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Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5′-deoxy-5′-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis (KlSpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species. [ABSTRACT FROM AUTHOR]

Phosphoserine aminotransferase (PSAT) is a pyridoxal 5′-phosphate-dependent enzyme involved in the second step of the phosphorylated pathway of serine biosynthesis. PSAT catalyzes the transamination of 3-phosphohydroxypyruvate to 3-phosphoserine using L-glutamate as the amino donor. Although structural studies of PSAT have been performed from archaea and humans, no structural information is available from fungi. Therefore, to elucidate the structural features of fungal PSAT, we determined the crystal structure of Saccharomyces cerevisiae PSAT (ScPSAT) at a resolution of 2.8 Å. The results demonstrated that the ScPSAT protein was dimeric in its crystal structure. Moreover, the gate-keeping loop of ScPSAT exhibited a conformation similar to that of other species. Several distinct structural features in the halide-binding and active sites of ScPSAT were compared with its homologs. Overall, this study contributes to our current understanding of PSAT by identifying the structural features of fungal PSAT for the first time. [ABSTRACT FROM AUTHOR]

This study reports the effect of the not-calcining process on the bioresorption and biomineralization of hydroxyapatite through in vitro dissolution assessment. The prepared calcined hydroxyapatite (c-HAp) and uncalcined hydroxyapatite (unc-HAp) have a particle size of 2 μm and 13 μm, surface areas of 4.47 m2/g and 108.08 m2/g, and a Ca/P ratio of 1.66 and 1.52, respectively. In vitro dissolution assessments of c-HAp and unc-HAp were performed for 20 days at 37 °C in a citric acid buffer according to ISO 10993-14. During the dissolution, the c-HAp and unc-HAp confirmed an increase in weight, and the calcium and phosphorous ions were rapidly released. The calcium ions released from c-HAp formed rod-shaped particles with a longer and thinner morphology, while in unc-HAp, they appeared thicker and shorter. In the ICP-OES results, the concentrations of calcium elements were initially increased and then decreased by this formation. The rod-shaped particles identified as calcium citrate (Ca-citrate) through the XRD pattern. The calcium content of Ca-citrate particles from unc-HAp was higher than that from c-HAp. The unc-HAp demonstrated non-toxic properties in a cytotoxicity evaluation. Therefore, due to its higher bioresorption and biomineralization, unc-HAp exhibits enhanced biocompatibility compared to c-HAp. [ABSTRACT FROM AUTHOR]

This paper reports the controlled release of citrus unshiu extract from spherical silica hybrid liposome (silicified liposomes) particles. Silicified liposome particles were synthesized by silicification through the sol-gel reaction with TEOS as a silica source of the hydrophilic region of lecithin. In addition, we achieved the various characterization analyses such as SEM-EDS, DLS, FT-IR, and TGA, respectively. The silicified liposomes particles effectively entrapped as much as 314.2 mg/L solution of the citrus unshiu peel extract. After the citrus unshiu peel extract was entrapped in the silicified liposomes, the controlled release profile was investigated and the results showed that the maximum release was 41.4%. The release kinetics were fitted to various kinetic models, such as pseudo-first, pseudo-second-order kinetic and intra-particle diffusion models. The pseudo-second-order kinetic model showed good matching with the experimental release results. Furthermore, the antioxidant activity of citrus unshiu peel extract was measured by the DPPH free radical scavenging method. [ABSTRACT FROM AUTHOR]

In this study, the effective elimination of Cr(VI) was achieved by thermo-responsive polymer-grafted amino-functionalized mesoporous silica (MS@APTES@PNIPAm) in aqueous solution. The MS@APTES@PNIPAm was successfully synthesized by the coupling of 3-MOP and N -isopropyl acrylamide (NIPAm) in 3-aminoproyltriethoxysilane (APTES) grafted mesoporous silica surface. The thermo-responsive elimination of Cr(VI) was demonstrated at various pH levels and at room temperature and 40 °C, respectively. The characterization of the synthesized materials was achieved by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FT-IR) and nitrogen (N 2 ) adsorption-desorption. The maximum adsorption of hexavalent chromium on MS@APTES@PNIPAm in aqueous solution was 123.8 mg g −1 at 40 °C in pH 2.5. Furthermore, the results of isotherm and kinetic experiments demonstrated that the adsorption behavior of Cr(VI) on MS@APTES@PNIPAm was well fitted to a Langmuir plot with a pseudo-second-order and intra-particle diffusion model. [ABSTRACT FROM AUTHOR]

This study reports the preparation of silica-coated and nano-fructosome encapsulated Candida antarctica lipase B particles (CalB@NF@SiO2) and a demonstration of their enzymatic hydrolysis and acylation. CalB@NF@SiO2 particles were prepared as a function of TEOS concentration (3–100 mM). Their mean particle size was 185 nm by TEM. Enzymatic hydrolysis was performed to compare catalytic efficiencies of CalB@NF and CalB@NF@SiO2. The catalytic constants (Km, Vmax, and Kcat) of CalB@NF and CalB@NF@SiO2 were calculated using the Michaelis–Menten equation and Lineweaver–Burk plot. Optimal stability of CalB@NF@SiO2 was found at pH 8 and a temperature of 35 °C. Moreover, CalB@NF@SiO2 particles were reused for seven cycles to evaluate their reusability. In addition, enzymatic synthesis of benzyl benzoate was demonstrated via an acylation reaction with benzoic anhydride. The efficiency of CalB@NF@SiO2 for converting benzoic anhydride to benzyl benzoate by the acylation reaction was 97%, indicating that benzoic anhydride was almost completely converted to benzyl benzoate. Consequently, CalB@NF@SiO2 particles are better than CalB@NF particles for enzymatic synthesis. In addition, they are reusable with high stability at optimal pH and temperature. [ABSTRACT FROM AUTHOR]

