Relevant bibliographies by topics / Variation (biology)

Academic literature on the topic 'Variation (biology)'

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Published: 4 June 2021
Last updated: 30 July 2024

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Journal articles on the topic "Variation (biology)"

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Antia, Bassey E., and Richard A. Kamai. "Writing biology, assessing biology." Terminology 22, no. 2 (December 31, 2016): 201–22. http://dx.doi.org/10.1075/term.22.2.03ant.

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There has been substantial research into terminology as an issue in learning science, especially against the backdrop of concerns over school literacy in science and as sometimes reflected in the poor performance of high school students in assessment tasks. Relevant research has emphasized issues such as lexical load, complexity and metaphor. Variation in the use of terminology has, however, been relatively under researched, although there is evidence that terminology use does vary within and across high school textbooks of science. Drawing on an eclectic theoretical framework comprising transitivity analysis (Halliday 1994), legitimation code theory semantics (Maton 2013a), and the context-specific term model (Gerzymisch-Arbogast 2008), this article identifies and classifies variations in the terminology employed in three high school textbooks of biology in Nigeria. It then determines what impact assessment tasks which use terms that differ from those employed in students’ study materials have on students. Examples are found of variant terminology impeding science literacy and task performance, even though there is reason to suspect such variation might in fact have been leveraged to enhance cognition.
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Przytycka, Teresa M. "Phenotypic variation meets systems biology." Genome Biology 10, no. 8 (2009): 313. http://dx.doi.org/10.1186/gb-2009-10-8-313.

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Thompson, R. C. A., and A. J. Lymbery. "Echinococcus: Biology and strain variation." International Journal for Parasitology 20, no. 4 (July 1990): 457–70. http://dx.doi.org/10.1016/0020-7519(90)90193-q.

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Montévil, Maël, Matteo Mossio, Arnaud Pocheville, and Giuseppe Longo. "Theoretical principles for biology: Variation." Progress in Biophysics and Molecular Biology 122, no. 1 (October 2016): 36–50. http://dx.doi.org/10.1016/j.pbiomolbio.2016.08.005.

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Donelson, J. E., and A. C. Rice-Ficht. "Molecular biology of trypanosome antigenic variation." Microbiological Reviews 49, no. 2 (1985): 107–25. http://dx.doi.org/10.1128/mmbr.49.2.107-125.1985.

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Donelson, J. E., and A. C. Rice-Ficht. "Molecular biology of trypanosome antigenic variation." Microbiological Reviews 49, no. 2 (1985): 107–25. http://dx.doi.org/10.1128/mr.49.2.107-125.1985.

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Safran, Rebecca J., and Mark E. Hauber. "Evolutionary Biology: Variation Isn't Always Sexy." Current Biology 17, no. 10 (May 2007): R368—R370. http://dx.doi.org/10.1016/j.cub.2007.03.041.

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Furmaga, Jacek, Marek Kowalczyk, Tomasz Zapolski, Olga Furmaga, Leszek Krakowski, Grzegorz Rudzki, Andrzej Jaroszyński, and Andrzej Jakubczak. "BK Polyomavirus—Biology, Genomic Variation and Diagnosis." Viruses 13, no. 8 (July 30, 2021): 1502. http://dx.doi.org/10.3390/v13081502.

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The BK polyomavirus (BKPyV), a representative of the family Polyomaviridae, is widespread in the human population. While the virus does not cause significant clinical symptoms in immunocompetent individuals, it is activated in cases of immune deficiency, both pharmacological and pathological. Infection with the BKPyV is of particular importance in recipients of kidney transplants or HSC transplantation, in which it can lead to the loss of the transplanted kidney or to haemorrhagic cystitis, respectively. Four main genotypes of the virus are distinguished on the basis of molecular differentiation. The most common genotype worldwide is genotype I, with a frequency of about 80%, followed by genotype IV (about 15%), while genotypes II and III are isolated only sporadically. The distribution of the molecular variants of the virus is associated with the region of origin. BKPyV subtype Ia is most common in Africa, Ib-1 in Southeast Asia, and Ib-2 in Europe, while Ic is the most common variant in Northeast Asia. The development of molecular methods has enabled significant improvement not only in BKPyV diagnostics, but in monitoring the effectiveness of treatment as well. Amplification of viral DNA from urine by PCR (Polymerase Chain Reaction) and qPCR Quantitative Polymerase Chain Reaction) is a non-invasive method that can be used to confirm the presence of the genetic material of the virus and to determine the viral load. Sequencing techniques together with bioinformatics tools and databases can be used to determine variants of the virus, analyse their circulation in populations, identify relationships between them, and investigate the directions of evolution of the virus.
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Breslow, J. L. "Human Apolipoprotein Molecular Biology and Genetic Variation." Annual Review of Biochemistry 54, no. 1 (June 1985): 699–727. http://dx.doi.org/10.1146/annurev.bi.54.070185.003411.

