Noise-independent route toward the genesis of a COMPACT ansatz for molecular energetics: A dynamic approach

Recent advances in quantum information and quantum science have inspired the development of various compact, dynamically structured ansätze that are expected to be realizable in Noisy Intermediate-Scale Quantum (NISQ) devices. However, such ansätze construction strategies hitherto developed involve considerable measurements, and thus, they deviate significantly in the NISQ platform from their ideal structures. Therefore, it is imperative that the usage of quantum resources be minimized while retaining the expressivity and dynamical structure of the ansatz that can adapt itself depending on the degree of correlation. We propose a novel ansatz construction strategy based on the ab initio many-body perturbation theory that requires no pre-circuit measurement and, thus, remains structurally unaffected by any hardware noise. The accuracy and quantum complexity associated with the ansatz are solely dictated by a pre-defined perturbative order, as desired, and, hence, are tunable. Furthermore, the underlying perturbative structure of the ansatz construction pipeline enables us to decompose any high-rank excitation that appears in higher perturbative orders into the product of various low-rank operators, and it thus keeps the execution gate-depth to its minimum. With a number of challenging applications on strongly correlated systems, we demonstrate that our ansatz performs significantly better, both in terms of accuracy, parameter count, and circuit depth, in comparison to the allied unitary coupled cluster based ansätze.

Do nanoparticles delivered to roots affect plant secondary metabolism? A comprehensive analysis in float seedling cultures of Hypericum perforatum L

Since nanoparticles (NPs) released into the environment from household or industrial wastes and applied directly on plants as agrochemicals can accumulate in the rhizosphere, it is imperative to understand how these NPs affect plant secondary metabolism upon their contact with the roots of intact plants. Here, the effects of Pd, Au, ZnO and Fe2O3 NPs on secondary metabolism were comprehensively investigated in Hypericum perforatum L float seedlings by analyzing 41 major secondary metabolites using ultra-performance liquid chromatography coupled with photodiode array, fluorescence detector and high-resolution mass spectrometry (UPLC-PDA-FLR-HRMS). The results showed that exposure of H. perforatum roots to Pd, Au, ZnO and Fe2O3 NPs rapidly led to fluctuations in the levels of secondary metabolites. Although these fluctuations did not correlate with NP type, concentration and duration of treatment, a total of 22 compounds were significantly altered by the NPs tested. In particular, 1 ppm Au increased the content of quercetin 3-(2″-acetylgalactoside), cadensin G and leutoskyrin by 5.02-, 2.12- and 2.58-fold, respectively after 24 h; 25 ppm Pd NPs led to a 2.1-fold increase in miquelianin content after 6 h; 50 ppm Fe2O3 NPs increased the level of furohyperforin by 3.09-fold and decreased the content of miquelianin 5.22-fold after 24 h and 50 ppm ZnO led to a 2.13-fold increase in hypericin after 48 h. These results emphasise the need to understand the intricate interplay between NPs and plant secondary metabolism in order to enable safer and efficient applications of NPs in agriculture.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

A thermo-mechanically loaded rotating FGM cylindrical pressure vessels under parabolic changing properties: An analytical and numerical analysis

This study aims to develop an exact analytical solution for steady-state thermo-mechanical stress in a functionally graded (FG) thick-walled cylindrical vessel. The cylinder is subjected to combined rotational speed and internal pressures while the thermal load is with convective and radiative boundary conditions. The dimensionless governing equations and boundary conditions, represented as a quartic equation, are derived and solved using Ferrari's method. The temperature, displacement, and stress fields across the thick-walled cylindrical vessel are calculated by finding the roots of the quartic equation. In order to investigate the accuracy of the exact analytical solution, a numerical model is constructed based on a standard Galerkin discretization approach of the finite element method (FEM). The analytical solutions and the results obtained through FEM show a high level of agreement. Furthermore, the study analyzes the effects of material parameters on temperature, displacement, and stress fields. Displacement, temperature, and stress fields are presented in the form of dimensionless graphs along the radial direction. For the considered parametric studies, results revealed that parabolic grading is beneficial than conventional grading. This study reveals that for the thermal loading, the maximum temperature, displacement, and tangential stress decrease for the parabolic grading. A similar but lower value of temperature, displacement, and tangential stress is also observed in the case of thermomechanical loading. This study is expected to assist in the assessment of the reliability of load calculations and contribute to the overall durability of pressure vessels. The results obtained from this study can provide valuable insights into thermo-elasticity and the thermo-mechanical behavior of thick-walled cylindrical vessels and can aid in the design and optimization of such systems.

Suitability of Adenosine Derivatives in Improving the Activity and Stability of Cytochrome c under Stress: Insights into the Effect of Phosphate Groups

It is well known that adenosine and its phosphate derivatives play a crucial role in biological phenomena such as apoptosis and cell signaling and act as the energy currency of the cell. Although their interactions with various proteins and enzymes have been described, the focus of this work is to demonstrate the effect of the phosphate group on the activity and stability of the native heme metalloprotein cytochrome c (Cyt c), which is important from both biological and industrial aspects. In situ and in silico characterizations are used to correlate the relationship between the binding affinity of adenosine and its phosphate groups with unfolding behavior, corresponding peroxidase activities, and stability factors. Interaction of adenosine (ADN), adenosine monophosphate (AMP), adenosine 5'-diphosphate (ADP), and adenosine 5'-triphosphate (ATP) with Cyt c increases peroxidase-like activity by up to 1.8-6.5-fold compared to native Cyt c. This activity is significantly maintained even after multiple stress conditions such as oxidative stress and the presence of a chaotropic agent such as guanidine hydrochloride (GuHCl). With binding affinities on the order of ADN < AMP < ADP < ATP, adenosine derivatives were found to stabilize Cyt c by varying the secondary structural features of the protein. Thus, in addition to being a fundamental study, the current work also proposes a way of stabilizing protein systems to be used for real-time biocatalytic applications.

