Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases

Oxidative damage represents a major threat to genomic stability, as the major product of DNA oxidation, 8-oxoguanine (GO), frequently mispairs with adenine during replication. In order to prevent these mutagenic events, organisms have evolved GO-DNA glycosylases that remove this oxidized base from DNA. We were interested to find out how GO is processed in the hyperthermophilic archaeon Pyrobaculum aerophilum, which lives at temperatures around 100 degrees C. To this end, we searched its genome for open reading frames (ORFs) bearing the principal hallmark of GO-DNA glycosylases: a helix-hairpin-helix motif and a glycine/proline-rich sequence followed by an absolutely conserved aspartate (HhH-GPD motif). Interestingly, although the P.aerophilum genome encodes three such ORFs, none of these encodes the potent GO-processing activity detected in P.aerophilum extracts. Fractionation of the extracts, followed by analysis of the active fractions by denaturing polyacrylamide gel electrophoresis, showed that the GO-processing enzyme has a molecular size of approximately 30 kDa. Mass spectrometric analysis of proteins in this size range identified several peptides originating from P.aerophilum ORF PAE2237. We now show that PAE2237 encodes AGOG (Archaeal GO-Glycosylase), the founding member of a new family of DNA glycosylases, which can remove GO from single- and double-stranded substrates with great efficienc

A Reconfigurable Quantum Local Area Network Over Deployed Fiber

Practical quantum networking architectures are crucial for scaling the connection of quantum resources. Yet quantum network testbeds have thus far underutilized the full capabilities of modern lightwave communications, such as flexible-grid bandwidth allocation. In this work, we implement flex-grid entanglement distribution in a deployed network for the first time, connecting nodes in three distinct campus buildings time-synchronized via the Global Positioning System (GPS). We quantify the quality of the distributed polarization entanglement via log-negativity, which offers a generic metric of link performance in entangled bits per second. After demonstrating successful entanglement distribution for two allocations of our eight dynamically reconfigurable channels, we demonstrate remote state preparation -- the first realization on deployed fiber -- showcasing one possible quantum protocol enabled by the distributed entanglement network. Our results realize an advanced paradigm for managing entanglement resources in quantum networks of ever-increasing complexity and service demands

Searching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase

To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, like AAG, to interact with DNA using two affinities: a lower-affinity interaction in a searching process and a higher-affinity interaction for catalytic repair. Here, we present crystal structures of AAG trapped in two DNA-bound states. The lower-affinity depiction allows us to investigate, for the first time, the conformation of this protein in the absence of a tightly bound DNA adduct. We find that active site residues of AAG involved in binding lesion bases are in a disordered state. Furthermore, two loops that contribute significantly to the positive electrostatic surface of AAG are disordered. Additionally, a higher-affinity state of AAG captured here provides a fortuitous snapshot of how this enzyme interacts with a DNA adduct that resembles a one-base loop.National Institutes of Health (U.S.) (grant no. P30-ES002109)National Institutes of Health (U.S.) (grant no. GM65337)National Institutes of Health (U.S.) (grant no. GM65337-03S2)National Institutes of Health (U.S.) (grant no. CA055042)National Institutes of Health (U.S.) (grant no. CA092584)Repligen Corporation (KIICR Graduate Fellowship

The Role of Purported Mucoprotectants in Dealing with Irritable Bowel Syndrome, Functional Diarrhea, and Other Chronic Diarrheal Disorders in Adults

Chronic diarrhea is a frequent presenting symptom, both in primary care medicine and in specialized gastroenterology units. It is estimated that more than 5% of the global population suffers from chronic diarrhea. and that about 40% of these subjects are older than 60 years. The clinician is frequently faced with the need to decide which is the best therapeutic approach for these patients. While the origin of chronic diarrhea is diverse, impairment of intestinal barrier function, dysbiosis. and mucosal micro-inflammation are being increasingly recognized as underlying phenomena characterizing a variety of chronic diarrheal diseases. In addition to current pharmacological therapies, there is growing interest in alternative products such as mucoprotectants, which form a mucoadhesive film over the epithelium to reduce and protect against the development of altered intestinal permeability, dysbiosis, and mucosal micro-inflammation. This manuscript focuses on chronic diarrhea in adults, and we will review recent evidence on the ability of these natural compounds to improve symptoms associated with chronic diarrhea and to exert protective effects for the intestinal barrier

Identification of highly penetrant Rb-related synthetic lethal interactions in triple negative breast cancer.