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Lemaitre, H., V. S. Mattay, F. Sambataro, B. Verchinski, R. E. Straub, J. H. Callicott, R. Kittappa, et al. "Genetic Variation in FGF20 Modulates Hippocampal Biology." Journal of Neuroscience 30, no. 17 (April 28, 2010): 5992–97. http://dx.doi.org/10.1523/jneurosci.5773-09.2010.

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Dissertations / Theses on the topic "Variation (biology)"

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Franks, Alexander M. "Quantifying Sources of Variation in High-throughput Biology." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17463988.

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One of the central challenges in systems biology research is disentangling relevant and irrelevant sources of variation. While the relevant quantities are always context dependent, an important distinction can be drawn between variability due to biological processes and variability due measurement error. Biological variability includes variability between mRNA or protein abundances within a well defined condition, variability of these abundances across conditions (physiological variability), and between species or between subject variability. Technical variability includes measurement error, technological bias, and variability due to missing data. In this dissertation, we explore statistical challenges associated with disentangling sources of variability, both biological and technical, in the analysis of high-throughput biological data. In the first chapter, we present a careful meta-analysis of 27 yeast data sets supported by a multilevel model to separate biological variability from structured technical variability. In the second chapter, we suggest a simple and general approach for deconvolving the contributions of orthogonal sources of biological variability, both between and within molecules, across multiple physiological conditions. The results discussed in these two chapters elucidate the relative importance of transcriptional and post-transcriptional regulation of protein levels. Finally, in the third chapter we introduce a novel approach for modeling non-ignorable missing data. We illustrate the utility of this methodology on missing data in mRNA and protein measurements.
Statistics
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Herfindal, Ivar. "Life history consequences of environmental variation along ecological gradients in northern ungulates." Doctoral thesis, Norwegian University of Science and Technology, Department of Biology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-706.

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Temporal and spatial variation in the environment can influence the performance of individuals in wild ungulate populations. Of particular importance is an understanding of the mechanisms that shape variation in individual body mass, because several important life history traits are directly related to body mass. Body mass is one of the first traits that is influenced by environmental variation, and often the effect operates through variation in the components of the foraging niche of ungulates. In this thesis, I aim to demonstrate how measurements of environmental variation relate to variation in the foraging niche of ungulates. Furthermore, I aim to explore how variation in ungulate life history traits relates to these variables, and finally, how the management of ungulates could benefit from the incorporation of knowledge about the effects of environmental variation on population dynamics. I use weather observations, large-scale climate indices, and indices of environmental phenology based on satellite-derived vegetation indices (NDVI) to analyse the effect of environmental variation on plants and body mass in moose (Alces alces) and roe deer (Capreolus capreolus) populations.

The environmental variables that explained most of the variation in plant performance, measured as radial growth in common juniper (Juniper communis) also explained variation in ungulate body mass. These variables were related to conditions in spring and early summer. Plant growth was low in cold summers, and in spring where the green-up curve as measured by change in photosynthetic activity during spring was moderate. Such growing conditions are recognised to increase the quality of the plants as forage for ungulates. Consequently, moose body mass in autumn showed the opposite pattern than juniper to environmental conditions, indicating that quality of plants, rather than the quantity, is an important component in temperate ungulate foraging niche. Further, regional variation in moose body mass was associated with environmental variables related to forage quality. Roe deer body mass was associated with availability of forage during winter, and not with factors related to summer conditions. Factors related to forage quantity neither influenced temporal nor spatial variation in body mass in the two species.

Accordingly, it appears that both weather observations and satellite-derived vegetation indices are able to effectively predict variation in plant performance related to variation in foraging conditions for ungulates. The variation in forage quality in space and time created variation in body mass between populations and between cohorts within a population. Further, the variation in body mass between moose population, caused by variation in the foraging conditions, predicted how the populations differentially respond to the effects of environmental stochastisity. In populations with a high mean body mass, or a low density relative to plant biomass production, available resources buffered environmental stochastisity, and were less influenced by environmental variation than populations with relatively fewer resources available.

If wildlife managers fail to incorporate the effects of environmental variation on population performance, e.g. on the recruitment rate, the population may show unexpected and large fluctuations in size. Therefore, managers should attempt to incorporate knowledge of recent environmental conditions on the population when setting harvesting quotas.

In face of the large variation in environmental conditions experienced by the ungulate populations in Norway, and the fact that responses to environmental variation varies between populations, management should be regionally adapted, and aim to incorporate variation in vital rates caused by environmental conditions. This is likely to create more stable and predictable populations. In face of the predicted climate and landscape changes in Norwegian forests, environmental variables, e.g. from satellite-derived vegetation indices, have the potential to be a powerful tool for a sustainable management of ungulate populations. Consequently, such information should be incorporated into the management of ungulates in order to a) obtain a management of ungulate populations that is adapted to regional mechanisms of environmental variation, and b) acquire a management that is sustainable in face of future change in climate and landscape that may vary regionally. This calls for a regional differentiation in management strategies.

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Larsson, Jobs Karl. "Population Fragmentation and Genetic Variation in Grouse." Doctoral thesis, Uppsala University, Department of Ecology and Evolution, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6006.

