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Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
Joel E Abbott, Roger L Sur
The aim of this paper was to evaluate the current technology and designs of flexible ureterorenoscopes. We will review contemporary fiberoptic and digital ureteroscopes, including a discussion on ureteroscope damage and repair, and lastly present the projected future of flexible ureterorenoscopy. Ureterorenoscopy has evolved dramatically over the past several decades, which has led to landscape reshaping of stone disease treatment and upper tract pathology. Advancements in tip control, miniaturization of scopes, introduction of a digital chip on the tip, disposable devices to augment surgery, surgical experience/familiarity and most recently single use scopes are all independent factors that have increased flexible ureterorenoscopy adoption and success...
October 19, 2016: Minerva Urologica e Nefrologica, the Italian Journal of Urology and Nephrology
Antonino Neri, Katia Todoerti, Marta Lionetti, Vittorio Simeon, Marzia Barbieri, Filomena Nozza, Gabriella Vona, Alessandra Pompa, Luca Baldini, Pellegrino Musto
Primary plasma cell leukemia (PPCL) is a rare and aggressive variant of multiple myeloma. The introduction of novel agents and modern technologies has recently partially changed the clinical and biological scenario of this malignancy, allowing limited, but not negligible, progresses. Areas covered: We will discuss the complex landscape of genetic alterations in PPCL, derived from conventional and high-throughput technologies; the best available treatments for PPCL; the possible future therapeutic perspectives...
October 19, 2016: Expert Review of Hematology
Daniel Nava Rodrigues, Gunther Boysen, Semini Sumanasuriya, George Seed, Angelo M De Marzo, Johann de Bono
Prostate cancer (PCa) is a clinically heterogeneous disease and current treatment strategies are based largely on anatomical and pathological parameters. In the recent past, several DNA sequencing studies of primary and advanced PCa have revealed recurrent patterns of genomic aberrations that expose mechanisms of resistance to available therapies and potential new drug targets. Suppression of androgen receptor (AR) signalling is the cornerstone of advanced prostate cancer treatment. Genomic aberrations of the androgen receptor or alternative splicing of its mRNA are increasingly recognized as biomarkers of resistance to AR-targeted therapy such as abiraterone or enzalutamide...
October 18, 2016: Journal of Pathology
Sharon Downes, Darren Kriticos, Hazel Parry, Cate Paull, Nancy Schellhorn, Myron P Zalucki
Helicoverpa armigera is a major pest of agriculture, horticulture and floriculture throughout the old world and recently invaded parts of the new world. We overview of the evolution in thinking about the application of area-wide approaches to assist with its control by the Australian Cotton Industry to highlight important lessons and future challenges to achieving the same in the New World. An over-reliance of broad-spectrum insecticides led to Helicoverpa spp. in Australian cotton rapidly became resistant to DDT, synthetic pyrethroids, organophosphates, carbamates and endosulfan...
October 17, 2016: Pest Management Science
Jan-Dieter Ludwigs, Markus Ebeling, Timothy B Fredricks, Roger C Murfitt, Steven Kragten
The registration of pesticides follows guidance published by the European Food Safety Authority, EFSA. As a default, the EFSA guidance document on risk assessment for birds and mammals assumes that animals feed exclusively on pesticide-treated fields. However, the guidance document suggests refining the risk via the proportion of food animals obtain from a treated field or specific crop (expressed via the so-called PT value). The EFSA guidance equalizes the portion of food taken from a treated area per day with the portion of time spent potentially foraging over the course of a day within this area...
October 18, 2016: Environmental Toxicology and Chemistry
Erina Takai, Yasushi Totoki, Hiromi Nakamura, Mamoru Kato, Tatsuhiro Shibata, Shinichi Yachida
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect molecular characteristics of tumors, supporting the concept of "liquid biopsy".We determined the mutational status of KRAS in plasma cfDNA using multiplex droplet digital PCR in 259 patients with PDAC, retrospectively...
2016: Advances in Experimental Medicine and Biology
Michael D Caggiano, Wade T Tinkham, Chad Hoffman, Antony S Cheng, Todd J Hawbaker
The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations...
