Journal articles on the topic '280102 Expanding knowledge in the biological sciences'
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1
Criales-Hernández, María I., Diana M. Sanchez-Lobo, and Johanna K. Almeyda-Osorio. "Expanding the knowledge of plankton diversity of tropical lakes from the Northeast Colombian Andes." Revista de Biología Tropical 68, S2 (October 22, 2020): S159—S176. http://dx.doi.org/10.15517/rbt.v68is2.44347.
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Introduction: A large number of planktonic communities found in tropical lakes have not yet been recorded, limiting understanding of how these ecosystems function and of the role that organisms play within them. Objective: Add new records of previously described species and to contribute to the knowledge of the planktonic communities present in tropical mountain and lowland lakes of the northeast Colombian Andes. Methods: Planktonic samples were collected and physicochemical variables measured in nine tropical lakes. Organisms were identified and a bibliographic search was carried out in databases and research articles to the identification of the new records to Colombia. Results: We present the data corresponding to six physicochemical variables measured in tropical lakes of this region and expand the existing information on organisms present in tropical lakes with a list of 391 taxa (299 phytoplankton and 92 zooplankton). The proportion of planktonic species unique to tropical lakes and the low similarity between lake types found with a Jaccard analysis indicated high heterogeneity of ecological conditions in the studied lakes. Conclusions: The 391 taxa found and 15 new records contribute to the list of planktonic organisms present in tropical lakes located in high and low areas of the Colombian northeast Andes.
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Graciá, Eva, Francisco Botella, José Daniel Anadón, Pim Edelaar, D. James Harris, and Andrés Giménez. "Surfing in tortoises? Empirical signs of genetic structuring owing to range expansion." Biology Letters 9, no. 3 (June 23, 2013): 20121091. http://dx.doi.org/10.1098/rsbl.2012.1091.
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Much of our current knowledge about the genetic dynamics in range expansions originates from models, simulations and microcosm experiments that need to be corroborated by field data. Here, we report a neutral genetic pattern that matches the predictions of the genetic surfing theory. Genetic surfing occurs when repeated founding events and genetic drift act on the wave of advance of an expanding population, promoting strong spatial structure. In the range expansion of the tortoise Testudo graeca from North Africa to southeastern Spain, we found several genetic signatures consistent with surfing: a decrease of genetic diversity with distance from the initial founder area, clinal patterns in allele frequencies, rare African alleles which have become common at distal sites in the Spanish range, and stronger spatial differentiation in the expanded range than in the original one. Our results provide support for the theory that genetic drift can be an important force in shaping the genetic structure of expanding populations.
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Manning, Patrick. "The Life Sciences, 1900–2000: Analysis and Social Welfare from Mendel and Koch to Biotech and Conservation." Asian Review of World Histories 6, no. 1 (January 30, 2018): 185–208. http://dx.doi.org/10.1163/22879811-12340030.
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Abstract The life sciences underwent a dramatic transformation during the twentieth century, with an expansion in fundamental knowledge of the process of evolution and its molecular basis, through advances in health care that greatly extended human life, and by the combination of these advances to address the problem of conserving the many forms of life threatened by expanding human society. The essay highlights the worldwide emphasis on social welfare in the years 1945–1980 and the expanding role of international collaboration, especially in the International Biological Program and its advances in ecology and the notion of the biosphere, and in the emergence of molecular biology. This was also the era of the Cold War, yet military confrontation had fewer implications for life sciences than for the natural sciences in that era. After 1980, deregulation and neoliberalism weakened programs for social welfare, yet links among the varying strands of life sciences continued to grow, bringing the development of genomics and its many implications, expanding epidemiology to include reliance on social sciences, and deepening ecological studies as the Anthropocene became more and more prevalent. In sum, the experience of the life sciences should make it clear to world historians that scientific advance goes beyond the achievements of brilliant but isolated researchers: those same advances rely substantially on social movements, migration, and the exchange of knowledge across intellectual and physical boundaries.
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Essl, Franz, Stefan Dullinger, Piero Genovesi, Philip E. Hulme, Jonathan M. Jeschke, Stelios Katsanevakis, Ingolf Kühn, et al. "A Conceptual Framework for Range-Expanding Species that Track Human-Induced Environmental Change." BioScience 69, no. 11 (September 25, 2019): 908–19. http://dx.doi.org/10.1093/biosci/biz101.
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Abstract For many species, human-induced environmental changes are important indirect drivers of range expansion into new regions. We argue that it is important to distinguish the range dynamics of such species from those that occur without, or with less clear, involvement of human-induced environmental changes. We elucidate the salient features of the rapid increase in the number of species whose range dynamics are human induced, and review the relationships and differences to both natural range expansion and biological invasions. We discuss the consequences for science, policy and management in an era of rapid global change and highlight four key challenges relating to basic gaps in knowledge, and the transfer of scientific understanding to biodiversity management and policy. We conclude that range-expanding species responding to human-induced environmental change will become an essential feature for biodiversity management and science in the Anthropocene. Finally, we propose the term neonative for these taxa.
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Pakeman, Robin J., Francisco I. Pugnaire, Richard Michalet, Chris J. Lortie, Katja Schiffers, Fernando T. Maestre, and Justin M. J. Travis. "Is the cask of facilitation ready for bottling? A symposium on the connectivity and future directions of positive plant interactions." Biology Letters 5, no. 5 (June 17, 2009): 577–79. http://dx.doi.org/10.1098/rsbl.2009.0384.
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The 2009 British Ecological Society's Annual Symposium entitled ‘Facilitation in Plant Communities’ was held at the University of Aberdeen, Scotland, from 20 to 22 April 2009. This was the first ever international meeting dedicated to the rapidly expanding field of facilitation. The aim of the symposium was to assess the current ‘state-of-play’ by contrasting findings from different systems and by looking outwards in an attempt to integrate this field with other related fields. It was also aimed at understanding how knowledge of facilitation can help understand community dynamics and be applied to ecosystem restoration. The symposium identified several key areas where future work is likely to be most profitable.
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Silva, G. G., A. J. Green, V. Weber, P. Hoffmann, Á. Lovas-Kiss, C. Stenert, and L. Maltchik. "Whole angiosperms Wolffia columbiana disperse by gut passage through wildfowl in South America." Biology Letters 14, no. 12 (December 2018): 20180703. http://dx.doi.org/10.1098/rsbl.2018.0703.
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For the first time to our knowledge, we demonstrate that whole angiosperm individuals can survive gut passage through birds, and that this occurs in the field. Floating plants of the genus Wolffia are the smallest of all flowering plants. Fresh droppings of white-faced whistling duck Dendrocygna viduata ( n = 49) and coscoroba swan Coscoroba coscoroba ( n = 22) were collected from Brazilian wetlands. Intact Wolffia columbiana were recovered from 16% of D. viduata and 32% of Coscoroba samples (total = 164 plantlets). The viability of plants was tested, and asexual reproduction was confirmed. Wolffia columbiana is an expanding alien in Europe. Avian endozoochory of asexual angiosperm propagules may be an important, overlooked dispersal means for aquatic plants, and may contribute to the invasive character of alien species.
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Braga, Jacqueline Ramos Machado, Relrison Dias Ramalho, José Cleidvan Cândido de Sousa, and Ivan Luiz De Almeida. "Scorpions from Ceará State, Brazil: Distribution and ecological comments." Revista Peruana de Biología 29, no. 1 (March 15, 2022): e21205. http://dx.doi.org/10.15381/rpb.v29i1.21205.