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In this thesis the genetic variation of two grouse species, the Chinese grouse (Bonasa sewersowi) and the Black grouse (Tetrao tetrix) was examined with neutral genetic markers: microsatellites. Habitat fragmentation and isolation leads to structuring among and loss of genetic variation within populations.

The Chinese grouse in a small population in Lianhuasan nature reserve was found to have undergone a population bottleneck and as a result of isolation and possible inbreeding showed genetic impoverishment hereof.

The Black grouse populations in Europe face various different conditions from widely distributed areas of suitable habitat in the northern and eastern parts of its range to highly naturally and anthropogenically fragmented habitat landscapes in the west.

Structure among populations was found in Great Britain where Wales, Scotland and England showed characteristics of three different genetic entities, indicating very little or no geneflow between these populations.

The Dutch population showed signs of loss of genetic variation as to be expected from a population that has historically decreased in population size from several thousands to tens of individuals in a matter of decades. However the possibility to spot signs of a bottleneck was impaired due to the short time-window in which this can be observed in a population with such a low effective population size (NE).

The sampled populations in Europe clustered into five different groups of genetic identities. The different clusters were: Great Britain-, the Netherlands-, Fenno-Scandian-, Alpine- and lowland German-Austrian populations. The level of genetic variation when compared over all these different populations decreased as a sign of isolation and small NE. However it was not feasible to separate the impact of these two factors.

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Jacobs, Jerry Dale. "Regulation of life history strategies with individuals in predictable and unpredictable environments /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/5169.

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Allen, J. B. "Geographical variation and population biology in wild Theobroma cacao." Thesis, University of Edinburgh, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.384148.

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Davids, Wagied. "Causes of Substitution Frequency Variation in Pathogenic Bacteria." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4838.

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Barrera, Luis A. "Towards a Systematic Approach for Characterizing Regulatory Variation." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718710.

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A growing body of evidence suggests that genetic variants that alter gene expression are responsible for many phenotypic differences across individuals, particularly for the risk of developing common diseases. However, the molecular mechanisms that underlie the vast majority of associations between genetic variants and their phenotypes remain unknown. An important limiting factor is that genetic variants remain difficult to interpret, particularly in noncoding sequences. Developing truly systematic approaches for characterizing regulatory variants will require: (a) improved annotations for the genomic sequences that control gene expression, (b) a more complete understanding of the molecular mechanisms through which genetic variants, both coding and noncoding, can affect gene expression, and (c) better experimental tools for testing hypotheses about regulatory variants. In this dissertation, I present conceptual and methodological advances that directly contribute to each of these goals. A recurring theme in all of these developments is the statistical modeling of protein-DNA interactions and its integration with other data types. First, I describe enhancer-FACS-Seq, a high-throughput experimental approach for screening candidate enhancer sequences to test for in vivo, tissue-specific activity. Second, I present an integrative computational analysis of the in vivo binding of NF-kappaB, a key regulator of the immune system, yielding new insights into how genetic variants can affect NF-kappaB binding. Next, I describe the first comprehensive survey of coding variation in human transcription factors and what it reveals about additional sources of genetic variation that can affect gene expression. Finally, I present SIFTED, a statistical framework and web tool for the optimal design of TAL effectors, which have been used successfully in genome editing and can thus be used to test hypotheses about regulatory variants. Together, these developments help fulfill key needs in the quest to understand the molecular basis of human phenotypic variation.
Biophysics
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Benmerzouga, Imaan A. "REGULATION OF ANTIGENIC VARIATION IN TRYPANOSOMA BRUCEI." Cleveland State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=csu1376047183.

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Foulkes, Nicholas F. "Molecular biology of the human G 6-PD gene." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253009.

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Wilson, David Francis. "Purposive variation in recordkeeping in the academic molecular biology laboratory." Thesis, University of Glasgow, 2011. http://theses.gla.ac.uk/2482/.

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This thesis presents an investigation into the role played by laboratory records in the disciplinary discourse of academic molecular biology laboratories. The motivation behind this study stems from two areas of concern. Firstly, the laboratory record has received comparatively little attention as a linguistic genre in spite of its central role in the daily work of laboratory scientists. Secondly, laboratory records have become a focus for technologically driven change through the advent of computing systems that aim to support a transition away from the traditional paper-based approach towards electronic recordkeeping. Electronic recordkeeping raises the potential for increased sharing of laboratory records across laboratory communities. However, the uptake of electronic laboratory notebooks has been, and remains, markedly low in academic laboratories. The investigation employs a multi-perspective research framework combining ethnography, genre analysis, and reading protocol analysis in order to evaluate both the organizational practices and linguistic practices at work in laboratory recordkeeping, and to examine these practices from the viewpoints of both producers and consumers of laboratory records. Particular emphasis is placed on assessing variation in the practices used by different scientists when keeping laboratory records, and on assessing the types of articulation work used to achieve mutual intelligibility across laboratory members. The findings of this investigation indicate that the dominant viewpoint held by laboratory staff other than principal investigators conceptualized laboratory records as a personal resource rather than a community archive. Readers other than the original author relied almost exclusively on the recontextualization of selected information from laboratory records into ‘public genres’ such as laboratory talks, research articles, and progress reports as the preferred means of accessing the information held in the records. The consistent use of summarized forms of recording experimental data rendered most laboratory records as both unreliable and of limited usability in the records management sense that they did not form full and accurate descriptions that could support future organizational activities. These findings offer a counterpoint to other studies, notably a number of studies undertaken as part of technology developments for electronic recordkeeping, that report sharing of laboratory records or assume a ‘cyberbolic’ view of laboratory records as a shared resource.
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Books on the topic "Variation (biology)"

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Rosemary, Feasey, ed. Variation. Oxford: Ginn, 2001.