October 2016: Heliyon
Michael Medinger, Claudia Lengerke, Jakob Passweg
Acute myeloid leukemia (AML) is a biologically complex and molecularly and clinically heterogeneous disease, and its incidence is increasing as the population ages. Cytogenetic anomalies and mutation testing remain important prognostic tools for tailoring treatment after induction therapy. Despite major advances in understanding the genetic landscape of AML and its impact on the pathophysiology and biology of the disease, as well as the rapid development of new drugs, standard treatment options have not experienced major changes during the past three decades...
2016: Leukemia Research Reports
Ann Boyle, Sophie Davies, Nisha Dogra, Jennifer Perry, Hannah Fosker
Aims and method There is a drive to increase the number of psychiatry foundation placements to ensure that training keeps up with the changing health and social care landscape. This qualitative study aimed to explore, by interview, the experiences of 17 doctors who have completed a foundation placement in psychiatry. Results The study highlights the benefits of foundation psychiatry placements and some of their positive and negative aspects. Clinical implications Those developing foundation placements will need to ensure they are of high quality...
October 2016: BJPsych Bulletin
Anthony G Hudetz, Jeannette A Vizuete, Siveshigan Pillay, George A Mashour
Consciousness has been linked to the repertoire of brain states at various spatiotemporal scales. Anesthesia is thought to modify consciousness by altering information integration in cortical and thalamocortical circuits. At a mesoscopic scale, neuronal populations in the cortex form synchronized ensembles whose characteristics are presumably state-dependent but this has not been rigorously tested. In this study, spontaneous neuronal activity was recorded with 64-contact microelectrode arrays in primary visual cortex of chronically instrumented, unrestrained rats under stepwise decreasing levels of desflurane anesthesia (8%, 6%, 4%, and 2% inhaled concentrations) and wakefulness (0% concentration)...
October 14, 2016: Neuroscience
Federica Parodi, Roberta Carosio, Marco Ragusa, Cinzia Di Pietro, Marco Maugeri, Davide Barbagallo, Fabio Sallustio, Giorgio Allemanni, Maria Pia Pistillo, Ida Casciano, Alessandra Forlani, Francesco P Schena, Michele Purrello, Massimo Romani, Barbara Banelli
In neuroblastoma, the epigenetic landscape is more profoundly altered in aggressive compared to lower grade tumors and the concomitant hypermethylation of many genes, defined as "methylator phenotype", has been associated with poor outcome. DNA methylation can interfere with gene expression acting at distance through the methylation or demethylation of the regulatory regions of miRNAs. The multiplicity of miRNA targets may result in the simultaneous alteration of many biological pathways like cell proliferation, apoptosis, migration and differentiation...
October 14, 2016: Biochimica et Biophysica Acta
Hiral Shah, Emiliano Albanese, Cynthia Duggan, Igor Rudan, Kenneth M Langa, Maria C Carrillo, Kit Yee Chan, Yves Joanette, Martin Prince, Martin Rossor, Shekhar Saxena, Heather M Snyder, Reisa Sperling, Mathew Varghese, Huali Wang, Marc Wortmann, Tarun Dua
At the First WHO Ministerial Conference on Global Action Against Dementia in March, 2015, 160 delegates, including representatives from 80 WHO Member States and four UN agencies, agreed on a call for action to reduce the global burden of dementia by fostering a collective effort to advance research. To drive this effort, we completed a globally representative research prioritisation exercise using an adapted version of the Child Health and Nutrition Research Initiative method. We elicited 863 research questions from 201 participants and consolidated these questions into 59 thematic research avenues, which were scored anonymously by 162 researchers and stakeholders from 39 countries according to five criteria...
November 2016: Lancet Neurology
Cecilia C S Yeung, H Joachim Deeg, Colin Pritchard, David Wu, Min Fang
Jumping translocations (JT) have been identified in numerous malignancies, including leukemia, but infrequently in patients with myelodysplastic syndromes (MDS). The responsible genetic region has been mapped to the JTB gene at 1q21, but breakpoints involving other chromosomal loci, such as 3q and 11q, have been described as well. We have characterized the pathological and mutational landscape, and the clinical course of 6 new MDS patients with jumping mutations using chromosome genomic array testing (CGAT) and target gene panel next generation sequencing...
