanthrene

A series of batch reactor experiments was carried out to examine the effect of a nonaqueous phase liquid (NAPL) on the biodegradation of a hydrophobic solute. A mathematical program model that describes physical processes of solute solubilization and partitioning between the NAPL and aqueous phases as well as microbial degradation and oxygen utilization was used to analyze the test data. The model calculates the cumulative changes in concentration of substrate, cell mass, carbon dioxide, and dissolved oxygen as a function of time. The equations incorporate the effects of solute solubilization, partitioning, biodegradation, as well as oxygen availability. Hexadecane was used as the model NAPL and was not biodegraded in the timeframe of the experiments performed. The model solute was the polyaromatic hydrocarbon, phenanthrene. In agreement with several previous studies, experimental measurements showed that hexadecane increased rates of mineralization of 15 mg phenanthrene when present at low mass but decreased rates at high mass. Model results suggest that partitioning of the phenanthrene into the hexadecane phase limits bioavailability at high NAPL mass. Further the model suggests that mineralization rates were higher with the low NAPL mass because aqueous phenanthrene concentrations were higher in those treatments from ca. 20 to 40 h than in other treatments. Finally, experiments showed that the presence of hexadecane, at all masses tested, resulted in a lower cell yield, effectively increasing the amount of CO₂ produced during the experiment. Model results suggest that this is due to changes in phenanthrene metabolism that are induced by the presence of the hexadecane phase. Model studies aimed at increasing rates of biodegradation by modifying operating conditions are described along with practical approaches to implementing these modifications.     

3,5-Bis(Phenylmethylene)-1-(N-arylmaleamoyl)-4-piperidones: A Novel Group of Cytotoxic Agents

A series of novel 3,5-bis(phenylmethylene)-1-(N-arylmaleamoyl)-4-piperidones 3 have been synthesized which displayed potent cytotoxicity towards human Molt 4/C8 and CEM T-lymphocytes as well as murine P388 and L1210 leukemic cells. In contrast, the related N-arylmaleamic acids 4 possessed little or no cytotoxicity in these four screens. Molecular modeling revealed certain interplanar and bond angles and interatomic distances which were perceived to contribute to the observed bioactivity as well as providing suggestions for future structural modifications of the piperidones 3. Evaluation of representative compounds in series 3 and 4 on the activity of human N-myristoyltransferase revealed that, at the maximum concentration utilized, namely 250?μM, only weak inhibiting properties were displayed by some of the compounds in series 4. Various members of series 3 and 4 were well tolerated in mice.     

Synthesis,molecular modeling studies and anticonvulsant activity of certain (1-(benzyl (aryl) amino) cyclohexyl) methyl esters

A series of (1-(benzyl (aryl) amino) cyclohexyl) methyl esters 7a-n were prepared and screened for their anticonvulsant profile. Screening of these esters 7a-n and their starting alcohols 6a and 6b revealed that compound 7k was the most potent one in the scPTZ screening test with an ED₅₀ value of 0.0056 mmol/kg being about 10- and 164-fold more potent than phenobarbital (ED₅₀ = 0.056 mmol/kg) and ethosuximide (ED₅₀ = 0.92 mmol/kg) as reference drugs, respectively. Meanwhile, in the MES test, compounds 7b and 7k at doses 0.0821 mmol/kg and 0.0334 mmol/kg, exerted 66% and 50% protection of the tested mice, respectively, compared with diphenylhydantoin, which exerted 100% protection at dose 0.16 mmol/kg. In the neurotoxicity screen test, almost all esters 7a-n did not show any minimal motor impairment at the maximum administrated dose. The anticonvulsant effectiveness of esters 7a-n was higher than their corresponding alcohols 6a and 6b. Compounds 7b and 7k exhibited pronounced anticonvulsant activity devoid of neurotoxicity in minimal motor impairment test and hepatotoxicity in the serum enzyme activity assay. 3D pharmacophore model using Discovery Studio 2.5 programs showed high fit value. The obtained experimental results of sc-PTZ activity of compounds 7a-n was consistent with the molecular modeling study.     

Modeling and simulation of oxygen-limited partial nitritation in a membrane-assisted bioreactor (MBR)