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Snedden, Robert. Variation in living things. Chicago, Ill: Raintree, 2012.

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Snedden, Robert. Variation in living things. Chicago, Ill: Raintree, 2012.

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Amaya, Julian A. Cervantes, and Miguel M. Franco Jimenez. Genetic diversity: New research. Hauppauge, N.Y: Nova Science Publisher's, Inc., 2011.

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Mielke, James H. Human biological variation. New York, NY: Oxford University Press, 2005.

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1958-, Weiner Michael P., Gabriel Stacey, and Stephens J. Claiborne, eds. Genetic variation: A laboratory manual. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press, 2007.

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Max, King. Species evolution: The role of chromosome change. Cambridge: Cambridge University Press, 1993.

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A, Mousseau Timothy, Sinervo Barry, and Endler John A. 1947-, eds. Adaptive genetic variation in the wild. New York: Oxford University Press, 2000.

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W, Konigsberg Lyle, and Relethford John, eds. Human biological variation. New York: Oxford University Press, 2006.

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Çalişkan, Mahmut. Analysis of genetic variation in animals. Rijeka, Croatia: InTech, 2012.

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Book chapters on the topic "Variation (biology)"

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Schmidt, Marco F. "Genomic Variation." In Chemical Biology, 49–65. Berlin, Heidelberg: Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-64412-6_6.

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Minkoff, Eli C., and Jennifer K. Hood-DeGrenier. "Human Variation." In Biology Trending, 235–74. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9781003391159-7.

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Walters, Kevin. "Epigenetic Variation." In Methods in Molecular Biology, 185–97. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-416-6_14.

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Antonovics, Janis, Norman C. Ellstrand, and Robert N. Brandon. "Genetic variation and environmental variation: expectations and experiments." In Plant Evolutionary Biology, 275–303. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-1207-6_11.

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Konigsberg, Lyle W. "Quantitative Variation and Genetics." In Human Biology, 143–73. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118108062.ch5.

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Sutton, Julian. "Life Cycles, Cell Division and Variation." In Biology, 181–98. London: Macmillan Education UK, 1998. http://dx.doi.org/10.1007/978-1-349-15201-8_11.

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Mitton, Jeffry B. "Physiological and Demographic Variation Associated With Allozyme Variation." In Isozymes in Plant Biology, 127–45. Dordrecht: Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-1840-5_7.

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Wain, Louise V., and Martin D. Tobin. "Copy Number Variation." In Methods in Molecular Biology, 167–83. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-416-6_13.

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Macé, Aurélien, Zoltán Kutalik, and Armand Valsesia. "Copy Number Variation." In Methods in Molecular Biology, 231–58. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7868-7_14.

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Crews, Douglas E., and Gillian H. Ice. "Aging, Senescence, and Human Variation." In Human Biology, 637–92. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118108062.ch13.

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Conference papers on the topic "Variation (biology)"

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Zare, Fatima, and Sheida Nabavi. "Copy Number Variation Detection Using Total Variation." In BCB '19: 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3307339.3342181.

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McNally, Ken. "Rice SNP-Seek database for gemic variation." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1053087.

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Beal, J. "Mathematical Foundations of Variation in Gene Expression." In IET/SynbiCITE Engineering Biology Conference. Institution of Engineering and Technology, 2016. http://dx.doi.org/10.1049/cp.2016.1228.

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BERWICK, ROBERT C. "INVARIANTS AND VARIATION IN BIOLOGY AND LANGUAGE EVOLUTION: EXTENDED ABSTRACT." In Proceedings of the 8th International Conference (EVOLANG8). WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814295222_0005.

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Arp, Jennifer. "Variation in C4 Photosynthetic Pathways over the Maize Life Cycle." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1050102.

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Cannataro, Mario. "Session details: Genomic variation." In BCB '21: 12th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3478666.

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Nabavi, Sheida. "Session details: Genomic variation." In BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2022. http://dx.doi.org/10.1145/3552480.

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Stuhrmann, H. B. "Neutron scattering in biology: from isotopic substitution to nuclear spin contrast variation." In Fifth International Conference on Applications of Nuclear Techniques: Neutrons in Research and Industry, edited by George Vourvopoulos. SPIE, 1997. http://dx.doi.org/10.1117/12.267880.

