| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Otto, Thomas D., et al.
(author)
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A comprehensive evaluation of rodent malaria parasite genomes and gene expression
- 2014
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In: BMC Biology. - : BioMed Central. - 1741-7007. ; 12
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Journal article (peer-reviewed)abstract
- BACKGROUND: Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.RESULTS: We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.CONCLUSIONS: Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
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| 4. |
- Mikkelsen, Tarjei S, et al.
(author)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Journal article (peer-reviewed)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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| 5. |
- Russell, Andrew J.C., et al.
(author)
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Regulators of male and female sexual development are critical for the transmission of a malaria parasite
- 2023
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In: Cell Host and Microbe. - : Cell Press. - 1931-3128 .- 1934-6069. ; 31:2, s. 305-319.e10
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Journal article (peer-reviewed)abstract
- Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of ten mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in the determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain as well as the protein interactors of a female-determining zinc-finger protein indicate that germ-granule-like ribonucleoprotein complexes complement transcriptional processes in the regulation of both male and female development of a malaria parasite.
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| 6. |
- Clegg, Simon L., et al.
(author)
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Chemical speciation models based upon the Pitzer activity coefficient equations, including the propagation of uncertainties. II. Tris buffers in artificial seawater at 25 °C, and an assessment of the seawater ‘Total’ pH scale
- 2022
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In: Marine Chemistry. - : Elsevier BV. - 0304-4203. ; 244
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Journal article (peer-reviewed)abstract
- The substance Tris (or THAM, 2-amino-2-hydroxymethyl-1,3-propanediol, CAS 77–86-1), and its protonated form TrisH+, is used in the preparation of pH buffer solutions for applications in seawater chemistry. The development of an acid-base chemical speciation model of buffer solutions containing Tris, TrisH+, and the major ions of seawater is desirable so that: (i) the effects of changes in the composition of the medium on pH can be calculated; (ii) pH on the free (a measure of [H+]) and total (a measure of ([H+] + [HSO4−])) scales can be interconverted; (iii) approximations inherent in the definition of the total pH scale can be quantified; (iv) electrode pairs such as H+/Cl− and H+/Na+ can more easily be calibrated for the measurement of pH. As a first step towards these goals we have extended the Pitzer-based speciation model of Waters and Millero (Mar. Chem. 149, 8–22, 2013) for artificial seawater to include Tris and TrisH+, at 25 °C. Estimates of the variances and covariances of the additional interaction parameters were obtained by Monte Carlo simulation. This enables the total uncertainty of any model-calculated quantity (e.g., pH, speciation) to be estimated, as well as the individual contributions of all interaction parameters and equilibrium constants. This is important for model development, because it allows the key interactions to be identified. The model was tested against measured EMFs of cells containing Tris buffer in artificial seawater at 25 °C, and the mean deviation was found to be 0.13 ± 0.070 mV for salinities 20 to 40. Total variances for calculated electromotive forces of the buffer solutions are dominated by contributions from just a few interaction parameters, making it likely that the model can readily be improved. The model was used to quantify the difference between various definitions of total pH and –log10([H+] + [HSO4−]) in Tris buffer solutions at 25 °C, for the first time (item (iii) above). The results suggest that the total pH scale can readily be extended to low salinities using the established approach for substituting TrisH+ for Na+ in the buffer solutions, especially if the speciation model is used to quantify the effect on pH of the substitution. The relationships between electromotive force (EMF), and pH on the total scale, with buffer molality in artificial seawater at constant salinity are shown to be linear above about 0.01 to 0.02 mol kg−1 buffer molality. The pH of Tris buffers containing ratios of TrisH+ to Tris that vary from unity can be calculated very simply. Technical aspects of the total pH scale, such as the extrapolation of pH to zero buffer (at constant salinity), are clarified. Recommendations are made for further work to extend the model to the temperature range 0–45 °C, and improve accuracy, so that requirements (i) to (iv) above can be fully met.
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| 7. |
- Humphreys, Matthew P., et al.
