A critical review on biochar for the removal of toxic pollutants from water environment.

As an effort to tackle some of the most pressing ecological issues we are currently experiencing, there has been an increasing interest in employing biomass-derived char products in various disciplines. Thermal combustion of biomass results in biochar production, which is a remarkably rich source of carbon. Not only does the biochar obtained by the thermochemical breakdown of biomass lower the quantity of carbon released into the environment, but it also serves as an eco-friendly substitute for activated carbon (AC) and further carbon-containing products. An overview of using biochar to remove toxic pollutants is the main subject of this article. Several techniques for producing biochar have been explored. The most popular processes for producing biochar are hydrothermal carbonization, gasification and pyrolysis. Carbonaceous materials, alkali, acid and steam are all capable of altering biochar. Depending on the environmental domains of applications, several modification techniques are chosen. The current findings on characterization and potential applications of biochar are compiled in this survey. Comprehensive discussion is given on the fundamentals regarding the formation of biochar. Process variables influencing the yield of biochar have been summarized. Several biochars' adsorption capabilities for expulsion pollutants under various operating circumstances are compiled. In the domain of developing biochar, a few suggestions for future study have been given.

A review on recent advancements in the treatment of polyaromatic hydrocarbons (PAHs) using sulfate radicals based advanced oxidation process.

Polyaromatic hydrocarbons (PAHs) are the most persistent compounds that get contaminated in the soil and water. Nearly 16 PAHs was considered to be a very toxic according US protection Agency. Though its concentration level is low in the environments but the effects due to it, is enormous. Advanced Oxidation Process (AOP) is an emergent methodology towards treating such pollutants with low and high molecular weight of complex substances. In this study, sulfate radical (SO4‾•) based AOP is emphasized for purging PAH from different sources. This review essentially concentrated on the mechanism of SO4‾• for the remediation of pollutants from different sources and the effects caused due to these pollutants in the environment was reduced by this mechanism is revealed in this review. It also talks about the SO4‾• precursors like Peroxymonosulfate (PMS) and Persulfate (PS) and their active participation in treating the different sources of toxic pollutants. Though PS and PMS is used for removing different contaminants, the degradation of PAH due to SO4‾• was presented particularly. The hydroxyl radical (•OH) mechanism-based methods are also emphasized in this review along with their limitations. In addition to that, different activation methods of PS and PMS were discussed which highlighted the performance of transition metals in activation. Also this review opened up about the degradation efficiency of contaminants, which was mostly higher than 90% where transition metals were used for activation. Especially, on usage of nanoparticles even 100% of degradation could be able to achieve was clearly showed in this literature study. This study mainly proposed the treatment of PAH present in the soil and water using SO4‾• with different activation methodologies. Particularly, it emphasized about the importance of treating the PAH to overcome the risk associated with the environment and humans due to its contamination.

Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen.

The timing, sequence, and scale of uplift of the Himalayan-Tibetan Orogen (HTO) are controversially debated. Many geoscientific studies assume paleoelevations close to present-day elevations and the existence of alpine environments across the HTO already in the late Paleogene, contradicting fossil data. Using molecular genetic data of ground beetles, we aim to reconstruct the paleoenvironmental history of the HTO, focusing on its southern margin (Himalayas, South Tibet). Based on a comprehensive sampling of extratropical Carabus, and ~ 10,000 bp of mitochondrial and nuclear DNA we applied Bayesian and Maximum likelihood methods to infer the phylogenetic relationships. We show that Carabus arrived in the HTO at the Oligocene-Miocene boundary. During the early Miocene, five lineages diversified in different parts of the HTO, initially in its southern center and on its eastern margin. Evolution of alpine taxa occurred during the late Miocene. There were apparently no habitats for Carabus before the late Oligocene. Until the Late Oligocene elevations must have been low throughout the HTO. Temperate forests emerged in South Tibet in the late Oligocene at the earliest. Alpine environments developed in the HTO from the late Miocene and, in large scale, during the Pliocene-Quaternary. Findings are consistent with fossil records but contrast with uplift models recovered from stable isotope paleoaltimetry.

Biodegradation of textile dye Rhodamine-B by Brevundimonas diminuta and screening of their breakdown metabolites.

