Physicochemcial Properties Research Articles

Review on The Impacts of Biochar and Soil Organic Matter (SOM) Habitation toward the Soil Physico-Chemical Properties Conjugating with Maize (Zea mays) Growth Performance

This study studies the complex relationships between maize growth, soil organic matter, and soil physico-chemcial properties, with an emphasis on biochar. It examines how soil organic matter affects pH, bulk density, Cation Exchange Capacity (CEC), porosity, and nutrient levels. Biochar and soil organic matter increase soil pH by decomposing organic anions. With biochar, increasing soil organic matter concentration reduces bulk density, improving soil structure, porosity, and water retention. By increasing Cation Exchange Capacity (CEC), biochar and soil organic matter improve soil nutrient retention and delivery, which is essential for soil fertility. As a soil organic matter component, biochar provides macro and micronutrients, boosting soil production. The study also highlights the importance of soil porosity in plant growth, with sandy soils having high porosity and leaching susceptibility and soil organic matter. However, loam soils, made of sand, clay, and silt, have a balanced porosity and soil organic matter concentration that makes them ideal for agriculture. These data show how organic matter, and biochar, affect maize growth and soil physico-chemical properties. This finding has major implications for protecting the environment and sustainable agriculture.

Petroleum pollution and microbial community structure in the soil of Liaohe Oilfield.

We analyzed the soil physico-chemcial properties, microbial community structure, petroleum hydrocarbon contents and components in soil samples from the well sites of Shuguang, Huanxi-ling and Jinzhou oil exploitation sites in Liaohe Oilfield, with uncontaminated paddy soil as a control. The results showed that: 1) The soil around all the three oil exploitation sites were seriously polluted by petroleum with certain differences in the petroleum hydrocarbon contents and components. The average content of petroleum hydrocarbon in the soil of Shuguang and Huanxiling oil exploitation sites was two times higher than that of Jinzhou oil exploitation site. The content of resins and asphaltenes in the soil of Shuguang oil exploitation site was the highest, while the soils of Huan-xiling and Jinzhou oil exploitation sites had the highest alkane content, which accounting for more than 40% in all the sites. 2)Compared with the paddy soil, the microbial OTU numbers, Chao1 and Shannon indices in the soil of Jinzhou oil exploitation site increased. The dominant phyla and genera were similar in the soil of all oil exploitation sites but with large differences in abundance. The soil in Jinzhou oil exploitation site had higher abundance of Mycobacterium and Pseudomonas, while Sphingomonas and Nocardioides, Massilia in the soil of Shuguang oil exploitation site, and Lysobacter, Thiobacillus and Pseudomonas in the soil of Huanxiling oil exploitation site. 3) The abundances of Sphingomonas, Nocardioides, Thiobacillus, Massilia, Pseudomonas and the contents of total petroleum hydrocarbons, total organic carbon and resins and asphaltenes were significantly positively correlated, while Mycobacterium, Lysobacter and Pseudomonas were significantly positively correlated with the contents of total nitrogen and total phosphorus. This study systematically analyzed the petroleum hydrocarbon, physico-chemcial properties and microbial communities in the soil of different oil exploitation sites, and revealed the specific dominant bacterial genera and microbial communities in the soil of Liaohe Oilfield. Our results provided a theoretical basis for functional bacterium screening and microbial community construction in the remediation process of petroleum contaminated soil in Liaohe Oilfield, and a reference for efficient degradation bacteria screening in other oilfields.

Quantifying Protein-Protein Interactions in Molecular Simulations.

Interactions among proteins, nucleic acids, and other macromolecules are essential for their biological functions and shape the physicochemcial properties of the crowded environments inside living cells. Binding interactions are commonly quantified by dissociation constants Kd, and both binding and nonbinding interactions are quantified by second osmotic virial coefficients B2. As a measure of nonspecific binding and stickiness, B2 is receiving renewed attention in the context of so-called liquid–liquid phase separation in protein and nucleic acid solutions. We show that Kd is fully determined by B2 and the fraction of the dimer observed in molecular simulations of two proteins in a box. We derive two methods to calculate B2. From molecular dynamics or Monte Carlo simulations using implicit solvents, we can determine B2 from insertion and removal energies by applying Bennett’s acceptance ratio (BAR) method or the (binless) weighted histogram analysis method (WHAM). From simulations using implicit or explicit solvents, one can estimate B2 from the probability that the two molecules are within a volume large enough to cover their range of interactions. We validate these methods for coarse-grained Monte Carlo simulations of three weakly binding proteins. Our estimates for Kd and B2 allow us to separate out the contributions of nonbinding interactions to B2. Comparison of calculated and measured values of Kd and B2 can be used to (re-)parameterize and improve molecular force fields by calibrating specific affinities, overall stickiness, and nonbinding interactions. The accuracy and efficiency of Kd and B2 calculations make them well suited for high-throughput studies of large interactomes.

