Preferences of University Academic Staff for Their Surrounding Environment: Uludag University as a Case Study

As a result of the damage to natural areas, open and green spaces in cities shrink in area and even disappear. This has caused an increase in the number of studies concerned with human-nature relations in urban landscaping. Contrary to the fact that the major part of our lives is spent in our workplaces, there are not many studies that investigate human-nature relations in workspaces. However, workspaces cover big areas of the urban landscape, their arrangement is of major importance in both an ecological and economical sense. The present study aims to shed light on how the academic staffs working at the Uludag University campus perceive the nature that surrounds their workspace and what their expectations concerning their natural surroundings are. Although the employees wish to see arranged landscapes surrounding their workplace, they significantly prefer naturally arranged spaces. It is evident that the staffs are concerned about the surroundings of the buildings they work in and that they make correct assumptions about and descriptions of the surroundings of their buildings

Immunostimulatory activity of polysaccharide-poly(I:C) nanoparticles

Cataloged from PDF version of article.Immunostimulatory properties of mushroom derived polysaccharides (PS) as stand-alone agents were tested. Next. PS were nanocomplexed with polyI:C (pIC) to yield stable nanoparticles around 200 nm in size evidenced by atomic force microscopy and dynamic light scattering analyses. PSs were selectively engaged by cells expressing TLR2 and initiated NF kappa B dependent signaling cascade leading to a Th1-biased cytokine/chemokine secretion in addition to bactericidal nitric oxide (NO) production from macrophages. Moreover, cells treated with nanoparticles led to synergistic IL6, production and upregulation of TNF alpha, MIP3 alpha, IFN gamma and IP10 transcript expression. In mice, PS-Ovalbumin-pIC formulation surpassed anti-OVA IgG responses when compared to either PS-OVA or pIC-OVA mediated immunity. Our results revealed that signal transduction initiated both by TLR2 and TLR3 via co-delivery of pIC by PS in nanoparticle depot delivery system is an effective immunization strategy. The present work implicate that the PS and nucleic acid based nanoparticle approach along with protein antigens can be harnessed to prevent infectious diseases. (C) 2011 Elsevier Ltd. All rights reserve

Regulatory de novo mutations underlying intellectual disability

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents. In addition, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific enhancers as compared with adult brain enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the prefrontal cortex. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1, and POU3F3). Most of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France

The zinc transporter ZIP12 regulates the pulmonary vascular response to chronic hypoxia

The typical response of the adult mammalian pulmonary circulation to a low oxygen environment is vasoconstriction and structural remodelling of pulmonary arterioles, leading to chronic elevation of pulmonary artery pressure (pulmonary hypertension) and right ventricular hypertrophy. Some mammals, however, exhibit genetic resistance to hypoxia-induced pulmonary hypertension1, 2, 3. We used a congenic breeding program and comparative genomics to exploit this variation in the rat and identified the gene Slc39a12 as a major regulator of hypoxia-induced pulmonary vascular remodelling. Slc39a12 encodes the zinc transporter ZIP12. Here we report that ZIP12 expression is increased in many cell types, including endothelial, smooth muscle and interstitial cells, in the remodelled pulmonary arterioles of rats, cows and humans susceptible to hypoxia-induced pulmonary hypertension. We show that ZIP12 expression in pulmonary vascular smooth muscle cells is hypoxia dependent and that targeted inhibition of ZIP12 inhibits the rise in intracellular labile zinc in hypoxia-exposed pulmonary vascular smooth muscle cells and their proliferation in culture. We demonstrate that genetic disruption of ZIP12 expression attenuates the development of pulmonary hypertension in rats housed in a hypoxic atmosphere. This new and unexpected insight into the fundamental role of a zinc transporter in mammalian pulmonary vascular homeostasis suggests a new drug target for the pharmacological management of pulmonary hypertension

Detection of conjugation related type four secretion machinery in Aeromonas culicicola

