Bulk Chemical and Optical Spectroscopy Characterisations of Dissolved Organic Matter Extracted from the Tropical Coastal Sediment

The study of organic matter characterisation in coastal sediment is useful for understanding how dissolved organic matter (DOM) reactivity influences the fate of pollutants in the aquatic environment. However, there is little information available on the structural properties of DOM in coastal sediment. Chemical analysis, UV-Visible (UV-Vis) absorbance, fluorescence, and Fourier-transform infrared (FTIR) spectroscopy were used in this work to characterise and compare the components of water-extractable organic matter (WEOM) fractions from sediment from an estuary, a coastal area, and a port in Peninsular Malaysia, Malaysia. The elemental analysis (H/C and C/N ratios) of the three samples differed, which coincided with the findings of optical indices estimated from UV-Visible and fluorescent spectroscopy analyses. WEOM had an average output of 7.05 to 8.47 mg/L and was very dominating with heavy fraction organic carbon (HFOC). In DOM-KS and DOM-K sediments, the allochthonous component with a high degree of condensation and the aromatic compound was the dominating composition. Meanwhile, the DOM-KT possessed a high autochthonous composition as well as carboxylic and phenolic content. Correlation analysis indicates that the aromaticity index SUVA254 and humification index (HIX) have positive correlations. The combined results of the chemical and spectroscopic analyses indicate that different coastal ecosystems, with the integration of various human and land activities, produce variations in DOM in the coastal area.

Accumulation of straw derived carbon, and changes in soil humic acid structural characteristics during corn straw decomposition

Appropriate application of corn straw residues increase soil organic carbon (SOC) sequestration. Yet, sequestration and stabilization of added carbon (C) during corn straw transformation is not fully understood. Here, we present changes in soil humus C and humic acid (HA) molecular structure during corn straw decomposition in an incubation experiment carried out for 270 days at 25 °C. Corn straw was applied at the amount of 74.76 g per 18 kg soil (i.e., 1.57 g C kg-1), in the soil surface (CS1), incorporated within 0–10 cm (CS2), applied below 10 cm soil depth (CS3), and no corn straw applied. The results showed that after corn straw application (CS1, CS2 and CS3), accumulation of SOC content was rapid in the first 90 days. The HA spectral results of straw amended soils showed a slight increase in aliphatic C compounds and amino acids in day 90. In day 180, the degree of condensation was less, and aliphatic C compounds were present in large quantities in soil HA. As decomposition advanced to day 270, the aliphatic character of HA appeared to slightly weaken, and soil HA was enriched with aromatic structures. These results suggest that corn straw application enrich soil HA with more aliphatic C compounds in the early stages of decomposition, and aromatic C structures are formed in the later stage of decomposition. Incorporation of corn straw into the soil (CS2 treatment) is more conducive in increasing SOC and aliphaticity in HA during corn straw decomposition, which can potentially increase C sequestration.

Bacillus aryabhattai TFG5-mediated synthesis of humic substances from coir pith wastes

Background Humic substances (HS) form the largest proportion among all the constituents of soil organic matter and are a key component of the terrestrial ecosystem. HS plays a multifunctional role in the environment by controlling the biogeochemical carbon cycle, providing nutrients and bio-stimulants for plant growth, and interacting with inorganic and organic pollutants. The rate of formation of HS in soils determines its productivity and carbon sequestration capacity. Enhancement of HS synthesis in the soil through the microbial route not only increases CO2 sequestration but also mitigates the greenhouse gas emissions in the environment. Result In this study, we attempted to understand the mechanism of formation and enhancement of HS from coir pith wastes using the tyrosinase produced by Bacillus aryabhattai TFG5. The bacterium TFG5 isolated from the termite garden produced the tyrosinase (1.34 U mL−1) and laccase (2.1 U mL−1) at 48 h and 60 h of fermentation, respectively. The extracellular tyrosinase from B. aryabhattai TFG5 was designated as TyrB. Homology modeling of TyrB revealed a structure with a predicted molecular mass of 35.23 kDa and two copper ions in the active center with its conserved residues required for the tyrosinase activity. TyrB efficiently transformed and polymerized standard phenols, such as p-cresol, p-hydroxyl benzoic acid, Levo DOPA, and 2,6 DMP, besides transforming free phenols in coir pith wash water (CWW). Additionally, UV–Vis and FT-IR spectra of the degradation products of the coir pith treated with TyrB revealed the formation of HS within 3 days of incubation. Furthermore, the E472/664 ratio of the degradation products revealed a higher degree of condensation of the aromatic carbons and the presence of more aliphatic structures in the HS. Conclusion The results confirmed the influence of TyrB for the effective synthesis of HS from coir pith wastes. The results of the present study also confirm the recently accepted theory of humification proposed by the International Humic Substances Society.

Synthesis of Silicon Hybrid Phenolic Resins with High Si-Content and Nanoscale Phase Separation Structure

In this paper, a set of silicon hybrid phenolic resins (SPF) with high Si-content were prepared by mixing phenolic resins with self-synthesized silicon resins. In order to obtain the nanoscale phase structure, condensation degree and the amount of Si-OH groups in silicon resins were controlled by the amount of inhibitor ethanol in the hydrolytic condensation polymerization of siloxane. Increasing the amount of ethanol resulted in more silanol groups and a lower degree of condensation for silicon resins, which then led to more formation of Si-O-Ph bonds in hybrid resin and improved compatibility between silicon resin and phenolic resin. When 400% ethanol by weight of siloxane was used in the sample SPF-4, nanoscale phase separation resulted. The residual weight of the cured SPF-4 at 1000 °C (R1000) significantly increased compared to pure phenolic resins. The result of the oxyacetylene flame ablation and the Cone Calorimeter test confirmed the improved ablative property and flammability after the modification. The performance improvement of the cured SPF-4 was attributed to the nanoscale phase structure and high silicon content, which promoted the formation of dense silica protective layers during pyrolysis.