September 2016: Cancer Genetics
Koning Shen, Barbara Calamini, Jonathan A Fauerbach, Boxue Ma, Sarah H Shahmoradian, Ivana L Serrano Lachapel, Wah Chiu, Donald C Lo, Judith Frydman
Many neurodegenerative diseases are linked to amyloid aggregation. In Huntington's disease (HD), neurotoxicity correlates with increased aggregation propensity of a polyglutamine (polyQ) expansion in exon 1 of mutant huntingtin protein (mHtt). Here we establish how the domains flanking the polyQ tract shape the mHtt conformational landscape in vitro and in neurons. In vitro, the flanking domains have opposing effects on the conformation and stabilities of oligomers and amyloid fibrils. The N-terminal N17 promotes amyloid fibril formation, while the C-terminal Proline Rich Domain destabilizes fibrils and enhances oligomer formation...
October 18, 2016: ELife
Shanshan Xu, Lanlan Dong, Yingying Shi, Liujun Chen, Peipei Yuan, Shuang Wang, Zhi Li, Yan Sun, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu
Human foamy virus (HFV) is a complex and unique retrovirus with the longest genomes among retroviruses used as vectors for gene therapy. Long non-coding RNAs (lncRNAs) are regarded as key regulators that involved in diverse biological processes during viral infection. However, the role of lncRNAs in HFV infection remains unknown. In this study, we utilized next-generation sequencing to first characterize lncRNAs in 293T cells after HFV infection, evaluating length distribution, exon number distribution, volcano picture and lncRNA class distribution...
October 18, 2016: AIDS Research and Human Retroviruses
Irsan E Kooi, Saskia E van Mil, David MacPherson, Berber M Mol, Annette C Moll, Hanne Meijers-Heijboer, Gertjan J L Kaspers, Jacqueline Cloos, Hein Te Riele, Josephine C Dorsman
Several murine retinoblastoma models have been generated by deleting the genes encoding for retinoblastoma susceptibility protein pRb and one of its family members p107 or p130. In Rb(-/-) p107(-/-) retinoblastomas, somatic copy number alterations (SCNAs) like Mdm2 amplification or Cdkn2a deletion targeting the p53-pathway occur, which is uncommon for human retinoblastoma. In our study, we determined SCNAs in retinoblastomas developing in Rb(-/-) p130(-/-) mice and compared this to murine Rb(-/-) p107(-/-) tumors and human tumors...
October 17, 2016: Genes, Chromosomes & Cancer
Dennis Wang, Nhu-An Pham, Jiefei Tong, Shingo Sakashita, Ghassan Allo, Lucia Kim, Naoki Yanagawa, Vibha Raghavan, Yuhong Wei, Christine To, Quang M Trinh, Maud H W Starmans, Michelle A Chan-Seng-Yue, Dianne Chadwick, Lei Li, Chang-Qi Zhu, Ni Liu, Ming Li, Sharon Lee, Vladimir Ignatchenko, Dan Strumpf, Paul Taylor, Nadeem Moghal, Geoffrey Liu, Paul C Boutros, Thomas Kislinger, Melania Pintilie, Igor Jurisica, Frances A Shepherd, John D McPherson, Lakshmi Muthuswamy, Michael F Moran, Ming-Sound Tsao
Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice...
October 17, 2016: International Journal of Cancer. Journal International du Cancer
Antoine Adde, Emmanuel Roux, Morgan Mangeas, Nadine Dessay, Mathieu Nacher, Isabelle Dusfour, Romain Girod, Sébastien Briolant
Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l'Oyapock (French Guiana). Longitudinal sampling sessions of An...
2016: PloS One
Daniel H Hovelson, Scott A Tomlins
Molecular biomarkers play little role in the current treatment of metastatic castration-resistant prostate cancer (CRPC). The advent of next-generation sequencing (NGS) has enabled the comprehensive molecular characterization of the genomic and transcriptomic landscape of both untreated primary prostate cancer and CRPC. Recent studies demonstrating the feasibility of interinstitution studies obtaining and NGS profiling of metastatic biopsies, targeted NGS approaches applicable to routine formalin-fixed, paraffin-embedded specimens, and NGS approaches applicable to circulating DNA and circulating tumor cells portend near-term adoption of NGS approaches in the management and treatment of CRPC...
September 2016: Cancer Journal
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