The carcinogenic Rhodamine-B dye is recalcitrant which could cause serious hazards to human beings. Degradation with the application of unique bacterial strain is a sustainable technique. The bioremediation technique showed great potential to degrade a variety of recalcitrant pollutants like dyes. In this study, Brevundimonas diminuta, was selected for the breakdown of toxic textile dye Rhodamine-B. This bacterium showed 90-95% of degradation at the optimum conditions like 10 mg L-1 of concentration of dye, pH 7 and temperature of 30 °C. Further UV-Visible spectrophotometry, FT-IR spectral scan, GC-MS analysis depicted the breakdown products like Methyl 18-fluoro-octadec-9-enoate, Methyl 18-fluoro-octadec-9-enoate and d-Homo-24-nor-17-oxachola-20,22-diene-3,16-dione,7-(acetyloxy)-1, 23 tri-epoxy-4,4,8-trimethyl. The degradation was confirmed by the changes in the functional groups, change in molecular weight and charge to-mass ratio. These results suggested that this strain is a deserving organism for the degradation of dye compounds.

Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA.

Uracil-DNA glycosylase (UDG) is one of the most important base excision repair (BER) enzymes involved in the repair of uracil-induced DNA lesion by removing uracil from the damaged DNA. Uracil in DNA may occur due to cytosine deamination or deoxy uridine monophosphate (dUMP) residue misincorporation during DNA synthesis. Medical evidences show that an abnormal expression of UDG is related to different types of cancer, including colorectal cancer, lung cancer, and liver cancer. Therefore, the research of UDG is crucial in cancer treatment and prevention as well as other clinical activities. Here we applied multiple computational methods to study UDG in several perspectives: Understanding the stability of the UDG enzyme in different pH conditions; studying the differences in charge distribution between the pocket side and non-pocket side of UDG; analyzing the field line distribution at the interfacial area between UDG and DNA; and performing electrostatic binding force analyses of the special region of UDG (pocket area) and the target DNA base (uracil) as well as investigating the charged residues on the UDG binding pocket and binding interface. Our results show that the whole UDG binding interface, and not the UDG binding pocket area alone, provides the binding attractive force to the damaged DNA at the uracil base.

Stimulation of Bacillus sp. by lipopeptide biosurfactant for the degradation of aromatic amine 4-Chloroaniline.

This study aims to reveal that the biosurfactant act as a stimulant in aromatic amine 4-Chloroaniline (4-CA) degradation. Isolated degrading strain Bacillus sp. was used for the production of biosurfactant with help of substrate such as engine oil. The surfactant production by the strain was studied by using various screening methods and the results showed best emulsification activity (75%), surface tension reduction activity (28.6 mNm-1) and oil spreading activity (5.9 cm). The obtained surfactant was characterized using Fourier transform infrared spectroscopy (FT-IR), Gas chromatography-Mass Spectrometry (GC-MS), Matrix-Assisted Laser Desorption/ Ionization Time of Flight (MALDI-TOF) which confirmed that the nature of surfactant is lipopeptide. The maximum removal of 4-CA was achieved in different environmental conditions at concentration 100 mg L-1, neutral pH and temperature 30 °C. In the degradation studies, the 4-CA was removed upto 76% by Bacillus sp but in the presence of lipopeptide surfactant, the Bacillus sp removed 4-CA upto 100%. The degraded metabolites were further characterized using High-Pressure Liquid Chromatography (HPLC) and GC-MS. This research indicated that strain Bacillus sp along with the lipopeptide biosurfactant possesses higher potential in the bioremediation of 4-CA compound from the environment.

Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2.

The ongoing outbreak of COVID-19 has been a serious threat to human health worldwide. The virus SARS-CoV-2 initiates its infection to the human body via the interaction of its spike (S) protein with the human Angiotensin-Converting Enzyme 2 (ACE2) of the host cells. Therefore, understanding the fundamental mechanisms of how SARS-CoV-2 S protein receptor binding domain (RBD) binds to ACE2 is highly demanded for developing treatments for COVID-19. Here we implemented multi-scale computational approaches to study the binding mechanisms of human ACE2 and S proteins of both SARS-CoV and SARS-CoV-2. Electrostatic features, including electrostatic potential, electric field lines, and electrostatic forces of SARS-CoV and SARS-CoV-2 were calculated and compared in detail. The results demonstrate that SARS-CoV and SARS-CoV-2 S proteins are both attractive to ACE2 by electrostatic forces even at different distances. However, the residues contributing to the electrostatic features are quite different due to the mutations between SARS-CoV S protein and SARS-CoV-2 S protein. Such differences are analyzed comprehensively. Compared to SARS-CoV, the SARS-CoV-2 binds with ACE2 using a more robust strategy: The electric field line related residues are distributed quite differently, which results in a more robust binding strategy of SARS-CoV-2. Also, SARS-CoV-2 has a higher electric field line density than that of SARS-CoV, which indicates stronger interaction between SARS-CoV-2 and ACE2, compared to that of SARS-CoV. Key residues involved in salt bridges and hydrogen bonds are identified in this study, which may help the future drug design against COVID-19.

