Genome sequence of white spot syndrome virus (WSSV) infecting cultured black tiger shrimp (Penaeus monodon) in Bangladesh

The white spot syndrome virus (WSSV) is a causative agent of white spot disease (WSD) in crustaceans, especially in cultivated black tiger shrimp (Penaeus monodon), leading to significant economic losses in the aquaculture sector. The present study describes four whole genome sequences of WSSV obtained from coastal regions of Bangladesh.

A-Site Cation Replacement of Hydrazinium Lead Iodide Perovskites by Borane Ammonium Ions: A DFT Calculation

Organometallic perovskites have become one of the most common multifunctional materials in optoelectronic research fields. This research studies density functional theory calculation on orthorhombic hydrazinium lead iodide (N2 H5 PbI3 ) perovskite by replacing A-site cation with a borane ammonium (BH2 NH3 + ) ion. The perovskite showed a significant structural deformation and an orthorhombic to triclinic phase transition due to A-site ion replacement. The N2 H5 PbI3 perovskite has a band gap of 1.64 eV, suitable for the solar cell absorber layer. The band gap has increased to 2.12 eV after complete A-site ion replacement. All structures showed a high absorption coefficient over 104  cm-1 in the low wavelength region and an increase in refractive index from 2.5 to 2.75 due to ion replacement. All the structures showed high optical conductivity of 1015  s-1 order in the blue wavelength region. These new perovskite structures hold the potential to provide a revolution in optoelectronic research.

Role of the redox state of the Pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways

Persistent cellular stress induced perpetuation and uncontrolled amplification of inflammatory response results in a shift from tissue repair toward collateral damage, significant alterations of tissue functions, and derangements of homeostasis which in turn can lead to a large number of acute and chronic pathological conditions, such as chronic heart failure, atherosclerosis, myocardial infarction, neurodegenerative diseases, diabetes, rheumatoid arthritis, and cancer. Keeping the vital role of balanced inflammation in maintaining tissue integrity in mind, the way to combating inflammatory diseases may be through identification and characterization of mediators of inflammation that can be targeted without hampering normal body function. Pirin (PIR) is a non-heme iron containing protein having two different conformations depending on the oxidation state of the iron. Through exploration of the Pirin interactome and using molecular docking approaches, we identified that the Fe2+-bound Pirin directly interacts with BCL3, NFKBIA, NFIX and SMAD9 with more resemblance to the native binding pose and higher affinity than the Fe3+-bound form. In addition, Pirin appears to have a function in the regulation of inflammation, the transition between the canonical and non-canonical NF-κB pathways, and the remodeling of the actin cytoskeleton. Moreover, Pirin signaling appears to have a critical role in tumor invasion and metastasis, as well as metabolic and neuro-pathological complications. There are regulatory variants in PIR that can influence expression of not only PIR but also other genes, including VEGFD and ACE2. Disparity exists between South Asian and European populations in the frequencies of variant alleles at some of these regulatory loci that may lead to differential occurrence of Pirin-mediated pathogenic conditions.

Simplified engineering geomorphic unit-based seismic site characterization of the detailed area plan of Dhaka city, Bangladesh

Severe failure of improperly designed and poorly constructed structures may occur due to the amplified and prolonged ground motion during an earthquake, and hence prediction of the ground motion characteristics at the soil surface is crucial. In this study, based on the prepared simplified engineering geomorphic map, we performed a one-dimensional (1D) nonlinear site response analysis for seismic site characterization of the recently proposed Detailed Area Plan (DAP) area of Dhaka City, the Capital of Bangladesh. The engineering geomorphic unit-based map was prepared from image analysis and verified with the collected borehole data and surface geology map. The study area was classified into three major geomorphic units and seven sub-units subject to the subsurface soil profiles. Nine earthquake time histories, seven from the PEER NGA WEST2 data set and two synthetics, and seven identified subsurface soil profiles were used for nonlinear site response analysis, along with the BNBC 2020 uniform hazard spectrum as the target spectrum. For the selected earthquake ground motions, the near-surface soil response of the DAP area showed de-amplification of acceleration in the short period and amplification of acceleration in the long period. The amplified long-period acceleration could cause severe damage in inappropriately designed and poorly constructed long-period structures. The outcome of this study could be used to prepare a seismic risk-sensitive land use plan for the future development of the DAP of Dhaka City.

