The ROK kinase N-acetylglucosamine kinase uses a sequential random enzyme mechanism with successive conformational changes upon each substrate binding.

N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.

The new institutional economic approach to land development game: Integrating transaction cost and efficient institutional framework in synergic urban land use-transport development model.

Land and property development process includes a series of multifaceted activities ranging from purchasing to converting it for development purposes and everything in between. The process itself encompasses multiple stakeholders, drivers, and contributions from diversified public and private actors and transaction cost arises out of their complex interaction. Transaction costs incurred during any kind of human interaction (i.e., transactions). Every actor involved in the process wishes to maximize his achievement under various constraints and hence institutional arrangement (i.e., set of humanly devised rules to administer the constraints) is necessary for efficient management of the development process. Therefore, to devise an optimum outcome out of economic and social transactions in the property development process, cooperative and competitive relationships between individuals should be understood from a broader socio-political and governance structure. In this research, it is critically argued that the land and property development process should implicate a multifaceted set of formal and informal rules or institutional arrangements to govern the intrinsic interaction, action and thereby reducing the related transaction cost. The central argument is further reproachfully evaluated and implicated in the urban development process through the myopic lens of the Transit-oriented development (TOD) pathway. A vigilant combination of descriptive and explanatory research approaches is adopted to analyze the connection between theory and practice.

Reusable Sugar-Based Gelator for Marine Oil-Spill Recovery and Waste Water Treatment.

In this work, the gelation ability of a series of novel pyridine-based glucose tailored gelators (DPHAEN, DPHABN, and DPHAHN) with a flexible alkyl chain has been examined in binary solvent mixtures using a number of techniques, for example, UV spectroscopy, FT-IR spectroscopy, NMR spectroscopy, rheology measurement, SEM, XRD, and computational study. Proposed herein is an environment-friendly method to realize toxic dye separation and oil/water separation. It has been found that gels in a selective binary solvent mixture are efficient reusable absorbers of toxic dye molecules. A new gravitational force-driven, simple one-step, toxic dye removal and oil-water separation method is presented for sustainable filtration of waste water and simultaneous collection of oil. The gel column also showed high stability and reusability over repeated use and can be easily scaled for efficient clean-up of a large number of toxic dyes and oil spills present in water. Studies also exposed that the gel column can simultaneously separate dye molecules and mineral oils from water. This simple, green, and efficient method overcomes a nontrivial hurdle for environmentally safe separation of toxic dyes as well as oil/water mixtures and offers insights into the design of advanced materials for practical oil/water separation.

Pineal Parenchymal Tumor of Intermediate Differentiation and DICER1 Syndrome: A Case Report.

DICER1 syndrome is a rare inherited tumor predisposition syndrome associated with an increased risk for several malignant and benign tumors. We present a patient with pineal parenchymal tumor of intermediate differentiation who was found to have a germline pathogenic variant in DICER1 gene. Pineoblastoma is a known DICER1-related tumor; however, the association between pineal parenchymal tumor of intermediate differentiation and DICER1 mutation is rare with only 1 recent large molecular study that has reported this association. This report adds to the evolving tumor spectrum of DICER1 and highlights the importance of molecular evaluation of pediatric brain tumors, for both therapeutic decisions and long-term surveillance.

Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells.

The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.

Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases.

The sugars streptose and dihydrohydroxystreptose (DHHS) are unique to the bacteria Streptomyces griseus and Coxiella burnetii, respectively. Streptose forms the central moiety of the antibiotic streptomycin, while DHHS is found in the O-antigen of the zoonotic pathogen C. burnetii. Biosynthesis of these sugars has been proposed to follow a similar path to that of TDP-rhamnose, catalyzed by the enzymes RmlA, RmlB, RmlC, and RmlD, but the exact mechanism is unclear. Streptose and DHHS biosynthesis unusually requires a ring contraction step that could be performed by orthologs of RmlC or RmlD. Genome sequencing of S. griseus and C. burnetii has identified StrM and CBU1838 proteins as RmlC orthologs in these respective species. Here, we demonstrate that both enzymes can perform the RmlC 3'',5'' double epimerization activity necessary to support TDP-rhamnose biosynthesis in vivo. This is consistent with the ring contraction step being performed on a double epimerized substrate. We further demonstrate that proton exchange is faster at the 3''-position than the 5''-position, in contrast to a previously studied ortholog. We additionally solved the crystal structures of CBU1838 and StrM in complex with TDP and show that they form an active site highly similar to those of the previously characterized enzymes RmlC, EvaD, and ChmJ. These results support the hypothesis that streptose and DHHS are biosynthesized using the TDP pathway and that an RmlD paralog most likely performs ring contraction following double epimerization. This work will support the elucidation of the full pathways for biosynthesis of these unique sugars.

