Biophysico-Chemical Processes Research Articles

A phenotypic drug discovery approach by latent interaction in deep learning

Contemporary drug discovery paradigms rely heavily on binding assays about the bio-physicochemical processes. However, this dominant approach suffers from overlooked higher-order interactions arising from the intricacies of molecular mechanisms, such as those involving cis -regulatory elements. It introduces potential impairments and restrains the potential development of computational methods. To address this limitation, I developed a deep learning model that leverages an end-to-end approach, relying exclusively on therapeutic information about drugs. By transforming textual representations of drug and virus genetic information into high-dimensional latent representations, this method evades the challenges arising from insufficient information about binding specificities. Its strengths lie in its ability to implicitly consider complexities such as epistasis and chemical–genetic interactions, and to handle the pervasive challenge of data scarcity. Through various modeling skills and data augmentation techniques, the proposed model demonstrates outstanding performance in out-of-sample validations, even in scenarios with unknown complex interactions. Furthermore, the study highlights the importance of chemical diversity for model training. While the method showcases the feasibility of deep learning in data-scarce scenarios, it reveals a promising alternative for drug discovery in situations where knowledge of underlying mechanisms is limited.

Effect of lignocellulose/montmorillonite immobilized Bacillus sp. on monosodium glutamate wastewater.

A group of Bacillus sp. was extracted from monosodium glutamate wastewater. Lignocellulose/montmorillonite composite was selected as the carrier. Lignocellulose/montmorillonite composite immobilized Bacillus sp./calcium alginate microspheres were prepared by immobilized microorganism techniques. The microspheres were used to treat monosodium glutamate wastewater with significantly reduced ammonia nitrogen (NH3-N) and chemical oxygen demand (COD) concentrations. The optimum preparation conditions of microspheres in the treatment of NH3-N and COD of monosodium glutamate wastewater were studied. The concentration of sodium alginate was 2.0 wt%, lignocellulose/montmorillonite was 0.06 wt%, Bacillus sp. was 1.0 wt%, CaCl2 solution was 2.0 wt%, coagulation time was 12h, and the removal capacities of NH3-N and COD were 44832 and 78345mg/L, respectively. The surface structure, element content, functional group change, and crystal structure of the microspheres were characterized by SEM, EDS, and other methods. The results showed that the -COOH in lignocellulose/montmorillonite and the -OH in the Bacillus sp. form intermolecular hydrogen bonds. The Si-O and Al-O bonds in lignocellulose/montmorillonite reacted with sodium ions in sodium alginate. New crystal structures appear inside the material after crosslinking, and the microspheres was formed. Thus, the study has shown that the microspheres were successfully prepared and contributes to the treatment of NH3-N and COD in monosodium glutamate wastewater. This work can provide an interesting strategy for the removal of COD and NH3-N in industrial wastewater by reasonably combining bio-physicochemical processes.

Biochar Amendment Increases C and N Retention in the Soil–Plant Systems: Its Implications in Enhancing Plant Growth and Water-Use Efficiency Under Reduced Irrigation Regimes of Maize (Zea mays L.)

Biochar influences soil biophysicochemical processes and nutrient availability, yet the effects of different biochar and soil water dynamics on carbon (C) and nitrogen (N) retention in the soil–plant systems remain unknown. Maize plants were grown in split-root pots filled with clay loam soil amended with wheat straw pellet biochar (WSP) and softwood pellet biochar (SWP) at 2% (w/w) and were either irrigated daily to 90% of water-holding capacity (FI) or irrigated with 70% volume of water used for FI to the whole root-zone (DI) or alternately to half root-zone (PRD) from the fourth leaf to grain-filling stage. Compared to the unamended controls, biochar amendment enhanced plant biomass and water-use efficiency, particularly when combined with PRD. Although the WSP amendment tended to decrease soil net N mineralization rate, it significantly increased C and N retention in the soil–plant systems. Compared to DI, PRD significantly increased soil respiration rate while lowering soil total organic C content. Moreover, PRD increased soil inorganic N content, which might be related to increased mineralization of soil organic C (SOC) and soil organic N (SON). Such effects might implicate that PRD outperformed DI in enhancing the mineralization of soil organic matter. Although PRD alone might not be a sustainable irrigation method because of greater C and N losses, biochar addition could alleviate these undesirable effects via depressing SOC and SON mineralization. Biochar amendment, especially WSP combined with PRD, could be a promising practice to increase maize growth and water-use efficiency while sustaining C and N retention in the soil–plant systems.