Engineering two-dimensional metal oxides via surface functionalization for biological applications.

Two-dimensional (2D) metal oxides (MOs) have attracted a considerable amount of attention for various biological applications due to their unique physicochemcial properties such as high photothermal response, temperature superconductivity, photoluminescence, flexibility, unique catalytic capability, plasmonic tunability and relatively low toxicity. However, the sophisticated physiological environments in biosystems stimulate various explorations of surface functionalization to improve the dispersity, stability and biocompatibility of 2D MOs. Moreover, 2D MOs exhibit remarkably tuneable properties via creating oxygen vacancies or doping, which endow 2D MOs with additional capabilities in biological applications. The large surface to volume ratio inherent in these materials also allows easy functionalization and maximal interaction with the external environment. Much work has been done in tailoring 2D MOs through physical/chemical functionalization for use in a diverse range of biomedical applications such as biosensors, bioimaging, drug/gene delivery carriers or even as therapeutic agents. In this review, current progress on 2D MOs functionalized for various biological applications will be presented. Additional relevant issues concerning the research challenges, technology limitations, and future trends have also been discussed.

Polyethyleneimine anchored copper(II) complexes: Synthesis, characterization, in vitro DNA binding studies and cytotoxicity studies

The water soluble polyethyleneimine–copper(II) complexes, [Cu(phen)(L-tyr)BPEI]ClO4 (where phen=1,10-phenanthroline, L-tyr=L-tyrosine and BPEI=branched polyethyleneimine) with various degree of copper(II) complex units in the polymer chain were synthesized and characterized by elemental analysis and electronic, FT-IR, EPR spectroscopic techniques. The binding of these complexes with CT-DNA was studied using UV–visible absorption titration, thermal denaturation, emission, circular dichroism spectroscopy and cyclic voltammetric methods. The changes observed in the physicochemcial properties indicated that the binding between the polymer–copper complexes and DNA was mostly through electrostatic mode of binding. Among these complexes, the polymer–copper(II) complex with the highest degrees of copper(II) complex units (higher degrees of coordination) showed higher binding constant than those with lower copper(II) complex units (lower degrees of coordination) complexes. The complex with the highest number of metal centre bound strongly due to the cooperative binding effect. Therefore, anticancer study was carried out using this complex. The cytotoxic activity for this complex on MCF-7 breast cancer cell line was determined adopting MTT assay, acridine orange/ethidium bromide (AO/EB) staining and comet assay techniques, which revealed that the cells were committed to specific mode of cell death either apoptosis or necrosis.

Complex Self-Assembly of Reverse Poly(butylene oxide)-Poly(ethylene oxide)-Poly(butylene oxide) Triblock Copolymers with Long Hydrophobic and Extremely Lengthy Hydrophilic Blocks

Amphiphilic block copolymers have emerged during last years as a fascinating substrate material to develop micellar nanocontainers able to solubilize, protect, transport, and release under external or internal stimuli different classes of cargos to diseased cells or tissues. However, this class of materials can also induce biologically relevant actions, which complement the therapeutic activity of their cargo molecules through their mutual interactions with biologically relevant entities (cellular membranes, proteins, organelles...); these interactions at the same time, are regulated by the nature, conformation, and state of the copolymeric chains. For these reasons, in this paper we investigated the self-assembly process and physico-chemcial properties of two reverse triblock poly(butylene oxide)-poly(ethylene oxide)-poly(butylene oxide) block copolymers, BO14EO378BO14 and BO21EO385BO21, which have been recently found to be very useful as drug delivery nanovehicles and biological response modifiers under certain conditions (A. Cambón et al. Int. J. Pharm. 2013, 445, 47-57) in order to obtain a clear picture of the solution behavior of this class or block copolymers and to understand their biological activity. These block copolymers are characterized by possessing long BO blocks and extremely lengthy central EO ones, which provide them with a rich rheological behavior characterized by the formation of flowerlike micelles with sizes ranging from 20 to 40 nm in aqueous solution and the presence of intermicellar bridging even at low copolymers concentrations as denoted by atomic force microscopy. Bridging is also clearly observed by analyzing the rheological response of these block copolymers both storage and loss moduli upon changes on time, temperature, and or concentration. Strikingly, the relatively wide Poisson distribution of the polymeric chains make the present copolymers behave rather distinctly to conventional associative thickeners. The observed rich rheological behavior and their tunability also make these copolymers promising materials to configure drug gelling depots.

