DNA G-Quadruplexes Contribute to CTCF Recruitment

G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment.     

Influence of heat shock on glycerol production in alcohol fermentation

The influence of single and double heat shocks induced during the exponential growth phase of the Saccharomyces cerevisiae fermentation of cultivar Sauvignon Blanc grape must was examined. Rapid temperature changes from 18 degrees C to 34 degrees C have been applied. The effect of the duration of exposure to a high temperature has been analyzed. By the applications of a single heat shock and a double heat shock, up to 8.2 g l(-1) and 11.0 g l(-1) glycerol have been produced, respectively. To prevent the evaporation of fine wine bouquet compounds during the temperature changes, reflux coolers on the top of bioreactors have been employed. By using this method, glycerol production was increased by up to 65%.     

Short communication: Effect of commercial or depurinized milk diet on plasma advanced oxidation protein products,cardiovascular markers,and bone marrow CD34 stem cell potential in rat experimental hyperuricemia

Cardiovascular repair and myocardial contractility may be improved by migration of bone marrow stem cells (BMSC) and their delivery to the site of injury, a process known as BMSC homing. The aim of our study was to examine the dietary effect of a newly patented depurinized milk (DP) that is almost free of uric acid and purine and pyrimidine compounds compared with a standard commercial 1.5% fat UHT milk diet or allopurinol therapy in rat experimental hyperuricemia. Bone marrow stem cell potential (BMCD34⁺, CD34-postive bone marrow cells), plasma oxidative stress parameters [advanced oxidation protein products, AOPP) and thiobarbituric acid reactive substances (TBARS)], myocardial damage markers [creatine phosphokinase (CPK), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH)], plasma cholesterol, and high-density lipoprotein cholesterol were investigated. The DP milk diet significantly increased the number of BMCD34⁺ stem cells compared with commercial UHT milk. Allopurinol given alone also increased the number of BMCD34⁺. Hyperuricemia caused a significant increase in all plasma enzyme markers for myocardial damage (CPK, LDH, and AST). A cardioprotective effect was achieved with allopurinol but almost equally with DP milk and more than with commercial milk. Regarding plasma AOPP, TBARS, and cholesterol levels, the most effective treatment was DP milk. In conclusion, the protective role of a milk diet on cardiovascular function may be enhanced through the new depurinized milk diet, which may improve cardiovascular system function via increased bone marrow stem cell regenerative potential, decreased plasma oxidative stress parameters, and decreased levels of myocardial damage markers and cholesterol. New dairy technology strategies focused on eliminating harmful milk compounds should be completely nontoxic. Novel milk products should be tested for their ability to improve tissue repair and function.     

Issues in the Analysis of Proof-Search Strategies in Sequential Presentations of Logics

Many proof search strategies can be expressed as restrictions on the order of application of the rules of the sequent calculus. Properties of these strategies are then shown by permutation arguments, such as showing that a given strategy is complete by transforming an arbitrary proof into one which obeys the strategy. Such analyses involve some very tedious manipulations of proofs, and are potentially overwhelming for humans. In this paper we investigate the development of systematic techniques for the analysis of sequent calculi. We show how a particular specification of inference rules leads to a detailed analysis of permutation properties for these rules, and we also investigate how to detect redundancies in proofs resulting from these rules.     

Nanoparticles for Applications in Cellular Imaging

In the following review we discuss several types of nanoparticles (such as TiO₂, quantum dots, and gold nanoparticles) and their impact on the ability to image biological components in fixed cells. The review also discusses factors influencing nanoparticle imaging and uptake in live cells in vitro. Due to their unique size-dependent properties nanoparticles offer numerous advantages over traditional dyes and proteins. For example, the photostability, narrow emission peak, and ability to rationally modify both the size and surface chemistry of Quantum Dots allow for simultaneous analyses of multiple targets within the same cell. On the other hand, the surface characteristics of nanometer sized TiO₂ allow efficient conjugation to nucleic acids which enables their retention in specific subcellular compartments. We discuss cellular uptake mechanisms for the internalization of nanoparticles and studies showing the influence of nanoparticle size and charge and the cell type targeted on nanoparticle uptake. The predominant nanoparticle uptake mechanisms include clathrin-dependent mechanisms, macropinocytosis, and phagocytosis.     