Although defects in the RB1 tumour suppressor are one of the more common driver alterations found in triple-negative breast cancer (TNBC), therapeutic approaches that exploit this have not been identified. By integrating molecular profiling data with data from multiple genetic perturbation screens, we identified candidate synthetic lethal (SL) interactions associated with RB1 defects in TNBC. We refined this analysis by identifying the highly penetrant effects, reasoning that these would be more robust in the face of molecular heterogeneity and would represent more promising therapeutic targets. A significant proportion of the highly penetrant RB1 SL effects involved proteins closely associated with RB1 function, suggesting that this might be a defining characteristic. These included nuclear pore complex components associated with the MAD2 spindle checkpoint protein, the kinase and bromodomain containing transcription factor TAF1, and multiple components of the SCFSKP Cullin F box containing complex. Small-molecule inhibition of SCFSKP elicited an increase in p27Kip levels, providing a mechanistic rationale for RB1 SL. Transcript expression of SKP2, a SCFSKP component, was elevated in RB1-defective TNBCs, suggesting that in these tumours, SKP2 activity might buffer the effects of RB1 dysfunction

Tight junctions: from simple barriers to multifunctional molecular gates

Epithelia and endothelia separate different tissue compartments and protect multicellular organisms from the outside world. This requires the formation of tight junctions, selective gates that control paracellular diffusion of ions and solutes. Tight junctions also form the border between the apical and basolateral plasma-membrane domains and are linked to the machinery that controls apicobasal polarization. Additionally, signalling networks that guide diverse cell behaviours and functions are connected to tight junctions, transmitting information to and from the cytoskeleton, nucleus and different cell adhesion complexes. Recent advances have broadened our understanding of the molecular architecture and cellular functions of tight junctions

4-5-(Benzo{\-}furan-2-yl)-1-phenyl-1{\it H}-pyrazol-3-yl-{\it N},{\it N}-di{\-}methyl{\-}aniline

In the title compound, C\sb 25H\sb 21N\sb 3O, the dihedral angles between the pyrazole ring and its phenyl, aniline and benzo\-furan (r.m.s. deviation = 0.006Å) substituents are 47.64(8), 4.00(8) and 29.12(7)\circ, respectively. The methyl C atoms of the aniline group deviate from their attached ring by 0.521(3) and 0.010(3)Å. In the crystal, aromatic π—π stacking between the pyrazole rings centroid{--}centroid separation = 3.7899(9){\AA} and slippage = 0.66{\AA} generates inversion dimers

Real-time Interactive Steerable Scientific Visualisation of Free Surface Flow in the Context of Synthetic Vision