The size-controlling of mesoporous silica particles (MSPs) are achieved by various metal-chelating surfactant micelle complexes using alkali (Na + , K + , and Cs + ), alkaline earth (Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ ), and transition metal ions (Co 2+ , Ni 2+ , Cu 2+ , and Zn 2+ ), respectively. These metal ions form a metal-surfactant micelle complex in an aqueous solution, while the metal ions are chelated to the hydrophilic domain of the surfactant such as the poly(ethylene oxide) group of a P123 surfactant. The differences in the complexation degree between the metal ions and surfactant plays an important role in determining the formation of nano-sized ordered MSPs due to the different stability constant for metal-P123 surfactant complexation. The complete hydrolysis of a silica precursor under an acidic condition and the subsequent steady assembly of negative silicate species and positive metal ions can effectively improve highly ordered MSPs. Consequently, the particle size can be reduced from a particle length of 1700 nm to a range of 250–800 nm with the transition metal ions. [ABSTRACT FROM AUTHOR]

We determined the crystal structure of Ec L-DER to elucidate protein function and substrate specificity. Unlike other asp/glu racemases, Ec L-DER has an unbalanced pair of catalytic residues, Thr83/Cys197, at the active site that is crucial for l - to d -unidirectional racemase activity. Ec L-DER exhibited racemase activity for both l -glutamate and l -aspartate, but had threefold higher activity for l -glutamate. Based on the structure of the Ec L-DER C197S mutant in complex with l -glutamate, we determined the binding mode of the l -glutamate substrate in Ec L-DER and provide a structural basis for how the protein utilizes l -glutamate as a main substrate. The unidirectionality, despite an equilibrium constant of unity, can be understood in terms of the Haldane relationship. [ABSTRACT FROM AUTHOR]

The type VI secretion system (T6SS) is a macromolecular complex that is conserved in Gram-negative bacteria. The T6SS secretes effector proteins into recipient cells in a contact-dependent manner in order to accomplish cooperative and competitive interactions with the cells. Although the composition and mechanism of the T6SS have been intensively investigated across many Gram-negative bacteria, to date structural information on T6SS components from the important pathogen Vibrio cholerae has been rare. Here, the cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the cytoplasmic domain of TssL, an inner membrane protein of the T6SS, from V. cholerae are reported. Diffraction data were collected to 1.5 Å resolution using synchrotron radiation. The crystal belonged to the hexagonal space group P61, with unit-cell parameters a = 78.4, b = 78.4 , c = 49.5 Å. The successful structural characterization of TssL from V. cholerae will contribute to understanding the role of the membrane-associated subunits of the T6SS in more detail. [ABSTRACT FROM AUTHOR]

Candida antarctica lipase B (CalB) enzyme was encapsulated and cross-linked by silica matrix to enhance its thermal stability and reusability, and demonstrated an enzymatic ability for rapid hydrolysis and esterification. Silica encapsulated CalB particles (Si-E-CPs) and silica cross-linked CalB particles (Si-CL-CPs) were prepared as a function of TEOS concentration. The particle size analysis, thermal stability, catalytic activity in different pHs, and reusability of Si-E-CPs and Si-CL-CPs were demonstrated. Furthermore, the determination of the CalB enzyme in Si-E-CPs and Si-CL-CPs was achieved by Bradford assay and TGA analysis. Enzymatic hydrolysis was performed against the p-nitrophenyl butyrate and the catalytic parameters (Km, Vmax, and Kcat) were calculated by the Michaelis–Menten equation and a Lineweaver–Burk plot. Moreover, enzymatic synthesis for benzyl benzoate was demonstrated by esterification with an acyl donor of benzoic acid and two acyl donors of benzoic anhydride. Although the conversion efficiency of Si-CL-CPs was not much higher than that of native CalB, it has an efficiency of 91% compared to native CalB and is expected to be very useful because it has high thermal and pH stability and excellent reusability. [ABSTRACT FROM AUTHOR]

Highlights: [•] We determined a crystal structure of 3-hydroxy-butyryl-CoA reductase from Ralstonia eutropha H16 (RePaaH1). [•] Structures in complex with NAD+ and acetoacetyl-CoA revealed cofactor and substrate binding modes of the enzyme. [•] Kinetic and biochemical properties of RePaaH1 were revealed. [ABSTRACT FROM AUTHOR]

Highlights: [•] We determined a crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha. [•] Complex structure with NADP reveals a unique cofactor binding mode. [•] The Clamp domain undersgoes a structural change uopn the binding of substrate. [ABSTRACT FROM AUTHOR]

Summary: Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5′ end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5′-to-3′ exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5Å provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5′ end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5′ end capping and subsequent pre-mRNA processing. [Copyright &y& Elsevier]

Recent studies showed that Rai1 is a crucial component of the mRNA 5?-end-capping quality-control mechanism in yeast. The yeast genome encodes a weak homolog of Rai1, Ydr370C, but little is known about this protein. Here we report the crystal structures of Ydr370C from Kluyveromyces lactis and the first biochemical and functional studies on this protein. The overall structure of Ydr370C is similar to Rai1. Ydr370C has robust decapping activity on RNAs with unmethylated caps, but it has no detectable pyrophosphohydrolase activity. Unexpectedly, Ydr370C also possesses distributive, 5?-3? exoRNase activity, and we propose the name Dxo1 for this new eukaryotic enzyme with both decapping and exonuclease activities. Studies of yeast in which both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process. [ABSTRACT FROM AUTHOR]

Abstract: This work describes the development of highly efficient human DNA separation with functionalized mesoporous silica (FMS) materials. To demonstrate the electrostatic interaction effect between the target DNA molecules and FMS, three aminofunctionality types comprised of a mono-, a di-, and a tri-amine functional group were introduced on the inner surfaces of mesoporous silica particles. Systematic characterization of the synthesized materials was achieved by solid-state 29Si and 13C-NMR techniques, BET, FT-IR, and XPS. The DNA separation efficiency was explored via the function of the amino-group number, the amount used, and the added NaCl concentration. The DNA adsorption yields were high in terms of the use of triaminofunctionalized FMS at the 10ng/L level, and the DNA desorption efficiency showed the optimum level at over 3.0M NaCl concentration. The use of FMS in a DNA separation process provides numerous advantages over the conventional silica-based process. [Copyright &y& Elsevier]