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Shamouilian, Michael, and Ivan Selesnick. "Total Variation Denoising for Optical Coherence Tomography." In 2019 IEEE Signal Processing in Medicine and Biology Symposium (SPMB). IEEE, 2019. http://dx.doi.org/10.1109/spmb47826.2019.9037832.

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Beverly, Daniel. "Spatial and temporal variation of whole plant conductivity and its influence on conifer transpiration." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1052920.

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Reports on the topic "Variation (biology)"

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Del Mauro, Diana, and William Fischer. Vaccines and Viral Variation Will Fischer LANL Theoretical Biology. Office of Scientific and Technical Information (OSTI), February 2021. http://dx.doi.org/10.2172/1766971.

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Grumet, R., J. Burger, Y. Tadmor, A. Gur, C. Barry, A. Schäffer, and M. Petreikov. Cucumis fruit surface biology: Genetic analysis of fruit exocarp features in melon (C. melo) and cucumber (C. sativus). Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134155.bard.

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The fruit surface (exocarp) is a unique tissue with multiple roles influencing fruit growth and development, disease susceptibility, crop yield, post-harvest treatments, shipping and storage quality, and food safety. Furthermore, highly visible exocarp traits are the consumer's first exposure to the fruit, serving to identify fruit type, variety, attractiveness, and market value. Cucurbit fruit, including the closely related Cucumis species, melon (C. melo) and cucumber (C. sativus), exhibit tremendous diversity for fruit surface properties that are not present in model species. In this project, we identified genetic factors influencing Cucumis fruit surface morphology with respect to important quality determinants such as exocarp and flesh color, cuticle deposition, and surface netting. We employed a combination of approaches including: genome-wide association studies (GWAS) utilizing an extensive melon population and the U.S. Plant Introduction (PI) collection for cucumber to identify genomic regions associated with natural variation in fruit surface traits; bulked segregant RNA-seq (BSR-seq) analysis of bi-parental F2:3 or RIL (recombinant inbred line) populations to genomic regions and candidate genes segregating for fruit surface traits; and comparison of syntenic genomic regions and identification of homologous candidate genes. Candidate genes were examined for sequence and/or expression differences during fruit development that correspond with phenotypic differences. Primary outcomes of the work included identification of candidate genes influencing cuticle deposition, epidermal cell structure, surface netting, and intensity of rind and flesh color. Parallel studies identified mutations within the cucumber and melon homologs of the transcription factor WIN1 (WAX INDUCER1) as a significant factor influencing these surface properties. Additional QTL (quantitative trait loci) were identified in both species, and candidate genes in melon include a novel beta-glucosidase involved in lignin production and an integral membrane protein potentially involved in cuticle metabolism. Genetic resources and biochemical approaches have been developed to study cuticle and wax deposition in both species: segregating populations of melon were developed and sequenced for bulked segregant analysis and samples collected for metabolic analysis; an isolation procedure was developed for lipid droplets from cucumber peel and metabolomic analyses have been initiated. Genetic studies in melon identified mutations in a candidate gene (APRR2), associated with light immature rind, and further indicated that this gene is also associated with color intensity of both mature rinds and flesh, making it a good target for breeding. GWAS studies utilizing the cucumber core diversity population are being performed to identify additional sources of variation for fruit surface properties, map QTL, and examine for synteny with melon. Collectively these studies identified genetic regions associated with important quality traits and contributed to our understanding of underlying biological processes associated with fruit surface development. Knowledge of genetic control of these characteristics can facilitate more efficient breeding for important fruit surface traits.
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Bloch, G., and H. S. Woodard. regulation of size related division of labor in a key pollinator and its impact on crop pollination efficacy. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134168.bard.

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Despite the rapid increase in reliance on bumble bees for food production and security, there are many critical knowledge gaps in our understanding of bumble bee biology that limit their colony production, commercial management, and pollination services. Our project focuses on the social, endocrine, and molecular processes regulating body size in the two bumble bee species most important to agriculture: Bombus terrestris in Israel, and B. impatiens in the USA. Variation in body size underline both caste (queen/worker) differentiation and division of labor among workers (foragers are typically larger than nest bees), two hallmarks of insect sociality which are also crucial for the commercial rearing and crop pollination services of bumble bees. Our project has generated several fundamental new insights into the biology of bumble bees, which can be integrated into science-based management strategies for commercial pollination. Using transcriptomic and behavioral approaches we show that in spite of high flexibility, task performance (brood care or foraging) in bumble bee colonies is associated with physiological variation and differential brain gene expression and RNA editing patterns. We further showed that interactions between the brood, the queen, and the workers determine the developmental program of the larva. We identified two important periods. The first is a critical period during the first few days after hatching. Larvae fed by queens during this period develop over less days, are not likely to develop into gynes, and commonly reach a smaller ultimate body size compared to workers reared mostly or solely by workers. The facial exocrine (mandibular and hypopharangeal) glands are involved in this queen effect on larva development. The second period is important for determining the ultimate body size which is positively regulated by the number of tending workers. The presence of the queen during this stage has little, if at all, influence. We further show that stressors such as agrochemicals that interfere with foraging or brood care specific processes can compromise bumble bee colony development and their pollination performance. We also developed new technology (an RFID system) for automated collection of foraging trip data, for future deployment in agroecosystems. In spite of many similarities, our findings suggest important differences between the Eurasian model species (B. terrestris) and the North American model species (B. impatiens) that impact how management strategies translate across the two species. For example, there is a similar influence of the queen on offspring body size in both species, but this effect does not appear to be mediated by development time in B. impatiens as it is in B. terrestris. Taken together, our collaboration highlights the power of comparative work, to show that considerable differences that exist between these two key pollinator species, and in the organization of young bumble bee nests (wherein queens provide the majority of care and then transition away from brood care) relative to later stages of nest development.
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4

Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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5

Burns, Malcom, and Gavin Nixon. Literature review on analytical methods for the detection of precision bred products. Food Standards Agency, September 2023. http://dx.doi.org/10.46756/sci.fsa.ney927.

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The Genetic Technology (Precision Breeding) Act (England) aims to develop a science-based process for the regulation and authorisation of precision bred organisms (PBOs). PBOs are created by genetic technologies but exhibit changes which could have occurred through traditional processes. This current review, commissioned by the Food Standards Agency (FSA), aims to clarify existing terminologies, explore viable methods for the detection, identification, and quantification of products of precision breeding techniques, address and identify potential solutions to the analytical challenges presented, and provide recommendations for working towards an infrastructure to support detection of precision bred products in the future. The review includes a summary of the terminology in relation to analytical approaches for detection of precision bred products. A harmonised set of terminology contributes towards promoting further understanding of the common terms used in genome editing. A review of the current state of the art of potential methods for the detection, identification and quantification of precision bred products in the UK, has been provided. Parallels are drawn with the evolution of synergistic analytical approaches for the detection of Genetically Modified Organisms (GMOs), where molecular biology techniques are used to detect DNA sequence changes in an organism’s genome. The scope and limitations of targeted and untargeted methods are summarised. Current scientific opinion supports that modern molecular biology techniques (i.e., quantitative real-time Polymerase Chain Reaction (qPCR), digital PCR (dPCR) and Next Generation Sequencing (NGS)) have the technical capability to detect small alterations in an organism’s genome, given specific prerequisites of a priori information on the DNA sequence of interest and of the associated flanking regions. These techniques also provide the best infra-structure for developing potential approaches for detection of PBOs. Should sufficient information be known regarding a sequence alteration and confidence can be attributed to this being specific to a PBO line, then detection, identification and quantification can potentially be achieved. Genome editing and new mutagenesis techniques are umbrella terms, incorporating a plethora of approaches with diverse modes of action and resultant mutational changes. Generalisations regarding techniques and methods for detection for all PBO products are not appropriate, and each genome edited product may have to be assessed on a case-by-case basis. The application of modern molecular biology techniques, in isolation and by targeting just a single alteration, are unlikely to provide unequivocal evidence to the source of that variation, be that as a result of precision breeding or as a result of traditional processes. In specific instances, detection and identification may be technically possible, if enough additional information is available in order to prove that a DNA sequence or sequences are unique to a specific genome edited line (e.g., following certain types of Site-Directed Nucelase-3 (SDN-3) based approaches). The scope, gaps, and limitations associated with traceability of PBO products were examined, to identify current and future challenges. Alongside these, recommendations were made to provide the infrastructure for working towards a toolkit for the design, development and implementation of analytical methods for detection of PBO products. Recognition is given that fully effective methods for PBO detection have yet to be realised, so these recommendations have been made as a tool for progressing the current state-of-the-art for research into such methods. Recommendations for the following five main challenges were identified. Firstly, PBOs submitted for authorisation should be assessed on a case-by-case basis in terms of the extent, type and number of genetic changes, to make an informed decision on the likelihood of a molecular biology method being developed for unequivocal identification of that specific PBO. The second recommendation is that a specialist review be conducted, potentially informed by UK and EU governmental departments, to monitor those PBOs destined for the authorisation process, and actively assess the extent of the genetic variability and mutations, to make an informed decision on the type and complexity of detection methods that need to be developed. This could be further informed as part of the authorisation process and augmented via a publicly available register or database. Thirdly, further specialist research and development, allied with laboratory-based evidence, is required to evaluate the potential of using a weight of evidence approach for the design and development of detection methods for PBOs. This concept centres on using other indicators, aside from the single mutation of interest, to increase the likelihood of providing a unique signature or footprint. This includes consideration of the genetic background, flanking regions, off-target mutations, potential CRISPR/Cas activity, feasibility of heritable epigenetic and epitranscriptomic changes, as well as supplementary material from supplier, origin, pedigree and other documentation. Fourthly, additional work is recommended, evaluating the extent/type/nature of the genetic changes, and assessing the feasibility of applying threshold limits associated with these genetic changes to make any distinction on how they may have occurred. Such a probabilistic approach, supported with bioinformatics, to determine the likelihood of particular changes occurring through genome editing or traditional processes, could facilitate rapid classification and pragmatic labelling of products and organisms containing specific mutations more readily. Finally, several scientific publications on detection of genome edited products have been based on theoretical principles. It is recommended to further qualify these using evidenced based practical experimental work in the laboratory environment. Additional challenges and recommendations regarding the design, development and implementation of potential detection methods were also identified. Modern molecular biology-based techniques, inclusive of qPCR, dPCR, and NGS, in combination with appropriate bioinformatics pipelines, continue to offer the best analytical potential for developing methods for detecting PBOs. dPCR and NGS may offer the best technical potential, but qPCR remains the most practicable option as it is embedded in most analytical laboratories. Traditional screening approaches, similar to those for conventional transgenic GMOs, cannot easily be used for PBOs due to the deficit in common control elements incorporated into the host genome. However, some limited screening may be appropriate for PBOs as part of a triage system, should a priori information be known regarding the sequences of interest. The current deficit of suitable methods to detect and identify PBOs precludes accurate PBO quantification. Development of suitable reference materials to aid in the traceability of PBOs remains an issue, particularly for those PBOs which house on- and off-target mutations which can segregate. Off-target mutations may provide an additional tool to augment methods for detection, but unless these exhibit complete genetic linkage to the sequence of interest, these can also segregate out in resulting generations. Further research should be conducted regarding the likelihood of multiple mutations segregating out in a PBO, to help inform the development of appropriate PBO reference materials, as well as the potential of using off-target mutations as an additional tool for PBO traceability. Whilst recognising the technical challenges of developing and maintaining pan-genomic databases, this report recommends that the UK continues to consider development of such a resource, either as a UK centric version, or ideally through engagement in parallel EU and international activities to better achieve harmonisation and shared responsibilities. Such databases would be an invaluable resource in the design of reliable detection methods, as well as for confirming that a mutation is as a result of genome editing. PBOs and their products show great potential within the agri-food sector, necessitating a science-based analytical framework to support UK legislation, business and consumers. Differentiating between PBOs generated through genome editing compared to organisms which exhibit the same mutational change through traditional processes remains analytically challenging, but a broad set of diagnostic technologies (e.g., qPCR, NGS, dPCR) coupled with pan-genomic databases and bioinformatics approaches may help contribute to filling this analytical gap, and support the safety, transparency, proportionality, traceability and consumer confidence associated with the UK food chain.
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6