Biosensing Technologies: A Focus Review on Recent Advancements in Surface Plasmon Coupled Emission.

In the past decade, novel nano-engineering protocols have been actively synergized with fluorescence spectroscopic techniques to yield higher intensity from radiating dipoles, through the process termed plasmon-enhanced fluorescence (PEF). Consequently, the limit of detection of analytes of interest has been dramatically improvised on account of higher sensitivity rendered by augmented fluorescence signals. Recently, metallic thin films sustaining surface plasmon polaritons (SPPs) have been creatively hybridized with such PEF platforms to realize a substantial upsurge in the global collection efficiency in a judicious technology termed surface plasmon-coupled emission (SPCE). While the process parameters and conditions to realize optimum coupling efficiency between the radiating dipoles and the plasmon polaritons in SPCE framework have been extensively discussed, the utility of disruptive nano-engineering over the SPCE platform and analogous interfaces such as 'ferroplasmon-on-mirror (FPoM)' as well as an alternative technology termed 'photonic crystal-coupled emission (PCCE)' have been seldom reviewed. In light of these observations, in this focus review, the myriad nano-engineering protocols developed over the SPCE, FPoM and PCCE platform are succinctly captured, presenting an emphasis on the recently developed cryosoret nano-assembly technology for photo-plasmonic hotspot generation (first to fourth). These technologies and associated sensing platforms are expected to ameliorate the current biosensing modalities with better understanding of the biophysicochemical processes and related outcomes at advanced micro-nano-interfaces. This review is hence envisaged to present a broad overview of the latest developments in SPCE substrate design and development for interdisciplinary applications that are of relevance in environmental as well as biological heath monitoring.

Modeling Thrombin Generation in Plasma under Diffusion and Flow

We investigate the capacity of published numerical models of thrombin generation to reproduce experimentally observed threshold behavior under conditions in which diffusion and/or flow are important. Computational fluid dynamics simulations incorporating species diffusion, fluid flow, and biochemical reactions are compared with published data for thrombin generation in vitro in 1) quiescent plasma exposed to patches of tissue factor and 2) plasma perfused through a capillary coated with tissue factor. Clot time is correctly predicted in individual cases, and some models qualitatively replicate thrombin generation thresholds across a series of tissue factor patch sizes or wall shear rates. Numerical results suggest that there is not a genuine patch size threshold in quiescent plasma—clotting always occurs given enough time—whereas the shear rate threshold observed under flow is a genuine physical limit imposed by flow-mediated washout of active coagulation factors. Despite the encouraging qualitative results obtained with some models, no single model robustly reproduces all experiments, demonstrating that greater understanding of the underlying reaction network, and particularly of surface reactions, is required. In this direction, additional simulations provide evidence that 1) a surface-localized enzyme, speculatively identified as meizothrombin, is significantly active toward the fluorescent thrombin substrate used in the experiments or, less likely, 2) thrombin is irreversibly inhibited at a faster-than-expected rate, possibly explained by a stimulatory effect of plasma heparin on antithrombin. These results highlight the power of simulation to provide novel mechanistic insights that augment experimental studies and build our understanding of complex biophysicochemical processes. Further validation work is critical to unleashing the full potential of coagulation models as tools for drug development and personalized medicine.