Combination of a partial nitritation process and an anaerobic ammonium oxidation process for the treatment of sludge reject water has some general cost-efficient advantages compared to nitrification-denitrification. The integrated process features two-stage autotrophic conversion of ammonium via nitrite to dinitrogen gas with lower demand for oxygen and no external carbon requirement. A nitrifying membrane-assisted bioreactor (MBR) for the treatment of sludge reject water was operated under continuous aeration at low dissolved oxygen (DO) concentrations with the purpose of generating nitrite accumulation. Microfiltration was applied to allow a high sludge retention time (SRT), resulting in a stable partial nitritation process. During start-up of the MBR, oxygen-limited conditions were induced by increasing the ammonium loading rate and decreasing the oxygen transfer. At a loading rate of 0.9 kg N m(-3) d(-1) and an oxygen concentration below 0.1 mg DO L(-1), conversion to nitrite was close to 50% of the incoming ammonium, thereby yielding an optimal effluent within the stoichiometric requirements for subsequent anaerobic ammonium oxidation. A mathematical model for ammonium oxidation to nitrite and nitrite oxidation to nitrate was developed to describe the oxygen-limited partial nitritation process within the MBR. The model was calibrated with in situ determinations of kinetic parameters for microbial growth, reflecting the intrinsic characteristics of the ammonium oxidizing growth system at limited oxygen availability and high sludge age. The oxygen transfer coefficient (K(L)a) and the ammonium-loading rate were shown to be the appropriate operational variables to describe the experimental data accurately. The validated model was used for further steady state simulation under different operational conditions of hydraulic retention time (HRT), K(L)a, temperature and SRT, with the intention to support optimized process design. Simulation results indicated that stable nitrite production from sludge reject water was feasible with this process even at a relatively low temperature of 20 degrees C with HRT down to 0.25 days.     

Modeling the spatial distribution of the striped dolphin (Stenella coeruleoalba) and common bottlenose dolphin (Tursiops truncatus) in the Gulf of Taranto (Northern Ionian Sea,Central-eastern Mediterranean Sea)

Although the EU Marine Strategy Framework Directive (MSFD) is largely based on the establishment of environmental targets and associated proxies to achieve Good Environmental Status (GES), a full suite of ecological indicators for all the ecosystem components is not currently available for ongoing assessment and regular update of GES targets. This is because effective indicators and management actions aimed at preserving/rebuilding marine biodiversity should be found from the knowledge of the spatial distribution of target species and extension of critical habitats as well as their overlapping with human activities, pressure and impacts. In this regard, the spatial distributions of the striped dolphin Stenella coeruleoalba and the common bottlenose dolphin Tursiops truncatus in the Gulf of Taranto (Northern Ionian Sea, Central-eastern Mediterranean Sea) were investigated by means of a generalized additive model (GAM) and a Random Forest (RF) based on sighting data collected during standardized vessel-based surveys carried out from 2009 to 2015. Eight predictive variables were considered, taking into account both the local physiographic features and human activities existing in the investigated area, suggesting an innovative approach to habitat modeling. In particular, the explanatory variables depth, distance from industrial areas and distance from the coast proved to significantly influence the distribution of both dolphin species. In addition, the distribution of S. coeruleoalba and T. truncatus were also significantly shaped by the distance from the navy exercise areas and the fishing areas, respectively. On the contrary, the slope and the distance from the main commercial routes never provided any significant influence. The reliability of GAM and RF models in predicting the spatial distribution of both dolphins was tested by applying the Youden Index method to the ROC curves. The RF model allowed the projection of the expected presence/absence pattern of S. coeruleoalba and T. truncatus to produce the preference habitat versus non habitat map. In particular, the RF model predicted that the striped dolphin is widely present in the central and deeper part of the Gulf of Taranto. In contrast, the common bottlenose dolphin seems to be mainly distributed along the coasts in both the eastern and western sector of the basin. A clear overlapping of the preference habitats estimated for S. coeruleoalba and T. truncatus is shown north of Punta Alice and in front of Policoro as well as offshore from Ugento in the eastern and western parts of the investigated area, respectively. Finally, the critical habitats of S. coeruleoalba and T. truncatus are the outcome of both the influence of environmental conditions and anthropogenic pressures presently occurring in the Gulf of Taranto, basically indicating the need for conservation measures, especially considering that the area is expected to be considered for hydrocarbon prospecting. These results contribute to setting up a baseline reference for future assessment of environmental marine disturbances using cetaceans, which are considered a key group in the MSFD, as an ecological indicator.     

Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs)

Mathematical modeling of complex gene expression programs is an emerging tool for understanding disease mechanisms. However, identification of large models sometimes requires training using qualitative, conflicting or even contradictory data sets. One strategy to address this challenge is to estimate experimentally constrained model ensembles using multiobjective optimization. In this study, we used Pareto Optimal Ensemble Techniques (POETs) to identify a family of proof-of-concept signal transduction models. POETs integrate Simulated Annealing (SA) with Pareto optimality to identify models near the optimal tradeoff surface between competing training objectives. We modeled a prototypical-signaling network using mass-action kinetics within an ordinary differential equation (ODE) framework (64 ODEs in total). The true model was used to generate synthetic immunoblots from which the POET algorithm identified the 117 unknown model parameters. POET generated an ensemble of signaling models, which collectively exhibited population-like behavior. For example, scaled gene expression levels were approximately normally distributed over the ensemble following the addition of extracellular ligand. Also, the ensemble recovered robust and fragile features of the true model, despite significant parameter uncertainty. Taken together, these results suggest that experimentally constrained model ensembles could capture qualitatively important network features without exact parameter information.     

