Meiotic Recombination Hotspots of Fission Yeast Are Directed to Loci that Express Non-Coding RNA

Polyadenylated, mRNA-like transcripts with no coding potential are abundant in eukaryotes, but the functions of these long non-coding RNAs (ncRNAs) are enigmatic. In meiosis, Rec12 (Spo11) catalyzes the formation of dsDNA breaks (DSBs) that initiate homologous recombination. Most meiotic recombination is positioned at hotspots, but knowledge of the mechanisms is nebulous. In the fission yeast genome DSBs are located within 194 prominent peaks separated on average by 65-kbp intervals of DNA that are largely free of DSBs.). Furthermore, we tested and rejected the hypothesis that the ncRNA loci and DSB peaks localize preferentially, but independently, to a third entity on the chromosomes.Meiotic DSB hotspots are directed to loci that express polyadenylated ncRNAs. This reveals an unexpected, possibly unitary mechanism for what directs meiotic recombination to hotspots. It also reveals a likely biological function for enigmatic ncRNAs. We propose specific mechanisms by which ncRNA molecules, or some aspect of RNA metabolism associated with ncRNA loci, help to position recombination protein complexes at DSB hotspots within chromosomes

School closures during the 2009 influenza pandemic: national and local experiences

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Physics of leptoquarks in precision experiments and at particle colliders

We present a comprehensive review of physics effects generated by leptoquarks (LQs), i.e., hypothetical particles that can turn quarks into leptons and vice versa, of either scalar or vector nature. These considerations include discussion of possible completions of the Standard Model that contain LQ fields. The main focus of the review is on those LQ scenarios that are not problematic with regard to proton stability. We accordingly concentrate on the phenomenology of light leptoquarks that is relevant for precision experiments and particle colliders. Important constraints on LQ interactions with matter are derived from precision low-energy observables such as electric dipole moments, (g-2) of charged leptons, atomic parity violation, neutral meson mixing, Kaon, B, and D meson decays, etc. We provide a general analysis of indirect constraints on the strength of LQ interactions with the quarks and leptons to make statements that are as model independent as possible. We address complementary constraints that originate from electroweak precision measurements, top, and Higgs physics. The Higgs physics analysis we present covers not only the most recent but also expected results from the Large Hadron Collider (LHC). We finally discuss direct LQ searches. Current experimental situation is summarized and self-consistency of assumptions that go into existing accelerator-based searches is discussed. A progress in making next-to-leading order predictions for both pair and single LQ productions at colliders is also outlined.Comment: 136 pages, 22 figures, typographical errors fixed, the Physics Reports versio

ИССЛЕДОВАНИЕ НЕЙРОРЕТИНОПРОТЕКТОРНОЙ АКТИВНОСТИ ТИОФАНА ПРИ ИНВОЛЮЦИОННОЙ ХОРИОРЕТИНАЛЬНОЙ ДЕГЕНЕРАЦИИ КРЫС ЛИНИИ OXYS

The method of spontaneous and induced luminol -dependent chemiluminescence in homogenates of rat retinas OXYS registered increase in the generation of free radicals against decrease in total antioxidant  activity.  With  the  ultra-microscopic  and  quantitative  analysis  revealed  degenerative retinal neurons rats OXYS: the percentage increase in neurosensory cells with pyknosis of nuclei, hyperchromatic piknomorfnyh associative neurons and ganglion n eurons that have been modified on a light and dark type. Thiophane, limiting free radical reactions in the retina and protects retinal neurons from damage.С помощью метода спонтанной и индуцированной люминолзависимой хемилюминесценции в гомогенатах сетчаток крыс линии OXYS зарегистрировано повышение уровня генерации свободных радикалов на фоне снижения общей антиокислительной активности. С помощью ультрамикроскопического и количественного анализа выявлены дегенеративные изменения нейронов сетчатки крыс линии OXYS: увеличение содержания нейросенсорных клеток с пикнозом ядра, гиперхромных  пикноморфных  ассоциативных нейронов и ганглионарных нейронов, измененных по светлому и темному типу. Установлено, что тиофан, ограничивая свободнорадикальные реакции в сетчатке, защищает нейроны сетчатки от повреждения