Influence of sugar concentration on the vesicle compactness, deformation and membrane poration induced by anionic nanoparticles

Sugar plays a vital role in the structural and functional characteristics of cells. Hence, the interaction of NPs with cell membranes in the presence of sugar concentrations is important for medicinal and pharmacological innovations. This study integrated three tools: giant unilamellar vesicles (GUVs), anionic magnetite nanoparticles (NPs), and sugar concentrations, to understand a simplified mechanism for interactions between the vesicle membranes and NPs under various sugar concentrations. We focused on changing the sugar concentration in aqueous solution; more precisely, sucrose inside the GUVs and glucose outside with equal osmolarity. 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (sodium salt) (DOPG) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were used to prepare the charged membranes of 40mole%DOPG/60mole%DOPC-GUVs, whereas only DOPC was used to prepare the neutral membranes. Phase contrast fluorescence microscopy shows that the adherence of 18 nm magnetite NPs with anionic charge depends on the sugar concentration. The alterations of GUVs induced by the NPs are characterized in terms of i) vesicle compactness, ii) deformation, and iii) membrane poration. The presence of sugar provides additional structural stability to the GUVs and reduces the effects of the NPs with respect to these parameters; more precisely, the higher the sugar concentration, the smaller the alteration induced by the NPs. The differences in NPs effects are explained by the change in the type of interaction between sugar molecules and lipid membranes, namely enthalpy and entropy-driven interaction, respectively. In addition, such alterations are influenced by the surface charge density of the lipid bilayer. The surface pressure of membranes due to the adsorption of NPs is responsible for inducing the poration in membranes. The differences in deformation and poration in charged and neutral GUVs under various sugar concentrations are discussed based on the structure of the head of lipid molecules.

A comprehensive in silico exploration of the impacts of missense variants on two different conformations of human pirin protein

BACKGROUND

Pirin, a member of the cupin superfamily, is an iron-binding non-heme protein. It acts as a coregulator of several transcription factors, especially the members of NFκB transcription factor family. Based on the redox state of its iron cofactor, it can assume two different conformations and thereby act as a redox sensor inside the nucleus. Previous studies suggested that pirin may be associated with cancer, inflammatory diseases as well as COVID-19 severities. Hence, it is important to explore the pathogenicity of its missense variants. In this study, we used a number of in silico tools to investigate the effects of missense variants of pirin on its structure, stability, metal cofactor binding affinity and interactions with partner proteins. In addition, we used protein dynamics simulation to elucidate the effects of selected variants on its dynamics. Furthermore, we calculated the frequencies of haplotypes containing pirin missense variants across five major super-populations (African, Admixed American, East Asian, European and South Asian).

RESULTS

Among a total of 153 missense variants of pirin, 45 were uniformly predicted to be pathogenic. Of these, seven variants can be considered for further experimental studies. Variants R59P and L116P were predicted to significantly destabilize and damage pirin structure, substantially reduce its affinity to its binding partners and alter pirin residue fluctuation profile via changing the flexibility of several key residues. Additionally, variants R59Q, F78V, G98D, V151D and L220P were found to impact pirin structure and function in multiple ways. As no haplotype was identified to be harboring more than one missense variant, further interrogation of the individual effects of these seven missense variants is highly recommended.

CONCLUSIONS

Pirin is involved in the transcriptional regulation of several genes and can play an important role in inflammatory responses. The variants predicted to be pathogenic in this study may thus contribute to a better understanding of the underlying molecular mechanisms of various inflammatory diseases. Future studies should be focused on clarifying if any of these variants can be used as disease biomarkers.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s42269-022-00917-7.

Effects of cholesterol on the size distribution and bending modulus of lipid vesicles

The influence of cholesterol fraction in the membranes of giant unilamellar vesicles (GUVs) on their size distributions and bending moduli has been investigated. The membranes of GUVs were synthesized by a mixture of two elements: electrically neutral lipid 1, 2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol and also a mixture of three elements: electrically charged lipid 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DOPG), DOPC and cholesterol. The size distributions of GUVs have been presented by a set of histograms. The classical lognormal distribution is well fitted to the histograms, from where the average size of vesicle is obtained. The increase of cholesterol content in the membranes of GUVs increases the average size of vesicles in the population. Using the framework of Helmholtz free energy of the system, the theory developed by us is extended to explain the experimental results. The theory determines the influence of cholesterol on the bending modulus of membranes from the fitting of the proper histograms. The increase of cholesterol in GUVs increases both the average size of vesicles in population and the bending modulus of membranes.

First characterization of a newly emerging phytopathogen, Sclerotinia sclerotiorum causing white mold in pea

