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https://www.readbyqxmd.com/read/29880426/3d-genome-mapping-and-analysis-methods
#1
EDITORIAL
Josée Dostie, Mathieu Blanchette
No abstract text is available yet for this article.
June 1, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29692173/droplet-behavior-in-open-biphasic-microfluidics
#2
Jing J Lee, Jean Berthier, Kenneth A Brakke, Ashley M Dostie, Ashleigh B Theberge, Erwin Berthier
Capillary open microsystems are attractive and increasingly used in biotechnology, biology, and diagnostics as they allow simple and reliable control of fluid flows. In contrast to closed microfluidic systems, however, two-phase capillary flows in open microfluidics have remained largely unexplored. In this work, we present the theoretical basis and experimental demonstration of a spontaneous capillary flow (SCF) of two-phase systems in open microchannels. Analytical results show that an immiscible plug placed in an open channel can never stop the SCF of a fluid in a uniform cross-section microchannel...
May 8, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29381840/swimming-against-the-current-a-qualitative-review-of-the-work-experiences-and-adaptations-made-by-employees-with-arthritis
#3
R J Purc-Stephenson, Jessica Dostie, Hailey J Smith
OBJECTIVE: To describe the experiences and strategies of employees with arthritis (EwA) to maintain employment and to use this information to build a conceptual model. METHODS: We conducted a systematic review of qualitative studies that examined the work experiences of EwA. Published studies on arthritis and employment were searched from electronic databases (1980-2017) and bibliographical reviews of relevant studies. We used meta-ethnography to synthesize the findings...
January 30, 2018: Arthritis Care & Research
https://www.readbyqxmd.com/read/29309079/fundamentals-of-rapid-injection-molding-for-microfluidic-cell-based-assays
#4
Ulri N Lee, Xiaojing Su, David J Guckenberger, Ashley M Dostie, Tianzi Zhang, Erwin Berthier, Ashleigh B Theberge
Microscale cell-based assays have demonstrated unique capabilities in reproducing important cellular behaviors for diagnostics and basic biological research. As these assays move beyond the prototyping stage and into biological and clinical research environments, there is a need to produce microscale culture platforms more rapidly, cost-effectively, and reproducibly. 'Rapid' injection molding is poised to meet this need as it enables some of the benefits of traditional high volume injection molding at a fraction of the cost...
January 30, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29244631/initial-results-of-peripheral-blood-stem-cell-mobilization-collection-cryopreservation-and-engraftment-after-autologous-transplantation-confirm-that-the-capacity-building-approach-offers-good-chances-of-success-in-critical-contexts-a-kurdish-italian-cooperative
#5
Ignazio Majolino, Dereen Mohammed, Dastan Hassan, Francesco Ipsevich, Chra Abdullah, Rebar Mohammed, Angelo Palmas, Marco Possenti, Diana Noori, Dlir Ali, Harem Karem, Salah Salih, Michele Vacca, Claudia Del Fante, Angelo Ostuni, Andrea Frigato, Maria Speranza Massei, Annunziata Manna, Stefania Vasta, Marcela Gabriel, Marta Verna, Attilio Rovelli, Valentino Conter, Kosar Ali, Dosti Othman
Introduction At Hiwa Cancer Hospital (Sulaymaniyah, Iraqi Kurdistan) after the center was started by a cooperative project in June 2016, autologous transplantation was developed. Patients and Methods To develop the project, the capacity-building approach was adopted, with on-site training and coaching of personnel, educational meetings, lectures, on-the-job training, and the implementation of quality management planning. Results Here, we report initial results of peripheral-blood stem-cell mobilization and collection of the first 27 patients (age 12 to 61 years; 19 males and 8 females; multiple myeloma, n = 10; plasma cell leukemia, n = 1; Hodgkin lymphoma, n = 12; non-Hodgkin lymphoma, n = 3; and acute myeloid leukemia, n = 1)...