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Scorpions are venomous synanthropic arachnids, in 2019 they were responsible for more than 37000 cases of envenomation in the state of Ceará, Northeastern Brazil. To update the knowledge about the scorpiofauna in Ceará, a distribution list of scorpions collected/received by municipal agents of the Health Surveillance Service was performed in 165 municipalities (89%) of Ceará (2018 – 2019) and deposited in the Dr. Thomaz Corrêa Aragão Entomology Laboratory scientific collection, including species distribution maps and ecological data. This study included a total of 999 scorpions from two families (Buthidae and Bothriuridae) and eleven species. The most abundant species were: Tityus stigmurus (40.1%), Jaguajir rochae (37.2%), Bothriurus asper (8.3%) and Bothriurus rochai (6.7%), mainly inhabiting municipalities in the Caatinga biome. The first record of Tityus confluens and Tityus maranhensis in the Sobral mesoregion is herein presented, expanding the distribution of these species in Brazil.
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Liseev, Igor K. "Ecology as a Way to Combine Knowledge about the Natural and Social in Human Being." Epistemology & Philosophy of Science 57, no. 4 (2020): 133–37. http://dx.doi.org/10.5840/eps202057466.
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The article considers the process of expanding the subject and methods of research in modern environmental science. It is shown how, following the traditional biological science of ecology, new directions of ecological knowledge arise under the influence of research activities: social ecology, anthropoecology. Knowledge about a human being is achieved through the use of both natural and human sciences. A great step in expanding the subject of modern ecology was the intensive formation of human ecology in recent years, in which the need for the formation of a unity of natural science and socio-humanitarian research methods was reflected most clearly. In contrast to biological ecology, in which the main focus of research was the principles of natural science research, in social ecology, socio-humanitarian issues become dominant, and in human ecology-the synthesis of natural science and socio-humanitarian approaches. It's time to abandon the progressive illusions of the past and move on to the awareness of the specifics of sustainable civilizational development at the present stage. This sustainable development presupposes the co-evolution of society and nature, such a co-development of society and nature, in which both components of this single system do not oppose each other, do not conflict, but organically presuppose each other in their combined, harmonious development. Thus, now acting as a unified science that studies the interaction of the central coreof the system and its environment, ecology sets new guidelines for understanding the organization of scientific knowledge, the mood of the modern world picture is falling. A promising way for ecology is to grow into a modern universal organizational science. But this is a distant prospect. However, even now, such a renewed ecology can provide much for Russia’s search for its modern civilizational path, clarifying the organization of scientific knowledge, specifying the contours of the modern scientific picture of the world.
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Devaux, Andre, Maximo Torero, Jason Donovan, and Douglas Horton. "Agricultural innovation and inclusive value-chain development: a review." Journal of Agribusiness in Developing and Emerging Economies 8, no. 1 (March 12, 2018): 99–123. http://dx.doi.org/10.1108/jadee-06-2017-0065.
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Purpose The purpose of this paper is twofold: first, to take stock of the current state of knowledge about inclusive value-chain development (VCD) in the context of international agricultural research; and second, to draw out the implications for future research and action. Design/methodology/approach This paper is based on a review of recent research papers authored by professionals affiliated with international agricultural research centers and their partners in Africa, Asia, and Latin America. Findings The studies reviewed in the paper identify the opportunities emerging from new and expanding markets for agricultural products and challenges to smallholder participation in these markets. It identifies key attributes of successful value-chain interventions, emphasizing the importance of combining value-chain approaches with other approaches, including those emerging from innovation systems and rural livelihoods frameworks. Methods are offered for evaluating complex value-chain interventions. Research limitations/implications The paper summarizes the state of knowledge as of early 2016 in a dynamic field. Important contributions to knowledge may have been made since then. Originality/value The paper summarizes the state of knowledge in the field, and identifies emerging issues and policy implications, knowledge gaps, and priorities for future applied research.
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Solanki, Kundan, Sajjan Rajpoot, Evgeny E. Bezsonov, Alexander N. Orekhov, Rohit Saluja, Anita Wary, Cassondra Axen, Kishore Wary, and Mirza S. Baig. "The expanding roles of neuronal nitric oxide synthase (NOS1)." PeerJ 10 (July 7, 2022): e13651. http://dx.doi.org/10.7717/peerj.13651.
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The nitric oxide synthases (NOS; EC 1.14.13.39) use L-arginine as a substrate to produce nitric oxide (NO) as a by-product in the tissue microenvironment. NOS1 represents the predominant NO-producing enzyme highly enriched in the brain and known to mediate multiple functions, ranging from learning and memory development to maintaining synaptic plasticity and neuronal development, Alzheimer’s disease (AD), psychiatric disorders and behavioral deficits. However, accumulating evidence indicate both canonical and non-canonical roles of NOS1-derived NO in several other tissues and chronic diseases. A better understanding of NOS1-derived NO signaling, and identification and characterization of NO-metabolites in non-neuronal tissues could become useful in diagnosis and prognosis of diseases associated with NOS1 expression. Continued investigation on the roles of NOS1, therefore, will synthesize new knowledge and aid in the discovery of small molecules which could be used to titrate the activities of NOS1-derived NO signaling and NO-metabolites. Here, we address the significance of NOS1 and its byproduct NO in modifying pathophysiological events, which could be beneficial in understanding both the disease mechanisms and therapeutics.
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Cárdenas, Melissa Querido, Márcia Cristina Nascimento Justo, Diego Carvalho Viana, and Simone Chinicz Cohen. "New host record and geographical distribution of Nematoda parasitizing Hypophthalmus marginatus Valenciennes (Siluriformes) from the Tocantins River, Brazil." Acta Scientiarum. Biological Sciences 43 (December 10, 2021): e58014. http://dx.doi.org/10.4025/actascibiolsci.v43i1.58014.
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Hypophthalmus marginatus is among the most commercialized fish from the Amazon region, with fish fillets exported to Southeastern Brazil and other countries. In the present study, the H. marginatus analyzed were parasitized by third-stage larvae of Hysterothylacium sp. and Anisakis sp. These nematodes are being reported for the first time in H. marginatus collected from the Tocantins River, representing a new host and geographical records, and expanding knowledge of the hosts of these nematodes in the Neotropical Region. A brief description with original measurements is presented.
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Sousa, Sebastiana Adriana Pereira, Helcileia Dias Santos, Cristiane América de Carvalho, Aline Marinho Machado, Letícia Espindola de Oliveira, Taiã Mairon Peixoto Ribeiro, Adriana Genelhá Carreira, et al. "Acute visceral leishmaniasis in a domestic cat (Felis silvestris catus) from the state of Tocantins, Brazil." Semina: Ciências Agrárias 40, no. 4 (June 7, 2019): 1723. http://dx.doi.org/10.5433/1679-0359.2019v40n4p1723.
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Visceral leishmaniasis (VL) is expanding in the Brazilian territory. Dogs are considered an important urban reservoir; however, studies have demonstrated the presence of infected cats in some Brazilian states. This report aimed to describe a case of Leishmania (Leishmania) infantum infection in a two-month-old domestic feline from a Brazilian region with a high incidence of human visceral leishmaniasis. The analyzed samples were the cat’s blood, conjunctiva, spleen, liver, popliteal, submandibular and mesenteric lymph nodes, skin, lung and kidney. The diagnostic methods were: parasitological examination, polymerase chain reaction (PCR) and an immunoflurescence antibody test (IFAT). All tissues were positive. The title obtained using the IFAT was 1:160. The animal was negative for feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV). This work addresses the first case of feline leishmaniasis in the state of Tocantins, and reveals data that may contribute to the knowledge of the disease, since it has been shown to be able to develop rapidly and fatally in kittens, with the ability to infect several tissues.