(author)
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Chemical speciation models based upon the Pitzer activity coefficient equations, including the propagation of uncertainties: Artificial seawater from 0 to 45 °C
- 2022
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In: Marine Chemistry. - : Elsevier BV. - 0304-4203. ; 244
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Journal article (peer-reviewed)abstract
- Accurate chemical speciation models of solutions containing the ions of seawater have applications in the calculation of carbonate system equilibria and trace metal speciation in natural waters, and the determination of pH. Existing models, based on the Pitzer formalism for the calculation of activity coefficients, do not yet agree with key experimental data (potentiometric determinations of H+ and Cl− activity products in acidified artificial seawaters) and, critically, do not include uncertainty estimates. This hampers applications of the models, and also their further development (for which the uncertainty contributions of individual ion interactions and equilibrium constants need to be known). We have therefore implemented the models of Waters and Millero (Mar. Chem. 149, 8-22, 2013) and Clegg and Whitfield (Geochim. et Cosmochim. Acta 59, 2403-2421, 1995) for artificial seawater, within a generalised treatment of uncertainties, as a first step towards a more complete model of standard seawater and pH buffers. This addition to the models enables both the total uncertainty of any model-calculated quantity (e.g., pH, speciation) to be estimated, and also the contributions of all interaction parameters and equilibrium constants. Both models have been fully documented (and some corrections made). Estimates of the variances and covariances of the interaction parameters were obtained by Monte Carlo simulation, with simplifying assumptions. The models were tested against measured electromotive forces (EMFs) of cells containing acidified artificial seawaters. The mean offsets (measured – calculated) at 25 °C for the model of Waters and Millero are: 0.046 ± 0.11 mV (artificial seawater without sulphate, 0.280 mol kg−1 to 0.879 mol kg−1 ionic strength); and −0.199 ± 0.070 mV (artificial seawater, salinities 5 to 45). Results are similar at other temperatures. These differences compare with an overall uncertainty in the measured EMFs of about 0.04 mV. Total uncertainties for calculated EMFs of the solutions were dominated by just a few contributions: mainly H+-Cl−, Na+-Cl−, and H+-Na+-Cl− ionic interactions, and the thermodynamic dissociation constant of HSO4−. This makes it likely that the accuracy of the models can readily be improved, and recommendations for further work are made. It is shown that standard EMFs used in the calibration of the marine ‘total’ pH scale can be accurately predicted with only slight modification to the original models, suggesting that they can contribute to the extension of the scale to lower salinities.
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| 8. |
- Kent, Robyn S, et al.
(author)
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Inducible developmental reprogramming redefines commitment to sexual development in the malaria parasite Plasmodium berghei
- 2018
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In: Nature Microbiology. - : Nature Publishing Group. - 2058-5276. ; 3:11, s. 1206-1213
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Journal article (peer-reviewed)abstract
- During malaria infection, Plasmodium spp. parasites cyclically invade red blood cells and can follow two different developmental pathways. They can either replicate asexually to sustain the infection, or differentiate into gametocytes, the sexual stage that can be taken up by mosquitoes, ultimately leading to disease transmission. Despite its importance for malaria control, the process of gametocytogenesis remains poorly understood, partially due to the difficulty of generating high numbers of sexually committed parasites in laboratory conditions1. Recently, an apicomplexa-specific transcription factor (AP2-G) was identified as necessary for gametocyte production in multiple Plasmodium species2,3, and suggested to be an epigenetically regulated master switch that initiates gametocytogenesis4,5. Here we show that in a rodent malaria parasite, Plasmodium berghei, conditional overexpression of AP2-G can be used to synchronously convert the great majority of the population into fertile gametocytes. This discovery allowed us to redefine the time frame of sexual commitment, identify a number of putative AP2-G targets and chart the sequence of transcriptional changes through gametocyte development, including the observation that gender-specific transcription occurred within 6 h of induction. These data provide entry points for further detailed characterization of the key process required for malaria transmission.
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| 9. |
- Moon, Robert W, et al.
