Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine**

5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay‘s potential for epigenetic evaluation of clinical samples, benefiting research and patient management.     

Benzene physical and chemical organogels: Effect of network scaffolding on the thermodynamic behavior of entrapped solvent molecules

This paper presents a thermodynamic investigation of the benzene physical and chemical organogels, using differential scanning calorimetry (DSC) and intends to draw an appropriate relationship between the gel network structure and the properties. Physical gels, formed by an aluminium soap of fatty acid, and chemical gels, created by in situ cross‐linking of a siloxane copolymer are investigated. The effects of the type and quantity of the gelators and their corresponding network mesh size distribution in the gels on crystallization, melting, and their kinetics are examined. It appears that the kinetics of crystallization of the entrapped solvent is significantly affected by the quality of the gel network scaffolding and can be treated successfully by the Avrami equation of crystallization. From the melting behavior of the entrapped solvent crystallites, quantitative information about the number of solvent molecules bound per molecule of the gelator has been extracted. DSC proves to be a reliable technique to evaluate the population distribution of solvent molecules trapped in the physical and chemical organogel network scaffolding. The state of the solvent may be treated as a probe to understand the structure of the gels. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 94: 1253–1264, 2004     

Calculating the Thermal Conductivity of Heated Powder Compacts

This work is devoted to the theoretical understanding of the microstructure and thermal conductivity relationships of compacted ceramic powders in the initial, nondensifying stage of sintering. A model based on surface diffusion of vacancies for the growth of the neck between particles is combined with numerical fully three-dimensional code calculations, which solve for the effective heat conductivity coefficient of lightly sintered particles. The predictions of the model are in agreement with experimental observations. The approach presented can be applied to solve a series of related problems, like dielectric properties, with arbitrary microstructure and multicomponent composite of the powders.     

Antibacterial modification of nylon-6 nanofibers: structure,properties and antibacterial activity.

Antibacterial nylon 6 (PA6) nanofibers have been prepared in one-step procedure using Nanospider technology. Chlorhexidine (CHX), 1-dodecyltrimethylamonium bromide (DTAB) and benzyltrimethylamonium bromide (BTAB) have been used as antibacterial agents. Samples were characterized by a series of analytical and testing methods to investigate the surface chemistry, zeta potential, structure, morphology, phase composition, mechanical properties and antibacterial activity. Experimental characterization has been combined with molecular modeling to analyze the interaction of nanofibers with modifying molecules for better understanding the effect of nanofibers modification on their properties. Antibacterial modification of PA6 led to significant changes of zeta potential (from -31 mV for PA 6 up to -49 mV for PA6/BTAB), changes in phase composition (decrease of alpha phase content and increase of gamma phase content for PA6/BTAB and PA6/CHX) and to significant increase of fiber diameter for PA6/BTAB. Antibacterial modification resulted in the straightening of nanofibers and to higher permeability of nanofiber textile for all investigated samples. Tensile tests showed the the increase of Young modulus for all the investigated samples. All the modified samples: PA6/DTAB, PA6/BTAB and PA6/CHX exhibit good antibacterial activity.     

Structural Study of the Partially Disordered Full‐Length δ Subunit of RNA Polymerase from Bacillus subtilis

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well‐folded N‐terminal domain was determined based on inter‐proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C‐terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C‐terminal domain. Various ¹⁵N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C‐terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C‐terminal tail with the N‐terminal domain and with itself were identified. A propensity of the C‐terminal domain to form β‐type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well‐balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C‐terminal domain. The results showed that the δ subunit consists of a well‐ordered N‐terminal domain and a flexible C‐terminal domain that exhibits a complex hierarchy of partial ordering.     

Direct evidence of oxygen evolution from Li1+ x (Ni1/3Mn1/3Co1/3)1? x O2 at high potentials

Li_1+x (Ni_1/3Mn_1/3Co_1/3)_1−x O₂ (NMC) oxides are among the most promising positive electrode materials for future lithium–ion batteries. A voltage “plateau” was observed on the first galvanostatic charging curve of NMC in the extended voltage region positive to 4.5 V vs. Li/Li⁺ for compounds with x > 0 (overlithiated compounds). Differences were observed in the cycling stability of the overlithiated and stoichiometric (x = 0) NMC oxides in this potential region. A differential plot of the charge vs. potential profile in the first cycle revealed that, for the overlithiated compounds, a large irreversible oxidative peak arises positive to 4.5 V vs. Li/Li⁺, while in the same potential region only a small peak due to the electrolyte oxidation is detected for the stoichiometric material. Differential Electrochemical Mass Spectrometry (DEMS) was used to investigate the high voltage region for both compounds and experimental evidence for oxygen evolution was provided for the overlithiated compounds at potentials positive to 4.5 V vs. Li/Li⁺. No oxygen evolution was detected for the stoichiometric compound.     