Non-Native Site-Selective Enzyme Catalysis

The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.

Development of a compact Ansatz via operator commutativity screening: Digital quantum simulation of molecular systems

Recent advancements in quantum information and quantum technology have stimulated a good deal of interest in the development of quantum algorithms toward the determination of the energetics and properties of many-fermionic systems. While the variational quantum eigensolver is the most optimal algorithm in the noisy intermediate scale quantum era, it is imperative to develop compact Ansätze with low-depth quantum circuits that are physically realizable in quantum devices. Within the unitary coupled cluster framework, we develop a disentangled Ansatz construction protocol that can dynamically tailor an optimal Ansatz using the one- and two-body cluster operators and a selection of rank-two scatterers. The construction of the Ansatz may potentially be performed in parallel over multiple quantum processors through energy sorting and operator commutativity prescreening. With a significant reduction in the circuit depth toward the simulation of molecular strong correlation, our dynamic Ansatz construction protocol is shown to be highly accurate and resilient to the noisy circumstances of the near-term quantum hardware.

Machine learning aided dimensionality reduction toward a resource efficient projective quantum eigensolver: Formal development and pilot applications

In recent times, a variety of hybrid quantum-classical algorithms have been developed that aim to calculate the ground state energies of molecular systems on Noisy Intermediate-Scale Quantum (NISQ) devices. Albeit the utilization of shallow depth circuits in these algorithms, the optimization of ansatz parameters necessitates a substantial number of quantum measurements, leading to prolonged runtimes on the scantly available quantum hardware. Through our work, we lay the general foundation for an interdisciplinary approach that can be used to drastically reduce the dependency of these algorithms on quantum infrastructure. We showcase these pertinent concepts within the framework of the recently developed Projective Quantum Eigensolver (PQE) that involves iterative optimization of the nonlinearly coupled parameters through repeated residue measurements on quantum hardware. We demonstrate that one may perceive such a nonlinear optimization problem as a collective dynamic interplay of fast and slow relaxing modes. As such, the synergy among the parameters is exploited using an on-the-fly supervised machine learning protocol that dynamically casts the PQE optimization into a smaller subspace by reducing the effective degrees of freedom. We demonstrate analytically and numerically that our proposed methodology ensures a drastic reduction in the number of quantum measurements necessary for the parameter updates without compromising the characteristic accuracy. Furthermore, the machine learning model may be tuned to capture the noisy data of NISQ devices, and thus the predicted energy is shown to be resilient under a given noise model.

Designing protein nano-construct in ionic liquid: a boost in efficacy of cytochrome C under stresses

Herein, we present a simple approach to fabricate protein nanoconstructs by complexing cytochrome C (Cyt C) with silk nanofibrils (SNF) and choline dihydrogen phosphate ionic liquid (IL). The peroxidase activity of the IL modified Cyt C nanoconstruct (Cyt C + SNF + IL) increased significantly (2.5 to 10-fold) over unmodified Cyt C and showed enhanced catalytic activity and stability under harsh conditions, proving its potential as a suitable protein packaging strategy.

Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds

FeII - and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C-H bonds via a variety of C-X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C-H functionalization with other non-native functional groups.

A Synergistic Approach towards Optimization of Coupled Cluster Amplitudes by Exploiting Dynamical Hierarchy

The coupled cluster iteration scheme for determining the cluster amplitudes involves a set of nonlinearly coupled difference equations. In the space spanned by the amplitudes, the set of equations are analyzed as a multivariate time-discrete map where the concept of time appears in an implicit manner. With the observation that the cluster amplitudes have difference in their relaxation timescales with respect to the distributions of their magnitudes, the coupled cluster iteration dynamics are considered as a synergistic motion of coexisting slow and fast relaxing modes, manifesting a dynamical hierarchical structure. With the identification of the highly damped auxiliary amplitudes, their time variation can be neglected compared to the principal amplitudes which take much longer time to reach the fixed points. We analytically establish the adiabatic approximation where each of these auxiliary amplitudes are expressed as unique parametric functions of the collective principal amplitudes, allowing us to study the optimization with the latter taken as the independent degrees of freedom. Such decoupling of the amplitudes significantly reduces the computational scaling without sacrificing the accuracy in the ground state energy as demonstrated by a number of challenging molecular applications. A road-map to treat higher order post-adiabatic effects is also discussed.

The Single-Component Flavin Reductase/Flavin-Dependent Halogenase AetF is a Versatile Catalyst for Selective Bromination and Iodination of Arenes and Olefins

Flavin-dependent halogenases (FDHs) natively catalyze selective halogenation of electron rich aromatic and enolate groups. Nearly all FDHs reported to date require a separate flavin reductase to supply them with FADH2 , which complicates biocatalysis applications. In this study, we establish that the single component flavin reductase/flavin dependent halogenase AetF catalyzes halogenation of a diverse set of substrates using a commercially available glucose dehydrogenase to drive its halogenase activity. High site selectivity, activity on relatively unactivated substrates, and high enantioselectivity for atroposelective bromination and bromolactonization was demonstrated. Site-selective iodination and enantioselective cycloiodoetherification was also possible using AetF. The substrate and reaction scope of AetF suggest that it has the potential to greatly improve the utility of biocatalytic halogenation.

Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3-Aryl-4(3H)-Quinazolinones via Kinetic or Dynamic Kinetic Resolution

In this study, we engineer a variant of the flavin-dependent halogenase RebH that catalyzes site- and atroposelective halogenation of 3-aryl-4(3H)-quinazolinones via kinetic or dynamic kinetic resolution. The required directed evolution uses a combination of random and site-saturation mutagenesis, substrate walking using two probe substrates, and a two-tiered screening approach involving the analysis of variant conversion and then enantioselectivity of improved variants. The resulting variant, 3-T, provides >99:1 e.r. for the (M)-atropisomer of the major brominated product, 25-fold improved conversion, and 91-fold improved site selectivity relative to the parent enzyme on the probe substrate used in the final rounds of evolution. This high activity and selectivity translate well to several additional substrates with varied steric and electronic properties. Computational modeling and docking simulations are used to rationalize the effects of key mutations on substrate binding. Given the range of substrates that have been used for atroposelective synthesis via electrophilic halogenation in the literature, these results suggest that flavin-dependent halogenases (FDHs) could find many additional applications for atroposelective catalysis. More broadly, this study highlights how RebH can be engineered to accept structurally diverse substrates that enable its use for enantioselective catalysis.

Presenting B-DNA as macromolecular crowding agent to improve efficacy of cytochrome c under various stresses

Existence of numerous biomolecules results in biological fluids to be extremely crowded. Thus, Macromolecular crowding is an essential phenomenon to sustain active conformation of proteins in biological systems. Herein, double helical deoxyribonucleic acid (B-DNA) is presented for the first time as a biomacromolecular crowding system for sustainable packaging of cytochrome c (Cyt C). The peroxidase activity of Cyt C was investigated in the presence of various concentrations of B-DNA (from salmon milt). At an optimized concentration of 0.125 mg/mL B-DNA, an 11-fold higher catalytic activity was found than in native Cyt C with improved stability. Molecular docking and spectroscopic analyses revealed that electrostatic and H-bonding are the main interactions between DNA and Cyt C that affect the structural stability and activity of the protein. Moreover, the catalytic activity and stability of the protein were further investigated in the presence of severe process conditions by UV-visible, circular dichroism, and Fourier-transform infrared spectroscopies. Molecularly crowded Cyt C showed significantly higher activity and stability under severe environments such as high temperature (110 °C), oxidative stress, high pH (pH 10) and biological (trypsin) and chemical denaturants (urea) compared to bare Cyt C. The observed results support the suitability of DNA-based macromolecular crowding media as a viable and effective stabilizer of proteins against multiple stresses.

Etiology of Chronic Abnormal Uterine Bleeding According to the FIGO's PALM-COEIN Classification in Bangladeshi Women of Reproductive Age: A Cross-Sectional Study

Chronic abnormal uterine bleeding (AUB) is common, but there is a lack of standardized methods for investigating and etiological categorization of AUB. The PALM-COEIN classification system of AUB is getting important to overcome this issue. This cross-sectional study was conducted from January 2019 to December 2019 at Mymensingh Medical College Hospital, Mymensingh, Bangladesh, to determine the causes of AUB in women of the reproductive age group and categorize the causes of AUB as per the PALM-COEIN classification. A total of 380 women with chronic AUB were evaluated. The distribution of PALM-COEIN causes of AUB were AUB-P (1.8%), AUB-A (9.2%), AUB-L (13.2%), AUB-M (5.8%), AUB-C (1.1%), AUB-O (24.7%), AUB-E (1.6%), AUB-I (6.6%), and AUB-N (36.1%). The participants' mean age was 29.6 (±10.5) years, the majority (78.2%) of them was married, only a few (9.5%) had comorbid diseases, including hypertension (HTN) (1.1%), diabetes mellitus (DM) (5.3%), and hypothyroidism (8.7%). Women in the AUB-M classification had higher age than others; anemia was more prevalent in the AUB-P group, the AUB-O group had the highest TSH levels and hypothyroidism frequency. The PALM-COEIN classification helps ascertain the cause of AUB practically and should be used in routine clinical practices to manage these patients better.

Efficacy of Nebulized Hypertonic Saline (3%) Versus Normal Saline and Salbutamol in Treating Acute Bronchiolitis in A Tertiary Hospital: A Randomized Controlled Trial

Acute bronchiolitis is a viral respiratory illness of infants and young children that occurs in the first two years of life. It is a major cause of hospital admissions in Bangladesh. Management of bronchiolitis is a great challenge for the pediatrician both in the outpatient and inpatient department. Because mainstay of treatment options are usually supportive like cool humidified oxygen, fluids, bronchodilators, epinephrine and corticosteroids. A number of agents have been proposed as adjunctive therapies, but their effects are controversial. Nebulized hypertonic saline (3%) has been reported to have some benefit in recent studies. So the objective of this study was to compare the efficacy of nebulized 3% hypertonic saline (HS) with salbutamol and normal saline (0.9%) nebulization in children with acute bronchiolitis. A double-blind randomized controlled trial was conducted in the Department of Paediatrics, Mymensingh Medical College Hospital, Bangladesh from November 2015 to October 2016. A total of 100 children aged one month to two years with acute bronchiolitis admitted in the Pediatric wards of MMCH were included in the study and were randomly assigned to either 3% nebulized hypertonic saline (n=50) or to 0.9% nebulized isotonic saline with salbutamol solution (n=50). The main outcome variables were clinical severity score, length of hospital stay, duration of oxygen therapy and oxygen saturation (SpO2). The therapy was repeated three times on every hospitalization day and the outcome was evaluated two times daily (12 hourly) for 60 hours. Mean duration of oxygen therapy in study group was 33.6±21.7 hours and in control group was 36.8±22.5 hours. But their difference was not statistically significant (p>0.05). The mean clinical severity score and mean oxygen saturation of the entire study patients in both groups decreased and increased respectively during hospital stay. There was significant difference of mean clinical severity score and oxygen saturation between admission and follow up-5 in each group (p<0.001). But their difference between two groups was not statistically significant (p>0.05). Mean duration of hospital stay was 2.91±1.54 days in study group and 3.09±1.85 days in control group. But their difference between two groups was not statistically significant (p>0.05). So in acute bronchiolitis nebulized hypertonic saline (3%) is as effective as normal saline (0.9%) and salbutamol nebulization.