Lers, Amnon, Majid R. Foolad, and Haya Friedman. genetic basis for postharvest chilling tolerance in tomato fruit. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600014.bard.

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ABSTRACT Postharvest losses of fresh produce are estimated globally to be around 30%. Reducing these losses is considered a major solution to ensure global food security. Storage at low temperatures is an efficient practice to prolong postharvest performance of crops with minimal negative impact on produce quality or human health and the environment. However, many fresh produce commodities are susceptible to chilling temperatures, and the application of cold storage is limited as it would cause physiological chilling injury (CI) leading to reduced produce quality. Further, the primary CI becomes a preferred site for pathogens leading to decay and massive produce losses. Thus, chilling sensitive crops should be stored at higher minimal temperatures, which curtails their marketing life and in some cases necessitates the use of other storage strategies. Development of new knowledge about the biological basis for chilling tolerance in fruits and vegetables should allow development of both new varieties more tolerant to cold, and more efficient postharvest storage treatments and storage conditions. In order to improve the agricultural performance of modern crop varieties, including tomato, there is great potential in introgression of marker-defined genomic regions from wild species onto the background of elite breeding lines. To exploit this potential for improving tomato fruit chilling tolerance during postharvest storage, we have used in this research a recombinant inbred line (RIL) population derived from a cross between the red-fruited tomato wild species SolanumpimpinellifoliumL. accession LA2093 and an advanced Solanum lycopersicumL. tomato breeding line NCEBR-1, developed in the laboratory of the US co-PI. The original specific objectives were: 1) Screening of RIL population resulting from the cross NCEBR1 X LA2093 for fruit chilling response during postharvest storage and estimation of its heritability; 2) Perform a transcriptopmic and bioinformatics analysis for the two parental lines following exposure to chilling storage. During the course of the project, we learned that we could measure greater differences in chilling responses among specific RILs compared to that observed between the two parental lines, and thus we decided not to perform transcriptomic analysis and instead invest our efforts more on characterization of the RILs. Performing the transcriptomic analysis for several RILs, which significantly differ in their chilling tolerance/sensitivity, at a later stage could result with more significant insights. The RIL population, (172 lines), was used in field experiment in which fruits were examined for chilling sensitivity by determining CI severity. Following the field experiments, including 4 harvest days and CI measurements, two extreme tails of the response distribution, each consisting of 11 RILs exhibiting either high sensitivity or tolerance to chilling stress, were identified and were further examined for chilling response in greenhouse experiments. Across the RILs, we found significant (P < 0.01) correlation between field and greenhouse grown plants in fruit CI. Two groups of 5 RILs, whose fruits exhibited reproducible chilling tolerant/sensitive phenotypes in both field and greenhouse experiments, were selected for further analyses. Numerous genetic, physiological, biochemical and molecular variations were investigated in response to postharvest chilling stress in the selected RILs. We confirmed the differential response of the parental lines of the RIL population to chilling stress, and examined the extent of variation in the RIL population in response to chilling treatment. We determined parameters which would be useful for further characterization of chilling response in the RIL population. These included chlorophyll fluorescence Fv/Fm, water loss, total non-enzymatic potential of antioxidant activity, ascorbate and proline content, and expression of LeCBF1 gene, known to be associated with cold acclimation. These parameters could be used in continuation studies for the identification and genetic mapping of loci contributing to chilling tolerance in this population, and identifying genetic markers associated with chilling tolerance in tomato. Once genetic markers associated with chilling tolerance are identified, the trait could be transferred to different genetic background via marker-assisted selection (MAS) and breeding. The collaborative research established in this program has resulted in new information and insights in this area of research and the collaboration will be continued to obtain further insights into the genetic, molecular biology and physiology of postharvest chilling tolerance in tomato fruit. The US Co-PI, developed the RIL population that was used for screening and measurement of the relevant chilling stress responses and conducted statistical analyses of the data. Because we were not able to grow the RIL population under field conditions in two successive generations, we could not estimate heritability of response to chilling temperatures. However, we plan to continue the research, grow the RIL progeny in the field again, and determine heritability of chilling tolerance in a near future. The IS and US investigators interacted regularly and plan to continue and expand on this study, since combing the expertise of the Co-PI in genetics and breeding with that of the PI in postharvest physiology and molecular biology will have great impact on this line of research, given the significant findings of this one-year feasibility project.
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7