Abstract: The correlation between the thermal fatigue resistance and microstructure of untreated and plasma surface engineered nodular cast irons was investigated. Both the ferrite and pearlite matrix nodular cast irons were evaluated. During the tests, 60mm long cylinders with 20mm diameter were subjected to 1000 high frequency induction heating and water cooling cycles, lasting 7 and 5s, respectively. The thermal fatigue damage was evaluated by analyzing the crack dimensions and distributions. The results showed that the plasma surface treatment increased thermal fatigue resistance. When thermal cracking occurred, the cracks always nucleated at the surface of the specimen. In addition, the nodular cast iron with a pearlite matrix had a better resistance to thermal fatigue than that of the ferrite matrix. [Copyright &y& Elsevier]

Abstract: This work describes the development of high efficiency protein separation with functionalized organosilanes on the surface of silica coated magnetic nanoparticles. The magnetic nanoparticles were synthesized with average particle size of 9 nm and silica coated magnetic nanoparticles were obtained by controlling the coating thicknesses on magnetic nanoparticles. The silica coating thickness could be uniformly sized with a diameter of 10–40 nm by a sol–gel approach. The surface modification was performed with four kinds of functionalized organosilanes such as carboxyl, aldehyde, amine, and thiol groups. The protein separation work with organosilane assembled silica coated magnetic nanoparticles was achieved for model proteins such as bovine serum albumin (BSA) and lysozyme (LSZ) at different pH conditions. Among the various functionalities, the thiol group showed good separation efficiency due to the change of electrostatic interactions and protein conformational structure. The adsorption efficiency of BSA and LSZ was up to 74% and 90% corresponding pH 4.65 and pH 11. [Copyright &y& Elsevier]

Abstract: This work showed the formation of phospholipid vesicle coating on inorganic sericite surface with characterization by combining electron microscopy of FE-SEM, TEM, AFM, and qualitatively evaluated the coated phospholipid vesicle by XPS as a function of etching time. The possibility of phospholipid vesicle mobility on the surface was restrained by the chelation effect of magnesium cation. The stabilization properties of phospholipid vesicles on sericite surface were demonstrated by the various concentration of magnesium cation. The presence of magnesium was found to have a much more pronounced influence on the lipid deposition process. The Mg cation plays an important role for attaching the phospholipids with optimum concentration of 7 mM. Totally, the phospholipid vesicles coating on inorganic powder could be useful for bio-related fields such as cosmetics and drug delivery system as the key functional compounds. We hope this basic result lead to a general and simple approach to prepare a wide a range of controlled releasing materials including an encapsulation with cosmetics or drugs. [Copyright &y& Elsevier]

Abstract: This work described the development of high throughput human DNA purification process with the amino-functionalized silica coated magnetic nanoparticles. The magnetic nanoparticles were synthesized with average particle size of 9 nm and silica-coated magnetic nanoparticles were obtained by controlling the coating thicknesses on magnetic nanoparticles. The silica coating thickness could be uniform-sized in the diameter of 10–40 nm by a sol–gel approach. The surface modification was performed with amino-functionalized organic silanes on silica coated magnetic nanoparticles. The spectroscopic measurements such as a FT-IR (ATR-method) and Vibrational Sample Magnetometer (VSM) were used to characterize the chemical structures and magnetic strengths. To elucidate the relationship among the surface area, pore size distribution and reactivity of the materials, XRD, TEM, BET and Zeta potential were used. The use of functionalized self-assembled magnetic nanoparticles for human DNA separation process gives a lot of advantages rather than the conventional silica based process. [Copyright &y& Elsevier]

Abstract: A novel approach to the hydrophobic partitioning effect on efficient separation of protein such as BSA was demonstrated by the modification of hydrophobic pockets on the surface of silica-coated magnetic nanoparticles with various alkyl groups at various pH levels. The separation efficiency is strongly reflected and can be attained by controlling the size of the hydrophobic pocket and other factors such as the alkyl chain length, the salt concentration, and the pH levels. Furthermore, the adsorption constant (k ad) was calculated for the hydrophobic partitioning interaction between BSA and the hydrophobic pocket size at various pH levels. [Copyright &y& Elsevier]

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria, respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children. [ABSTRACT FROM AUTHOR]

Glucose-6-phosphate dehydrogenase is the first enzyme in the pentose phosphate pathway. The reaction catalyzed by the enzyme is considered to be the main source of reducing power for nicotinamide adenine dinucleotide phosphate (NADPH) and is a precursor of 5-carbon sugar used by cells. To uncover the structural features of the enzyme, we determined the crystal structures of glucose-6-phosphate dehydrogenase from Kluyveromyces lactis (Kl G6PD) in both the apo form and a binary complex with its substrate glucose-6-phosphate. Kl G6PD contains a Rossman-like domain for cofactor NADPH binding; it also presents a typical antiparallel β sheet at the C-terminal domain with relatively the same pattern as those of other homologous structures. Moreover, our structural and biochemical analyses revealed that Lys153 contributes significantly to substrate G6P recognition. This study may provide insights into the structural variation and catalytic features of the G6PD enzyme. • Crystal structures of G6PD from K. lactis were determined in both the apo form and a complex with its substrate. • The conserved active site residue Lys153 may critically be involved in substrate recognition. • Two distinct structural features were shown by comparison with G6PD homologs. [ABSTRACT FROM AUTHOR]