Post-Acute Covid Neurological Symptoms among Doctors and Nurses in A Tertiary Care Hospital: An Observational Study from Bangladesh

A good number of patients experience post-Covid complications. Doctors and nurses are the front liners who are at greater risk of having this disease. Neurological symptoms are frequent in patients with post-COVID-19 infection. The study aims to observe the post-acute neurological symptoms among doctors and nurses of Mymensingh Medical College Hospital, a tertiary care hospital in Bangladesh, after they recover from initial infection or among the asymptomatic cases. It was a retrospective observational study among the doctors and nurses who became RT PCR positive from late April to mid-September 2020. A total of 100 subjects were interviewed over the phone for the presence or absence of neurological symptoms four weeks post Covid-19 infection. Total 54 doctors and 46 nurses were evaluated; the male-female ratio was 1:1.77, the mean age was 35.6±7.6 years. Post-acute COVID neurological symptoms (PACNS) were present in 60% of respondents. Fatigue (51%) was the most common symptom, followed by sleep disturbance, headache, myalgia, loss of taste and smell. PACNS were more in symptomatic patients at the initial Covid infection than asymptomatic cases.

Bioinspired engineering protein nanofibrils-based multilayered self-cleaning membranes for universal water purification

Proteinaceous materials are promising for membranes due to greater mechanical strength, in-built functionalities, amphiphilicity and high molecular loading capacity. Herein, a novel strategy of functionalization of silk nanofibrils with metal oxyhydroxide and fabrication of ultrafast permeable multi-layered and self-cleaning membrane was demonstrated. Typically, 1.9 µm thick multilayered membrane efficiently purifies macromolecules, dyes, pharmaceutical, surfactants and oil-water emulsion contaminated wastewater with rejection rate > 89% with the flux rate > 883 Lm²h^-1. Further, the potential of the multilayered membrane was tested for series of different feed concentrations of fluoride and As (V) to validate the commercial applicability of the multilayered membranes for industry wastewater. Notably, even at higher concentration of 10-30 mgL^-1, >96% for fluoride and >87% for As (V) rejection was obtained. Furthermore, the functionalized multilayered membrane exhibited outstanding performance for fluoride removal in real water streams, where, it purifies approximately 4710 L.m^-2 in two consecutive cycles, before the quality of the effluents no longer meets WHO criteria. However, the remarkable separation efficiency principally attributed to adsorption sites on the surface of the membrane. Thus, various regeneration strategies were established based on the nature of pollutants. More importantly, photocatalytic Fenton-like reaction assisted self-cleaning property of the multilayered membrane is demonstrated for regeneration of organic fouled membrane. Overall, the present multilayered membrane exhibits superior performance in purifying organic, inorganic contaminated water and oil-water emulsion with excellent recyclability; hence, envisaged its application for Universal water purification.

Histidine protonation states are key in the LigI catalytic reaction mechanism

Lignin is one of the world's most abundant organic polymers, and 2-pyrone-4,6-dicarboxylate lactonase (LigI) catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) in the degradation of lignin. The pH has profound effects on enzyme catalysis and therefore we studied this in the context of LigI. We found that changes of the pH mostly affects surface residues, while the residues at the active site are more subject to changes of the surrounding microenvironment. In accordance with this, a high pH facilitates the deprotonation of the substrate. Detailed free energy calculations by the empirical valence bond (EVB) approach revealed that the overall hydrolysis reaction is more likely when the three active site histidines (His31, His33 and His180) are protonated at the ɛ site, however, protonation at the δ site may be favored during specific steps of the reaction. Our studies have uncovered the determinant role of the protonation state of the active site residues His31, His33 and His180 in the hydrolysis of PDC.

Exploring the Activation Process of the β2AR-Gs Complex

G-Protein-coupled receptors (GPCRs) belong to an important family of integral membrane receptor proteins that are essential for a variety of transmembrane signaling process, such as vision, olfaction, and hormone responses. They are also involved in many human diseases (Alzheimer's, heart diseases, etc.) and are therefore common drug targets. Thus, understanding the details of the GPCR activation process is a task of major importance. Various types of crystal structures of GPCRs have been solved either at stable end-point states or at possible intermediate states. However, the detailed mechanism of the activation process is still poorly understood. For example, it is not completely clear when the nucleotide release from the G protein occurs and how the key residues on α5 contribute to the coupling process and further affect the binding specificity. In this work we show by free energy analysis that the guanosine diphosphate (GDP) molecule could be released from the G_s protein when the binding cavity is half open. This occurs during the transition to the G_s open state, which is the rate-determining step in the system conformational change. We also account for the experimentally observed slow-down effects by the change of the reaction barriers after mutations. Furthermore, we identify potential key residues on α5 and validated their significance by site-directed mutagenesis, which illustrates that computational works have predictive value even for complex biophysical systems. The methodology of the current work may be applied to other biophysical systems of interest.