Predicting changes in land use/land cover and seasonal land surface temperature using multi-temporal landsat images in the northwest region of Bangladesh.

Land use/land cover (LULC) variations are accelerated by rapid urbanization and significantly impacted global Land Surface Temperature (LST). The dynamic increase in LST results in the Urban Heat Island (UHI) effect. In this study, future LULC change scenarios, seasonal (summer & winter) LST variations, and LST distribution over different LULC classes were predicted using Landsat satellite images for 1999, 2009, and 2019 in Rajshahi District, Bangladesh. Cellular Automata (CA) and Artificial Neural Network (ANN) procedures were used to predict the LULC changes and seasonal LST variations for 2029 and 2039. In addition, Focus Group Discussions (FGDs) and Key Informants Interviews (KIIs) were conducted to identify the possible impacts of LULC change, LST shifts, and climate change on agricultural productivity and developed a sustainable land use management plan for the study area. Validation of the CA model demonstrated an excellent accuracy with a kappa value of 0.82. Similarly, the ANN model's validation using Mean Square Error (0.523 and 0.796 for summer) and Correlation coefficient (0.6023 and 0.831 for winter) values demonstrated a good prediction accuracy. The LULC prediction result indicated that the built-up area will be expanded by 58.03 km2 and 79.90 km2, respectively, from 2019 to 2029 and 2039. The predicted seasonal LST indicated that in 2029 and 2039, more than 23.30 % and 50.46 % of the summer and 3.02 % and 13.02 % of the winter seasons will likely be experienced LSTs greater than 35 °C. The results of public participation exposed that changes in LULC classes, variations in LST, and climate change significantly impact the regional biodiversity (loss of farmland and water bodies), reduce agricultural productivity, and increase extreme weather events (flood, heavy rainfall, and cold/warm temperature). This study provides the useful guidelines for agricultural officers, urban planners, and environmental engineers to understand the spatial configurations of built-up area enlargement and provide effective policy measures to conserve farming lands to ensure environmental sustainability.

Zoonoses under our noses.

One Health is an effective approach for the management of zoonotic disease in humans, animals and environments. Examples of the management of bacterial zoonoses in Europe and across the globe demonstrate that One Health approaches of international surveillance, information-sharing and appropriate intervention methods are required to successfully prevent and control disease outbreaks in both endemic and non-endemic regions. Additionally, a One Health approach enables effective preparation and response to bioterrorism threats.

Synthesis and characterization of biogenic metal nanoparticles and its cytotoxicity and anti-neoplasticity through the induction of oxidative stress, mitochondrial dysfunction and apoptosis.

In the present study, we demonstrate a simple, cost-effective and eco-friendly method for biogenic synthesis of silver nanoparticles (AgNPCGs) using ethanolic extract of Calotropis gigantea latex. Attempts were made to characterize these biogenic silver nanoparticles AgNPCGs and also to test its cytotoxic, anti-neoplastic and apoptotic potential through the induction of oxidative stress, mitochondrial dysfunction. AgNPCGs were characterized by UV-vis spectroscopy, dynamic light scattering (DLS) and surface zeta potential measurement, Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM) and selected area electron diffraction, scanning electron microscopy (SEM), energy-dispersive X-ray fluorescence spectrometry (EDX). UV visible spectroscopy showed an intense surface plasmon resonance band at 431nm which clearly reflected the formation of silver nanoparticles. FTIR study revealed that latex extract acted as reducing and stabilizing agent for the synthesis of AgNPCGs. Energy dispersive X-ray spectroscopy confirmed the presence of silver as a major component of synthesized AgNPCGs. SEM and TEM studies showed that the synthesized AgNPCGs were nearly spherical in shape with an average size of 2.338nm. The selected area electron diffraction pattern and XRD studies confirmed the crystalline nature of AgNPCGs. AgNPCGs exhibited in-vitro cytotoxic activity against Ehrlich's ascites carcinoma (EAC), Jurkat and MCF-7 cells at respective IC50 doses without producing cytotoxicity to mice and human lymphocytes. Significant chromatin condensation, DNA fragmentation, cell cycle arrest at G2/M phase, up-regulation of Bax and caspase-3 and down-regulation of Bcl-2 were observed in AgNPCGs treated EAC cells. The results suggest that biogenic silver nanoparticles AgNPCGs could be a potential chemotherapeutic formulation for cancer therapy.

Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species.

Many human-dwelling bacteria acquire sialic acid for growth or surface display. We identified previously a sialic acid utilization operon in Tannerella forsythia that includes a novel outer membrane sialic acid-transport system (NanOU), where NanO (neuraminate outer membrane permease) is a putative TonB-dependent receptor and NanU (extracellular neuraminate uptake protein) is a predicted SusD family protein. Using heterologous complementation of nanOU genes into an Escherichia coli strain devoid of outer membrane sialic acid permeases, we show that the nanOU system from the gut bacterium Bacteroides fragilis is functional and demonstrate its dependence on TonB for function. We also show that nanU is required for maximal function of the transport system and that it is expressed in a sialic acid-responsive manner. We also show its cellular localization to the outer membrane using fractionation and immunofluorescence experiments. Ligand-binding studies revealed high-affinity binding of sialic acid to NanU (Kd ~400 nM) from two Bacteroidetes species as well as binding of a range of sialic acid analogues. Determination of the crystal structure of NanU revealed a monomeric SusD-like structure containing a novel motif characterized by an extended kinked helix that might determine sugar-binding specificity. The results of the present study characterize the first bacterial extracellular sialic acid-binding protein and define a sialic acid-specific PUL (polysaccharide utilization locus).

Effect of pH and oxygen atom of the hydrophobic chain on the self-assembly property and morphology of the pyridyl boronic acid based amphiphiles.

The surface activity and aggregation behavior of two synthesized boronic acid based anionic surfactants, sodium salt of 2-dodecyl pyridine-5-boronic acid (SDDPB) and sodium salt of 2-oxydodecyl pyridine-5-boronic acid (SODDPB), were studied in buffer solution at pH 9 and 13 containing carbohydrates. The self-assembly formation was investigated by use of a number of techniques including surface tension, conductivity, fluorescence spectroscopy, dynamic light scattering, X-ray diffraction, and transmission electron microscopy (TEM). Both of the amphiphiles exhibit a single break in the surface tension vs log(concentration) plots, indicating existence of one critical aggregation concentration. Steady state fluorescence spectroscopy was used to determine the polarity indexes using pyrene and the rigidity of the microenvironments of the aggregates using 1,6-diphenyl-1,3,5-hexatriene (DPH) as fluorescence probe molecules. The pKa's of both amphiphiles were determined in buffer solutions of different pH's. XRD studies were performed to shed light on the morphology of the self-assemblies. TEM micrographs revealed the existence of vesicles for both the amphiphiles in buffer solution of pH 9, but at pH 13, TEM pictures indicate the existence of closed vesicles in SDDPB solution and at concentrated solution the vesicles are fused to form sponge-like micelles. After aging the vesicular solution of pH 13 of SDDPB, the closed vesicles are destroyed. In contrast, for SODDPB at pH 13, TEM pictures suggest the existence of spherical and complex micelles in solution which were further transformed into crystal-like structure upon aging. The average hydrodynamic radii were determined by dynamic light scattering measurement. Therefore, for the first time, we have successfully synthesized two new surfactants containing pyridyl-boronic acid as a headgroup which shows remarkable tuning of morphology in two different pH's and in the presence of two different carbohydrates.

Effect of amide hydrogen bonding on spontaneously formed gel-emulsions by two pyridyl carboxylic acid based amphiphiles, sodium salt of 2-dodecylpyridine-5-carboxylic acid and sodium salt of [2-dodecylpyridine-5-carboxylic]glycine: entrapment and release of vitamin B12.