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Shalamova, E. A. "Methodological issues in the History of origin and development of the Foundation Engineering from Ancient times to the beginning of the XVII century." Construction and Geotechnics 12, no. 2 (December 15, 2021): 51–63. http://dx.doi.org/10.15593/2224-9826/2021.2.05.
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The article is devoted to the methodology of the history of the emergence and development of knowledge in the field of foundation building from ancient times to the beginning of the XVII century. It is suggested that for the full-fledged formation of general cultural and professional competencies of graduates of higher education in the specialty 08.03.01 «Construction», it is necessary to build relatively deeper historical and theoretical connections in the methodology of the history of foundation construction. The object of the research is the history of the foundation building sciences. The purpose of this work is to analyze the history of the emergence and development of the foundation sciences in the «horizontal cross-section» of scientific periodization at the stage of pre-science within the framework of methodological issues. The research method is system-historical. Results of the research: during the research, the structures of the foundations of individual famous architectural monuments erected during the chronology of world history from the beginning of the primitive society age to the beginning of the New Time are considered. The role of sections of scientific works of the epochs of Antiquity, the Middle Ages and the Renaissance devoted to the structure of foundations and foundations in modern issues of methodology is analyzed. Conclusions are drawn about the rationality of expanding the chronological boundaries in the study of the history of the emergence and development of the sciences of foundation construction to form students of the specialty 08.03.01 «Construction» theoretical knowledge that meets the requirements of modern professional standards.
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Robertson, M. J., R. C. Muchow, R. A. Donaldson, N. G. Inman-Bamber, and A. W. Wood. "Estimating the risk associated with drying-off strategies for irrigated sugarcane before harvest." Australian Journal of Agricultural Research 50, no. 1 (1999): 65. http://dx.doi.org/10.1071/a98051.
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The development of recommendations for drying-off management in sugarcane is difficult due to climatic variability and lack of knowledge of the sensitivity of changes in sucrose content and cane yield to severity of water deficit. Relative cane biomass targets were developed for drying-off irrigated sugarcane before harvest based on derived relationships between cane yield, cane dry weight, and sucrose concentration, using pooled data from previous field studies. These targets were then linked to a crop–soil model and long-term climate data to determine the economically optimum duration of drying-off, and its variability from season to season for 2 locations in Australia and one location in South Africa, for a range of harvest dates and soil types. The crop–soil model was validated on yields measured in 37 drying-off treatments conducted in South Africa and Australia. The simulation results show that the required drying-off duration can be highly variable, although the level of variability is not necessarily correlated with rainfall per se. There were interactions between soil type and harvest date, but not at every location. The systems approach outlined here can be useful in developing recommendations for drying-off where experience is limited, such as in expanding areas of sugar industries, for districts in which the practice of irrigation is increasing, or for harvest dates outside the current harvesting season.
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Vallee, Mickey. "The Science of Listening in Bioacoustics Research: Sensing the Animals' Sounds." Theory, Culture & Society 35, no. 2 (August 31, 2017): 47–65. http://dx.doi.org/10.1177/0263276417727059.
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Bioacoustics is an interdisciplinary field bridging biological and acoustic sciences, which uses sound technologies to record, preserve, and analyse large datasets of animal communications. But it is also a world, made of the meanings created through inter- and intra-species communication. This article empirically explores a variety of bioacoustics research, including interviews with researchers, as part of a broader qualitative study, in order to theorize the expanding sense and sensation of a global biosphere and sonic data. By giving a sustained and detailed account of the science of bioacoustics, particularly how its modes of measurement allow for a new way of understanding what is involved in the de-centred modes of hearing that re-centre acts of listening and, by extension, the nature of the relation between researcher and researched, the article contributes to methodological discussions regarding the longstanding questions of how researchers and scientists are implicated in the knowledge and objects they collectively produce.
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Schluter, Dolph, Kerry B. Marchinko, R. D. H. Barrett, and Sean M. Rogers. "Natural selection and the genetics of adaptation in threespine stickleback." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1552 (August 27, 2010): 2479–86. http://dx.doi.org/10.1098/rstb.2010.0036.
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Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection—mechanism, form and history—from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus ( Ectodysplasin ) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.
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Solvang, Hiroko K., Tore Haug, Tor Knutsen, Harald Gjøsæter, Bjarte Bogstad, Siri Hartvedt, Nils Øien, and Ulf Lindstrøm. "Distribution of rorquals and Atlantic cod in relation to their prey in the Norwegian high Arctic." Polar Biology 44, no. 4 (March 14, 2021): 761–82. http://dx.doi.org/10.1007/s00300-021-02835-2.
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AbstractRecent warming in the Barents Sea has led to changes in the spatial distribution of both zooplankton and fish, with boreal communities expanding northwards. A similar northward expansion has been observed in several rorqual species that migrate into northern waters to take advantage of high summer productivity, hence feeding opportunities. Based on ecosystem surveys conducted during August–September in 2014–2017, we investigated the spatial associations among the three rorqual species of blue, fin, and common minke whales, the predatory fish Atlantic cod, and their main prey groups (zooplankton, 0-group fish, Atlantic cod, and capelin) in Arctic Ocean waters to the west and north of Svalbard. During the surveys, whale sightings were recorded by dedicated whale observers on the bridge of the vessel, whereas the distribution and abundance of cod and prey species were assessed using trawling and acoustic methods. Based on existing knowledge on the dive habits of these rorquals, we divided our analyses into two depth regions: the upper 200 m of the water column and waters below 200 m. Since humpback whales were absent in the area in 2016 and 2017, they were not included in the subsequent analyses of spatial association. No association or spatial overlap between fin and blue whales and any of the prey species investigated was found, while associations and overlaps were found between minke whales and zooplankton/0-group fish in the upper 200 m and between minke whales and Atlantic cod at depths below 200 m. A prey detection range of more than 10 km was suggested for minke whales in the upper water layers.
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Wang, Enli, and Chris J. Smith. "Modelling the growth and water uptake function of plant root systems: a review." Australian Journal of Agricultural Research 55, no. 5 (2004): 501. http://dx.doi.org/10.1071/ar03201.
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Crop models have been intensively used as a tool to analyse the performance of cropping systems under variable climate in terms of productivity, profitability, and off-site impact. The importance of modelling the function of plant roots in water and nutrient uptake from the soil is becoming increasing clear with the expanding application areas of crop models. This paper reviews the approaches and assumptions used in growth and uptake modelling of plant roots, and how the responses of plant root system to internal and external factors are captured in the widely used crop models. Most modelling approaches are based on one of the following assumptions: (i) that plant roots are uniformly distributed in homogenous soil layers and all roots have the same ability for uptake, or (ii) that plant root length is always sufficient for resource uptake in rooted soil layers. In structured soils, an overestimation of water uptake is likely to be expected. Further studies on root growth, distribution, and function in structured soils will require quantification of soil structures and root distribution patterns; and for non-uniformly distributed plant populations, spatial distribution of plant roots and non-uniform uptake need to be modelled. Root architecture modelling may help to address such issues. However, in order for the model to be useful at the field production level, simplified approaches that require easily measurable inputs need to be developed. Some examples are given. The oversimplification of root response to soil drying and hardness is likely to lead to overestimation of root growth and water uptake in dense soils. A soil strength factor needs to be incorporated so that the improved model can help evaluate the effect of subsoil compaction on production and resource use. Responses of root growth and uptake to soil salinity, boron toxicity, and extreme pH need to be further investigated if models are to be used for evaluation of crop performance in such environments. Effect of waterlogging also needs to be added for use of the model on heavy clay soils under irrigation or concentrated rainfall. There is an urgent need for joint efforts of crop physiologists, agronomists, breeders, and soil scientists to integrate interdisciplinary knowledge and to collect data that better describe the crop root system and its growth and uptake ability, to quantify plant process level responses, and for better soil quantification. Such knowledge and data are essential for improvement of model performance and successful applications.