VLBI measurement of the vector baseline between geodetic antennas at Kokee Park Geophysical Observatory, Hawaii

We measured the components of the 31-m-long vector between the two very-long-baseline interferometry (VLBI) antennas at the Kokee Park Geophysical Observatory (KPGO), Hawaii, with approximately 1 mm precision using phase delay observables from dedicated VLBI observations in 2016 and 2018. The two KPGO antennas are the 20 m legacy VLBI antenna and the 12 m VLBI Global Observing System (VGOS) antenna. Independent estimates of the vector between the two antennas were obtained by the National Geodetic Survey (NGS) using standard optical surveys in 2015 and 2018. The uncertainties of the latter survey were 0.3 and 0.7 mm in the horizontal and vertical components of the baseline, respectively. We applied corrections to the measured positions for the varying thermal deformation of the antennas on the different days of the VLBI and survey measurements, which can amount to 1 mm, bringing all results to a common reference temperature. The difference between the VLBI and survey results are 0.2 ± 0.4 mm, -1.3 ± 0.4 mm, and 0.8 ± 0.8 mm in the East, North, and Up topocentric components, respectively. We also estimate that the Up component of the baseline may suffer from systematic errors due to gravitational deformation and uncalibrated instrumental delay variations at the 20 m antenna that may reach ± 10 and -2 mm, respectively, resulting in an accuracy uncertainty on the order of 10 mm for the relative heights of the antennas. Furthermore, possible tilting of the 12 m antenna increases the uncertainties in the differences in the horizontal components to 1.0 mm. These results bring into focus the importance of (1) correcting to a common reference temperature the measurements of the reference points of all geodetic instruments within a site, (2) obtaining measurements of the gravitational deformation of all antennas, and (3) monitoring local motions of the geodetic instruments. These results have significant implications for the accuracy of global reference frames that require accurate local ties between geodetic instruments, such as the International Terrestrial Reference Frame (ITRF).

Designing biopolymer-based artificial peroxidase for oxidative removal of dibenzothiophene from a model diesel fuel

Naturally occurring peroxidases are important for living organisms and have manifold utility in industries. However, lack of stability in harsh reaction conditions hinders wide applicability of such enzymes. Thus, suitable alternative is vital which can endure severe reaction conditions. As a substitute of natural peroxidase, herein, biopolymer-based polyelectrolyte complexes (PECs) coordinated with Feⁿ⁺ is proposed as macromolecular peroxidase mimicking systems. Three PECs were engineered via complexation of protonated chitosan and alginate with Fe²⁺ (Fe²⁺-PEC), Fe³⁺ (Fe³⁺-PEC), and Fe₃O₄ (Fe₃O₄-PEC), respectively. Computational study showed the Fe³⁺-PEC was highly stable with abundant electrostatic and intramolecular hydrogen bonding interactions. The versatility of the Fe-PECs as artificial peroxidase biocatalysts was probed by two types of peroxidase assays - ABTS oxidation in buffer systems (pH 4.0 and 7.0) and pyrogallol oxidation in organic solvents (acetonitrile, ethyl acetate and toluene). Overall, Fe³⁺-PEC showed remarkably high peroxidase activity both in aqueous buffers and in organic solvents, whereas, Fe₃O₄-PEC showed least catalytic activity. Finally, as a proof of concept, the ability of the biocatalyst to carry out deep oxidative desulphurization was demonstrated envisaging removal of dibenzothiophene from model fossil fuel in a sustainable way.

407 Incidental Focal Intrahepatic Duct Dilatation (FIDD) – A Finding That Mandates Further Investigation That May Include Liver Resection

Background

The increasing use of imaging has led to incidental findings in the liver. The Western experience of managing focal intrahepatic duct dilatation (FIDD) is not well recorded. We present our experience based on a large prospectively maintained database at a tertiary hepatobiliary surgical unit.

Method

Patients with liver resection for FIDD between January 2003-December 2019 were retrospectively identified from the liver unit database. The demographics, symptomatology, blood test results, imaging, type of liver resection, morbidity, mortality, and histology of resected specimens were recorded.

Results

9 patients had FIDD among 994 liver resections performed (0.9%). 6 patients were asymptomatic, 2 upper abdominal pain and 1 recurrent gram-negative sepsis. Liver function tests were normal in all patients. Two patients had cholangiocarcinoma (CCA), 4 intrahepatic stones, 1 intraductal papillary neoplasm of bile duct (IPN –B) and 2 benign strictures.

Conclusions

FIDD is rare in the Western population. Most patients are asymptomatic with an incidental finding of FIDD on cross-sectional imaging. Differentiating benign and malignant pathology is difficult warranting liver resection in fit patients to resolve the diagnosis. Liver resection is safe and can be potentially curative in patients with a neoplasm, which can occur in 30% of patients with FIDD.

Diversity of Vibrio parahaemolyticus in marine fishes of Bangladesh

AIMS

To determine the occurrence, diversity, antibiotic resistance and biofilm formation of Vibrio parahaemolyticus isolated from marine fishes in Bangladesh.