Agresar, Grenmarie, and Michael A. Savageau. Final Report, December, 1999. Sloan - US Department of Energy joint postdoctoral fellowship in computational molecular biology [Canonical nonlinear methods for modeling and analyzing gene circuits and spatial variations during pattern formation in embryonic development]. Office of Scientific and Technical Information (OSTI), December 1999. http://dx.doi.org/10.2172/811376.

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8

Bartolino, Valerio, Birgit Koehler, and Lena Bergström, eds. Climate effects on fish in Sweden : Species-Climate Information Sheets for 32 key taxa in marine and coastal waters. Department of Aquatic Resources, Swedish University of Agricultural Sciences, 2023. http://dx.doi.org/10.54612/a.4lmlt1tq5j.

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The purpose of this publication is to summarize the state of knowledge on the effects of environmental variability and climate change for individual species and stocks based on literature review, giving species-climate information for 32 key taxa in Swedish marine and coastal waters. The report is written in English. The extent and scale of recent changes in climate due to global warming is unprecedented and causes increasing effects on ecosystems. In oceans, ongoing warming leads to, for example, increased water temperatures, decreased ice cover and effects on hydrology and water circulation patterns that can in turn influence salinity. The environmental alterations affect species distribution, biology, and hence also the delivery of marine ecosystem services and human well-being. The results of this review on the effects of environmental variability and climate change on marine taxa are presented as species-climate information sheets designed in a user-friendly format aimed to enhance accessibility for professionals spanning different fields and roles, including e.g. scientific experts, NGOs affiliates and managers. The species-climate information sheets presented here cover 32 key taxa selected among the economically and ecologically most important coastal and marine fish and crustacean species in Swedish waters. The species-wise evaluations show that climate change leads to a wide range of effects on fish, reflecting variations in their biology and physiological tolerances. The review also highlights important data and knowledge gaps for each species and life stage. Despite the high variability and prevailing uncertainties, some general patterns appeared. On a general level, most fish species in Swedish marine and coastal waters are not expected to benefit from climate change, and many risks are identified to their potential for recruitment, growth and development. Boreal, marine and cold-adapted species would be disadvantaged at Swedish latitudes. However, fish of freshwater origin adapted to warmer temperature regimes could benefit to some extent in the Baltic Sea under a warming climate. Freshwater fish could also be benefitted under further decreasing salinity in the surface water in the Baltic Sea. The resulting effects on species will not only depend on the physiological responses, but also on how the feeding conditions for fish, prey availability, the quality of essential fish habitats and many other factors will develop. A wide range of ecological factors decisive for the development of fish communities are also affected by climate change but have not been explored here, where we focused on the direct effects of warming. The sensitivity and resilience of the fish species to climate change will also depend on their present and future health and biological status. Populations exposed to prolonged and intense fishing exploitation, or affected by environmental deterioration will most likely have a lower capacity to cope with climate change effects over time. For both the Baltic Sea and the North Sea, it is important to ensure continued work to update and improve the species-climate information sheets as results from new research become available. It can also be expected that new important and relevant biological information and improved climate scenarios will emerge continuously. Continued work is therefore important to update and refine the species-climate information sheets, help filling in currently identified knowledge gaps, and extend to other species not included here. Moreover, there is need to integrate this type of species-level information into analyses of the effects of climate change at the level of communities and ecosystems to support timely mitigation and adaptation responses to the challenges of the climate change.
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