December 15, 2017: Journal of Global Oncology
https://www.readbyqxmd.com/read/29203104/evaluating-the-effect-of-myrtus-communis-on-programmed-cell-death-in-hydatid-cyst-protoscolices
#6
Mojtaba Shahnazi, Abbas Azadmehr, Moazzam Dosti Jondabeh, Reza Hajiaghaee, Reza Norian, Hamidreza Aghaei, Mehrzad Saraei, Mahmood Alipour
OBJECTIVE: To evaluate the possible involvement of programmed cell death strategy in hydatid cyst protoscolices following treatment with Myrtus communis (M. communis) as an herbal medicine. METHODS: Protoscolices were aseptically collected from sheep liver hydatid cysts. Evaluating the effect of M. communis extract on programmed cell death and increased activity of caspases 3, 8, and 9 in hydatid cyst protoscolices was conducted by treating the protoscolices with different concentration (5, 50, and 100 mg/mL) of M...
November 2017: Asian Pacific Journal of Tropical Medicine
https://www.readbyqxmd.com/read/28639807/the-impact-of-time-and-repeated-exposure-on-famous-person-knowledge-in-amnestic-mild-cognitive-impairment-and-alzheimer-s-disease
#7
Sophie Benoit, Isabelle Rouleau, Roxane Langlois, Valérie Dostie, Marie-Jeanne Kergoat, Sven Joubert
OBJECTIVE: Famous people knowledge has been shown to be impaired early in Alzheimer's disease (AD) and amnestic mild cognitive impairment (aMCI). However, the question of whether recently acquired knowledge is more impaired than remotely acquired knowledge remains a matter of debate. The aim of this study was to investigate the patterns of semantic memory impairment in aMCI and AD by investigating 2 factors that may influence the retrieval of such knowledge, namely remoteness and frequency of repetition of information over time...
October 2017: Neuropsychology
https://www.readbyqxmd.com/read/28512560/the-start-up-of-the-first-hematopoietic-stem-cell-transplantation-center-in-the-iraqi-kurdistan-a-capacity-building-cooperative-project-by-the-hiwa-cancer-hospital-sulaymaniyah-and-the-italian-agency-for-development-cooperation-an-innovative-approach
#8
Ignazio Majolino, Dosti Othman, Attilio Rovelli, Dastan Hassan, Luqman Rasool, Michele Vacca, Nigar Abdalrahman, Chra Abdullah, Zhalla Ahmed, Dlir Ali, Kosar Ali, Chiara Broggi, Cinzia Calabretta, Marta Canesi, Gloria Ciabatti, Claudia Del Fante, Elisabetta De Sapio, Giovanna Dore, Andrea Frigato, Marcela Gabriel, Francesco Ipsevich, Harem Kareem, Dana Karim, Rosa Leone, Tavan Mahmood, Annunziata Manna, Maria Speranza Massei, Andrea Mastria, Dereen Mohammed, Rebar Mohammed, Khoshnaw Najmaddin, Diana Noori, Angelo Ostuni, Angelo Palmas, Marco Possenti, Ali Qadir, Giorgio Real, Rebwar Shrif, Caterina Valdatta, Stefania Vasta, Marta Verna, Mariangela Vittori, Awder Yousif, Francesco Zallio, Alessandro Calisti, Sergio Quattrocchi, Corrado Girmenia
We describe the entire process leading to the start-up of a hematopoietic stem cell transplantation center at the Hiwa Cancer Hospital, in the city of Sulaymaniyah, Kurdistan Iraqi Region. This capacity building project was funded by the Italian Development Cooperation Agency and implemented with the support of the volunteer work of Italian professionals, either physicians, nurses, biologists and technicians. The intervention started in April 2016, was based exclusively on training and coaching on site, that represent a significant innovative approach, and led to a first autologous transplant in June 2016 and to the first allogeneic transplant in October...
2017: Mediterranean Journal of Hematology and Infectious Diseases
https://www.readbyqxmd.com/read/28273065/complex-multi-enhancer-contacts-captured-by-genome-architecture-mapping
#9
Robert A Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C A Kraemer, Mita Chotalia, Sheila Q Xie, Mariano Barbieri, Inês de Santiago, Liron-Mark Lavitas, Miguel R Branco, James Fraser, Josée Dostie, Laurence Game, Niall Dillon, Paul A W Edwards, Mario Nicodemi, Ana Pombo
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation)...