MULTIRESOLUTION ANALYSIS UNCOVERS HIDDEN CONSERVATION OF PROPERTIES IN STRUCTURALLY AND FUNCTIONALLY SIMILAR PROTEINS

Physicochemcial properties of amino acids are important factors in determining protein structure and function. Most approaches make use of averaged properties over entire domains or even proteins to analyze their structure or function. This level of coarseness tends to hide the richness of the variability in the different properties across functional domains. This paper studies the conservation of physicochemical properties in a functionally similar family of proteins using a novel wavelet-based technique known as multiresolution analysis. Such an analysis can help uncover characteristics that can otherwise remain hidden. We have studied the protein kinase family of sequences and our findings are as follows: (a) a number of different properties are conserved over the functional catalytic domain irrespective of the sequence identities; (b) conservation of properties can be observed at different frequency levels and they agree well with the known structural/functional properties of the subdomains for the protein kinase family; (c) structural differences between the different kinase family members are reflected in the waveforms; and (d) functionally important mutations show distortions in the waveforms of conserved properties. The potential usefulness of the above findings in identifying functionally similar sequences in the twilight and midnight zones is demonstrated through a simple prediction model for the protein kinase family which achieved a recall of 93.7% and a precision of 96.75% in cross-validation tests.

Spectrochemical and electrochemical studies of 21-thiatetra( p-tolyl)porphyrin and its copper(II) complexes

Electrochemistry, NMR, ESR and UV-Vis spectroscopy of 21-thiatetra( p-tolyl)porphyrin (STpTPH) and respective copper(II) (21-tiatetra( p-tolyl)porphyrin) X Cu(STpTP)X (X=Cl −, Br −, HCO 3 −, ClO 4 −, PPh 3) complexes have been investigated. Monothiaporphyrin is an analogue of widely studied tetraphenylporphyrin, where one of the pyrrole rings has been replaced by a thiophene moiety. The impact of the replacement and the coordinating abilities of thiophene sulfur have been studied. STpTPH undergoes a two step proton addition in dichloromethane. Mono- and dication formations result in distorting the planar thiaporphyrin structure as confirmed by NMR and UV-Vis data. The electronic spectra of Cu(STpTP)X have a similar pattern to the monocation form but the pronounced dependence of the band positions on the ligand character has been established. An ESR spectrum pattern is typical for quasi-tetragonal Cu(II)systems. Parallel features show well resolved seven lines associated with coordination of three nearly equivalent nitrogens. The ESR parameters, particularly hyperfine coupling constant A, have been correlated with the geometry of Cu(II) porphyrins or porphyrin- like ligands. The influence of the axial ligand on the ESR parameters has also been discussed. Cyclic voltammetry studies show that Cu(STpTP)X exhibits a well defined Cu(II)/Cu(I) reduction ( E 1/2= −0.14 ±0.03 V depending on the axial ligand), reported previously only for Cu(II) N-substituted porphyrins but not for Cu(II) porphyrins. The second reduction step results in demetalation. The physicochemcial properties of Cu(STpTP)X are considerably different from Cu(TTP) and closely resemble those of Cu(II) N-substituted porphyrin. Comparison between the electrochemical and spectroscopical properties has been discussed in terms of the general stability of a Cu(II)-axial ligand bond.

Studies on Aspergillus proteinase. 3. Physicochemical properties and amino acid composition of Aspergillus melleus proteinases. (Studies on enzymes. 39)

Some physicochemcial properties and amino acid compositions of the Aspergillus melleus proteinases were investigated. 1) Semi-alkaline proteinase from Aspergillus melleus : The molecular weight was 30300 using the Svedverg's formula, based upon the values of the sedimentation coefficient (S020, w=2.98S), the diffusion coefficient (D020, w=8.75×10-7 cm2/sec), and the partial specific volume (V=0.728). The enzyme contains 16.35% of nitrogen and is composed of 314 residues of amino acid ; Asp. 36, Glu. 18, Ser. 37, Thr. 25, Gly. 45, Ala. 46, Val. 33, Leu. 21, Ileu. 15, Pro. 9, Phe. 7, Tyr. 11, Trp. 2, Arg. 2, Lys. 5, His. 2, (amide-NH3)16. 2) Alkaline proteinase from Aspergillus melleus : The molecular weight was 27900 using the Svedverg's formula, based upon the value of the sedimentation coefficient (S020, w=2.85S), the diffusion coefficient (D020, w=9.05×10-7 cm2/sec), and the partial specific volume (V=0.726). The enzyme contains 16.10% of nitrogen and is composed of 282 residues of amino acid ; Asp. 33, Glu. 16, Ser. 33, Tyr. 17, Gly. 45, Ala. 39, Val. 22, Leu. 16, Ileu. 10, Pro. 6, Phe. 5, Tyr. 15, Trp. 3, Arg. 5, Lys. 12, His. 5, (amide-NH3)16.