Characterization of the First Fungal Glycosyl Hydrolase Family 19 Chitinase (NbchiA) from Nosema bombycis (Nb)

Chitinases (EC 3.2.1.14), as one kind of glycosyl hydrolase, hydrolyze the β‐(1,4) linkages of chitin. According to the sequence similarity, chitinases can be divided into glycoside hydrolase family 18 and family 19. Here, a chitinase from Nosema bombycis (NbchiA) was cloned and purified by metal affinity chromatography and molecular exclusion chromatography. Sequence analysis indicated that NbchiA belongs to glycoside hydrolase family 19 class IV chitinase. The optimal pH and temperature of NbchiA are 7.0 and 40 °C, respectively. This purified chitinase showed high activity toward soluble substrates such as ethylene glycol chitin and soluble chitosan. The degradation of chitin oligosaccharides (GlcNAc)_2–5 detected by high‐performance liquid chromatography showed that NbchiA hydrolyzed mainly the second glycosidic linkage from the reducing end of (GlcNAc)_3‐5. On the basis of structure‐based multiple‐sequence alignment, Glu51 and Glu60 are believed to be the key catalytic residues. The site‐directed mutation analysis revealed that the enzymatic activity was decreased upon mutation of Glu60, whereas mutation of Glu51 totally abolished the enzymatic activity. This is the first report of a GH19 chitinase in fungi and in Microsporidia.     

Simple criteria for finding (nearly) optimal vaccination strategies

Strategies for best controlling the spread of the diseases with limited vaccine available are explored. I use influenza as a representative disease in point. The model describes the dynamics of influenza spread among multiple groups that have different risks and activity levels. I define a core group consisting of individuals with occupations that brings them in contact with many other people in a day. These occupations may include service industries, teachers, health care, and government workers, to name a few. High-risk individuals are those as typically designated for: children under 5 and adults over 50, people with weakened immune systems as well as emergency and health care personnel. Under certain conditions, shifting vaccination resources away from the high-risk group to the high-activity group will result in improved herd immunity in both the high-risk group and the population as whole. This results in more high-risk people protected even though less of them are being vaccinated, with the obvious implications that current vaccination policies may be far less then optimal. I show that the criteria for the optimal strategy can be derived from simple expressions gleaned from the expression for the basic reproductive number.     

Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1)

Adrenodoxin reductase homologue (Arh1) and yeast adrenodoxin homologue (Yah1) are essential Saccharomyces cerevisiae mitochondrial proteins involved in heme A biosynthesis and in iron-sulfur cluster (FeSC) assembly. Although the role of Arh1 and Yah1 in heme A biosynthesis is fairly well established, their systemic role on FeSC synthesis is not well understood. Also, while it is thought that the reductase Arh1 provides electrons for the ferredoxin Yah1, two hybrid experiments do not show interaction between the two proteins. In the first part of this article, we use structural bioinformatics methods to evaluate the possibility of interaction between Arh1 and Yah1. Using protein model building and docking algorithms, we predict a complex between Arh1 and Yah1 that is similar to that of their bovine homologues (adrenodoxin reductase-adrenodoxin), suggesting that Arh1 can indeed reduce Yah1. The predicted complex allows us to suggest point mutations to either molecule that could hinder Arh1-Yah1 interaction and test the role of Arh1 as the reductase for Yah1. In the second part of this article, we investigate the physiological role of Arh1-Yah1 on FeSC assembly by deriving alternative mathematical models of the process, based on published information. Comparing the dynamical behavior of each model with that observed in reported experiments emphasizes the importance of Arh1-Yah1 providing electrons for in situ FeSC repair. Only when this mode of action of either of the two proteins in FeSC synthesis is considered can previously reported results be reproduced.     

Potential distribution of the invasive freshwater dinoflagellate Ceratium furcoides (Levander) Langhans (Dinophyta) in South America

Dinoflagellates of the genus Ceratium are predominantly found in marine environments, with a few species in inland waters. Over the last decades, the freshwater species Ceratium hirundinella and Ceratium furcoides have colonized and invaded several South American basins. The purpose of this study was to create a distribution model for the invasive dinoflagellate C. furcoides in South America in order to further investigate the basins at potential risk, as well as the environmental conditions that influence its expansion. This species is known to develop blooms due to its mobility, resistance to sedimentation, and optimized use of resources. Although nontoxic, blooms of the species cause many problems to both the natural ecosystems and water users. Potential distribution was predicted by using a maximum entropy algorithm (MaxEnt). Model was run with 101 occurrences obtained from the scientific literature, and climatic, hydrological and topographic variables. The developed model had a very good performance for the study area. The most susceptible areas identified were mainly concentrated in the basins between southeastern Brazil and northeastern Argentina. Besides already affected regions, new potentially suitable areas were identified in temperate regions of South America. The information generated here will be useful for authorities responsible for water and watershed management to monitor the spread of this species and address problems related to its establishment in new environments.