March 23, 2017: Nature
https://www.readbyqxmd.com/read/28180285/reciprocal-regulation-of-chromatin-state-and-architecture-by-hotairm1-contributes-to-temporal-collinear-hoxa-gene-activation
#10
Xue Q D Wang, Josée Dostie
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammals, many of which represent important regulators of gene expression. However, the mechanisms used by lncRNAs to control transcription remain largely uncharacterized. Here, we report on HOTAIRM1, a promising lncRNA biomarker in leukemia and solid tumors. We find that HOTAIRM1 contributes to three-dimensional chromatin organization changes required for the temporal collinear activation of HOXA genes. We show that distinct HOTAIRM1 variants preferentially associate with either UTX/MLL or PRC2 complexes to modulate the levels of activating and silencing marks at the bivalent domain...
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28146278/detection-and-manipulation-of-the-stress-response-protein-metallothionein
#11
REVIEW
Sadikshya Bhandari, Clare Melchiorre, Kristen Dostie, Debby Laukens, Lindsey Devisscher, Ariel Louwrier, Amy Thees, Michael A Lynes
Metallothioneins (MTs) are small molecular weight stress response proteins that play a central role as reservoir of essential divalent heavy metal cations such as zinc and copper, and also can diminish the effects of toxic heavy metals such as mercury and cadmium. Historically, MT has been considered to be an intracellular protein with roles to play in the management of heavy metals, as a regulator of cellular redox potential, and as a buffer of free radicals. Our recent studies have highlighted immunomodulatory role of MT in inflammatory diseases and also in the progression of metastatic cell movement...
February 1, 2017: Current Protocols in Toxicology
https://www.readbyqxmd.com/read/28117914/chemotherapeutic-decontamination-of-dental-implants-colonized-by-mature-multispecies-oral-biofilm
#12
Sebastien Dostie, Lubna T Alkadi, Gethin Owen, Jiarui Bi, Ya Shen, Markus Haapasalo, Hannu S Larjava
AIM: No studies have tested disinfectants on mature multispecies oral biofilms on titanium substrata. The aim of this study was to investigate the efficacy of commonly used antimicrobial agents in decontamination of multispecies mature oral biofilm on sandblasted, large-grit, acid-etched (SLA) titanium implants. METHODS: SLA titanium disks were inoculated with dental plaque and cultured anaerobically for 21 days. The disks were rinsed with 0.9% NaCl, exposed for 2 min...
January 24, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/27940207/chromosome-folding-and-its-regulation-in-health-and-disease
#13
REVIEW
Xue Qing David Wang, Josée Dostie
There are many ways in which cells may not adequately behave or respond to their environment, and the molecular mechanisms leading to these defects are as diverse as they are many. In this review, we report on how spatial chromatin organization contributes to the proper expression of genes, relating how CTCF-one of its main architects-contributes to gene regulation. We also touch on the emerging role of long noncoding RNAs in shaping chromatin organization and activity. The HOX gene clusters have been used as paradigm in the study of various biological pathways, and the overview we provide gives emphasis to what research on these loci has revealed about chromatin architecture and its regulation in the control of gene expression...
April 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27789700/reciprocal-regulation-of-chromatin-state-and-architecture-by-hotairm1-contributes-to-temporal-collinear-hoxa-gene-activation
#14
Xue Q D Wang, Josée Dostie
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammals, many of which represent important regulators of gene expression. However, the mechanisms used by lncRNAs to control transcription remain largely uncharacterized. Here, we report on HOTAIRM1, a promising lncRNA biomarker in leukemia and solid tumors. We find that HOTAIRM1 contributes to three-dimensional chromatin organization changes required for the temporal collinear activation of HOXA genes. We show that distinct HOTAIRM1 variants preferentially associate with either UTX/MLL or PRC2 complexes to modulate the levels of activating and silencing marks at the bivalent domain...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27736093/diastereoselective-synthesis-of-c2-fluorinated-nucleoside-analogues-using-an-acyclic-approach
#15
Starr Dostie, Michel Prévost, Philippe Mochirian, Kashif Tanveer, Nicholas Andrella, Ariana Rostami, Guillaume Tambutet, Yvan Guindon
Nucleoside analogues bearing a fluorine in the C2'-position have been synthesized by SN2-like cyclizations of acyclic thioaminal precursors. This strategy provides access to two scaffolds, d-1',2'-cis-thiofuranosides and d-1',2'-trans-furanosides, which are difficult to generate using the standard approach for nucleoside synthesis. The addition of silylated nucleobases onto model C2-fluorinated dithioacetal substrates resulted in 1,2-syn diastereoselectivity, which is consistent with the C2-F and S-alkyl moiety being in close proximity...