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Muchow, R. C., and B. A. Keating. "Assessing irrigation requirements in the Ord Sugar Industry using a simulation modelling approach." Australian Journal of Experimental Agriculture 38, no. 4 (1998): 345. http://dx.doi.org/10.1071/ea98023.
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Summary. Sustainable irrigation guidelines that maximise profitability and minimise water losses and accession to the watertable are required for the new Ord Sugar Industry. In addition, knowledge on crop water requirements is needed to guide water allocation and costing policies for the expanding Ord Irrigation Area where sugarcane is likely to be a dominant crop. Field data indicating water requirements for sugar in the Ord Irrigation Area are few and this paper deploys a modelling approach to extrapolate from knowledge of water requirements in other parts of the world. The approach links long-term climatic data with soil water characteristics of the main soil type, with a cropping systems model, to develop indicative estimates of irrigation water requirement and yield consequences for different management options for sugarcane production in the Ord. Analyses of the growth of 12-month old ratoon crops were conducted using the APSIM–Sugarcane model with historical climatic data from 1960 to 1985 and either a deep (188 mm available water to 160 cm depth) or shallow (144 mm of water to 120 cm depth) Cununurra clay soil. Under maximum attainable growth conditions where crops were irrigated after half the soil water supply was depleted, average sucrose yield ranged from 26.7 to 29.0 t/ha, and the irrigation requirement (assuming 100% application efficiency) ranged from 22.7 to 23.8 ML/ha depending on ratooning date. Soil water holding capacity had a major effect on the number of irrigations and the interval between irrigation for a given irrigation schedule but little effect on yield or irrigation requirement. Varying the irrigation schedule by changing the level of soil water depletion before irrigation and thus the irrigation frequency, showed the tradeoff between yield and irrigation requirement with the most profitable irrigation schedule depending on the price of sucrose and the cost of irrigation relative to other costs. Most of the year-to-year variation in irrigation water requirement could be explained by the highly variable effectiveness in soil storage of rainfall which ranged from 44 to 93%. This study has provided insight and indicative estimates of the yield and irrigation requirements for different irrigation management options for use in the establishment of an Ord River sugar industry. These estimates will be further refined as field data become available.
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Marsden, Russell L., Juan A. G. Ranea, Antonio Sillero, Oliver Redfern, Corin Yeats, Michael Maibaum, David Lee, et al. "Exploiting protein structure data to explore the evolution of protein function and biological complexity." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1467 (February 2006): 425–40. http://dx.doi.org/10.1098/rstb.2005.1801.
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New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms. We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms. When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.
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Caruso, Alessandra, Alessandra Gaetano, and Sergio Scaccianoce. "Corticotropin-Releasing Hormone: Biology and Therapeutic Opportunities." Biology 11, no. 12 (December 8, 2022): 1785. http://dx.doi.org/10.3390/biology11121785.
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In 1981, Wylie Vale, Joachim Spiess, Catherine Rivier, and Jean Rivier reported on the characterization of a 41-amino-acid peptide from ovine hypothalamic extracts with high potency and intrinsic activity stimulating the secretion of adrenocorticotropic hormone and β-endorphin by cultured anterior pituitary cells. With its sequence known, this neuropeptide was determined to be a hormone and consequently named corticotropin-releasing hormone (CRH), although the term corticotropin-releasing factor (CRF) is still used and preferred in some circumstances. Several decades have passed since this seminal contribution that opened a new research era, expanding the understanding of the coding of stress-related processes. The characterization of CRH receptors, the availability of CRH agonists and antagonists, and advanced immunocytochemical staining techniques have provided evidence that CRH plays a role in the regulation of several biological systems. The purpose of this review is to summarize the present knowledge of this 41-amino-acid peptide.
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Coman, Ioana A., Caitlyn E. Cooper-Norris, Scott Longing, and Gad Perry. "It Is a Wild World in the City: Urban Wildlife Conservation and Communication in the Age of COVID-19." Diversity 14, no. 7 (July 4, 2022): 539. http://dx.doi.org/10.3390/d14070539.
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Most ecosystems are increasingly being degraded and reduced by human activities at the local and global scales. In contrast, urban environments are expanding as increasing portions of humanity move into cities. Despite the common perception among biologists that urban areas are biological deserts, cities offer habitat for many non-human species, but their ecology and conservation remain poorly studied. In this review, we first provide an update on the current state of knowledge on urban wildlife, then briefly examine the indirect effects of the COVID-19 pandemic on urban wildlife and add four components not previously included in comprehensive reviews. (1) We show that by reducing human activity, COVID-19 has temporarily enhanced urban habitat quality for some species and diminished it for others. (2) Thoughtful horticulture can contribute to urban wildlife by providing complex habitat structures that benefit biodiversity while enhancing human wellbeing. (3) Recent literature on urban invertebrate biodiversity has grown, though is still focused on pollinators. (4) Finally, employing insights from the discipline of communication can enhance the success of urban biodiversity conservation among both biologists and the public.
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Quamar, Md Firoze. "Late Holocene vegetation dynamics and monsoonal climatic changes in Jammu, India." Acta Palaeobotanica 62, no. 1 (June 2022): 36–49. http://dx.doi.org/10.35535/acpa-2022-0004.
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Knowledge of the Holocene Indian Summer Monsoon (ISM) variability is important for understanding the spatio-temporal dynamics of the ISM precipitation. In this study, a Late Holocene pollen proxy record of the changes in the ISM intensity from a 1.8 m deep lacustrine sedimentary deposit in Jammu District (Jammu and Kashmir State) in India is presented. The results show that between ~3205 and 2485 cal yr BP, mixed broad-leaved/conifer forests occurred in the region under a warm and humid climate, probably indicating high monsoon precipitation. Subsequently, the conifers, such as Pinus sp., Cedrus sp., Abies sp., Picea sp. and Larix sp. increased comparatively and show dominance over the existing broad-leaved taxa between ~2485 and 1585 cal yr BP under a cool and dry climate with reduced monsoon precipitation. The climate further deteriorated (towards attaining aridity under reduced monsoon condition) during ~1585 to 865 cal yr BP, which coincides with the Dark Ages Cold Period (DACP: CE/AD 400–765; 1185–1550 cal yr BP). Since ~865 cal yr BP (CE/AD 1085 onwards) to Present, the broad-leaved taxa, such as Alnus sp., Betula sp., Ulmus sp., Carpinus sp., Corylus sp. and Quercus sp. started expanding and showed their dominance over the conifers, indicating a warm and humid climate in the region with increased monsoon precipitation. This phase partly corresponds with the Medieval Climatic Anomaly (MCA) between CE/AD 950 and 1300. Thus, the ISM rainfall intensity is linked with some of the global climatic trends in the present study.
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Xu, Xingjian, Lili Hao, Junwei Zhu, Bixia Tang, Qing Zhou, Fuhai Song, Tingting Chen, et al. "Database Resources of the BIG Data Center in 2018." Nucleic Acids Research 46, no. D1 (October 3, 2017): D14—D20. http://dx.doi.org/10.1093/nar/gkx897.