METHODS AND RESULTS

A total of 80 marine fishes were obtained from the local markets and examined for the presence of V. parahaemolyticus. All the isolated V. parahaemolyticus were characterized for the presence of virulence markers, thermostable direct hemolysin (TDH) or thermostable direct hemolysin related hemolysin (TRH). Isolates were serotyped and further characterized by enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) typing to analyse the genetic diversity. Moreover, biofilm formation and antibiotic resistance patterns were also determined. About 63·75% (51/80) of the tested marine fishes were contaminated with V. parahaemolyticus. From the contaminated fishes, 71 representatives V. parahaemolyticus were isolated and none of them harboured tdh and trh virulence genes. Nine different O-groups and seven different K-types were found by serological analysis and the dominant serotype was O5:KUT. In ERIC-PCR analysis, eight clusters (A-H) were found and the most common pattern was A (46·5%). All of the isolates were resistant to ampicillin and 78·9% of isolates were resistant to streptomycin. The highest biofilm formation was found at 37°C compared to 25°C and 4°C.

CONCLUSION

Diverse V. parahaemolyticus are present in marine fishes in the local market of Bangladesh with antibiotic-resistant properties and biofilm formation capacity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The widespread prevalence of diverse V. parahaemolyticus in marine fishes is an issue of serious concern, and it entails careful monitoring to ascertain the safety of seafood consumers.

Restructuring thin film composite membrane interfaces using biopolymer as a sustainable alternative to prevent organic fouling

Replacing polyamide (PA) layer in commercially successful thin film composite (TFC) membranes prepared via interfacial polymerization has been challenging task. Lately, PA is under scrutiny due to its increasing fouling propensity for highly contaminated waters. To mitigate the bio and organic fouling on PA layer in nanofiltration (NF) membranes in a long run, present study attempts to create a new interfacial thin film asymmetric structure using biopolymer chitosan as sustainable alternative. Herein, the effect of chitosan-silver on porous support structure and filtration performance were systematically investigated. Further, the membranes were characterized for their functionality and surface characteristics using ATR-IR, FESEM, AFM, UV-vis spectroscopy and contact angle measurements, respectively. New asymmetric membrane performances in cross flow process were evaluated in terms of pure water flux, NaCl (∼40 %), red brown/organic dye (>98 %) and tannery wastewater flux and rejection (>98 %). With a higher pure water flux (>100 L m^-2 h^-1) compared to control (40 L m^-2 h^-1) at 4 bar, membrane showed exceptional antifouling behaviors in comparison to commercial PA membrane. Further, surface characteristics of the membranes before and after rigorous testing were evaluated using AFM micrographs and SEM imaging.

Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2

The development of reliable ways of predicting the binding free energies of covalent inhibitors is a challenge for computer-aided drug design. Such development is important, for example, in the fight against the SARS-CoV-2 virus, in which covalent inhibitors can provide a promising tool for blocking Mpro, the main protease of the virus. This work develops a reliable and practical protocol for evaluating the binding free energy of covalent inhibitors. Our protocol presents a major advance over other approaches that do not consider the chemical contribution of the binding free energy. Our strategy combines the empirical valence bond method for evaluating the reaction energy profile and the PDLD/S-LRA/β method for evaluating the noncovalent part of the binding process. This protocol has been used in the calculations of the binding free energy of an α-ketoamide inhibitor of Mpro. Encouragingly, our approach reproduces the observed binding free energy. Our study of covalent inhibitors of cysteine proteases indicates that in the choice of an effective warhead it is crucial to focus on the exothermicity of the point on the free energy surface of a peptide cleavage that connects the acylation and deacylation steps. Overall, we believe that our approach should provide a powerful and effective method for in silico design of covalent drugs.

Fe-Al based nanocomposite reinforced hydrothermal carbon: Efficient and robust absorbent for anionic dyes

Nanocomposites with ultrahigh adsorption capabilities are highly desired for efficient wastewater remediation. Unfortunately, most of the nanomaterial based adsorbents showing inevitable limitation such as leaching and agglomeration led to the emerging field of carbonaceous hybrid materials with nanocomposites. Herein, we demonstrated a simple and low-temperature hydrothermal assisted preparation of Fe-Al based nanocomposites immobilized using carbon spheres. Towards this, we have approached two different routes one is hybridizing with nanocomposite and another is doping on the surface of the carbon spheres. Iron doping played a dual-faceted role of active site for robust adsorption as well as induce magnetic property to the composites. The micro-cleaners have been extensively characterized for their physicochemical properties and adsorption capacities using FTIR, Raman, XRD, BET isotherms and XPS techniques. Remarkably, microcleaners shows robust adsorption where >99% removal was obtained within 10 min for 50 mg L^-1 concentrated Eriochrome Black T (EBT) dye using 0.01 g of materials. Further, adsorption data followed the pseudo second order kinetics while the equilibrium data fitted perfectly into the Langmuir adsorption equation. As synthesized user friendly microcleaner (HTC-2) exhibits maximum adsorption capacity (q_max) of 564.97 mg g^-1 for EBT dye at pH 4. Hence, the preliminary results highlight the potential of the composites to be used in pretreatment steps of industry effluents.

Exploring the activation pathway and Gi-coupling specificity of the μ-opioid receptor

Understanding the activation mechanism of the μ-opioid receptor (μ-OR) and its selective coupling to the inhibitory G protein (Gi) is vital for pharmaceutical research aimed at finding treatments for the opioid overdose crisis. Many attempts have been made to understand the mechanism of the μ-OR activation, following the elucidation of new crystal structures such as the antagonist- and agonist-bound μ-OR. However, the focus has not been placed on the underlying energetics and specificity of the activation process. An energy-based picture would not only help to explain this coupling but also help to explore why other possible options are not common. For example, one would like to understand why μ-OR is more selective to Gi than a stimulatory G protein (Gs). Our study used homology modeling and a coarse-grained model to generate all of the possible "end states" of the thermodynamic cycle of the activation of μ-OR. The end points were further used to generate reasonable intermediate structures of the receptor and the Gi to calculate two-dimensional free energy landscapes. The results of the landscape calculations helped to propose a plausible sequence of conformational changes in the μ-OR and Gi system and for exploring the path that leads to its activation. Furthermore, in silico alanine scanning calculations of the last 21 residues of the C terminals of Gi and Gs were performed to shed light on the selective binding of Gi to μ-OR. Overall, the present work appears to demonstrate the potential of multiscale modeling in exploring the action of G protein-coupled receptors.