The present study offers the demonstration and rational design of two synthesized single chain pyridyl carboxylic acid (nicotinic acid) based amphiphilic gelators named the sodium salt of 2-dodecylpyridine-5-carboxylic acid (SDDPC) and the sodium salt of [2-dodecylpyridine-5-carboxylic]glycine (SDDPCG). The gelation abilities were tested in a series of organic solvents, by a number of physical methods including X-ray diffraction, FTIR spectroscopy, rheology, DSC, optical and electron microscopy. The minimum gelation concentration and gelation number of the gelators in different solvents were determined. No gelation was observed when pure solvents were employed. The gelation properties of these two compounds found that the gelation depends on H-bonding of the amide linkage. X-ray diffraction study indicates the presence of two recognizable morphologies for SDDPC in a gel-emulsion, whereas for SDDPCG a single type of aggregate is predominant. FTIR spectra suggest that the presence of intermolecular hydrogen bonding facilitates the gelation process. Rheological measurements demonstrated that the gel-emulsions are mechanically stable and exhibit typical viscoelastic properties. Optical microscopy images show a network structure in the gel phase and a fibril structure in the xerogel. SEM images confirmed the presence of network as well as a flex-like thick fibrous network for both the amphiphiles, forming three dimensional (3-D) networks. Both the gelators showed a remarkable response toward external pH. The gel-emulsions were used in the controlled and/or pH triggered release of entrapped (within the gel-emulsions) vitamin B12 at different pHs.

Spontaneous formation of vesicles by sodium 2-dodecylnicotinate in water.

The surface activity and aggregation behavior of a synthesized nicotinic acid based anionic surfactant, sodium 2-dodecylnicotinate, were studied in aqueous solution. The self-assembly formation was investigated by use of a number of techniques, including surface tension and conductivity measurements, fluorescence spectroscopy, dynamic light scattering measurement, gel permeation chromatography, and microscopy. The amphiphile exhibits two breaks in the surface tension vs concentration plot, indicating stepwise aggregate formation and thus producing two values of the aggregation concentration. Stepwise aggregation of the amphiphile was further confirmed by steady-state fluorescence spectroscopy using pyrene as a probe molecule, and also the micropolarity of the aggregates was determined. The rigidity of the microenvironment was estimated by determining steady-state fluorescence anisotropy using 1,6-diphenyl-1,3,5-hexatriene as a fluorescence probe molecule. The average hydrodynamic radius and size distribution of the aggregate suggest formation of larger aggregates in aqueous solution. The formation of vesicles in water was established by conductivity measurement and a dye entrapment experiment. The entrapment of a small solute and the release capability have also been examined to demonstrate these bilayers form enclosed vesicles. Transmission electron micrographs revealed the existence of closed vesicles and closed tubules in aqueous solution. Therefore, for the first time, it has been observed that this simple single-chain nicotinic acid based amphiphile spontaneously assembles to vesicles in aqueous solution.

Beta-hexosaminidase activity of the oral pathogen Tannerella forsythia influences biofilm formation on glycoprotein substrates.

Tannerella forsythia is an important pathogen in periodontal disease. Previously, we showed that its sialidase activity is key to utilization of sialic acid from a range of human glycoproteins for biofilm growth and initial adhesion. Removal of terminal sialic acid residues often exposes ß-linked glucosamine or galactosamine, which may also be important adhesive molecules. In turn, these residues are often removed by a group of enzymes known as ß-hexosaminidases. We show here that T. forsythia has the ability to cleave glucosamine and galactosamine from model substrates and that this activity can be inhibited by the hexosaminidase inhibitor PugNAc (O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino N-phenyl carbamate). We now demonstrate for the first time that ß-hexosaminidase activity plays a role in biofilm growth on glycoprotein-coated surfaces because biofilm growth and initial cell adhesion are inhibited by PugNAc. In contrast, adhesion to siallo-glycoprotein-coated surfaces is unaltered by PugNAc in the absence of sialidase activity (using a sialidase-deficient mutant) or surprisingly on the clinically relevant substrates saliva or serum. These data indicate that ß-hexosaminidase activity has a significant role in biofilm formation in combination with sialidase activity in the biofilm lifestyle of T. forsythia.