BACKGROUND: Aeromonas sp. can now be considered relatively common enteropathogens due to the increase of diseases in humans. Aeromonas culicicola is a gram negative rod-shaped bacterium isolated for the first time from the mosquito mid-gut, but subsequently detected in other insects and waters also. Our previous study discovered that A. culicicola harbors three plasmids, which we designated as pAc3249A, pAc3249B and pAc3249C. We investigated and report here the existence and genetic organization of a Conjugal Type IV Secretion System (TFSS) in pAc3249A. METHODOLOGY/PRINCIPLE FINDING: The complete operon is 11,061 bp in length and has G+C content of 47.20% code for 12 ORFs. The gene order and orientation were similar to those found in other bacteria with some differences. We have designated this system as AcTra for Aeromonas culicicola transfer system. BLAST results of ORFs and phylogenetic analysis showed significant similarity towards the respective proteins of the IncI2 plasmid R721 of E. coli. Other bioinformatics studies have been performed to predict conserved motifs/domains, signal peptides, transmembrane helices, etc. of the ORFs. CONCLUSIONS/SIGNIFICANCE: BLAST results of ORFs and phylogenetic analysis showed significant similarity towards the respective proteins of the IncI2 plasmid R721 of E. coli

Immunostimulatory activity of polysaccharide-poly(I:C) nanoparticles

PubMedID: 21459434Immunostimulatory properties of mushroom derived polysaccharides (PS) as stand-alone agents were tested. Next, PS were nanocomplexed with polyI:C (pIC) to yield stable nanoparticles around 200 nm in size evidenced by atomic force microscopy and dynamic light scattering analyses. PSs were selectively engaged by cells expressing TLR2 and initiated NF?B dependent signaling cascade leading to a Th1-biased cytokine/chemokine secretion in addition to bactericidal nitric oxide (NO) production from macrophages. Moreover, cells treated with nanoparticles led to synergistic IL6, production and upregulation of TNF?, MIP3?, IFN? and IP10 transcript expression. In mice, PS-Ovalbumin-pIC formulation surpassed anti-OVA IgG responses when compared to either PS-OVA or pIC-OVA mediated immunity. Our results revealed that signal transduction initiated both by TLR2 and TLR3 via co-delivery of pIC by PS in nanoparticle depot delivery system is an effective immunization strategy. The present work implicate that the PS and nucleic acid based nanoparticle approach along with protein antigens can be harnessed to prevent infectious diseases. © 2011 Elsevier Ltd.203953 036615 108S316This work was supported by the Scientific and Technological Research Council of Turkey (TÜBİTAK, Grant No: 108S316 ). IG received grant support from EU/FP6/MC IRG (Grant # 036615 ) and EU 7th Framework Project UNAM-Regpot (Grant # 203953 ). GT and FCY received scholarship grants from SANTEZ ( 0448-STZ-2009-2 ) and TUBITAK . We thank to Dr. Aykutlu Dana and his group members for their invaluable support during AFM studies. Drs. Can K. Akcali and Mayda Gursel are sincerely acknowledged for their critical reading of the manuscript. Appendi

Regulatory de novo mutations underlying intellectual disability

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents. In addition, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific enhancers as compared with adult brain enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the prefrontal cortex. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1, and POU3F3). Most of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID.This work was funded by grants from the Wellcome Trust Institute Strategic Support and National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, Institute for Translational Medicine and Therapeutics (P70888) obtained by SS Atanur. J Ferrer and MG De Vas’s work was funded by grants from the Wellcome Trust (WT101033 to J Ferrer), Medical Research Council (MR/L02036X/1 to J Ferrer), and European Research Council Advanced Grant (789055 to J Ferrer). MM Pradeepa’s lab is funded by the UKRI/MRC (MR/T000783/1), and Barts charity (MGU0475) grants. TN Khan was partially supported by the Government of Pakistan under the PSDP project “Development of National University of Medical Sciences (NUMS), Rawalpindi.