ZnO Nanorods via Spray Deposition of Solutions Containing Zinc Chloride and Thiocarbamide

In this work we present the results on formation of ZnO nanorods prepared by spray of aqueous solutions containing ZnCl₂ and thiocarbamide (tu) at different molar ratios. It has been observed that addition of thiocarbamide into the spray solution has great impact on the size, shape and phase composition of the ZnO crystals. Obtained layers were characterized by scanning electron microscopy (SEM) equipped with energy selected backscattered electron detection system (ESB), X-ray diffraction (XRD) and photoluminescence spectroscopy (PL). Small addition of thiocarbamide into ZnCl₂ solution (ZnCl₂:tu = 1:0.25) supports development of significantly thinner ZnO nanorods with higher aspect ratio compared to those obtained from ZnCl₂ solution. Diameter of ZnO rods decreases from 270 to 100 nm and aspect ratio increases from ∼2.5 to 12 spraying ZnCl₂ and ZnCl₂:tu solutions, respectively. According to XRD, well crystallized (002) orientated pure wurtzite ZnO crystals have been formed. However, tiny ‘spot’—like formations of ZnS were detected on the side planes of hexagonal rods prepared from the thiocarbamide containing solutions. Being adsorbed on the side facets of the crystals ZnS inhibits width growth and promotes longitudinal c-axis growth.     

A latent class model of residential choice behaviour and ethnic segregation preferences

The nature of ethnic residential clustering involves diverse population segments which through their location decisions influence the spatial patterns of ethnic settlements. While residential location is in part determined by outside constraints, choice plays a role too, making the study of preferences an important research topic. Along with differences in socio-economic characteristics, literature often emphasizes the role of unobserved (behavioural) elements in the formation of preferences for ethnic neighbourhood composition. This paper tests the potential of latent class choice models to examine both observed and unobserved heterogeneity in residential choices across ethnic groups. The empirical example is estimated on stated preferences data from Lugano, Switzerland. The results indicate different ethnic attributes as key choice drivers for households belonging to three latent classes, where the origin of households is the best predictor of class membership. Swiss citizens are mainly concerned about high shares of foreigners, advantaged foreigners favour their co-nationals, while disadvantaged foreigners hold both of such preferences.     

An Exploratory Evaluation of Tyrosine Hydroxylase Inhibition in Planaria as a Model for Parkinsonism

Planaria are the simplest organisms with bilateral symmetry and a central nervous system (CNS) with cephalization; therefore, they could be useful as model organisms to investigate mechanistic aspects of parkinsonism and to screen potential therapeutic agents. Taking advantage of the organism’s anti-tropism towards light, we measured a significantly reduced locomotor velocity in planaria after exposure to 3-iodo-l-tyrosine, an inhibitor of tyrosine hydroxylase that is an enzyme catalyzing the first and rate-limiting step in the biosynthesis of catecholamines. A simple semi-automatic assay using videotaped experiments and subsequent evaluation by tracking software was also implemented to increase throughput. The dopaminergic regulation of locomotor velocity was confirmed by bromocriptine, a drug whose mechanisms of action to treat Parkinson’s disease is believed to be through the stimulation of nerves that control movement.     

Clock jitter generator with picoseconds resolution

The clock is one of the most critical signals in any synchronous system. As CMOS technology has scaled, supply voltages have dropped chip power consumption has increased and the effects of jitter due to clock frequency increase have become critical and jitter budget has become tighter. This article describes design and development of low-cost mixed-signal programmable jitter generator with high resolution. The digital technique is used for coarse-grain and an analogue technique for fine-grain clock phase shifting. Its structure allows injection of various random and deterministic jitter components in a controllable and programmable fashion. Each jitter component can be switched on or off. The jitter generator can be used in jitter tolerance test and jitter transfer function measurement of high-speed synchronous digital circuits. At operating system clock frequency of 220?MHz, a jitter with 4?ps resolution can be injected.     

Engineering highly thermostable xylanase variants using an enhanced combinatorial library method

A new directed evolution method was used to enhance the thermostability of the wild-type GH11 xylanase 2 (known as BD-11) from Hypocrea jecorina (Trichoderma reesei). Both Look-Through Mutagenesis (LTM?), which is a method for rapidly screening selected positions in the protein sequence for amino acids that introduce favorable properties, and Combinatorial Beneficial Mutagenesis (CBM?), which is a method for identifying the best ensemble of individual mutations, were employed to enhance the stability of an enzyme that has been thoroughly engineered by various means during the past 20 years. A diverse set of novel mutations was discovered, including N71D, Y73G, T95G and Y96Q. When these mutations were combined into a single construct (Hjx-81), the purified protein was active even after heating at 100°C for 20 min. This time-effective method should be generally applicable for quickly improving the physico-chemical properties of other industrial and therapeutic enzymes in only several months time.