Stability and Release Kinetics of an Advanced Gliclazide-Cholic Acid Formulation: The Use of Artificial-Cell Microencapsulation in Slow Release Targeted Oral Delivery of Antidiabetics

Introduction: In previous studies carried out in our laboratory, a bile acid (BA) formulation exerted a hypoglycaemic effect in a rat model of type-1 diabetes (T1D). When the antidiabetic drug gliclazide (G) was added to the bile acid, it augmented the hypoglycaemic effect. In a recent study, we designed a new formulation of gliclazide-cholic acid (G-CA), with good structural properties, excipient compatibility and exhibits pseudoplastic-thixotropic characteristics. The aim of this study is to test the slow release and pH-controlled properties of this new formulation. The aim is also to examine the effect of CA on G release kinetics at various pH values and different temperatures. Method: Microencapsulation was carried out using our Buchi-based microencapsulating system developed in our laboratory. Using sodium alginate (SA) polymer, both formulations were prepared: G-SA (control) and G-CA-SA (test) at a constant ratio (1:3:30), respectively. Microcapsules were examined for efficiency, size, release kinetics, stability and swelling studies at pH 1.5, pH 3, pH 7.4 and pH 7.8 and temperatures of 20 and 30 °C. Results: The new formulation is further optimised by the addition of CA. CA reduced microcapsule swelling of the microcapsules at pH 7.8 and pH 3 at 30 °C and pH 3 at 20 °C, and, even though microcapsule size remains similar after CA addition, percent G release was enhanced at high pH values (pH 7.4 and pH 7.8, p < 0.01). Conclusion: The new formulation exhibits colon-targeted delivery and the addition of CA prolonged G release suggesting its suitability for the sustained and targeted delivery of G and CA to the lower intestine

Direct Generation of Neurosphere-Like Cells from Human Dermal Fibroblasts

Neural stem cell (NSC) transplantation replaces damaged brain cells and provides disease-modifying effects in many neurological disorders. However, there has been no efficient way to obtain autologous NSCs in patients. Given that ectopic factors can reprogram somatic cells to be pluripotent, we attempted to generate human NSC-like cells by reprograming human fibroblasts. Fibroblasts were transfected with NSC line-derived cellular extracts and grown in neurosphere culture conditions. The cells were then analyzed for NSC characteristics, including neurosphere formation, gene expression patterns, and ability to differentiate. The obtained induced neurosphere-like cells (iNS), which formed daughter neurospheres after serial passaging, expressed neural stem cell markers, and had demethylated SOX2 regulatory regions, all characteristics of human NSCs. The iNS had gene expression patterns that were a combination of the patterns of NSCs and fibroblasts, but they could be differentiated to express neuroglial markers and neuronal sodium channels. These results show for the first time that iNS can be directly generated from human fibroblasts. Further studies on their application in neurological diseases are warranted

Up-regulated expression of LAMP2 and autophagy activity during neuroendocrine differentiation of prostate cancer LNCaP cells

Neuroendocrine (NE) prostate cancer (PCa) is a highly aggressive subtype of prostate cancer associated with resistance to androgen ablation therapy. In this study, we used LNCaP prostate cancer cells cultured in a serum-free medium for 6 days as a NE model of prostate cancer. Serum deprivation increased the expression of NE markers such as neuron-specific enolase (NSE) and βIII tubulin (βIII tub) and decreased the expression of the androgen receptor protein in LNCaP cells. Using cDNA microarrays, we compared gene expression profiles of NE cells and non-differentiated LNCaP cells. We identified up-regulation of 155 genes, among them LAMP2, a lysosomal membrane protein involved in lysosomal stability and autophagy. We then confirmed up-regulation of LAMP2 in NE cells by qRT-PCR, Western blot and confocal microscopy assays, showing that mRNA up-regulation correlated with increased levels of LAMP2 protein. Subsequently, we determined autophagy activity in NE cells by assessing the protein levels of SQSTM/p62 and LC3 by Western blot and LC3 and Atg5 mRNAs content by qRT-PCR. The decreased levels of SQSTM/p62 was accompanied by an enhanced expression of LC3 and ATG5, suggesting activation of autophagy in NE cells. Blockage of autophagy with 1μM AKT inhibitor IV, or by silencing Beclin 1 and Atg5, prevented NE cell differentiation, as revealed by decreased levels of the NE markers. In addition, AKT inhibitor IV as well as Beclin1 and Atg5 kwockdown attenuated LAMP2 expression in NE cells. On the other hand, LAMP2 knockdown by siRNA led to a marked blockage of autophagy, prevention of NE differentiation and decrease of cell survival. Taken together, these results suggest that LAMP2 overexpression assists NE differentiation of LNCaP cells induced by serum deprivation and facilitates autophagy activity in order to attain the NE phenotype and cell survival. LAMP2 could thus be a potential biomarker and potential target for NE prostate cancer