November 18, 2016: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/27559040/association-study-of-two-functional-single-nucleotide-polymorphisms-of-neuropeptide-y-gene-with-multiple-sclerosis
#16
Seyed Mahdi Mohammadi, Zeinab Shirvani Farsani, Rozita Dosti, Mohammad Ali Sahraian, Mehrdad Behmanesh
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by brain inflammation, demyelination and axonal loss. Neuropeptide Y (NPY) has a critical role in the maintenance of homeostasis in the immune system and coping of stress condition. In the current study we analyzed 188 patients suffering from MS and 204 unrelated healthy controls for two functional single nucleotide polymorphisms (SNPs), NPY 20T>C (rs16139) and NPY -485T>C (rs16147) using PCR-RFLP and Mismatch PCR-RFLP methods...
December 2016: Neuropeptides
https://www.readbyqxmd.com/read/26986719/spatial-organization-of-epigenomes
#17
Jonathan Christopher Dubé, Xue Qing David Wang, Josée Dostie
The role of genome architecture in transcription regulation has become the focus of an increasing number of studies over the past decade. Chromatin organization can have a significant impact on gene expression by promoting or restricting the physical proximity between regulatory DNA elements. Given that any change in chromatin state has the potential to alter DNA folding and the proximity between control elements, the spatial organization of chromatin is inherently linked to its molecular composition. In this review, we explore how modulators of chromatin state and organization might keep gene expression in check...
March 2016: Current Molecular Biology Reports
https://www.readbyqxmd.com/read/26836162/memory-for-public-events-in-mild-cognitive-impairment-and-alzheimer-s-disease-the-importance-of-rehearsal
#18
Roxane Langlois, Sven Joubert, Sophie Benoit, Valérie Dostie, Isabelle Rouleau
Ribot's law refers to the better preservation of remote memories compared with recent ones that presumably characterizes retrograde amnesia. Even if Ribot-type temporal gradient has been extensively studied in retrograde amnesia, particularly in Alzheimer's disease (AD), this pattern has not been consistently found. One explanation for these results may be that rehearsal frequency rather than remoteness accounts for the better preservation of these memories. Thus, the aim of present study was to address this question by studying retrograde semantic memory in subjects with amnestic mild cognitive impairment (aMCI) (n = 20), mild AD (n = 20) and in healthy older controls (HC; n = 19)...
2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/26700852/hierarchical-folding-and-reorganization-of-chromosomes-are-linked-to-transcriptional-changes-in-cellular-differentiation
#19
James Fraser, Carmelo Ferrai, Andrea M Chiariello, Markus Schueler, Tiago Rito, Giovanni Laudanno, Mariano Barbieri, Benjamin L Moore, Dorothee C A Kraemer, Stuart Aitken, Sheila Q Xie, Kelly J Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Colin A Semple, Josée Dostie, Ana Pombo, Mario Nicodemi
Mammalian chromosomes fold into arrays of megabase-sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher-order organization remains elusive. Here, we investigate TAD higher-order interactions with Hi-C through neuronal differentiation and show that they form a hierarchy of domains-within-domains (metaTADs) extending across genomic scales up to the range of entire chromosomes...
December 23, 2015: Molecular Systems Biology
https://www.readbyqxmd.com/read/26644285/pam-multiplicity-marks-genomic-target-sites-as-inhibitory-to-crispr-cas9-editing
#20
Abba Malina, Christopher J F Cameron, Francis Robert, Mathieu Blanchette, Josée Dostie, Jerry Pelletier
In CRISPR-Cas9 genome editing, the underlying principles for selecting guide RNA (gRNA) sequences that would ensure for efficient target site modification remain poorly understood. Here we show that target sites harbouring multiple protospacer adjacent motifs (PAMs) are refractory to Cas9-mediated repair in situ. Thus we refine which substrates should be avoided in gRNA design, implicating PAM density as a novel sequence-specific feature that inhibits in vivo Cas9-driven DNA modification.
December 8, 2015: Nature Communications
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