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Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn.
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Angell, Inga Leena, and Knut Rudi. "A game theory model for gut bacterial nutrient utilization strategies during human infancy." Proceedings of the Royal Society B: Biological Sciences 287, no. 1931 (July 15, 2020): 20200824. http://dx.doi.org/10.1098/rspb.2020.0824.
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Despite the fact that infant gut colonization patterns have been extensively studied, we have limited knowledge about the underlying ecological processes. This particularly relates to the ecological choice of nutrient utilization strategies. The aim of the current study was therefore to compare empirically determined nutrient utilization strategies with that expected from a combinatorial game theory model. Observational analyses for 100 mother–child pairs suggested mother–child transmission of specialists with the potential to use few nutrients. Generalists, on the other hand, with the potential to use many nutrients, peaked at three months of age for the children. The level of generalists was gradually replaced with specialists up to 12 months of age. Game theory simulation revealed a competitive advantage of generalists in an expanding population, while more specialized bacteria were favoured with the maturation of the population. This suggests that the observed increase in generalists in the three-month-old children could be due to an immature, expanding gut microbiota population while the increase of specialists at 12 months could be due to population maturation. The simulated and empirical data also correspond with respect to an increased α diversity and a decreased β diversity with the number of simulations and age, respectively. Taken together, game theory simulation of nutrient utilization strategies can therefore provide novel insight into the maturation of the human gut microbiota during infancy.
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Jiao, Yuannian, and Andrew H. Paterson. "Polyploidy-associated genome modifications during land plant evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1648 (August 5, 2014): 20130355. http://dx.doi.org/10.1098/rstb.2013.0355.
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The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.
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Gomez-Cabrero, David, Albert Compte, and Jesper Tegner. "Workflow for generating competing hypothesis from models with parameter uncertainty." Interface Focus 1, no. 3 (March 30, 2011): 438–49. http://dx.doi.org/10.1098/rsfs.2011.0015.
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Mathematical models are increasingly used in life sciences. However, contrary to other disciplines, biological models are typically over-parametrized and loosely constrained by scarce experimental data and prior knowledge. Recent efforts on analysis of complex models have focused on isolated aspects without considering an integrated approach—ranging from model building to derivation of predictive experiments and refutation or validation of robust model behaviours. Here, we develop such an integrative workflow, a sequence of actions expanding upon current efforts with the purpose of setting the stage for a methodology facilitating an extraction of core behaviours and competing mechanistic hypothesis residing within underdetermined models. To this end, we make use of optimization search algorithms, statistical (machine-learning) classification techniques and cluster-based analysis of the state variables' dynamics and their corresponding parameter sets. We apply the workflow to a mathematical model of fat accumulation in the arterial wall (atherogenesis), a complex phenomena with limited quantitative understanding, thus leading to a model plagued with inherent uncertainty. We find that the mathematical atherogenesis model can still be understood in terms of a few key behaviours despite the large number of parameters. This result enabled us to derive distinct mechanistic predictions from the model despite the lack of confidence in the model parameters. We conclude that building integrative workflows enable investigators to embrace modelling of complex biological processes despite uncertainty in parameters.
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Ambrosino, Luca, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, and Maria Luisa Chiusano. "Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives." Marine Drugs 17, no. 10 (October 11, 2019): 576. http://dx.doi.org/10.3390/md17100576.
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The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Snezhitskiy, V. A., E. A. Moiseenok, and L. S. Lukashevich. "JOURNAL OF THE GRODNO STATE MEDICAL UNIVERSITY IS 20 YEARS OLD: OUR ACHIEVEMENTS." Journal of the Grodno State Medical University 20, no. 6 (December 30, 2022): 575–78. http://dx.doi.org/10.25298/2221-8785-2022-20-6-575-578.
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Summary. The scientific and practical peer-reviewed "Journal of the Grodno State Medical University" celebrates its twentieth anniversary. The history of the journal began on November 27, 2002, when it was registered by the Ministry of Information of the Republic of Belarus. Over the years of its existence, the Journal of the Grodno State Medical University has gained the status of an authoritative periodical scientific journal that publishes review and original articles on medical and biomedical topics, the history of medicine, and the features of medical education. In just 20 years, 90 issues of the Journal of the Grodno State Medical University were published, where 2610 scientific articles and reviews appeared. The main purpose of the journal is to provide a wide coverage of scientific achievements in the field of preventive, clinical, experimental medicine and other medical and biological sciences, especially in the context of cross-border cooperation of medical specialists. The editorial policy of the Journal of the Grodno State Medical University is aimed at disseminating and exchanging scientific knowledge, expanding cooperation with domestic and foreign clinical, scientific and educational institutions in order to deepen integration in the field of medical research.
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Arvizu-Rubio, Verania J., Laura C. García-Carnero, and Héctor Manuel Mora-Montes. "Moonlighting proteins in medically relevant fungi." PeerJ 10 (September 13, 2022): e14001. http://dx.doi.org/10.7717/peerj.14001.
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Moonlighting proteins represent an intriguing area of cell biology, due to their ability to perform two or more unrelated functions in one or many cellular compartments. These proteins have been described in all kingdoms of life and are usually constitutively expressed and conserved proteins with housekeeping functions. Although widely studied in pathogenic bacteria, the information about these proteins in pathogenic fungi is scarce, but there are some reports of their functions in the etiological agents of the main human mycoses, such as Candida spp., Paracoccidioides brasiliensis, Histoplasma capsulatum, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. In these fungi, most of the described moonlighting proteins are metabolic enzymes, such as enolase and glyceraldehyde-3-phosphate dehydrogenase; chaperones, transcription factors, and redox response proteins, such as peroxiredoxin and catalase, which moonlight at the cell surface and perform virulence-related processes, contributing to immune evasion, adhesions, invasion, and dissemination to host cells and tissues. All moonlighting proteins and their functions described in this review highlight the limited information about this biological aspect in pathogenic fungi, representing this a relevant opportunity area that will contribute to expanding our current knowledge of these organisms’ pathogenesis.
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Sobral-Souza, Thadeu, Juliana Stropp, Jessie Pereira Santos, Victor Mateus Prasniewski, Neucir Szinwelski, Bruno Vilela, André Victor Lucci Freitas, Milton Cezar Ribeiro, and Joaquín Hortal. "Knowledge gaps hamper understanding the relationship between fragmentation and biodiversity loss: the case of Atlantic Forest fruit-feeding butterflies." PeerJ 9 (June 25, 2021): e11673. http://dx.doi.org/10.7717/peerj.11673.
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Background A key challenge for conservation biology in the Neotropics is to understand how deforestation affects biodiversity at various levels of landscape fragmentation. Addressing this challenge requires expanding the coverage of known biodiversity data, which remain to date restricted to a few well-surveyed regions. Here, we assess the sampling coverage and biases in biodiversity data on fruit-feeding butterflies at the Brazilian Atlantic Forest, discussing their effect on our understanding of the relationship between forest fragmentation and biodiversity at a large-scale. We hypothesize that sampling effort is biased towards large and connected fragments, which occur jointly in space at the Atlantic forest. Methods We used a comprehensive dataset of Atlantic Forest fruit-feeding butterfly communities to test for sampling biases towards specific geographical areas, climate conditions and landscape configurations. Results We found a pattern of geographical aggregation of sampling sites, independently of scale, and a strong sampling bias towards large and connected forest fragments, located near cities and roads. Sampling gaps are particularly acute in small and disconnected forest fragments and rare climate conditions. In contrast, currently available data can provide a fair picture of fruit-feeding butterfly communities in large and connected Atlantic Forest remnants. Discussion Biased data hamper the inference of the functional relationship between deforestation and biodiversity at a large-scale, since they are geographically clustered and have sampling gaps in small and disconnected fragments. These data are useful to inform decision-makers regarding conservation efforts to curb biodiversity loss in the Atlantic Forest. Thus, we suggest to expand sampling effort to small and disconnected forest fragments, which would allow more accurate evaluations of the effects of landscape modification.