(author)
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A cyclic GMP signalling module that regulates gliding motility in a malaria parasite
- 2009
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In: PLoS Pathogens. - : Public Library of Science. - 1553-7366 .- 1553-7374. ; 5:9
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Journal article (peer-reviewed)abstract
- The ookinete is a motile stage in the malaria life cycle which forms in the mosquito blood meal from the zygote. Ookinetes use an acto-myosin motor to glide towards and penetrate the midgut wall to establish infection in the vector. The regulation of gliding motility is poorly understood. Through genetic interaction studies we here describe a signalling module that identifies guanosine 3', 5'-cyclic monophosphate (cGMP) as an important second messenger regulating ookinete differentiation and motility. In ookinetes lacking the cyclic nucleotide degrading phosphodiesterase delta (PDEdelta), unregulated signalling through cGMP results in rounding up of the normally banana-shaped cells. This phenotype is suppressed in a double mutant additionally lacking guanylyl cyclase beta (GCbeta), showing that in ookinetes GCbeta is an important source for cGMP, and that PDEdelta is the relevant cGMP degrading enzyme. Inhibition of the cGMP-dependent protein kinase, PKG, blocks gliding, whereas enhanced signalling through cGMP restores normal gliding speed in a mutant lacking calcium dependent protein kinase 3, suggesting at least a partial overlap between calcium and cGMP dependent pathways. These data demonstrate an important function for signalling through cGMP, and most likely PKG, in dynamically regulating ookinete gliding during the transmission of malaria to the mosquito.
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| 10. |
- Raghavan, Maanasa, et al.
(author)
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Genomic evidence for the Pleistocene and recent population history of Native Americans
- 2015
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6250
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Journal article (peer-reviewed)abstract
- Howand when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericues and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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| 11. |
- Sinha, Abhinav, et al.
(author)
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A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
- 2014
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In: Nature. - : Macmillan Publishers Ltd.. - 0028-0836 .- 1476-4687. ; 507:7491, s. 253-257
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Journal article (peer-reviewed)abstract
- Commitment to and completion of sexual development are essential for malaria parasites (protists of the genus Plasmodium) to be transmitted through mosquitoes. The molecular mechanism(s) responsible for commitment have been hitherto unknown. Here we show that PbAP2-G, a conserved member of the apicomplexan AP2 (ApiAP2) family of DNA-binding proteins, is essential for the commitment of asexually replicating forms to sexual development in Plasmodium berghei, a malaria parasite of rodents. PbAP2-G was identified from mutations in its encoding gene, PBANKA_143750, which account for the loss of sexual development frequently observed in parasites transmitted artificially by blood passage. Systematic gene deletion of conserved ApiAP2 genes in Plasmodium confirmed the role of PbAP2-G and revealed a second ApiAP2 member (PBANKA_103430, here termed PbAP2-G2) that significantly modulates but does not abolish gametocytogenesis, indicating that a cascade of ApiAP2 proteins are involved in commitment to the production and maturation of gametocytes. The data suggest a mechanism of commitment to gametocytogenesis in Plasmodium consistent with a positive feedback loop involving PbAP2-G that could be exploited to prevent the transmission of this pernicious parasite.
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| 12. |
- Steffen, Will, et al.
(author)
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Stratigraphic and Earth System approaches to defining the Anthropocene
- 2016
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In: Earth's Future. - 2328-4277. ; 4:8, s. 324-345
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Research review (peer-reviewed)abstract
- Stratigraphy provides insights into the evolution and dynamics of the Earth System over its long history. With recent developments in Earth System science, changes in Earth System dynamics can now be observed directly and projected into the near future. An integration of the two approaches provides powerful insights into the nature and significance of contemporary changes to Earth. From both perspectives, the Earth has been pushed out of the Holocene Epoch by human activities, with the mid-20th century a strong candidate for the start date of the Anthropocene, the proposed new epoch in Earth history. Here we explore two contrasting scenarios for the future of the Anthropocene, recognizing that the Earth System has already undergone a substantial transition away from the Holocene state. A rapid shift of societies toward the UN Sustainable Development Goals could stabilize the Earth System in a state with more intense interglacial conditions than in the late Quaternary climate regime and with little further biospheric change. In contrast, a continuation of the present Anthropocene trajectory of growing human pressures will likely lead to biotic impoverishment and a much warmer climate with a significant loss of polar ice.
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