The extension project “Athletics for children and young people” which has been developed at Unesp-Rio Claro since 1999, had, in 2008, the objective of promoting, among students of the community, different experiences in the athletics field, with emphasis on regular classes, pictures exhibition and visit to the athletic track. These activities have provided among other things a greater knowledge about the athletics and different experiences such as games and specific competitions contributing to the disclosure of this sport. The children and young people that participated in the project, initially, did not have any idea of what they would learn, because, for most of them, the Athletics had not been taught in Physical Education classes at school. However, during the project, the students were able to know and recognize some of the competitions they had seen on television, especially considering that 2008 was an Olympic year. At the end of the year, we observed that in addition to the dissemination of the athletics, the project helped the trainee students and others responsible for organizing and implementing the proposal and the activities to expand their knowledge on the topic.El Proyeto de extensión “Atletismo para niños y jóvenes” desarrollado en la Unesp – Rio Claro desde 1999 tuvo, em 2008, como objetivo, promover, entre alumnos de la comunidad, diferentes vivencias en el campo del atletismo, con destaque a las clases regulares, a las exposiciones de imágenes y visita a la pista de atletismo. Tales actividades proporcionaron, entre otras cosas: un mayor conocimiento cerca el atletismo y vivencias variadas que explotan juegos pre deportivos y pruebas especificas, contribuyendo para la difusión de esta modalidad deportiva. Los niños y jóvenes, participantes del proyecto, no hacían, inicialmiente, idea de lo que iban a aprender, ya que, para la mayoría de ellos, el Atletismo no habia sido enseñado en classes de educación fisica en el campo de la escuela. Todavia, cuando participarón de las actividades del atletismo, los alumnos empiezaron poco a poco a conocer y reconocer algunas de las pruebas que habían visto por la tele, sobretodo considerando que 2008 fue un año de Olimpiadas. Al final de este año, verificamos que además de la difusión del atletismo, el proyecto contribuyó con la formación profesional de los pasantes y de los becarios, responsables por la organización e implementación de las actividades propuestas, contribuyendo para la ampliación del conocimiento de todos los arrollados.O projeto de extensão “Atletismo para crianças e jovens”, desenvolvido na Unesp-Rio Claro desde 1999, teve em 2008 como objetivo promover, entre alunos da comunidade, diferentes vivências no campo do atletismo, com destaque para as aulas regulares, para as exposições de imagens e para a visita à pista de atletismo. Tais atividades proporcionaram, entre outras coisas: um maior conhecimento acerca do atletismo e de vivências variadas que exploraram jogos pré-desportivos e provas específicas, contribuindo para a difusão dessa modalidade esportiva. As crianças e os jovens participantes do projeto não faziam, inicialmente, idéia do que iriam aprender, já que, para a maioria deles, o atletismo não havia sido ensinado em aulas de Educação Física no campo escolar. Entretanto, ao participarem das atividades de atletismo, os alunos foram pouco a pouco conhecendo e reconhecendo algumas das provas que assistiam pela televisão, sobretudo considerando que 2008 foi um ano olímpico. Ao final do ano verificamos que, para além da difusão do atletismo, o projeto contribuiu na formação profissional dos estagiários e da bolsista, responsáveis pela organização e implementação das atividades propostas, contribuindo para a ampliação do conhecimento de todos os envolvidos

Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large ΔC<SUB>p</SUB>'s

Maltose binding protein (MBP) is a large, monomeric two domain protein containing 370 amino acids. In the absence of denaturant at neutral pH, the protein is in the native state, while at pH 3.0 it forms a molten globule. The molten globule lacks a tertiary circular dichroism signal but has secondary structure similar to that of the native state. The molten globule binds 8-anilino-1-naphthalene sulfonate (ANS). The unfolding thermodynamics of MBP at both pHs were measured by carrying out a series of isothermal urea melts at temperatures ranging from 274-329 K. At 298 K, values of ΔG°, ΔC<SUB>p</SUB>, and C<SUB>m</SUB> were 3.1 ± 0.2 kcal mol<SUP>-1</SUP>, 5.9 ± 0.8 kcal mol<SUP>-1</SUP> K<SUP>-1</SUP> (15.9 cal (mol-residue)<SUP>-1</SUP> K<SUP>-1</SUP>), and 0.8 M, respectively, at pH3.0 and 14.5 ± 0.4 kcal mol<SUP>-1</SUP>, 8.3 ± 0.7 kcalmo<SUP>l-1</SUP> K<SUP>-1</SUP> (22.4kcal (mol-residue<SUP>-1</SUP> K<SUP>-1</SUP>), and 3.3 M, respectively, at pH 7.1. Guanidine hydrochloride denaturation at pH 7.1 gave values of ΔG° and ΔC<SUB>p</SUB> similar to those obtained with urea. The m values for denaturation are strongly temperature dependent, in contrast to what has been previously observed for small globular proteins. The value of ΔC<SUB>p</SUB> per mol-residue for the molten globule is comparable to corresponding values of ΔCp for the unfolding of typical globular proteins and suggests that it is a highly ordered structure, unlike molten globules of many small proteins. The value of ΔC<SUB>p</SUB> per mol-residue for the unfolding of the native state is among the highest currently known for any protein