Pea (Pisum sativum L.) is of global importance as a food crop for its edible pod and seed. A new disease causing the tan to light brown blighted stems and pods has occurred in pea (P. sativum L.) plants in Chapainawabganj district, Bangladesh. A fungus with white-appressed mycelia and large sclerotia was consistently isolated from symptomatic tissues. The fungus formed funnel-shaped apothecia with sac-like ascus and endogenously formed ascospores. Healthy pea plants inoculated with the fungus produced typical white mold symptoms. The internal transcribed spacer sequences of the fungus were 100% similar to Sclerotinia sclerotiorum, considering the fungus to be the causative agent of white mold disease in pea, which was the first record in Bangladesh. Mycelial growth and sclerotial development of S. sclerotiorum were favored at 20°C and pH 5.0. Glucose was the best carbon source to support hyphal growth and sclerotia formation. Bavistin and Amistar Top inhibited the radial growth of the fungus completely at the lowest concentration. In planta, foliar application of Amistar Top showed the considerable potential to control the disease at 1.0% concentration until 7 days after spraying, while Bavistin prevented infection significantly until 15 days after spraying. A large majority (70.93%) of genotypes, including tested released pea cultivars, were susceptible, while six genotypes (6.98%) appeared resistant to the disease. These results on identification, characterization, host resistance, and fungicidal control of white mold could be valuable to achieve improved management of a new disease problem for pea cultivation.

A new purification technique to obtain specific size distribution of giant lipid vesicles using dual filtration

A new purification technique is developed for obtaining distribution of giant unilamellar vesicles (GUVs) within a specific range of sizes using dual filtration. The GUVs were prepared using well known natural swelling method. For filtration, different combinations of polycarbonate membranes were implemented in filter holders. In our experiment, the combinations of membranes were selected with corresponding pore sizes-(i) 12 and 10 μm, (ii) 12 and 8 μm, and (iii) 10 and 8 μm. By these filtration arrangements, obtained GUVs size distribution were in the ranges of 6-26 μm, 5-38 μm and 5-30 μm, respectively. In comparison, the size distribution range was much higher for single filtration technique, for example, 6-59 μm GUVs found for a membrane with 12 μm pores. Using this technique, the water-soluble fluorescent probe, calcein, can be removed from the suspension of GUVs successfully. The size distributions were analyzed with lognormal distribution. The skewness became smaller (narrow size distribution) when a dual filtration was used instead of single filtration. The mode of the size distribution obtained in dual filtration was also smaller to that of single filtration. By continuing this process of purification for a second time, the GUVs size distribution became even narrower. After using an extra filtration with dual filtration, two different size distributions of GUVs were obtained at a time. This experimental observation suggests that different size specific distributions of GUVs can be obtained easily, even if GUVs are prepared by different other methods.

Effects of osmotic pressure on the irreversible electroporation in giant lipid vesicles

Irreversible electroporation (IRE) is a nonthermal tumor/cell ablation technique in which a series of high-voltage short pulses are used. As a new approach, we aimed to investigate the rupture of giant unilamellar vesicles (GUVs) using the IRE technique under different osmotic pressures (Π), and estimated the membrane tension due to Π. Two categories of GUVs were used in this study. One was prepared with a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol (chol) for obtaining more biological relevance while other with a mixture of DOPG and DOPC, with specific molar ratios. We determined the rate constant (kp) of rupture of DOPG/DOPC/chol (46/39/15)-GUVs and DOPG/DOPC (40/60)-GUVs induced by constant electric tension (σc) under different Π. The σc dependent kp values were fitted with a theoretical equation, and the corresponding membrane tension (σoseq) at swelling equilibrium under Π was estimated. The estimated membrane tension agreed well with the theoretical calculation within the experimental error. Interestingly, the values of σoseq were almost same for both types of synthesized GUVs under same osmotic pressure. We also examined the sucrose leakage, due to large osmotic pressure-induced pore formation, from the inside of DOPG/DOPC/chol(46/39/15)-GUVs. The estimated membrane tension due to large Π at which sucrose leaked out was very similar to the electric tension at which GUVs were ruptured without Π. We explained the σc and Π induced pore formation in the lipid membranes of GUVs.

Detection and removal of microplastics in wastewater: evolution and impact

The pervasiveness of microplastics in aquatic ecosystems has become a major environmental issue in recent years. The gradual dumping of plastic wastes, inadequate standard detection methods with specific removal techniques, and slow disposal rate of microplastics make it ubiquitous in the environment. Evidence shows that microplastics act as a potential vector by adsorbing different heavy metals, pathogens, and other chemical additives widely used in different raw plastic production. Microplastics are ingested by aquatic creatures such as fish and different crustaceans, and finally, people ingest them at the tertiary level of the food chain. This phenomenon is responsible for blocking the digestion tracts, disturbing the digestive behavior, finally decreasing the reproductive growth of entire living organisms. Because of these consequences, microplastics have become an increasing concern as a newly emerging potential threat, and therefore, the control of microplastics in aquatic media is required. This paper provides a critical analysis of existing and newly developed methods for detecting and separating microplastics from discharged wastewater, which are the ultimate challenges in the microplastic treatment systems. A critical study on the effect of microplastics on aquatic organisms and human health is also discussed. Thus, this analysis provides a complete understanding of entire strategies for detecting and removing microplastics and their associated issues to ensure a waste discharge standard to minimize the ultimate potential impact in aquatic environments.