Nα-Acetylation of the virulence factor EsxA is required for mycobacterial cytosolic translocation and virulence.

The Mycobacterium tuberculosis virulence factor EsxA and its chaperone EsxB are secreted as a heterodimer (EsxA:B) and are crucial for mycobacterial escape from phagosomes and cytosolic translocation. Current findings support the idea that for EsxA to interact with host membranes, EsxA must dissociate from EsxB at low pH. However, the molecular mechanism by which the EsxA:B heterodimer separates is not clear. In the present study, using liposome-leakage and cytotoxicity assays, LC-MS/MS-based proteomics, and CCF-4 FRET analysis, we obtained evidence that the Nα-acetylation of the Thr-2 residue on EsxA, a post-translational modification that is present in mycobacteria but absent in Escherichia coli, is required for the EsxA:B separation. Substitutions at Thr-2 that precluded Nα-acetylation inhibited the heterodimer separation and hence prevented EsxA from interacting with the host membrane, resulting in attenuated mycobacterial cytosolic translocation and virulence. Molecular dynamics simulations revealed that at low pH, the Nα-acetylated Thr-2 makes direct and frequent "bind-and-release" contacts with EsxB, which generates a force that pulls EsxB away from EsxA. In summary, our findings provide evidence that the Nα-acetylation at Thr-2 of EsxA facilitates dissociation of the EsxA:B heterodimer required for EsxA membrane permeabilization and mycobacterial cytosolic translocation and virulence.

StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions.

Studying biomolecular interactions is a crucial but challenging task. Due to their large scales, many biomolecular interactions are difficult to be simulated via all atom models. An effective approach to investigate the biomolecular interactions is highly demanded in many areas. Here we introduce a Structure Manipulation (StructureMan) program to operate the structures when studying the large-scale biomolecular interactions. This novel StructureMan tool provides comprehensive operations which can be utilized to study the interactions in various large biological systems. Combining with electrostatic calculation programs such as DelPhi and DelPhiForce, StructureMan was implemented to reveal the detailed electrostatic features in two large biological examples, the viral capsid and molecular motor-microtubule complexes. Applications on these two examples revealed interesting binding mechanisms in the viral capsid and molecular motor. Such applications demonstrated that the StructureMan can be widely used when studying the biomolecular interactions in large scale biological problems. This novel tool provides an alternative approach to efficiently study the biomolecular interactions, especially for large scale biology systems. The StructureMan tool is available at our website: http://compbio.utep.edu/static/downloads/script-for-munipulation2.zip.

Revealing the mechanism of SARS-CoV-2 spike protein binding with ACE2.

A large population in the world has been infected by COVID-19. Understanding the mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is important for management and treatment of the COVID-19. When it comes to the infection process, one of the most important proteins in SARS-CoV-2 is the spike (S) protein, which is able to bind to human Angiotensin-Converting Enzyme 2 (ACE2) and initializes the entry of the host cell. In this study, we implemented multi-scale computational approaches to study the electrostatic features of the interfaces of the SARS-CoV-2 S protein Receptor Binding Domain (RBD) and ACE2. The simulations and analyses were performed on high-performance computing resources in Texas Advanced Computing Center (TACC). Our study identified key residues on the SARS-CoV-2, which can be used as targets for future drug design. The results shed lights on future drug design and therapeutic targets for COVID-19.

The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses.

In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.

Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group.

Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.

Toxicity Evaluation of Purna Cantirotaya Centuram, a Siddha Medicine in Wistar Rats.

Purna Cantirotaya Centuram (PCC), a herbometallic formulation of Siddha medicine, consists of mercury, sulphur, and gold, processed with red cotton flower and plantain stem pith juices. To evaluate its safety, acute and 28-day repeated oral toxicity studies were performed following OECD test guidelines 423 and 407, respectively. In acute study, PCC was administered orally at 5, 50, 300, and 2000 mg/kg body weight. Animals were observed for toxic signs for 14 days. Gross pathology was performed at the end of the study. In repeated dose toxicity study, PCC was administered at 2.5, 25, and 50 mg/kg body weight daily for 28 days. Satellite groups (control and high dose) were also maintained to determine the delayed onset toxicity of PCC. In acute toxicity study, no treatment related death or toxic signs were observed. It revealed that the LD50 cut-off value of PCC is between 2000 and 5000 mg/kg body weight. The repeated dose study did not show evidence of any treatment related changes in all observations up to the high dose level, when compared with the control. Histopathological examination revealed no abnormalities except mild hyperplasia of stomach in high dose group. This study provides scientific validation for the safety of PCC.