Engineering a Biopolymer-Based Ultrafast Permeable Aerogel Membrane Decorated with Task-Specific Fe-Al Nanocomposites for Robust Water Purification

The present work demonstrates an innovative strategy for robust water purification using an engineered aerogel membrane fabricated from biopolymers and task-specific Fe-Al-based nanocomposites. The as-prepared ethylenediaminetetraacetate dianhydride cross-linked chitosan- and agarose (7:3 weight ratio)-based aerogel membrane decorated with α-FeOOH- and γ-AlOOH-based nanocomposites was characterized using various analytical tools, which suggested formation of a highly stable network interconnected through covalent and electrostatic interactions. The optimized bionanocomposite-based aerogel (BNC-AG-0.1) membrane showed macroporous and partial unidirectional short-range channels with an ultralow density of 0.021 g·m^-2, a high swelling ratio of 1974%, and a remarkable pure water flux of 19,228 L·m^-2·h^-1 (>6-fold higher flux compared to the reported aerogel membranes). The aerogel membranes were successfully utilized for purification of diverse pollutants such as dyes, emerging pollutants (EPs), arsenate, and fluoride in a continuous flow method under gravitational force. The BNC-AG-0.1 membrane exhibits high rejection (95-98.6%) for both cationic and anionic dyes with a flux rate of 1150-1375 L·m^-2·h^-1 and a rejection of 89-92% for EPs with a flux rate of 1098-1165 L·m^-2·h^-1. Moreover, the BNC-AG-0.1 membrane showed a q_max of 102.45 mg·g^-1 (at pH 6.5) for As(V) with >93% rejection at a flow rate of 1000 L·m^-2·h^-1. Furthermore, the aerogel membrane showed an excellent removal efficiency (92%) of arsenic up to the 10th cycle and hence demonstrated as a potential adsorption-based membrane for arsenic-free potable water. On the other hand, the BNC-AG-0.1 membrane showed a q_max of 81.56 mg·g^-1 (at pH 6.5) for F^- removal with >99% rejection at a flow rate of 250 L·m^-2·h^-1. When applied for real-water purification, approximately 4734 L of safe drinking water (the F^- concentration is less than the WHO permissible limit) per square meter of the aerogel membrane can be obtained with a flux rate of 250 L·m^-2·h^-1. Overall, the prepared aerogel membrane showed robust removal of a variety of contaminants with ultrafast water permeation and established excellent recyclability.

Exploring the Proteolysis Mechanism of the Proteasomes

The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.

Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design

Computer-aided enzyme design is a field of great potential importance for biotechnological applications, medical advances, and a fundamental understanding of enzyme action. However, reaching a predictive ability in this direction is extremely challenging. It requires both the ability to predict quantitatively the activation barriers in cases where the structure and sequence are known and the ability to predict the effect of different mutations. In this work, we propose a protocol for predicting reasonable starting structures of mutants of proteins with known structures and for calculating the activation barriers of the generated mutants. Our approach also allows us to use the predicted structures of the generated mutant to predict structures and activation barriers for subsequent set of mutations. This protocol is used to examine the reliability of the in silico directed evolution of Kemp eliminase and haloalkane dehalogenase. We also used the results of single and double mutations as a base for predicting the effect of transition-state stabilization by multiple concurrent mutations. This strategy seems to be useful in creating an activity funnel that provides a qualitative ranking of the catalytic power of different mutants.

Exploring alternative catalytic mechanisms of the Cas9 HNH domain

Understanding the reaction mechanism of CRISPR-associated protein 9 (Cas9) is crucial for the application of programmable gene editing. Despite the availability of the structures of Cas9 in apo- and substrate-bound forms, the catalytically active structure is still unclear. Our first attempt to explore the catalytic mechanism of Cas9 HNH domain has been based on the reasonable assumption that we are dealing with the same mechanism as endonuclease VII, including the assumption that the catalytic water is in the first shell of the Mg2+ . Trying this mechanism with the cryo-EM structure forced us to induce significant structural change driven by the movement of K848 (or other positively charged residue) close to the active site to facilitate the proton transfer step. In the present study, we explore a second reaction mechanism where the catalytic water is in the second shell of the Mg2+ and assume that the cryo-EM structure by itself is a suitable representation of a catalytic-ready structure. The alternative mechanism indicates that if the active water is from the second shell, then the calculated reaction barrier is lower compared with the corresponding barrier when the water comes from the first shell.

Exploring the structure of Xe isotopes in A ~ 130 region: Single particle and collective excitations

High and medium spin structures of 130,131Xe have been studied using α-induced fusion-evaporation reaction and the Indian National Gamma Array (INGA) coupled with a digital data acquisition system. Various new band structures and near yrast levels of 131Xe have been established. The multipolarities of the observed transitions have been assigned on the basis of the DCO ratios and the polarization asymmetry measurements. Band structures based on 1-quasi-particle (qp), 3-qp configurations have been observed. A new Magnetic Rotational (MR) band based on 5-qp configuration has also been established in 131Xe. The MR band has been interpreted in terms of shears mechanism with principal axis cranking (SPAC) calculations. Shell Model calculations are carried out to describe the non yrast states of 131Xe above the 11/2− isomer. New excited states have also been identified in 130Xe, produced in the same reaction.