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1—a ubiquitous nucleosome-binding protein—remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.

The resource-saving technology to restore the accumulation ability of tailing ponds

The accumulating capacity of tailing ponds by technology infusion of pulp preliminary clarification in the alluvium charts with its subsequent thickening and storage in the form of a highly concentrated pulp at the bottom of the pond is proposed by authors in the work. For the first time, the time dependence of filling a temporary pond on the ratio of the initial and condensed slurry concentrations for such technologies is obtained. The formula for calculating the degree of condensation is proposed. It provides the parameters selection and justification of equipment for removing water from a temporary pond as the map is filled with the accumulating capacity restoration of tailing ponds. The calculation results for the proposed dependencies allow us to establish: the necessary values of the thickening degree of the hydromixture, the possible intervals of the change in the pulp flow before and after thickening, as well as the volume of water taken from the temporary pond, depending on the concentration of the slurry entering the pond from the alluvium maps, its volumetric flow rate , geometric parameters of the technology for waste storage and the operation duration of a temporary pond.

Conventional Karyotype and Fluorescence in situ Hybridization (FISH) Technology

Karyotype analysis of cells has been in use for many years and has led to the causative genetic change in numerous clinical syndromes, including trisomy 21, Klinefelter, Turner, Prader-Willi and Angelman syndromes. The resolution of the test depends on the degree of condensation of the chromosomes in the karyotype, but even at high resolution (> 800 bands per haploid set) the changes identified are in the order of 5 Mb of DNA. Fluorescence in situ hybridization (FISH) bridges the gap between the relatively low resolution of karyotype analysis and the very high resolution of DNA analysis. With FISH it is possible to identify smaller changes in individual cells. The size of the change identified correlates with the size of the probe, which vary from 120 kb to 600 kb in size. FISH is widely used to confirm deletions or duplications identified by newer methods, such as array analysis. This review contains 8 figures, 3 tables, and 25 references. Keywords: Cytogenetics, chromosome, karyotype, chromosomal resolution, tissue culture, fluorescence, hybridization, probe

Contribution of Microbial Residues Obtained from Lignin and Cellulose on Humus Formation

The contribution of microbial residues formed on lignin and cellulose to the formation of humus (HS) was investigated. The microbial residues formed by Aspergillus niger (A. niger) in the cultures of cellulose and lignin in a fluid medium were structurally characterized by elemental analysis, differential thermal analysis (DTA), FTIR spectroscopy and CP/MAS 13C NMR spectroscopy. Compared to cellulose itself, the microbial residue from cellulose contains more aromatic compounds and N-containing compounds and fewer carbohydrates and carboxylic compounds. A. niger improved the thermal stability and aromaticity of the cellulose. However, compared with that on lignin, more N-containing compounds, carbohydrates and carboxylic acid derivatives and less aromatic material were found in the microbial residue from lignin. Regardless of whether the carbon source was cellulose or lignin, A. niger utilized the N in the fluid medium to synthesize its own cells, and eventually, they could transfer the N into the microbial residue; in addition, the O-alkyl species dominated over the alkyl and aromatic compounds in the microbial residue. Although the molecular structures of the components of the microbial residue from lignin tended to be simpler, they were more alkylated, more hydrophobic and less aliphatic than those from cellulose. During culture with A. niger, the cellulose underwent degradation and then a polymerization, which led to an increased degree of condensation but a lower degree of oxidation, providing essential precursor substances for HSs formation. However, lignin underwent oxidative degradation. The microbial residue from lignin had a lower degree of condensation and a higher degree of oxidation.

Prediction and Comparison of Shell Condensers With Straight or Helical Channels for Underwater Vehicles

The shell condenser is one of the key components of underwater vehicles. To study its thermal performance and to design a more efficient structure, a computational model is generated to simulate condensation inside straight and helical channels. The model combines empirical correlations and a MATLAB-based iterative algorithm. The vapor quality is used as a sign of the degree of condensation. Three calculation models are compared, and the optimal model is verified by a comparison of simulated results and available experimental data. Several cases are designed to reveal the effects of various inlet conditions and the diameter-over-radius (Dh/R) ratio. The results show that the inlet temperature and mass rate significantly affect the flow and heat transfer in the condensation process, the heat transfer capabilities of the helical channels are much better than that of the straight channel, and both the heat transfer coefficient and total pressure drop increase with the decrease of Dh/R. This study may provide a useful reference for performance prediction and structural design of shell condensers used for underwater vehicles and may provide a relatively universal prediction model for condensation in channels.

The basic structure of chromatin

In cells, DNA is associated with histones, non-histone proteins and RNA in a complex referred to as chromatin. Four different types of histones form octamers (nucleosomes), around which DNA is wrapped yielding a chromatin fiber with the configuration of “beads on a string.” Disassembly, followed by reassembly, of this structure occurs during DNA replication, damage repair and transcription. Core histones are replication-coupled; variants are replication-independent. Positioning of nucleosomes on the chromatin fiber is mediated by chromatin remodeling complexes and reflects the functional state of various regions along the fiber. Various biophysical methods have been utilized to study the physical association of nucleosomes and DNA. Chromatin can be differentiated on the basis of the activity of the genes that are present in a given region. Heterochromatin represents repressed or inactive regions of the genome and exhibits a greater degree of condensation than euchromatin, which refers to more unwound regions where active genes are located. The two types of chromatin are present in different nuclear locations.