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Orr, James A., Rolf D. Vinebrooke, Michelle C. Jackson, Kristy J. Kroeker, Rebecca L. Kordas, Chrystal Mantyka-Pringle, Paul J. Van den Brink, et al. "Towards a unified study of multiple stressors: divisions and common goals across research disciplines." Proceedings of the Royal Society B: Biological Sciences 287, no. 1926 (May 6, 2020): 20200421. http://dx.doi.org/10.1098/rspb.2020.0421.
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Anthropogenic environmental changes, or ‘stressors’, increasingly threaten biodiversity and ecosystem functioning worldwide. Multiple-stressor research is a rapidly expanding field of science that seeks to understand and ultimately predict the interactions between stressors. Reviews and meta-analyses of the primary scientific literature have largely been specific to either freshwater, marine or terrestrial ecology, or ecotoxicology. In this cross-disciplinary study, we review the state of knowledge within and among these disciplines to highlight commonality and division in multiple-stressor research. Our review goes beyond a description of previous research by using quantitative bibliometric analysis to identify the division between disciplines and link previously disconnected research communities. Towards a unified research framework, we discuss the shared goal of increased realism through both ecological and temporal complexity, with the overarching aim of improving predictive power. In a rapidly changing world, advancing our understanding of the cumulative ecological impacts of multiple stressors is critical for biodiversity conservation and ecosystem management. Identifying and overcoming the barriers to interdisciplinary knowledge exchange is necessary in rising to this challenge. Division between ecosystem types and disciplines is largely a human creation. Species and stressors cross these borders and so should the scientists who study them.
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Safandeev, Vitalij Vasilevich, and Tat’yana Alekseevna Sinitskaya. "The use of neurotoxins in fundamental, medical and biological sciences on the example of the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine." Toxicological Review 30, no. 5 (October 30, 2022): 307–14. http://dx.doi.org/10.47470/0869-7922-2022-30-5-307-314.
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Introduction. Neurotoxins are a class of chemicals that damage neurons. Some pesticides have a similar effect. The increase in areas with developed heavy industry and agriculture, uncontrolled use of pesticides contribute to the emergence and progression of Alzheimer’s and Parkinson’s disease (PD). The insidiousness of PD is that it is still incurable, since there is no early diagnosis: for decades it has been asymptomatic, and by the time of manifestation there are no target neurons for therapy. Considering that the diagnosis is made at the late stages of PD development, the treatment of the disease is ineffective. It follows that in order to increase the effectiveness of treatment, it should be started as early as possible - before the appearance of motor symptoms, at the preclinical stage. To do this, it is first necessary to develop an early (preclinical) diagnosis of PD based on an in-depth study of the cellular and molecular mechanisms of pathogenesis. In order to develop early diagnosis and preventive therapy of PD, proneurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was used in this study. Material and methods. To simulate the preclinical and clinical stages of PD, inbred lines of animals were injected with MPTP according to certain schemes. The behavior of experimental animals was assessed, and after their decapitation, the content of monoamines in the structures of the brain, peripheral organs, and blood plasma was determined by HPLC, and a morphofunctional analysis of the studied tissues and organs was performed. Results. The clinical stage of PD was modeled in animals, which corresponds to the key characteristics of PD in humans. A hypothetical preclinical stage of PD was modeled in animals, on which the method of early diagnosis was successfully tested. This model shows a number of important biochemical changes in peripheral organs, indicating the systemic nature of the disease and preceding the onset of the clinical stage of PD. Research limitations. The results of this study can only be applied to humans only after similar results have been obtained in monkeys. Limitations. Only after obtaining similar results in monkeys the results of this study can be translated to humans. Conclusion. Knowledge about the mechanisms of action of some neurotoxins is expanding, which are successfully used for the needs of fundamental, medical and biological sciences.
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Mokiy, Vladimir, and Tatiana Lukyanova. "Covid-19: Systems Transdisciplinary Generalization, Technical and Technological Ideas, and Solutions." Informing Science: The International Journal of an Emerging Transdiscipline 25 (2022): 001–21. http://dx.doi.org/10.28945/4893.
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Aim/Purpose: The Covid-19 pandemic has created many adverse effects. It overloads the healthcare system, causes deaths, and angers some at anti-covid restrictions. This study examines the feasibility of using technical and technological ideas to overcome these effects. The solution is based on new knowledge about the virus, its nature, formation, and activation in the environment. Background: The rapid spread of a new coronavirus infection is taking place against the background of a lack of time required to create new treatment scenarios for the disease, development, production, and vaccine safety research. In such a situation, it became necessary to gain this time for organizing and conducting events that could reduce the burden on the healthcare system. Methodology: The science that studies the morphology, physiology, genetics, ecology, and evolution of viruses is virology. The modern development of virology is moving towards a more accurate and comprehensive description of the mechanisms of interaction of viruses with the host organism. This contributed to the emergence of genomics, transcriptomics, proteomics, and immunomics. However, in virology, there is no particular discipline that sets itself three fundamental goals: to substantiate a single concept of the emergence of viruses; to study the natural mechanisms of formation of virus molecules in the environment; to describe the natural mechanisms of activation of certain viruses in the environment that cause viral pandemics. As a result, there are many articles among the published scientific articles on viruses dealing with the mechanisms of interaction of viruses with the host organism. However, there are no articles on the natural mechanisms of formation and activation of certain viruses in the environment. In the absence of such specialized articles, we were forced to use the method of systems transdisciplinary generalization of disciplinary knowledge to achieve our article’s purpose. Generalization created new knowledge about the nature of viruses, about the mechanisms of their formation and activation in the environment and cells of biological organisms. It is logical to assume that to synchronize the state of biological objects of all functional ensembles on the planet, it is necessary to create and activate appropriate “technological tools.” We have suggested and proved that RNA viruses play the role of such tools. Piezoelectricity activates viruses. It occurs during the compression and stretching of sedimentary rocks and bases of continental plates in different territories. Contribution: The systems transdisciplinary generalization of the knowledge of scientific disciplines made it possible to edit the concept of viruses, to eliminate stereotypes that arose due to the use of unsuccessful analogies. As a result of this generalization, it was possible to prove that viruses are not intracellular parasites. The virus is a “technological tool” of the planetary organizing component. This “tool” aims to correct the genetic programs of organisms of all functional ensembles (plants, animals, people), which will maintain the state of organisms and the parameters of their metabolism in changing environmental conditions. Findings: The viruses that triggered pandemics in the 20th century and early 21st century are RNA viruses. RNA molecules play the role of “technological tools” that the planetary organizing component uses to carry out short-term and long-term adjustments and constant support of the genetic programs of biological organisms. Therefore, in such a situation, it is advisable to talk not about the fight against the virus but only about eliminating the negative manifestations of the Covid-19 pandemic: reducing the number of people in need of emergency hospitalization, eliminating cases of the acute course of the disease and deaths. It is proposed to use certain technical and technological ideas and solutions to eliminate these negative manifestations. Recommendation for Researchers: This paper recommends that researchers use new interdisciplinary and transdisciplinary approaches. They challenge assumptions and conclusions about the nature of viruses, and the mechanisms of their formation and activation in the environment can initiate. Such new research might describe the mechanisms that form and activate viruses in the environment and the body’s cells. They also might provide practical use of this knowledge to eliminate the multiple speculations and fears that arise against the background of reports of the likely appearance of more deadly viruses and viral infections. Future Research: The results of a systems transdisciplinary generalization of disciplinary knowledge about the nature and purpose of viruses are essential for expanding the horizon of the scientific worldview. Future fundamental research on the mechanisms of objective organizing constituents, a general description given in this article, will contribute to a deeper understanding of chemical and biological evolution mechanisms in which modern humanity is involved. In due time, such an understanding will allow a new look at the existing scenarios of the world socio-economic order, explore and describe new principles of sustainable development of society.