Simulation of Microwave Sintering of Ceramic Bodies with Complex Geometry

Microwave sintering, an emerging technology in which the energy is applied directly to the material, enabling rapid sintering, shows potential for the synthesis of advanced ceramic materials with superior properties. The process is complex, combining the propagation and absorption of electromagnetic waves in the ceramic material, heat transport within the geometric body, and densification. The densification changes both macroscopic shape and microstructural morphology. A dynamic balance between the rate of electromagnetic energy absorbed within the bulk of the sample and the rate of energy loss from its surface generally results in temperature gradients. These temperature gradients may be especially important during the microwave sintering of bodies with a complex geometry, because neither the diffusion distance nor the electromagnetic penetration depth scale with sample dimensions. The gradients generated in a ZnO green body of a complex geometry were studied theoretically using various microwave-sintering approaches, and it was found that (1) dual-frequency (2.45 and 30 GHz) microwave processing leads to a decrease in the duration of the temperature gradients, and (2) an increase in the heating rate from 5°C/min to 1400°C/min at 2.45 GHz decreases the total required microwave energy by a factor of 55, while at the same time the internal temperature gradients are maintained over a substantially shorter time.     

Manufacture of Multilayered Artificial Cell Membranes through Sequential Bilayer Deposition on Emulsion Templates

Efforts to manufacture artificial cells that replicate the architectures, processes and behaviours of biological cells are rapidly increasing. Perhaps the most commonly reconstructed cellular structure is the membrane, through the use of unilamellar vesicles as models. However, many cellular membranes, including bacterial double membranes, nuclear envelopes, and organelle membranes, are multilamellar. Due to a lack of technologies available for their controlled construction, multilayered membranes are not part of the repertoire of cell-mimetic motifs used in bottom-up synthetic biology. To address this, we developed emulsion-based technologies that allow cell-sized multilayered vesicles to be produced layer-by-layer, with compositional control over each layer, thus enabling studies that would otherwise remain inaccessible. We discovered that bending rigidities scale with the number of layers and demonstrate inter-bilayer registration between coexisting liquid–liquid domains. These technologies will contribute to the exploitation of multilayered membrane structures, paving the way for incorporating protein complexes that span multiple bilayers.     

Maternal N-Acetyl-Cysteine Prevents Neonatal Hypoxia-Induced Brain Injury in a Rat Model

Perinatal hypoxia is a major cause of infant brain damage, lifelong neurological disability, and infant mortality. N-Acetyl-Cysteine (NAC) is a powerful antioxidant that acts directly as a scavenger of free radicals. We hypothesized that maternal-antenatal and offspring-postnatal NAC can protect offspring brains from hypoxic brain damage.Sixty six newborn rats were randomized into four study groups. Group 1: Control (CON) received no hypoxic intervention. Group 2: Hypoxia (HYP)-received hypoxia protocol. Group 3: Hypoxia-NAC (HYP-NAC). received hypoxia protocol and treated with NAC following each hypoxia episode. Group 4: NAC Hypoxia (NAC-HYP) treated with NAC during pregnancy, pups subject to hypoxia protocol. Each group was evaluated for: neurological function (Righting reflex), serum proinflammatory IL-6 protein levels (ELISA), brain protein levels: NF-κB p65, neuronal nitric oxide synthase (nNOS), TNF-α, and IL-6 (Western blot) and neuronal apoptosis (histology evaluation with TUNEL stain). Hypoxia significantly increased pups brain protein levels compared to controls. NAC administration to dams or offspring demonstrated lower brain NF-κB p65, nNOS, TNF-α and IL-6 protein levels compared to hypoxia alone. Hypoxia significantly increased brain apoptosis as evidenced by higher grade of brain TUNEL reaction. NAC administration to dams or offspring significantly reduce this effect. Hypoxia induced acute sensorimotor dysfunction. NAC treatment to dams significantly attenuated hypoxia-induced acute sensorimotor dysfunction. Prophylactic NAC treatment of dams during pregnancy confers long-term protection to offspring with hypoxia associated brain injury, measured by several pathways of injury and correlated markers with pathology and behavior. This implies we may consider prophylactic NAC treatment for patients at risk for hypoxia during labor.     

Molecular Mechanisms Underlying TDP-43 Pathology in Cellular and Animal Models of ALS and FTLD

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are neurodegenerative disorders that exist on a disease spectrum due to pathological, clinical and genetic overlap. In up to 97% of ALS cases and ~50% of FTLD cases, the primary pathological protein observed in affected tissues is TDP-43, which is hyperphosphorylated, ubiquitinated and cleaved. The TDP-43 is observed in aggregates that are abnormally located in the cytoplasm. The pathogenicity of TDP-43 cytoplasmic aggregates may be linked with both a loss of nuclear function and a gain of toxic functions. The cellular processes involved in ALS and FTLD disease pathogenesis include changes to RNA splicing, abnormal stress granules, mitochondrial dysfunction, impairments to axonal transport and autophagy, abnormal neuromuscular junctions, endoplasmic reticulum stress and the subsequent induction of the unfolded protein response. Here, we review and discuss the evidence for alterations to these processes that have been reported in cellular and animal models of TDP-43 proteinopathy.