| 1. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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In: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Research review (peer-reviewed)abstract
- Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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| 2. |
- Fagman, Henrik, 1975, et al.
(author)
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Morphogenetics of early thyroid development.
- 2010
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In: Journal of molecular endocrinology. - 1479-6813.
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Research review (peer-reviewed)abstract
- The thyroid develops from the foregut endoderm. Yet uncharacterized inductive signals specify endoderm progenitors to a thyroid cell fate that assemble in the pharyngeal floor from which the primordium buds and migrates to the final position of the gland. The morphogenetic process is regulated by both cell-autonomous (activated by e.g. Nkx2-1, Foxe1, Pax8 and Hhex) and mesoderm-derived (mediated by e.g. Tbx1 and Fgf) mechanisms acting in concert to promote growth and survival of progenitor cells. The developmental role of thyroid-stimulating hormone is limited to thyroid differentiation set to work after the gross anatomy of the gland is already sculptured. This review summarizes recent advances on the molecular genetics of thyroid morphogenesis put into context of endoderm developmental traits and highlights established and potentially novel mechanisms of thyroid dysgenesis of relevance to congenital hypothyroidism in man.
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| 3. |
- Tavella, T A, et al.
(author)
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Yeast-based high-throughput screens for discovery of kinase inhibitors for neglected diseases.
- 2021
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In: Advances in Protein Chemistry and Structural Biology. - : Elsevier. - 1876-1631. ; 124, s. 275-309
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Research review (peer-reviewed)abstract
- The discovery and development of a new drug is a complex, time consuming and costly process that typically takes over 10 years and costs around 1 billion dollars from bench to market. This scenario makes the discovery of novel drugs targeting neglected tropical diseases (NTDs), which afflict in particular people in low-income countries, prohibitive. Despite the intensive use of High-Throughput Screening (HTS) in the past decades, the speed with which new drugs come to the market has remained constant, generating doubts about the efficacy of this approach. Here we review a few of the yeast-based high-throughput approaches that can work synergistically with parasite-based, in vitro, or in silico methods to identify and optimize novel antiparasitic compounds. These yeast-based methods range from HTP screens to identify novel hits against promising parasite kinase targets to the identification of potential antiparasitic kinase inhibitors extracted from databases of yeast chemical genetic screens.
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| 4. |
- Sattar, Muhammad Naeem, et al.
(author)
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Cotton leaf curl disease - an emerging threat to cotton production worldwide
- 2013
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In: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 94, s. 695-710
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Research review (peer-reviewed)abstract
- Cotton leaf curl disease (CLCuD) is a serious disease of cotton which has characteristic symptoms, the most unusual of which is the formation of leaf-like enations on the undersides of leaves. The disease is caused by whitefly-transmitted geminiviruses (family Geminiviridae, genus Begomovirus) in association with specific, symptom-modulating satellites (betasatellites) and an evolutionarily distinct group of satellite-like molecules known as alphasatellites. CLCuD occurs across Africa as well as in Pakistan and north-western India. Over the past 25 years, Pakistan and India have experienced two epidemics of the disease, the most recent of which involved a virus and satellite that are resistance breaking. Loss of this conventional host-plant resistance, which saved the cotton growers from ruin in the late 1990s, leaves farmers with only relatively poor host plant tolerance to counter the extensive losses the disease causes. There has always been the fear that CLCuD could spread from the relatively limited geographical range it encompasses at present to other cotton-growing areas of the world where, although the disease is not present, the environmental conditions are suitable for its establishment and the whitefly vector occurs. Unfortunately recent events have shown this fear to be well founded, with CLCuD making its first appearance in China. Here, we outline recent advances made in understanding the molecular biology of the components of the disease complex, their interactions with host plants, as well as efforts being made to control CLCuD.
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| 5. |
- Guerra, Lina, et al.
(author)
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The biology of the cytolethal distending toxins
- 2011
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In: Toxins. - : MDPI. - 2072-6651. ; 3:3, s. 172-190
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Research review (peer-reviewed)abstract
- The cytolethal distending toxins (CDTs), produced by a variety of Gram-negative pathogenic bacteria, are the first bacterial genotoxins described, since they cause DNA damage in the target cells. CDT is an A-B(2) toxin, where the CdtA and CdtC subunits are required to mediate the binding on the surface of the target cells, allowing internalization of the active CdtB subunit, which is functionally homologous to the mammalian deoxyribonuclease I. The nature of the surface receptor is still poorly characterized, however binding of CDT requires intact lipid rafts, and its internalization occurs via dynamin-dependent endocytosis. The toxin is retrograde transported through the Golgi complex and the endoplasmic reticulum, and subsequently translocated into the nuclear compartment, where it exerts the toxic activity. Cellular intoxication induces DNA damage and activation of the DNA damage responses, which results in arrest of the target cells in the G1 and/or G2 phases of the cell cycle and activation of DNA repair mechanisms. Cells that fail to repair the damage will senesce or undergo apoptosis. This review will focus on the well-characterized aspects of the CDT biology and discuss the questions that still remain unanswered.