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McKiernan, Erin C., and Diano F. Marrone. "CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging." PeerJ 5 (September 19, 2017): e3836. http://dx.doi.org/10.7717/peerj.3836.
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Neuron types (e.g., pyramidal cells) within one area of the brain are often considered homogeneous, despite variability in their biophysical properties. Here we review literature demonstrating variability in the electrical activity of CA1 hippocampal pyramidal cells (PCs), including responses to somatic current injection, synaptic stimulation, and spontaneous network-related activity. In addition, we describe how responses of CA1 PCs vary with development, experience, and aging, and some of the underlying ionic currents responsible. Finally, we suggest directions that may be the most impactful in expanding this knowledge, including the use of text and data mining to systematically study cellular heterogeneity in more depth; dynamical systems theory to understand and potentially classify neuron firing patterns; and mathematical modeling to study the interaction between cellular properties and network output. Our goals are to provide a synthesis of the literature for experimentalists studying CA1 PCs, to give theorists an idea of the rich diversity of behaviors models may need to reproduce to accurately represent these cells, and to provide suggestions for future research.
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Kelly, Rachel, Aysha Fleming, Gretta T. Pecl, Julia von Gönner, and Aletta Bonn. "Citizen science and marine conservation: a global review." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1814 (November 2, 2020): 20190461. http://dx.doi.org/10.1098/rstb.2019.0461.
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Climate change, overfishing, marine pollution and other anthropogenic drivers threaten our global oceans. More effective efforts are urgently required to improve the capacity of marine conservation action worldwide, as highlighted by the United Nations Decade of Ocean Science for Sustainable Development 2021–2030. Marine citizen science presents a promising avenue to enhance engagement in marine conservation around the globe. Building on an expanding field of citizen science research and practice, we present a global overview of the current extent and potential of marine citizen science and its contribution to marine conservation. Employing an online global survey, we explore the geographical distribution, type and format of 74 marine citizen science projects. By assessing how the projects adhere to the Ten Principles of Citizen Science (as defined by the European Citizen Science Association), we investigate project development, identify challenges and outline future opportunities to contribute to marine science and conservation. Synthesizing the survey results and drawing on evidence from case studies of diverse projects, we assess whether and how citizen science can lead to new scientific knowledge and enhanced environmental stewardship. Overall, we explore how marine citizen science can inform current understanding of marine biodiversity and support the development and implementation of marine conservation initiatives worldwide. This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.
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Jones, Ghangela, Cesar Escalante, and Hofner Rusiana. "Reconciling information gaps in organic farm borrowers’ dealings with farm lenders." Agricultural Finance Review 75, no. 4 (November 2, 2015): 469–83. http://dx.doi.org/10.1108/afr-01-2015-0002.
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Purpose – Organic outputs have been increasing at much lower rates than growth in consumer demand. Organic farmers’ debt aversion hinders them from obtaining business funds through borrowing. The purpose of this paper is to clarify that the farmers’ reluctance to use debt as a funding option can be more attributed to gaps in existing borrower-lender relationships, beyond sustainability principles. Design/methodology/approach – Empirical evidence collected from organic farmers and farm lenders establish differing expectations and perceptions that reinforce the organic farmers’ debt aversion. The farm lender survey data set was analyzed using the Heckman approach applied to two lenders’ decisions: their interest in lending to organic farm borrowers and loan amounts approved for successful loan applicants. The econometric results were reconciled with the compiled inputs provided by organic farmers interviewed. Findings – Results validate the farmers’ lower reliance on loans due to suspicions that lenders lack knowledge and consideration of organic farming conditions and principles. Farm lenders must depart from employing a uniform credit risk appraisal model and adopt borrower-specific versions of the model, but not necessarily delineating organic-conventional farming dichotomy that may not substantially affect credit risk measurement. Organic farms, on the other hand, need to better understand the credit risk appraisal principles and use their inherent business strengths to compete for loans with conventional farms without any special consideration. Practical implications – Borrower-lender relationships can improve if information gaps between lenders and borrowers can be minimized with more extensive outreach education efforts. Better relationships would increase organic farms’ credit access to effectively address an impending supply gap in an expanding industry. Originality/value – To the knowledge, a specific focus on organic farms in understanding farm borrower-lender relationships has never been explored in literature.
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Illes, Anya E., and Laila Yunes-Jimenez. "A female songbird out-sings male conspecifics during simulated territorial intrusions." Proceedings of the Royal Society B: Biological Sciences 276, no. 1658 (December 2, 2008): 981–86. http://dx.doi.org/10.1098/rspb.2008.1445.
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While birdsong is a model system for animal communication studies, our knowledge is derived primarily from the study of only one sex and is therefore incomplete. The study of song in a role-reversed species would provide a unique opportunity to study selective pressures and mechanisms specific to females, and to test the robustness of current theories in an empirically novel manner. We investigated function of female song in stripe-headed sparrows ( Aimophila r. ruficauda ), a Neotropical, duetting passerine, and found that during simulated territorial intrusions by a female, male or duetting pair, females: (i) sang more than males to same-sex and duet playback, (ii) played a leading singing role in all contexts, and (iii) showed a longer term song response than males. These results suggest that females sing competitively against other females, and that intrasexual selection may be greater among females than among males. This is the first songbird study to show a stronger vocal role in territory defence for females than males. Stripe-headed sparrows are group-living cooperative breeders, and preliminary data suggest that polyandry and/or resource defence may explain strong female singing behaviour. Stripe-headed sparrows may be a useful study species for expanding our knowledge of vocal communication in female animals.
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Jepson, P., F. Schepers, and W. Helmer. "Governing with nature: a European perspective on putting rewilding principles into practice." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1761 (October 22, 2018): 20170434. http://dx.doi.org/10.1098/rstb.2017.0434.
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Academic interest in rewilding is moving from commentary to discussion on future research agendas. The quality of rewilding research design will be enhanced if it is informed by knowledge of the rewilding practice. Here, we describe the conceptual origins and six case study examples of a mode of rewilding that emerged in the Dutch Delta and is being promoted and supported by Rewilding Europe, an umbrella organization established in 2011. The case experiences presented help position this version of rewilding in relation to the US 3C's version and point towards a rewilding action philosophy characterized by pragmatic realism and pioneer projects around which multiactor networks interested in policy innovation and change form. We argue that scaling-up the models of rewilding presented is constrained by institutional cultures and will require innovations in conservation finance and business models. Nonetheless, we suggest that the expanding European Rewilding Network and associated facilities, such as the European Wildlife Bank, represent a valuable asset for natural science research, aimed at exploring the ecological impacts of grazing and the relationship between role of restored herbivore guilds and biotical expansion, and for social science research investigating concepts such as non-human agency and autonomy. Lastly, we ask applied scientists to view rewilding as an uncertain and unfolding conservation approach and to refrain from seeking to specify it as a management approach supporting the delivery of pre-determined targets and/or ideals. This is because such actions may constrain the transformative potential of rewilding practice. This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
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CIOBANU, Elena, Catalina CROITORU, Greta BALAN, Vladimir BERNIC, Olga BURDUNIUC, and Alina FERDOHLEB. "„Phage treatment and wetland technology as intervention strategy to prevent dissemination of antibiotic resistance in surface waters”- a project launch in low-middle in-come countries of Eastern Europe." One Health & Risk Management 3, no. 2S (March 20, 2022): 28. http://dx.doi.org/10.38045/ohrm.2022.2.05.