Protein packaging in ionic liquid mixtures: an ecofriendly approach towards the improved stability of β-lactoglobulin in cholinium-based mixed ionic liquids

The present work demonstrates a pioneering approach for the packaging of β-LG with improved stability in the presence of aqueous solutions containing cholinium-based ionic liquid mixtures.

Multifunctional solvothermal carbon derived from alginate using ‘water-in-deep eutectic solvents’ for enhancing enzyme activity

The use of a water-in-DES system for conversion of a seaweed biopolymer to a highly oxygenated functional carbon is reported for protein packaging with improved activity and stability.

Exploring the Effectiveness of Binding Free Energy Calculations

Increasing the accuracy of the evaluation of ligand-binding energies is one of the most important tasks of current computational biology. Here we explore the accuracy of free energy perturbation (FEP) approaches by comparing the performance of a "regular" FEP method to the one using replica exchange to enhance the sampling on a well-defined benchmark. The examination was limited to the so-called alchemical perturbations which are restricted to a fragment of the drug, and therefore, the calculation is a relative one rather than the absolute binding energy of the drug. Overall, our calculations reach the 1 kcal/mol accuracy limit. It is also shown that the accurate prediction of the position of water molecules around the binding pocket is important for FEP calculations. Interestingly, the replica exchange method does not significantly improve the accuracy of binding energies, suggesting that we reach the limit where the force field quality is a critical factor for accurate calculations.

Biomolecule-derived quantum dots for sustainable optoelectronics

The diverse chemical functionalities and wide availability of biomolecules make them essential and cost-effective resources for the fabrication of zero-dimensional quantum dots (QDs, also known as bio-dots) with extraordinary properties, such as high photoluminescence quantum yield, tunable emission, photo and chemical stability, excellent aqueous solubility, scalability, and biocompatibility. The additional advantages of scalability, tunable optical features and presence of heteroatoms make them suitable alternatives to conventional metal-based semiconductor QDs in the field of bioimaging, biosensing, drug delivery, solar cells, photocatalysis, and light-emitting devices. Furthermore, a recent focus of the scientific community has been on QD-based sustainable optoelectronics due to the primary concern of partially mitigating the current energy demand without affecting the environment. Hence, it is noteworthy to focus on the sustainable optoelectronic applications of biomolecule-derived QDs, which have tunable optical features, biocompatibility and the scope of scalability. This review addresses the recent advances in the synthesis, properties, and optoelectronic applications of biomolecule-derived QDs (especially, carbon- and graphene-based QDs (C-QDs and G-QDs, respectively)) and discloses their merits and disadvantages, challenges and future prospects in the field of sustainable optoelectronics. In brief, the current review focuses on two major issues: (i) the advantages of two families of carbon nanomaterials (i.e. C-QDs and G-QDs) derived from biomolecules of various categories, for instance (a) plant extracts including fruits, flowers, leaves, seeds, peels, and vegetables; (b) simple sugars and polysaccharides; (c) different amino acids and proteins; (d) nucleic acids, bacteria and fungi; and (e) biomasses and their waste and (ii) their applications as light-emitting diodes (LEDs), display systems, solar cells, photocatalysts and photo detectors. This review will not only bring a new paradigm towards the construction of advanced, sustainable and environment-friendly optoelectronic devices using natural resources and waste, but also provides critical insights to inspire researchers ranging from material chemists and chemical engineers to biotechnologists to search for exciting developments of this field and consequently make an advance step towards future bio-optoelectronics.

Designing biological fluid inspired molecularly crowded ionic liquid media as a sustainable packaging platform for cytochrome c

The present study demonstrated biological fluid inspired design of molecularly crowded IL media and disclosed an innovative and sustainable way for the packaging of Cyt c with enhanced activity and stability.

High concentration solubility and stability of ɛ-poly-l-lysine in an ammonium-based ionic liquid: A suitable media for polypeptide packaging and biomaterial preparation

Packaging of structurally sensitive biomolecules such as proteins, peptides and DNA in non-aqueous media at ambient conditions with chemical and structural stability is important to explore the potential of such biomacromolecules as substrate for functional biomaterial design and for biotechnological applications. In this perspective, solubility, chemical and structural stability of ɛ-poly-l-lysine (ɛ-PL), a homopolypeptide produced by Streptomyces albulus in different ionic liquids (ILs) namely 2-hydroxyethyl ammonium formate (2-HEAF), 2-hydroxyethyl ammonium acetate (2-HEAA), choline formate (Ch-Formate) and choline acetate (Ch-Acetate) was studied. Maximum solubility (15% w/v) of the homopolypeptide was observed in 2-HEAF and lowest was found in Ch-Formate (2% w/v). After regeneration of the dissolved polypeptide in the IL, the IL could be recycled and reused in the dissolution process. Unlike in other ILs, 3-15% w/v of ɛ-PL in 2-HEAF gave formation of a thixotropic thermoreversible soft gel. Molecular docking studies established favourable interactions of [2-HEA]⁺ cation over [Ch]⁺ with ɛ-PL indicating [2-HEA]⁺ as the most promising cation for the dissolution process. However, the role of the anions was also found to be important, which could lead to improvement in polypeptide solubility when combined to the selected cation. The findings demonstrate suitability of the ionic liquids for functionalization of polypeptides for biomaterial preparation.