Machine learning for regulatory analysis and transcription factor target prediction in yeast

High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps—the identity and location of regulatory binding sites within genomes. Still, the full identification of sites, even in lower eukaryotes, remains largely incomplete. In this paper we develop a supervised learning approach to site identification using support vector machines (SVMs) to combine 26 different data types. A comparison with the standard approach to site identification using position specific scoring matrices (PSSMs) for a set of 104 Saccharomyces cerevisiae regulators indicates that our SVM-based target classification is more sensitive (73 vs. 20%) when specificity and positive predictive value are the same. We have applied our SVM classifier for each transcriptional regulator to all promoters in the yeast genome to obtain thousands of new targets, which are currently being analyzed and refined to limit the risk of classifier over-fitting. For the purpose of illustration we discuss several results, including biochemical pathway predictions for Gcn4 and Rap1. For both transcription factors SVM predictions match well with the known biology of control mechanisms, and possible new roles for these factors are suggested, such as a function for Rap1 in regulating fermentative growth. We also examine the promoter melting temperature curves for the targets of YJR060W, and show that targets of this TF have potentially unique physical properties which distinguish them from other genes. The SVM output automatically provides the means to rank dataset features to identify important biological elements. We use this property to rank classifying k-mers, thereby reconstructing known binding sites for several TFs, and to rank expression experiments, determining the conditions under which Fhl1, the factor responsible for expression of ribosomal protein genes, is active. We can see that targets of Fhl1 are differentially expressed in the chosen conditions as compared to the expression of average and negative set genes. SVM-based classifiers provide a robust framework for analysis of regulatory networks. Processing of classifier outputs can provide high quality predictions and biological insight into functions of particular transcription factors. Future work on this method will focus on increasing the accuracy and quality of predictions using feature reduction and clustering strategies. Since predictions have been made on only 104 TFs in yeast, new classifiers will be built for the remaining 100 factors which have available binding data

Feshbach resonances and mesoscopic phase separation near a quantum critical point in multiband FeAs-based superconductors

High Tc superconductivity in FeAs-based multilayers (pnictides), evading temperature decoherence effects in a quantum condensate, is assigned to a Feshbach resonance (called also shape resonance) in the exchange-like interband pairing. The resonance is switched on by tuning the chemical potential at an electronic topological transition (ETT) near a band edge, where the Fermi surface topology of one of the subbands changes from 1D to 2D topology. We show that the tuning is realized by changing i) the misfit strain between the superconducting planes and the spacers ii) the charge density and iii) the disorder. The system is at the verge of a catastrophe i.e. near a structural and magnetic phase transition associated with the stripes (analogous to the 1/8 stripe phase in cuprates) order to disorder phase transition. Fine tuning of both the chemical potential and the disorder pushes the critical temperature Ts of this phase transition to zero giving a quantum critical point. Here the quantum lattice and magnetic fluctuations promote the Feshbach resonance of the exchange-like anisotropic pairing. This superconducting phase that resists to the attacks of temperature is shown to be controlled by the interplay of the hopping energy between stripes and the quantum fluctuations. The superconducting gaps in the multiple Fermi surface spots reported by the recent ARPES experiment of D. V. Evtushinsky et al. arXiv:0809.4455 are shown to support the Feshbach scenario.Comment: 31 pages, 7 figure