The small, the big, and the beautiful: Emerging challenges and opportunities for waste stabilization ponds in Australia

AbstractWaste stabilization ponds (WSPs) are used extensively for the treatment of wastewater in Australia, mostly in regional and remote areas. Wastewater treatment plants (WWTPs) using pond technologies are also distributed over the full geographical extent of Australia, encompassing many climatic zones. Predominantly used to service small to medium‐sized communities, WSPs are also used to service large metropolitan Australian populations, up to 2.5 million people. When well‐maintained, WSPs are a sustainable and resilient treatment option, and treatment is achieved at significantly lower cost when compared with conventional WWTPs. Increasing population, changing regulations, and climate variability are placing increasing pressure on Australian WSP systems. Sludge accumulation over time presents a significant challenge to pond maintenance, along with increasing occurrence of toxic cyanobacterial bloom events. These challenges are only enhanced by the wide geographical distribution and by increasing operational and maintenance costs. Increased demand for recycled water is placing further pressure on Australian WSP systems, as higher value treated water is expected from WSP infrastructure that is often overloaded or under‐designed. This increased demand for high‐quality treatment presents an opportunity for operators and researchers to develop a better understanding of the coupling between hydraulics and microbial ecology of these systems. With more stringent guidelines for greenhouse gas emissions (GHGs), a better understanding of biophysicochemical processes in WSPs will lead to better estimates of GHG fluxes and variability. This information will become critical for the future planning, maintenance and operation of WSPs, and will result in a better understanding of WSP systems overall.This article is categorized under:Engineering Water > Water, Health, and SanitationEngineering Water > Sustainable Engineering of Water

Comprehensive assessment of microbial aggregation characteristics of activated sludge bioreactors using fuzzy clustering analysis

Understanding microbial aggregation dynamics in response to the often violent environmental fluctuations is important for activated sludge wastewater biotreatment practice, yet remains poorly understood. We investigated microbial aggregation process of an activated sludge reactor in response to various operating conditions of resource limitations, disinfectant and pH stresses, and quantified aggregation characteristics by employing a fuzzy clustering analysis (FCA) method. The results revealed that the FCA provided a means for comprehensive assessment of microbial aggregation dynamics of the bioreactor relying solely on simple parameter estimation. Proper disinfectant stress (of NaClO 1.00% or 2.00%) is a promising strategy to improve the comprehensive performance of microbial aggregation and sludge settleability. Nitrogen– (of C/N ratio > 40) and dissolved oxygen–limitations (of DO < 0.2 mg/L) had medium influence on the comprehensive performance of the activated sludge system, while little impacts for acidic and alkaline conditions. These quantitative estimations offer insights into the underlying bio–physicochemical processes of an activated sludge bioreactor in response to practical fluctuations that is often beyond typical assessment practice. In addition, it may represent a step towards uncoupling the complex biophysical interactions that is essential for optimized designing and proper engineering practice of biological wastewater treatment reactors.

High Resolution 31P NMR Spectroscopy Generates a Quantitative Evolution Profile of Phosphorous Translocation in Germinating Sesame Seed

Phosphorus metabolism and circulation are essential bio-physicochemical processes during development of a plant and have been extensively studied and known to be affected by temperature, humidity, lighting, hormones etc. However, a quantitative description of how various phosphorous species evolve over time has not been reported. In this work, a combined 31P liquid and solid state NMR spectroscopic methodology is employed, supported by a new extraction scheme and data analysis method, to carry out a quantitative investigation of phosphorous circulation in germinating sesame seeds in dark and under illumination with and without adding a growth hormone. The spectra show that only slight changes occur for phosphorous metabolism at the initial stage but a rapid change takes place between 48–96 hours after germination is started. The metabolism is found to be temperature dependent and affected by illumination and hormone. However, neither illumination nor hormone affects the final residual concentration of phytin. Moreover, phytin does not flow out of cotyledon and the phosphorous flowing to other parts of the plant is always in the inorganic form. The overall evolution profile of phytate consumption is found to be a Gaussian decaying function. These findings can be explained with a dynamic model on phytin conversion.

Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity

Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity

Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity

Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Toxicity

Shewanella oneidensis MR-1-Induced Fe(III) Reduction Facilitates Roxarsone Transformation.

Although microbial activity and associated iron (oxy)hydroxides are known in general to affect the environmental dynamics of 4-hydroxy-3-nitrobenzenearsonic acid (roxarsone), the mechanistic understanding of the underlying biophysico-chemical processes remains unclear due to limited experimental information. We studied how Shewanella oneidensis MR-1 –a widely distributed metal-reducing bacterium, in the presence of dissolved Fe(III), affects roxarsone transformations and biogeochemical cycling in a model aqueous system. The results showed that the MR-1 strain was able to anaerobically use roxarsone as a terminal electron acceptor and to convert it to a single product, 3-amino-4-hydroxybenzene arsonic acid (AHBAA). The presence of Fe(III) stimulated roxarsone transformation via MR-1-induced Fe(III) reduction, whereby the resulting Fe(II) acted as an efficient reductant for roxarsone transformation. In addition, the subsequent secondary Fe(III)/Fe(II) mineralization created conditions for adsorption of organoarsenic compounds to the yielded precipitates and thereby led to arsenic immobilization. The study provided direct evidence of Shewanella oneidensis MR-1-induced direct and Fe(II)-associated roxarsone transformation. Quantitative estimations revealed a candidate mechanism for the early-stage environmental dynamics of roxarsone in nature, which is essential for understanding the environmental dynamics of roxarsone and successful risk assessment.

Geophysical signatures of disseminated iron minerals: A proxy for understanding subsurface biophysicochemical processes

Previous studies have linked biogeophysical signatures to the presence of iron minerals resulting from distinct biophysicochemical processes. Utilizing geophysical methods as a proxy of such biophysicochemical processes requires an understanding of the geophysical signature of the different iron minerals. Laboratory experiments were conducted to investigate the complex conductivity and magnetic susceptibility signatures of five iron minerals disseminated in saturated porous media under variable iron mineral content and grain size. Both pyrite and magnetite show high quadrature and inphase conductivities compared to hematite, goethite, and siderite, whereas magnetite was the highly magnetic mineral dominating the magnetic susceptibility measurements. The quadrature conductivity spectra of both pyrite and magnetite exhibit a well-defined characteristic relaxation peak below 10 kHz, not observed with the other iron minerals. The quadrature conductivity and magnetic susceptibility of individual and a mixture of iron minerals are dominated and linearly proportional to the mass fraction of the highly conductive (pyrite and magnetite) and magnetic (magnetite) iron minerals, respectively. The quadrature conductivity magnitude increased with decreasing grain size diameter of magnetite and pyrite with a progressive shift of the characteristic relaxation peak toward higher frequencies. The quadrature conductivity response of a mixture of different grain sizes of iron minerals is shown to be additive, whereas magnetic susceptibility measurements were insensitive to the variation in grain size diameters (1–0.075 mm). The integration of complex conductivity and magnetic susceptibility measurements can therefore provide a complimentary tool for the successful investigation of in situ biophysicochemical processes resulting in biotransformation or secondary iron mineral precipitation.

Using protein nanofibrils to remove azo dyes from aqueous solution by the coagulation process