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| 6. |
- Radecka, Dorota, et al.
(author)
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Looking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation
- 2015
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In: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 15:6
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Research review (peer-reviewed)abstract
- Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiaerecombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii(osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha(thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).
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| 7. |
- Richter-Boix, Alexander, et al.
(author)
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Fine-grained adaptive divergence in an amphibian : genetic basis of phenotypic divergence and the role of nonrandom gene flow in restricting effective migration among wetlands
- 2013
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 22:5, s. 1322-1340
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Research review (peer-reviewed)abstract
- Adaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High gene flow, on the other hand, is expected to homogenize genetic variation among populations and therefore prevent local adaptation. Understanding how local adaptation can persist at the spatial scale at which gene flow occurs has remained an elusive goal, especially for wild vertebrate populations. Here, we explore the roles of natural selection and nonrandom gene flow (isolation by breeding time and habitat choice) in restricting effective migration among local populations and promoting generalized genetic barriers to neutral gene flow. We examined these processes in a network of 17 breeding ponds of the moor frog Rana arvalis, by combining environmental field data, a common garden experiment and data on variation in neutral microsatellite loci and in a thyroid hormone receptor (TR) gene putatively under selection. We illustrate the connection between genotype, phenotype and habitat variation and demonstrate that the strong differences in larval life history traits observed in the common garden experiment can result from adaptation to local pond characteristics. Remarkably, we found that haplotype variation in the TR gene contributes to variation in larval development time and growth rate, indicating that polymorphism in the TR gene is linked with the phenotypic variation among the environments. Genetic distance in neutral markers was correlated with differences in breeding time and environmental differences among the ponds, but not with geographical distance. These results demonstrate that while our study area did not exceed the scale of gene flow, ecological barriers constrained gene flow among contrasting habitats. Our results highlight the roles of strong selection and nonrandom gene flow created by phenological variation and, possibly, habitat preferences, which together maintain genetic and phenotypic divergence at a fine-grained spatial scale.
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| 8. |
- Berdan, Emma L, 1983, et al.
(author)
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How chromosomal inversions reorient the evolutionary process
- 2023
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In: Journal of Evolutionary Biology. - 1010-061X .- 1420-9101. ; 36:12, s. 1761-1782
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Research review (peer-reviewed)abstract
- Inversions are structural mutations that reverse the sequence of a chromosome seg-ment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as spe-ciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given re-cent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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| 9. |
- Vargas, Alexander O, et al.
(author)
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An Epigenetic Perspective on the Midwife Toad Experiments of Paul Kammerer (1880-1926)
- 2017
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In: Journal of Experimental Zoology Part B. - : John Wiley & Sons. - 1552-5007 .- 1552-5015. ; 328:1-2, s. 179-192
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Research review (peer-reviewed)abstract
- Paul Kammerer was the most outstanding neo-Lamarckian experimentalist of the early 20th century. He reported spectacular results in the midwife toad, including crosses of environmentally modified toads with normal toads, where acquired traits were inherited in Mendelian fashion. Accusations of fraud generated a great scandal, ending with Kammerer's suicide. Controversy reignited in the 1970s, when journalist Arthur Koestler argued against these accusations. Since then, others have argued that Kammerer's results, even if real, were not groundbreaking and could be explained by somatic plasticity, inadvertent selection, or conventional genetics. More recently, epigenetics has uncovered mechanisms by which inheritance can respond directly to environmental change, inviting a reanalysis of Kammerer's descriptions. Previous arguments for mere somatic plasticity have ignored the description of experiments showing heritable germ line modification. Alleged inadvertent selection associated with egg mortality can be discarded, since mortality decreased in a single generation, upon repeated exposures. The challenging implications did not escape the attention of Kammerer's noted contemporary, William Bateson, but he reacted with disbelief, thus encouraging fraud accusations. Nowadays, formerly puzzling phenomena can be explained by epigenetic mechanisms. Importantly, Kammerer described parent-of-origin effects, an effect of parental sex on dominance. Epigenetic mechanisms underlie these effects in genomic imprinting and experiments of transgenerational epigenetic inheritance. In the early 20th century, researchers had no reason to link them with the inheritance of acquired traits. Thus, the parent-of-origin effects in Kammerer's experiments specifically suggest authenticity. Ultimate proof should come from renewed experimentation. To encourage further research, we present a model of possible epigenetic mechanisms.
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| 10. |
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