SiO 2 coated platy TiO 2 (S-pTi) was prepared as a noble UV/IR(Ultraviolet/Infrared)-shielding material by a modified Stöber method. S-pTi consists of a dense and uniform SiO 2 shell onto platy TiO 2 (pTi) core, and the thickness of SiO 2 shell layer was coated about 8–20 nm by tuning SiO 2 coating amount. The zeta-potential of S-pTi was decreased from −12 to −32 mV with increasing amounts of coated SiO 2 , indicating the improvement of dispersibility between the particles. The UV-shielding ability of S-pTi was improved by enhancing UV absorption of the SiO 2 coating layer onto pTi and thus the photocatalytic activity was suppressed effectively. Compared to nanosized TiO 2 (nTi), S-pTi showed higher UV absorption at the shorter wavelength and exhibited higher IR reflectance because of high reflective index and the crystal shape and size of pTi to reflect the IR effectively under its wide shielding area. These results can contribute to the prevention of harmful UV and the maintenance of a cool environment from IR heat source as noble UV/IR-shielding materials on the skin. [ABSTRACT FROM AUTHOR]

L-aspartate aminotransferase is a pyridoxal 5ʹ-phosphate-dependent transaminase that catalyzes reversible transfer of an α-amino group from aspartate to α-ketoglutarate or from glutamate to oxaloacetate. L-aspartate aminotransferase not only mediates amino acid and carbohydrate metabolism but also regulates the cellular level of amino acids by catalyzing amino acid degradation and biosynthesis. To expand our structural information, we determined the crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe at 2.1 Å resolution. A structural comparison between two yeast L-aspartate aminotransferases revealed conserved enzymatic mechanism mediated by the open–closed conformational change. Compared with higher eukaryotic species, L-aspartate aminotransferases showed distinguishable inter-subunit interaction between the N-terminal arm and a large domain of the opposite subunit. Interestingly, structural homology search showed varied conformation of the N-terminal arm among 71 structures of the family. Therefore, we classified pyridoxal 5ʹ-phosphate-dependent enzymes into eight subclasses based on the structural feature of N-terminal arms. In addition, structure and sequence comparisons showed strong relationships among the eight subclasses. Our results may provide insights into structure-based evolutionary aspects of pyridoxal 5ʹ-phosphate-dependent enzymes. [ABSTRACT FROM AUTHOR]

In soybean, flavonoid 3′5′-hydroxylase (F3′5′H) and dihydroflavonol-4-reductase (DFR) play a crucial role in the production of anthocyanin pigments. Loss-of-function of the W1 locus, which encodes the former, or W3 and W4, which encode the latter, always produces white flowers. In this study, we searched for new genetic components responsible for the production of white flowers in soybean and isolated four white-flowered mutant lines, i.e., two Glycine soja accessions (CW12700 and CW13381) and two EMS-induced mutants of Glycine max (PE1837 and PE636). F3′5′H expression in CW12700, PE1837, and PE636 was normal, whereas that in CW13381 was aberrant and missing the third exon. Sequence analysis of F3′5′H of CW13381 revealed the presence of an indel (~90-bp AT-repeat) in the second intron. In addition, the F3′5′H of CW12700, PE1837, and PE636 harbored unique single-nucleotide substitutions. The single nucleotide polymorphisms resulted in substitutions of amino acid residues located in or near the SRS4 domain of F3′5′H, which is essential for substrate recognition. 3D structure modeling of F3′5′H indicated that the substitutions could interfere with an interaction between the substrate and heme group and compromise the conformation of the active site of F3′5′H. Recombination analysis revealed a tight correlation between all of the mutant alleles at the W1 locus and white flower color. On the basis of the characterization of the new mutant alleles, we discussed the biological implications of F3′5′H and DFR in the determination of flower colors in soybean. [ABSTRACT FROM AUTHOR]

AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3′-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding. [ABSTRACT FROM AUTHOR]

Polyhydroxyalkanoates are linear polyesters that are produced by bacterial fermentation and are used as biodegradable bioplastics. β-Ketothiolase B (BktB) from Ralstonia eutropha ( ReBktB) is a key enzyme for the production of various types of copolymers by catalyzing the condensation reactions of acetyl-CoA with propionyl-CoA and butyryl-CoA. The ReBktB protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 25% polyethylene glycol 3350, 0.1 M bis-tris pH 6.5, 0.2 M lithium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å on a synchrotron beamline. The crystal belonged to space group C2221, with unit-cell parameters a = 106.95, b = 107.24, c = 144.14 Å. With two molecules per asymmetric unit, the crystal volume per unit protein weight ( VM) is 2.54 Å3 Da−1, which corresponds to a solvent content of approximately 51.5%. The structure was solved by the molecular-replacement method and refinement of the structure is in progress. [ABSTRACT FROM AUTHOR]

Summary: Poly(A) polymerases (PAPs) are found in most living organisms and have important roles in RNA function and metabolism. Here, we report the crystal structure of human PAPD1, a noncanonical PAP that can polyadenylate RNAs in the mitochondria (also known as mtPAP) and oligouridylate histone mRNAs (TUTase1). The overall structure of the palm and fingers domains is similar to that in the canonical PAPs. The active site is located at the interface between the two domains, with a large pocket that can accommodate the substrates. The structure reveals the presence of a previously unrecognized domain in the N-terminal region of PAPD1, with a backbone fold that is similar to that of RNP-type RNA binding domains. This domain (named the RL domain), together with a β-arm insertion in the palm domain, contributes to dimerization of PAPD1. Surprisingly, our mutagenesis and biochemical studies show that dimerization is required for the catalytic activity of PAPD1. [ABSTRACT FROM AUTHOR]

Abstract: This study shows the optimization of biotin labeling to antibodies using mouse IgG. Several parameters of the biotin labeling, including the molar ratio of biotin to antibody, the coupling time and the dialysis time, were studied to optimum conditions. The biotin-tagged mouse IgGs were immobilized on avidin-coated PMMA (Polymethyl Methacrylate) plates via a biotin–avidin linkage. The immobilization of the IgG to the chip was quantified using goat anti-mouse IgG bound fluorescent beads. It was found that the binding of the fluorescent beads saturated when a 10-fold or higher molar ratio of biotin to antibody was used. In biotin coupling time tests, sixty minutes was sufficient for the capture probes to bind to the surface. However, the results from the dialysis experiments showed no difference, indicating that 2hours was sufficient to remove any unbound biotin. Finally, to prove the universality of this protocol using mouse antibodies, the optimum conditions were successfully applied in sandwich immunoassays designed to detect troponin I (TnI) and N-terminal probrain natriuretic peptide (NT-proBNP). [ABSTRACT FROM AUTHOR]