Study of the effect of oral gabapentin used as preemptive analgesia to attenuate post-operative pain in patients undergoing abdominal surgery under general anesthesia.

AIMS: To study the effect of oral gabapentin used as preemptive analgesia to attenuate post operative pain in patients undergoing abdominal surgery under general anesthesia. MATERIALS AND METHODS: In a randomized double blind study, 60 patients were divided into two groups. Group A received 600mg gabapentin and group B oral received placebo 1 h prior to surgery. Anesthesia was induced with Propofol 2 mg/kg and Vecuronium 0.1mg/kg and maintained with 60% N(2)O in O(2) and Vecuronium 0.02 mg/kg. All cases were given Fentanyl 2µg/kg as pre medication and a repeat dose 1µg/kg at the end of the first hour. Assessment of post-operative pain was made with the visual analog score (VAS) at extubation (0 h), 2, 4, 6, 12, and 24 h post-operatively. Post-operative analgesia was provided with intravenous Tramadol. The first dose was given in the Post Anesthesia Care Unit as 2mg/kg, and repeated at 8 and 16 h. Rescue analgesia was given with Diclofenac 1.5mg/kg, slow intravenous. The number of doses of rescue analgesia in both the groups was noted. RESULTS: The VAS scores at 0, 2, 4, 6, 12, and 24 h were 1.9 vs. 2.4 (P=0.002), 2.3 vs. 3.0 (P=0.000), 3.2 vs. 3.7 (P=0.006), 2.9 vs. 4.4 (P=0.000), 3.6 vs. 4.6 (P=0.000), and 3.7 vs.4.6 (P=0.000), respectively. Numbers of patients requiring rescue analgesia with Diclofenac were 3 vs. 14 (P=0.004). CONCLUSION: A single oral dose of gabapentin given pre-operatively enhanced the analgesic effect of Tramadol as it also reduced the requirement of rescue analgesia with Diclofenac.

Perioperative anesthetic management of patients with hypertrophic cardiomyopathy for noncardiac surgery: a case series.

Hypertrophic cardiomyopathy with or without left ventricular outflow tract obstruction is characterized by asymmetric hypertrophy of the interventricular septum causing intermittent obstruction of the left ventricular outflow tract. Because Hypertrophic cardiomyopathy is the most common genetic cardiovascular disease, it may present to the anesthesiologist more often than anticipated, sometimes in undiagnosed form during routine preoperative visit. Surgery and anesthesia often complicate the perioperative outcome if adequate monitoring and proper care are not taken. Therefore, a complete understanding of the pathophysiology, hemodynamic changes and anesthetic implications is needed for successful perioperative outcome. We hereby describe the perioperative management of three patients with Hypertrophic cardiomyopathy for different surgical procedures.

Use of medetomidine-ketamine and atipamezole for reversible immobilization of free-ranging hog deer (Axis porcinus) captured in drive nets.

A combination of 0.05 mg/kg medetomidine and 1.5 mg/kg ketamine was used to immobilize nine adult free-ranging hog deer (Axis porcinus) captured in drive nets in the Royal Bardia National Park, Nepal, 22-23 February 2000. The drugs were administered intramuscularly from separate syringes and the mean time (+/-SD) to complete immobilization was 4.6+/-1.0 min. Muscle relaxation was good and no major clinical side effects were seen. Mean values for physiologic parameters, recorded at 10-12 and 18-20 min after drug administration, were 40.6+/-0.5 and 41.1+/-0.6 C, 87+/-5 and 84+/-4%, 107+/-16 and 113+/-16 beats/ min, and 46+/-9 and 40+/-8 breaths/min for rectal temperature, SpO2, pulse rate, and respiratory rate, respectively. All animals received 0.25 mg/ kg atipamezole intramuscularly 20-22 min after administration of medetomidine-ketamine and the mean time to coordinated running was 4.8+/-0.8 min. All animals survived for at least 5 mo post-capture. To reduce stress and to facilitate handling, medetomidine-ketamine and atipamezole are recommended for reversible immobilization of free-ranging hog deer captured in drive nets.