Role of sialidase in glycoprotein utilization by Tannerella forsythia.

The major bacterial pathogens associated with periodontitis include Tannerella forsythia. We previously discovered that sialic acid stimulates biofilm growth of T. forsythia, and that sialidase activity is key to utilization of sialoconjugate sugars and is involved in host-pathogen interactions in vitro. The aim of this work was to assess the influence of the NanH sialidase on initial biofilm adhesion and growth in experiments where the only source of sialic acid was sialoglycoproteins or human oral secretions. After showing that T. forsythia can utilize sialoglycoproteins for biofilm growth, we showed that growth and initial adhesion with sialylated mucin and fetuin were inhibited two- to threefold by the sialidase inhibitor oseltamivir. A similar reduction (three- to fourfold) was observed with a nanH mutant compared with the wild-type. Importantly, these data were replicated using clinically relevant serum and saliva samples as substrates. In addition, the ability of the nanH mutant to form biofilms on glycoprotein-coated surfaces could be restored by the addition of purified NanH, which we show is able to cleave sialic acid from the model glycoprotein fetuin and, much less efficiently, 9-O-acetylated bovine submaxillary mucin. These data show for the first time that glycoprotein-associated sialic acid is likely to be a key in vivo nutrient source for T. forsythia when growing in a biofilm, and suggest that sialidase inhibitors might be useful adjuncts in periodontal therapy.

A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen Tannerella forsythia.

Tannerella forsythia is a Gram-negative anaerobe that is one of the most prominent inhabitants of the sub-gingival plaque biofilm, which is crucial for causing periodontitis. We have used iTRAQ proteomics to identify and quantify alterations in global protein expression of T. forsythia during growth in a biofilm. This is the first proteomic study concentrating on biofilm growth in this key periodontal pathogen, and this study has identified several changes in protein expression. Moreover, we introduce a rigorous statistical method utilising peptide-level intensities of iTRAQ reporters to determine which proteins are significantly regulated. In total, 348 proteins were identified and quantified with the expression of 44 proteins being significantly altered between biofilm and planktonic cells. We identified proteins from all cell compartments, and highlighted a marked upregulation in the relative abundances of predicted outer membrane proteins in biofilm cells. These included putative transport systems and the T. forsythia S-layer proteins. These data and our finding that the butyrate production pathway is markedly downregulated in biofilms indicate possible alterations in host interaction capability. We also identified upregulation of putative oxidative stress response proteins, and showed that biofilm cells are 10 to 20 fold more resistant to oxidative stress. This may represent an important adaptation of this organism to prolonged persistence and immune evasion in the oral cavity.

A novel sialic acid utilization and uptake system in the periodontal pathogen Tannerella forsythia.

Tannerella forsythia is a key contributor to periodontitis, but little is known of its virulence mechanisms. In this study we have investigated the role of sialic acid in biofilm growth of this periodontal pathogen. Our data show that biofilm growth of T. forsythia is stimulated by sialic acid, glycolyl sialic acid, and sialyllactose, all three of which are common sugar moieties on a range of important host glycoproteins. We have also established that growth on sialyllactose is dependent on the sialidase of T. forsythia since the sialidase inhibitor oseltamivir suppresses growth on sialyllactose. The genome of T. forsythia contains a sialic acid utilization locus, which also encodes a putative inner membrane sialic acid permease (NanT), and we have shown this is functional when it is expressed in Escherichia coli. This genomic locus also contains a putatively novel TonB-dependent outer membrane sialic acid transport system (TF0033-TF0034). In complementation studies using an Escherichia coli strain devoid of its outer membrane sialic acid transporters, the cloning and expression of the TF0033-TF0034 genes enabled an E. coli nanR nanC ompR strain to utilize sialic acid as the sole carbon and energy source. We have thus identified a novel sialic acid uptake system that couples an inner membrane permease with a TonB-dependent outer membrane transporter, and we propose to rename these novel sialic acid uptake genes nanO and nanU, respectively. Taken together, these data indicate that sialic acid is a key growth factor for this little-characterized oral pathogen and may be key to its physiology in vivo.