Simple Summary: Antimicrobial resistance acquired an endemic status in the Pakistan poultry sector. A cross-sectional study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant Escherichia coli using next-generation sequencing. Results show the widespread presence of diverse antibiotic resistance genes, virulence-associated genes, plasmid replicon types, and dysbiotic fecal microbial communities. Results indicate that antibiotic resistance altered the fecal microbial community structure of broiler chickens. The use of next-generation sequencing in this study documents a robust and cost-effective approach to study the fecal microbiome and resistome diversities of broiler chickens. The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS. [ABSTRACT FROM AUTHOR]

Melanosomes are specialized membrane-bound organelles that are involved in melanin synthesis. Unlike melanosome biogenesis, the melanosome degradation pathway is poorly understood. Among the cellular processes, autophagy controls degradation of intracellular components by cooperating with lysosomes. In this study, we showed that ursolic acid inhibits skin pigmentation by promoting melanosomal autophagy, or melanophagy, in melanocytes. We found that B16F1 cells treated with ursolic acid suppressed alpha-melanocyte stimulating hormone (α-MSH) stimulated increase in melanin content and activated autophagy. In addition, we found that treatment with ursolic acid promotes melanosomal degradation, and bafilomycin A1 inhibition of autophagosome–lysosome fusion blocked the removal of melanosomes in α-MSH-stimulated B16F1 cells. Furthermore, depletion of the autophagy-related gene 5 (ATG5) resulted in significant suppression of ursolic acid–mediated anti-pigmentation activity and autophagy in α-MSH-treated B16F1 cells. Taken together, our results suggest that ursolic acid inhibits skin pigmentation by increasing melanosomal degradation in melanocytes. • Ursolic acid suppressed the α-MSH-stimulated increase of melanin contents. • Ursolic acid increased the autophagic flux of melanosome, whereas combination with bafilomycin A1 suppressed their degradation in B16F1 cells. • Depletion of ATG5 blocked ursolic acid-mediated depigmentation and autophagy in α-MSH-treated cells. [ABSTRACT FROM AUTHOR]

The melanosome is a specialized membrane-bound organelle that is involved in melanin synthesis, storage, and transportation. In contrast to melanosome biogenesis, the processes underlying melanosome degradation remain largely unknown. Autophagy is a process that promotes degradation of intracellular components' cooperative process between autophagosomes and lysosomes, and its role for process of melanosome degradation remains unclear. Here, we assessed the regulation of autophagy and its contributions to depigmentation associated with Melasolv (3,4,5-trimethoxycinnamate thymol ester). B16F1 cells-treated with Melasolv suppressed the α-MSH-stimulated increase of melanin content and resulted in the activation of autophagy. However, introduction of bafilomycin A1 strongly suppressed melanosome degradation in Melasolv-treated cells. Furthermore, inhibition of autophagy by ATG5 resulted in significant suppression of Melasolv-mediated depigmentation in α-MSH-treated cells. Taken together, our results suggest that treatment with Melasolv inhibits skin pigmentation by promoting melanosome degradation via autophagy activation. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria acquire the acquisition of iron from the host to ensure their survival. Salmonella spp. utilizes siderophores, including salmochelin, for high affinity aggressive import of iron. Although the iroBCDEN operon is reportedly responsible for the production and the transport of salmochelin, the molecular mechanisms underlying the regulation of its gene expression have not yet been characterized. Here, we analyzed the expression pattern of iroB using the lacZY transcriptional reporter system and determined the transcription start site in response to iron availability using primer extension analysis. We further examined the regulation of iroB expression by the ferric uptake regulator (Fur), a key regulatory protein involved in the maintenance of iron homeostasis in various bacteria, including Salmonella. Using sequence analysis followed by a gel shift assay, we verified that the Fur box lies within the promoter region of iroBCDE. The Fur box contained the consensus sequence (GATATTGGTAATTATTATC) and overlapped with the −10-element region. The expression of iroB was repressed by Fur in the presence of iron, as determined using an in vitro transcription assay. Therefore, we found that the iron acquisition system is regulated in a Fur-dependent manner in Salmonella. • The expression of iroB encoding the salmochelin siderophore system was regulated by. • Fur in response to iron availability in Salmonella. • The fur box is located between the −35 and −10 region of iroB promoter, which overlaps with −10 region. • Under Iron-deplete conditions, Fur repress the transcription of iroB by steric hindrance for RNAP binding. [ABSTRACT FROM AUTHOR]

Mitochondria are essential for providing the energy necessary for neuronal function. Dysregulation of mitochondrial dynamics has been linked with the pathogenesis of many neurodegenerative diseases. Dynamin related protein 1 (Drp1) participates in fission activity in the mitochondria, and post-translational modifications to Drp1 modulate complex mitochondrial dynamics. However, the regulation of Drp1 at the post-transcriptional level remains poorly understood. In this study, we found that the RNA-binding protein Hu antigen R (HuR) post-transcriptionally regulates Drp1 expression. HuR interacts with Drp1 mRNA at its 3′ untranslated region. Depletion of HuR reduces Drp1 expression, which leads to mitochondrial elongation in SH-SY5Y neuroblastoma cells. In contrast, ectopic expression of HuR enhances Drp1 expression, which promotes mitochondrial fragmentation in response to treatment with the mitochondrial complex 1 inhibitor MPP+. In addition, depletion of HuR suppressed the generation of mitochondrial ROS and cytotoxicity in MPP+ treated cells. Taken together, these findings suggest that HuR controls mitochondrial morphology via regulation of Drp1. • Inhibition of HuR decreases Drp1 expression and leads to mitochondrial elongation. • HuR interacts with Drp1 mRNA at its 3′-untranslated region. • Over-expression of HuR enhances Drp1 expression, which leads to fragmentation. • Depletion of HuR suppressed the generation of mitochondrial ROS and cytotoxicity in MPP+-treated cells. [ABSTRACT FROM AUTHOR]