The ever-increasing applications of hazardous azo dyes as industrialized coloring agents have led to serious remediation challenges. In this study, proteinaceous nanofibrils were examined as coagulants for decolorization of azo dyes in aqueous solutions. The results provided some insight regarding the mechanism of dye removal. The strength of nanofibrils to remove dyes from solution was evaluated by remediation of acid red 88, Bismarck brown R, direct violet 51, reactive black 5, and Congo red. However, the efficiency of nanofibrils to coagulate with different dyes was variable (60–98%) and dependent on the structures of dyes and the physicochemical conditions of the solutions. Increasing the temperature or ionic strength declined the coagulation time and induced the rate of dye removal. Changing pH had contradictory effects on the dye removal efficiency which was more affected by the chemical structure of the dye rather than the change in stability of the coagulant. The efficiency of nanofibrils to remove dyes was more than that of charcoal, which is considered as one of the most common substances used for azo dye remediation which may be due to its well dispersion in the aqueous solutions, and slower rates of the coagulation than that of the adsorption process. Furthermore, cytotoxicity was not detected after treating cell cultures with the decolorized solutions. Accordingly, by integrating biological and biophysicochemical processes, proteinaceous nanofibrils can be promising candidates for treatment of colored wastewaters. Ease of production, proper and quick dispersion in water, without the production of dangerous dye by-products and derivatives, are some of the main advantages of nanofibrils.

Nanotoxicology: in Vitro–in Vivo Dosimetry

Nanotoxicology: in Vitro–in Vivo Dosimetry

Molecular environmental soil science at the interfaces in the Earth’s critical zone

The International Symposium of Molecular Environmental Soil Science at the Interfaces in the Earth’s Critical Zone (ISMESS 2009) was successfully held during 10–14 October 2009 at Zhejiang University in Hangzhou, China. Two hundred sixty-six participants from 21 countries attended the symposium. The scientific program featured 2 plenary lecturers, 19 invited lecturers, 29 oral presentations, and 65 poster presentations. The five main sessions were included in the symposium: (1) The role of mineral colloids in carbon turnover and sequestration and the impact on climate change; (2) Biogeochemical interfacial reactions and the transformation, transport, and fate of vital and toxic elements; (3) Anthropogenic organics, crop protection, and ecotoxicology; (4) Environmental nanoparticles: distribution, formation, transformation, structural, and surface chemistry and biogeochemical and ecological impacts; and (5) Environmental processes and ecosystem health (Xu and Huang 2009). Following the peer reviewing process, a selection of articles arising from the symposium is published in this issue of Journal of Soils and Sediments. This symposium provided a forum for the interactions and communication of soil chemists, mineralogists, microbiologists, and physicists with allied scientists including pure chemists, biologists, environmental scientists, ecologists, and ecotoxicologists to address the current state-ofthe-art on “Molecular Environmental Soil Science”. No doubt this symposium contributed to identification of gaps in knowledge and to future research directions and research on soil processes at the interfaces at the molecular level in the Earth’s critical zone. It is significant to advance the frontiers of knowledge on biophysicochemical processes in soil and related environmental systems and their biogeochemical and ecological impacts and to promote education in this extremely important and challenging area of science for years to come. The symposium was highly evaluated by all the participants, and major knowledge shared include the following: (1) The concept of the Earth’s critical zone was highlighted, which is a system of coupled chemical, biological, physical, and geological processes operating together to support life at the Earth’s surface. (2) Further efforts are required by scientists to cross-disciplines for the study of the interactive processes in the critical zone and their impact on the globe and humankind, ranging in scale from the environmental mineral–organism–humus–water–air interfaces. (3) Discussion on carbon turnover improved the understanding of the role of mineral colloids in carbon transformation, dynamics, and sequestration and their impact on climate change in the environment. (4) Microbes are involved in important natural biogeochemical processes relating to metal–mineral transformations, element cycling, bioweathering, biocorrosion, bioremediation, revegetation, phytoremediation, and containment of pollution in the Earth’s critical zone. (5) The importance of nanoscience as a new frontier in soil science has been emphasized. The resolution is occurring for the study of Responsible editor: Jianming Xu

Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems - edited by Senesi, N., Xing, B. &amp; Huang, P.M.

Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems - edited by Senesi, N., Xing, B. &amp; Huang, P.M.

Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems

Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems

Biophysico-Chemical Processes of Heavy Metals and Metalloids in Soil Environments

Biophysico-Chemical Processes of Heavy Metals and Metalloids in Soil Environments

Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems

Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems

Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems

Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems