المؤلفون: Van den Broeck, Frederik, Savill, Nicholas J., Imamura, Hideo, Sanders, Mandy, Maes, Ilse, Cooper, Sinclair, Mateus, David, Jara, Marlene, Adaui, Vanessa, Arevalo, Jorge, Llanos-Cuentas, Alejandro, Garcia, Lineth, Cupolillo, Elisa, Miles, Michael, Berriman, Matthew, Schnaufer, Achim, Cotton, James A., Dujardin, Jean-Claude

المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2020 Oct 01. 117(40), 25159-25168.

URL الوصول: https://www.jstor.org/stable/26969486

المؤلفون: Levy, Cooper Sinclair

مصطلحات موضوعية: Electrical engineering

الوصف: This dissertation addresses two distinct topics, namely circuits for radio-frequency and millimeter-wave transmitters with emphasis on power amplifiers, and control circuits and system design for linearizing atomic magnetometers.Power amplification for wireless transmitters, despite receiving myriad attention over the last few decades, is still one of the main bottlenecks in terms of complete transmitter integration and reducing system power dissipation. First, a distributed amplifier architecture aiming to improve peak efficiency by voltage supply scaling will be presented. By using multiple supplies, wasted headroom is eliminated in the early stages of the distributed amplifier where the output voltage swing is relatively low. Second, a class of Doherty power amplifiers that was rediscovered by the author by reverse engineering the canonical Doherty power amplifier, and a modern implementation, will be presented. The implementation stacks the voltage swings of the main and peaking amplifiers of the Doherty power amplifier, allowing increased output power in scaled CMOS without concern of breakdown. Finally, atomic magnetometers have shown promise as replacements in many applications where SQUIDs are currently used, with the benefits of no supercooling required, and the ability to operate in Earth's geomagnetic field. At the same time, operation outside of a magnetically-shielded environment has numerous side-effects. The last section will present a technique for linearizing the Bell-Bloom atomic magnetometer, improving its performance in interference-rich environments. The technique notes that the detected output signal of the magnetometer contains not only information about the spin precession of the optically pumped atoms, but also a large component due to the pumping laser modulation. By subtracting this known pumping modulation signal from the detected output, the system linearity can be significantly improved.

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URL الوصول: https://escholarship.org/uc/item/9q7877x4

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المؤلفون: Cooper, Sinclair, Wadsworth, Lizzie, Schnaufer, Achim, Savill, Nicholas Jon

المصدر: Cooper, S, Wadsworth, L, Schnaufer, A & Savill, N J 2022, ' Organization of minicircle cassettes and guide RNA genes of Trypanosoma brucei ', RNA, vol. 28, no. 7, pp. 972-992 . https://doi.org/10.1261/rna.079022.121

مصطلحات موضوعية: kinetoplast, minicircle, trypanosoma brucei, guide RNA

الوصف: Mitochondrial DNA of protists of order Kinetoplastida comprises thousands of interlinked circular molecules arranged in a network. There are two types of molecules called minicircles and maxicircles. Minicircles encode guide RNA (gRNA) genes whose transcripts mediate post-transcriptional editing of maxicircle encoded genes. Minicircles are diverse. The human sleeping sickness parasite Trypanosoma brucei has one of the most diverse sets of minicircle classes of all studied trypanosomatids with hundreds of different classes, each encoding one to four genes mainly within cassettes framed by 18 bp inverted repeats. A third of cassettes have no identifiable gRNA genes even though their sequence structures are similar to cassettes with identifiable genes. Only recently have almost all minicircle classes for some subspecies and isolates of T. brucei been sequenced and annotated with corresponding verification of gRNA expression by small-RNA transcriptome data. These data sets provide a rich resource for understanding the structure of minicircle classes, cassettes and gRNA genes and their transcription. Here, we provide a statistical description of the functionality, expression status, structure and sequence of gRNA genes in a differentiation-competent, laboratory-adapted strain of T. brucei We obtain a clearer definition of what is a gRNA gene. Our analysis supports the idea that many, if not all, cassettes without an identifiable gRNA gene contain decaying remnants of once functional gRNA genes. Finally, we report several new, unexplained discoveries such as the association between cassette position on the minicircle and gene expression and functionality, and the association between gene initiation sequence and anchor position.

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URL الوصول: https://explore.openaire.eu/search/publication?articleId=od______3094::7033a093b2f603ec254342d9dcb88f66
https://hdl.handle.net/20.500.11820/50b566c1-3bda-49f8-96e5-6380efe5da58

المؤلفون: Savill, Nick, Schnaufer, Achim, Cooper, Sinclair, Wadsworth, Elizabeth

الوصف: Trypanosoma brucei EATRO1125 AnTat1.1 assembled and annotated minicircle genome

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e7dc4fc79c12a40b0c17a9f3bd4f44d

المؤلفون: Dewar, Caroline E., MacGregor, Paula, Cooper, Sinclair, Gould, Matthew K., Matthews, Keith R., Savill, Nicholas J., Schnaufer, Achim

المساهمون: Dewar, Caroline E [0000-0002-0107-6985], MacGregor, Paula [0000-0003-0919-3745], Cooper, Sinclair [0000-0002-0371-1591], Savill, Nicholas J [0000-0002-9769-6168], Schnaufer, Achim [0000-0003-2132-5560], Apollo - University of Cambridge Repository

المصدر: Dewar, C E, MacGregor, P, Cooper, S, Gould, M K, Matthews, K R, Savill, N J & Schnaufer, A 2018, ' Mitochondrial DNA is critical for longevity and metabolism of transmission stage Trypanosoma brucei ', PLoS Pathogens, vol. 14, no. 7, pp. e1007195 . https://doi.org/10.1371/journal.ppat.1007195
PLoS Pathogens, Vol 14, Iss 7, p e1007195 (2018)
PLoS Pathogens

مصطلحات موضوعية: Life Cycles, Trypanosoma, Azides, QH301-705.5, Parasitic Life Cycles, Trypanosoma brucei gambiense, Trypanosoma brucei brucei, Bioenergetics, Biochemistry, Parasitic Cell Cycles, DNA, Mitochondrial, Host-Parasite Interactions, Mice, Parasitic cell cycles, parasitic diseases, Medicine and Health Sciences, Parasitic Diseases, Trypanosoma Brucei, Animals, Biology (General), Energy-Producing Organelles, Protozoans, DNA, Kinetoplast, Organisms, Chemical Compounds, Biology and Life Sciences, Eukaryota, Cell Differentiation, Cell Biology, RC581-607, Parasitic diseases, Parasitic Protozoans, Mitochondria, mitochondria, Chemistry, Kinetoplasts, Trypanosomiasis, African, Physical Sciences, Parasitology, Cellular Structures and Organelles, Immunologic diseases. Allergy, Research Article, Developmental Biology, Trypanosoma Brucei Gambiense

الوصف: The sleeping sickness parasite Trypanosoma brucei has a complex life cycle, alternating between a mammalian host and the tsetse fly vector. A tightly controlled developmental programme ensures parasite transmission between hosts as well as survival within them and involves strict regulation of mitochondrial activities. In the glucose-rich bloodstream, the replicative ‘slender’ stage is thought to produce ATP exclusively via glycolysis and uses the mitochondrial F1FO-ATP synthase as an ATP hydrolysis-driven proton pump to generate the mitochondrial membrane potential (ΔΨm). The ‘procyclic’ stage in the glucose-poor tsetse midgut depends on mitochondrial catabolism of amino acids for energy production, which involves oxidative phosphorylation with ATP production via the F1FO-ATP synthase. Both modes of the F1FO enzyme critically depend on FO subunit a, which is encoded in the parasite’s mitochondrial DNA (kinetoplast or kDNA). Comparatively little is known about mitochondrial function and the role of kDNA in non-replicative ‘stumpy’ bloodstream forms, a developmental stage essential for disease transmission. Here we show that the L262P mutation in the nuclear-encoded F1 subunit γ that permits survival of ‘slender’ bloodstream forms lacking kDNA (‘akinetoplastic’ forms), via FO-independent generation of ΔΨm, also permits their differentiation into stumpy forms. However, these akinetoplastic stumpy cells lack a ΔΨm and have a reduced lifespan in vitro and in mice, which significantly alters the within-host dynamics of the parasite. We further show that generation of ΔΨm in stumpy parasites and their ability to use α-ketoglutarate to sustain viability depend on F1-ATPase activity. Surprisingly, however, loss of ΔΨm does not reduce stumpy life span. We conclude that the L262P γ subunit mutation does not enable FO-independent generation of ΔΨm in stumpy cells, most likely as a consequence of mitochondrial ATP production in these cells. In addition, kDNA-encoded genes other than FO subunit a are important for stumpy form viability.
Author summary African trypanosomes are single cellular eukaryotes transmitted by tsetse flies that cause important diseases in humans and their livestock. For survival these parasites depend on their mitochondrion, an organelle that has its own genome (‘mtDNA’) and that is traditionally viewed as the ‘power plant’ of cells, but that has other essential roles as well. Interfering with mtDNA is an important part of how some anti-trypanosomatid drugs work. Most mitochondrial research in trypanosomes in the past has focused on forms of the sleeping sickness parasite that proliferate in the mammalian bloodstream or in the insect midgut, as these can be readily cultured in the laboratory. As a consequence, relatively little is known about mitochondrial biology of the so-called ‘stumpy’ form, a non-replicative stage that is critical for transmission to tsetse flies. In this study we use a mouse infection model to show that a certain gene mutation permits formation of stumpy forms that lack mtDNA. However, without mtDNA these parasites have an altered mitochondrial metabolism and a reduced life span, which tells us that stumpy forms depend on additional mtDNA-encoded genes that are not required by the proliferative bloodstream form.

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URL الوصول: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::cb3240bc3979bda79345ef6254b98a08
https://www.repository.cam.ac.uk/handle/1810/285590

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المؤلفون: Cooper Sinclair, Matthew Walliser, Jennifer Holmes, Jolene Northey, Luke Boechler, Robyn Despins, Jason Perepelkin

المصدر: Canadian Pharmacists Journal / Revue des Pharmaciens du Canada. 148:138-141

مصطلحات موضوعية: Professional services, business.industry, Pharmacist, Pharmaceutical Science, Pharmacy, Public relations, Nonverbal communication, Grassroots, Research and Clinical, Nursing, Health care, Medicine, Professional association, Strategic communication, business

الوصف: Pharmacists are moving from traditional and technical dispensing roles to professional and clinical patient-centred services. They have shown that these new professional services have an essential and positive effect on patient outcomes. However, we must advocate for and promote these new services to 4 key groups—pharmacists, other health care professionals, patients and the community—or what is the point? This advocacy must begin at the grassroots, with the individual pharmacist, rather than relying solely on our professional organizations. It begins with the pharmacist eliminating the mystery of “behind the counter.” Both verbal patient interaction tips and nonverbal strategic communication tools can be developed and used to aid in this venture. We invite all pharmacists across Canada to take ownership of their evolving profession and to share ideas and collaborate with their colleagues. ■

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::084a1eae89b6186065ddd0c0a30b05c9
https://doi.org/10.1177/1715163515577693

المؤلفون: Cooper, Sinclair

المساهمون: Savill, Nick, Schnaufer, Achim, Biotechnology and Biological Sciences Research Council (BBSRC)

مصطلحات موضوعية: minicircles, RNA-editing, parasitic diseases, mitochondrion, trypanosomatids, kinetoplast, Trypanosoma brucei

الوصف: The mitochondrial genome (kinetoplast or kDNA) of Trypanosoma brucei is highly complex in terms of structure, content and function. It is composed of two types of molecules: 10-50 copies of identical ~23-kb maxicircles and 5,000-10,000 highly heterogeneous 1-kb minicircles. Maxicircles and minicircles form a concatenated network that resembles chainmail. Maxicircles are the equivalent of mitochondrial DNA in other eukaryotes, but 12 out of the 18 protein-coding genes encoded on the maxicircle require post-transcriptional RNA editing by uridylate insertion and removal before a functional mRNA can be generated. The 1-kb minicircles make up the bulk of the kDNA content and facilitate the editing of the maxicircle-encoded mRNAs by encoding short guide RNAs (gRNAs) that are complementary to blocks of edited sequence. It is estimated that there are at least hundred classes of minicircle, each class encoding a different set of gRNAs. At each cycle of cell division the contents of the kDNA genome must be faithfully copied and segregated into the daughter cells. Mathematical modelling of kDNA replication has shown that failure to segregate evenly will eventually result in loss of low copy number minicircle classes from the population. Depending on the type of minicircle that is lost this can result in immediate parasite death or, if the loss occurred in the bloodstream stage, render the cells unable to complete the canonical life-cycle in the tsetse fly vector. In order to investigate minicircle complexity and replication in T. brucei further we i) first established the true complexity of the kDNA genome using a Illumina short read sequencing and a bespoke assembly pipeline, ii) annotated the minicircles to establish the editing capacity of the cells, iii) analysed expression levels of predicted gRNA gene cassettes using small RNA data, and iv) carried out a long term time course to measure how kDNA complexity changes over time and compared this to preliminary model predictions. The structure of this thesis follows these steps. Using these approaches, 365 unique and complete minicircle sequences were assembled and annotated, representing 99% of the minicircle genome of the differentiation competent (i.e. transmission competent) T. brucei strain AnTat90.13. These minicircles encode 593 canonical gRNAs, defined as having a match in the known editing space, and a further 558 non-canonical gRNAs with unknown function. Transcriptome analysis showed that the non-canonical gRNAs, like the canonical set, have 3' U-tails and showed the same length distribution. Canonical and non-canonical sets differ, however, in their sense to anti-sense transcript ratios. In vitro culturing of bloodstream form T. brucei for ~500 generations resulted in loss of ~30 minicircle classes. After incorporating parameters for network size and minicircle diversity determined above, model fitting to longitudinal kDNA complexity data will provide estimations for the fidelity of kDNA segregation. The refined mathematical model for kDNA segregation will permit insight into time constraints for transmissibility during chronic infections due to progressive minicircle loss. It also has the potential to shed light on the selective pressures that may have led to the apparent co-evolution of the concatenated kDNA network structure and parasitism in kinetoplastids.

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URL الوصول: https://explore.openaire.eu/search/publication?articleId=od_______463::656b482411ad4989fddc4008b6a2aeb3
http://hdl.handle.net/1842/28819