Cdc2-like kinases (CLKs) play a crucial role in the alternative splicing of eukaryotic pre-mRNAs through the phosphorylation of serine/arginine-rich proteins (SR proteins). Dysregulation of this processes is linked with various diseases including cancers, neurodegenerative diseases, and many genetic diseases. Thus, CLKs have been regarded to have a potential as a therapeutic target and significant efforts have been exerted to discover an effective inhibitor. In particular, the small molecule CX-4945, originally identified as an inhibitor of casein kinase 2 (CK2), was further revealed to have a strong CLK-inhibitory activity. Four isoforms of CLKs (CLK1, CLK2, CLK3, and CLK4) can be inhibited by CX-4945, with the highest inhibitory effect on CLK2. This study aimed to elucidate the structural basis of the selective inhibitory effect of CX-4945 on different isoforms of CLKs. We determined the crystal structures of CLK1, CLK2, and CLK3 in complex with CX-4945 at resolutions of 2.4 Å, 2.8 Å, and 2.6 Å, respectively. Comparative analysis revealed that CX-4945 was bound in the same active site pocket of the CLKs with similar interacting networks. Intriguingly, the active sites of CLK/CX-4945 complex structures had different sizes and electrostatic surface charge distributions. The active site of CLK1 was somewhat narrow and contained a negatively charged patch. CLK3 had a protruded Lys248 residue in the entrance of the active site pocket. In addition, Ala319, equivalent to Val324 (CLK1) and Val326 (CLK2), contributed to the weak hydrophobic interactions with the benzonaphthyridine ring of CX-4945. In contrast, the charge distribution pattern of CLK2 was the weakest, favoring its interactions with benzonaphthyridine ring. Thus, the relatively strong binding affinities of CX-4945 with CLK2 are consistent with its strong inhibitory effect defined in the previous study. These results may provide insights into structure-based drug discovery processes. [ABSTRACT FROM AUTHOR]

Summary: 2,3‐Dihydro‐2,5‐dihydroxy‐6‐methyl‐4H‐pyran‐4‐one (DDMP) saponins are one of the major saponin groups that are widely distributed in legumes such as pea, barrel medic, chickpea, and soybean. The steps involved in DDMP saponin biosynthesis remain uncharacterized at the molecular level.We isolated two recessive mutants that lack DDMP saponins from an ethyl methanesulfonate‐induced mutant population of soybean cultivar Pungsannamul.Segregation analysis showed that the production of DDMP saponins is controlled by a single locus, named Sg‐9. The locus was physically mapped to a 130‐kb region on chromosome 16. Nucleotide sequence analysis of candidate genes in the region revealed that each mutant has a single‐nucleotide polymorphism in the Glyma.16G033700 encoding a UDP‐glycosyltransferase UGT73B4. Enzyme assays and mass spectrum‐coupled chromatographic analysis reveal that the Sg‐9 protein has glycosyltransferase activity, converting sapogenins and group B saponins to glycosylated products, and that mutant proteins had only partial activities. The tissue‐specific expression profile of Sg‐9 matches the accumulation pattern of DDMP saponins.This is the first report on a new gene and its function in the biosynthesis of DDMP saponins. Our findings indicate that Sg‐9 encodes a putative DDMP transferase that plays a critical role in the biosynthesis of DDMP saponins. [ABSTRACT FROM AUTHOR]

RabGTPase is a member of the Ras superfamily of small GTPases, which share a GTP‐binding pocket containing highly conserved motifs that promote GTP hydrolysis. In Arabidopsis, the RabA group, which corresponds to the Rab11 group in animals, functions in the recycling of endosomes that control docking and fusion during vesicle transport. However, their molecular mechanisms remain unknown. In this study, we determined the crystal structures of the GDP‐bound inactive form and both GppNHp‐ and GTP‐bound active forms of RabA1a, at resolutions of 2.8, 2.6, and 2.6 Å, respectively. A bound sulfate ion in the active site of the GDP‐bound structure stabilized Switch II by bridging the interaction between a magnesium ion and Arg74. Comparisons of the two states of RabA1a with Rab11 proteins revealed clear differences in the Switch I and II loops. These results suggested that conformational change of the Switch regions of RabA1a, derived by GTP or GDP binding, could maintain subcellular membrane traffic through the specific interaction of effector molecules. In Arabidopsis, the RabA group, which corresponds to the Rab11 group in animals, functions in the recycling of endosomes during vesicle transport. In this study, we presented conformational changes of Switch I and II regions upon RabA1a activation via crystal structures of both GTP‐ and GDP‐bound forms. [ABSTRACT FROM AUTHOR]

Abnormal reorganization of the dentate gyrus and neuroinflammation in the hippocampus represent characteristic phenotypes of patients suffering from temporal lobe epilepsy. Hesperetin, a flavanone abundant in citrus fruit, is known to have protective effects by preventing inflammation and oxidative stress in neuronal cultures and in the adult murine brain. However, the protective effects of hesperetin against epileptic seizures in vivo remain unclear, despite one study reporting anticonvulsant effects in vitro. In this study, we report that oral administration of hesperetin not only delays the onset of seizures triggered by kainic acid (KA) but also contributes to the attenuation of granule cell dispersion in the KA-treated hippocampus. Moreover, we observed that hesperetin administration inhibited the expression of pro-inflammatory molecules produced by activated microglia in the hippocampus. Thus, administration of hesperetin might be beneficial for preventing epileptic seizures. [ABSTRACT FROM AUTHOR]

Abstract Alzheimer's disease (AD), which is the most common progressive neurodegenerative disease, causes learning and memory impairment. The pathological progress of AD can derive from imbalanced homeostasis of amyloid beta (Aβ) in the brain. In such cases, microglia play important roles in regulating the brain Aβ levels. In the present study, we found that human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) can increase, through paracrine action, the ability of microglial cells to clear Aβ. In order to identify the associated paracrine factors, a secretome of hUCB-MSCs co-cultured with Aβ-treated BV2 microglial cells was analyzed using a human cytokine protein array. As a result, growth differentiation factor-15 (GDF-15) was identified as a predominant candidate, and its association with Aβ clearance by microglial cells was investigated in vitro and in a 5XFAD mouse model. When Aβ-treated BV2 cells were treated with exogenous recombinant GDF-15, the Aβ levels in the culture medium decreased. Moreover, GDF-15 injection in the brain parenchyma of 5XFAD mice also led to decrease in Aβ plaques. In contrast, co-culture of BV2 cells and hUCB-MSCs treated with GDF-15-specific siRNA did not influence the Aβ levels in the culture medium. To elucidate how these phenomena are related, we confirmed that GDF-15 specifically increases insulin-degrading enzyme (IDE) expression in microglial cells through TGFβ receptor type II (TGFβRII), both in vitro and in vivo. These findings suggest that hUCB-MSCs promote the Aβ clearance ability of microglial cells through regulation of GDF-15 secretion, thus elucidating a therapeutic mechanism for AD. Highlights • Paracrine action of hUCB-MSCs enhances Aβ clearance through microglial modulation. • GDF-15 secreted from hUCB-MSCs promotes the decrease of Aβ levels via enhancing IDE expression in microglia. • TGFβRII is involved in GDF-15-enhanced IDE expression in microglia. [ABSTRACT FROM AUTHOR]

Abstract The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5′-3′ exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3′-NADP+. Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3′, 5′-bisphosphate (pAp), a known inhibitor of the 5′-3′ exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO–pAp-Mg2+ complex at 1.8 Å resolution. In comparison with the DXO–RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor. Highlights • pAp inhibits the exoribonuclease activity of DXO. • Crystal structure of DXO was obtained in complex with pAp and Mg2+ at 1.8 Å resolution. • pAp competitively inhibits DXO nuclease activity by sharing the binding site pocket. [ABSTRACT FROM AUTHOR]

In soybean, triterpenoid saponin is one of the major secondary metabolites and is further classified into group A and DDMP saponins. Although they have known health benefits for humans and animals, acetylation of group A saponins causes bitterness and gives an astringent taste to soy products. Therefore, several studies are being conducted to eliminate acetylated group A saponins. Previous studies have isolated and characterized the Sg-5 (Glyma.15g243300) gene, which encodes the cytochrome P450 72A69 enzyme and is responsible for soyasapogenol A biosynthesis. In this study, we elucidated the molecular identity of a novel mutant of Glycine soja, ′CWS5095′. Phenotypic analysis using TLC and LC-PDA/MS/MS showed that the mutant ′CWS5095′ did not produce any group A saponins. Segregation analysis showed that the absence of group A saponins is controlled by a single recessive allele. The locus was mapped on chromosome 15 (4.3 Mb) between Affx-89193969 and Affx-89134397 where the previously identified Glyma.15g243300 gene is positioned. Sequence analysis of the coding region for the Glyma.15g243300 gene revealed the presence of four SNPs in ′CWS5095′ compared to the control lines. One of these four SNPs (G1127A) leads to the amino acid change Arg376Lys in the motif, which is invariably conserved among the CYP450 superfamily proteins. Co-segregation analysis showed that the missense mutation (Arg376Lys) was tightly linked with the absence of group A saponins in ′CWS5095′. Even though Arg and Lys have similar chemical features, the 3D modelled protein structure indicates that the replacement of Arg with Lys may cause a loss-of-function of the Sg-5 protein by inhibiting the stable binding of a heme cofactor to the CYP72A69 apoenzyme. [ABSTRACT FROM AUTHOR]

Nanoporous silicified-phospholipids assembled boron nitride (nSPLs@BN) powder was prepared and demonstrated for use in controlled release of anti-oxidant astaxanthin (AX) as a cosmetic application. The nanoporous silicified phospholipids (nSPLs) were obtained by the silicification with tetraethyl orthosilicate (TEOS) of the hydrophilic region of phospholipid bilayers. This process involved the co-assembly of chemically active phospholipid bilayers within the porous silica matrix. In addition, nSPLs@BN was characterized using several analytical techniques and tested to assess their efficiency as drug delivery systems. We calculated the maximum release amounts as a function of time and various pH. The release rate of AX from the nSPLs@BN for the initial 24 h was 10.7 μmol/(h mg) at pH 7.4. Furthermore, we determined the antioxidant activity ( K D ) for the released AX with DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical and the result was 34.6%. [ABSTRACT FROM AUTHOR]

This paper describes an optimization of planetary mill pretreatment and saccharification processes for improving biosugar production. Pitch pine (Pinus rigida) wood sawdust waste was used as biomass feedstock and the process parameters optimized in this study were the buffering media, the milling time, the enzyme quantity, and the incubation time. Glucose yields were improved when acetate buffer was used rather than citrate buffer. Initially, with each process variable tests, the optimal values were 100 minutes of milling, an enzyme concentration of 16 FPU/g-biomass, and a 12-hour enzymatic hydrolysis. Typically, interactions between these experimental conditions and their effects on glucose production were next investigated using RSM. Glucose yields from the Pinus rigida waste exceeded 80% with several of the conditions tested, demonstrating that milling can be used to obtain high levels of glucose bioconversion from woody biomass for biorefinery purposes. [ABSTRACT FROM AUTHOR]

Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin ( Pygoscelis papua ), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3–β4 loop region (residues 57–62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein – ligand interactions. [ABSTRACT FROM AUTHOR]

We report rapid and accurate pathogen detection by coupling with high efficiency magnetic separation of pathogen by Ni2+-heterogeneous magnetic mesoporous silica (Ni-HMMS) and real time-polymerase chain reaction (RT-PCR) technique. Ni-HMMS was developed with a significant incorporation of Fe particles within the silica mesopores by programed thermal hydrogen reaction and functionalized with Ni2+ ion on the surface by the wet impregnation process. High abundant Ni2+ ions on the Ni-HMMS surface were able to assemble with cell wall component protein NikA (nickel-binding membrane protein), which contains several pathogenic bacteria including Escherichia coli O157:H7. NikA protein expression experiment showed the outstanding separation rate of the nikA gene-overexpressed E. coli (pSY-Nik) when comparing with wild-type E. coli (44.5±13%) or not over-expressed E. coli (pSY-Nik) (53.2±2.7%). Moreover, Ni-HMMS showed lower obstacle effect by large reaction volume (10mL) than spherical core/shell-type silica magnetic nanoparticles functionalized with Ni2+ (ca. 40nm-diameters). Finally, the Ni-HMMS was successfully assessed to separate pathogenic E. coli O157:H7 and applied to direct and rapid RT-PCR to quantitative detection at ultralow concentration (1Log10 cfumL−1) in the real samples (milk and Staphylococcus aureus culture broth) without bacterial amplification and DNA extraction step. [ABSTRACT FROM AUTHOR]

Abstract: Enzyme-inspired inorganic materials as biomimetic catalysts were synthesized for rapid hydrolysis of ester compounds through the surface functionalization of silica-coated magnetic nanoparticles (Si-MNPs). Three functional groups such as amine, imidazole, and carboxyl group were grafted onto the silica surface of Si-MNPs to mimic catalytic triad (Ser195, His57, and Asp102). Michaelis–Menten kinetic parameters show that the catalytic efficiency for substrate (p-nitrophenyl butyrate) was observed in the order of multi->imidazole>carboxyl>amine group functionality. Furthermore, the reaction rate of the multi-functionalized Si-MNPs was highly improved than natural enzyme for hydrolysis of esters with long-length carbon chain. [Copyright &y& Elsevier]

Abstract: This study describes the preparation of hydroxyapatite microspheres for local delivery of alendronate and BMP-2. The hydroxyapatite microsphere preparation was initiated by enzymatic decomposition of urea and accomplished using an emulsification process (water-in-oil) for nucleation and growth of hydroxyapatite within the microemulsion. The microspheres obtained were then sintered at 500°C. Scanning electron microscope (SEM) indicated that the microspheres have particle-in-sphere morphology, so called ‘microstructured microspheres’. The viability of L-929 cells in the presence of sintered microspheres was 85%. The adsorption efficiencies for alendronate varied from 27.2% to 84.1% depending on the loading conditions. For BMP-2 loading, 79.2% was absorbed on the microspheres when a BMP-2 concentration of 25μg/ml was used. [Copyright &y& Elsevier]

Abstract: This work demonstrates the development of novel antimicrobial and biodegradable suture coated by natural extract from grape fruit. The natural extract is loaded to PLGA suture and their optimum conditions are determined as a function of soaking time, loaded volume, and releasing time. Furthermore, the evaluation of antibacterial effect was achieved by Staphylococcus aureus and Escherchia DH5α with the used amounts and released time. The cell growth was calculated for several days through 2 months. The physicochemical properties of antimicrobial and biodegradable PLGA suture are demonstrated. [Copyright &y& Elsevier]

Abstract: Highly ordered mesoporous silica nanoparticles with tunable morphology and pore-size are prepared by the use of a transition metal-chelating surfactant micelle complex using Co2+, Ni2+, Cu2+, and Zn2+ ions. These metal ions formed a metal-P123 micelle complex in an aqueous solution, while the metal ions are chelated to the hydrophilic domain such as the poly(ethylene oxide) group of a P123 surfactant. The different complexation abilities of the utilized transition metal ions play an important role in determining the formation of nano-sized ordered MSNs due to the different stabilization constant of the metal-P123 complex. Consequently, from a particle length of 1700nm in the original mesoporous silica materials, the particle length of ordered MSNs through the metal-chelating P123 micelle templates can be reduced to a range of 180–800nm. Furthermore, the variation of pore size shows a slight change from 8.8 to 6.6nm. In particular, the Cu2+-chelated MSNs show only decreased particle size to 180nm. The stability constants for the metal-P123 complex are calculated on the basis of molar conductance measurements in order to elucidate the formation mechanism of MSNs by the metal-chelating P123 complex templates. In addition, solid-state 29Si, 13C-NMR and ICP-OES measurements are used for quantitative characterization reveal that the utilized metal ions affect only the formation of a metal-P123 complex in a micelle as a template. [Copyright &y& Elsevier]

Abstract: This paper describes a method for the effective and self-oriented immobilization of antibodies on magnetic silica-nanoparticles using a multimeric protein G. Cysteine-tagged recombinant dimers and trimers of protein G were produced in Escherichia coli BL21 by repeated linking of protein G monomers with a flexible (GGGGS)3 linker. Amino-functionalized silica-coated magnetic nanoparticles (SiO2-MNPs, Fe3O4@SiO2) were prepared and coupled to the protein G multimers, giving the final magnetic immunosensor. The optimal conditions for the reaction between the protein Gs and the SiO2-MNPs was a time of 60min and a concentration of 100μg/mL, resulting in coupling efficiencies of 77%, 67% and 55% for the monomeric, dimeric and trimeric protein Gs, respectively. Subsequently, anti-hepatitis B surface antigen (HBsAg) was immobilized onto protein G-coupled SiO2-MNPs. The quantitative efficiency of antibody immobilization found the trimeric protein G to be the best, followed by the dimeric and monomeric proteins, which differs from the coupling efficiencies. Using all three protein constructs in an HBsAg fluoroimmunoassay, the lowest detectable concentrations were 500, 250 and 50ng/mL for the monomeric, dimeric and trimeric protein G-coupled SiO2-MNPs, respectively. Therefore, multimeric protein Gs, particularly the trimeric form, can be employed to improve antibody immobilization and, ultimately, enhance the sensitivity of immunoassays. In addition, the multimeric protein Gs devised in this study can be utilized in other immunosensors to bind the antibodies at a high efficiency and in the proper orientation. [Copyright &y& Elsevier]