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Introduction. Antimicrobial resistance is a widespread and tough challenge, if not impossible, to limit by biological, physical or geographical barriers. This is the reason behind the "One Health" approach, which guides all rules and research plans on antimicrobial resistance worldwide. The abusive and excessive use of antimicrobials in human medicine, veterinary practices, agriculture and aquaculture has traditionally been considered the main reason for the global spread of antimicrobial resistance. The purpose was to assess the epidemiological risk of wastewater as a source of antimicrobial-resistant bacteria concerning public health, focusing on low- and middle-income Eastern European countries.
Material and methods. To achieve this goal, the development of a secure, cost-effective and sustainable technology has been planned, which could easily be introduced in low- and middle-income countries. There have been outlined the following steps: mapping the consumption of antimicrobial emulsions at the national level (primary, cross-sectional study, complete sampling, based on imported data and centralized public acquirement of medicines); research regarding the knowledge, attitudes and practices of the population on antimicrobial resistance (primary, cross-sectional, descriptive study); qualitative and descriptive evaluation of barriers to reduce the phenomenon of antimicrobial resistance by the healthcare services; research regarding the knowledge, attitudes and practices in human and veterinary healthcare on antimicrobial resistance (primary, cross-sectional, descriptive study); screening and investigation of the microbial resistance mechanisms to the strains isolated from patients with infectious pathological processes (preclinical study); analysis of the specific features and sampling of the Constructed Wetlands in Orhei (preclinical study). The Ethics Committee of the Ministry of Health of RM positively approved the Research PhageLand.
Results. The obtained results of this research will contribute to a better understanding of the involved factors that are generating the broadening of antimicrobial resistance and how they influence the transmission among different hosts (bacteria, animals and humans). Moreover, it can also have a major impact to the engineering field and wastewater management companies by expanding the range of tools with sophisticated technologies, designed to reduce the risk of transmitting antimicrobial resistance in wastewater and improve sewerage practices.
Conclusions. The effective use of knowledge and practices in the worldwide fight against antimicrobial resistance, providing useful data, applicable knowledge, efficient, environmentally friendly and cost-effective protocols and technologies, which can be scaled, implemented and used at the European and international levels with no economic or geographical obstacles.
Acknowledgment. The research was conducted in the Republic of Moldova within the JPIAMR projects (PhageLand), project number - 22.80013.8007.1.
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Muthuramalingam, Pandiyan, Rajendran Jeyasri, Kasinathan Rakkammal, Lakkakula Satish, Sasanala Shamili, Adhimoolam Karthikeyan, Alaguvel Valliammai, et al. "Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review." Biology 11, no. 7 (July 7, 2022): 1022. http://dx.doi.org/10.3390/biology11071022.
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Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.
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Magalhães, Alex Fernandes, and Luiz Alex Silva Saraiva. "In Defense of a Complex Notion of Subject in Organizational Studies." Organizações & Sociedade 29, no. 100 (January 2022): 20–50. http://dx.doi.org/10.1590/1984-92302022v29n0001en.
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Abstract This essay reflects on the need to expand the complexity of the notion of subject in the critical approaches used in organizational studies and to contribute with a new perspective on the human attribute in collective issues based on a new concept: the concrete procedural subject. The human and social sciences are faced with the challenge of delimiting their object of study (human beings in their manifestations) without excluding the biological, social, historical, and psychological dimensions that are inherent to them, thus avoiding reductionism. It is believed that this complex perspective is relevant to analyses of socio-organizational spaces since we take the subject as a fundamental analytical unit to understand organizational dynamics. Organizations emerge from the interrelationships between subjects, expanding, structuring, and institutionalizing themselves. Therefore, the subject and organization are inseparable, and dichotomies must be avoided in favor of knowledge production in organizational studies and other correlated areas. Based on a critical analysis and adopting a multifaceted and plural approach, with contributions from psychoanalysis, sociohistorical psychology, and post-structuralism, all of which address the complexity of the human being, this essay presents a notion of subject that is contradictory and fluid, which are the marks of its procedurality in contemporary times and the foundation for understanding the complex socio-organizational dynamic and its phenomena.
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Magalhães, Alex Fernandes, and Luiz Alex Silva Saraiva. "Em Defesa de uma Concepção Complexa de Sujeito nos Estudos Organizacionais." Organizações & Sociedade 29, no. 100 (January 2022): 20–50. http://dx.doi.org/10.1590/1984-92302022v29n0001pt.
Full textAbstract:
Abstract This essay reflects on the need to expand the complexity of the notion of subject in the critical approaches used in organizational studies and to contribute with a new perspective on the human attribute in collective issues based on a new concept: the concrete procedural subject. The human and social sciences are faced with the challenge of delimiting their object of study (human beings in their manifestations) without excluding the biological, social, historical, and psychological dimensions that are inherent to them, thus avoiding reductionism. It is believed that this complex perspective is relevant to analyses of socio-organizational spaces since we take the subject as a fundamental analytical unit to understand organizational dynamics. Organizations emerge from the interrelationships between subjects, expanding, structuring, and institutionalizing themselves. Therefore, the subject and organization are inseparable, and dichotomies must be avoided in favor of knowledge production in organizational studies and other correlated areas. Based on a critical analysis and adopting a multifaceted and plural approach, with contributions from psychoanalysis, sociohistorical psychology, and post-structuralism, all of which address the complexity of the human being, this essay presents a notion of subject that is contradictory and fluid, which are the marks of its procedurality in contemporary times and the foundation for understanding the complex socio-organizational dynamic and its phenomena.
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Purdon, Jean, Fannie W. Shabangu, Dawit Yemane, Marc Pienaar, Michael J. Somers, and Ken Findlay. "Species distribution modelling of Bryde’s whales, humpback whales, southern right whales, and sperm whales in the southern African region to inform their conservation in expanding economies." PeerJ 8 (September 22, 2020): e9997. http://dx.doi.org/10.7717/peerj.9997.
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In southern African waters, information about species distribution and habitat preferences of many cetacean species is limited, despite the recent economic growth that may affect them. We determined the relative importance of eight environmental variables (bathymetry, distance to shore, slope, chlorophyll-a, salinity, eastwards sea water velocity, northwards sea water velocity and sea surface temperature) as drivers of seasonal habitat preferences of Bryde’s whales (Balaenoptera brydei), humpback whales (Megaptera novaeangliae), southern right whales (Eubalaena australis) and sperm whales (Physeter macrocephalus). Using presence only data from multiple sources, we constructed predictive species distribution models (SDMs) consisting of ensembles of seven algorithms for these species during both summer and winter. Predicted distribution for all cetaceans was high in southern Africa and, in particular, within the South African Exclusive Economic Zone (EEZ). Predictive models indicated a more pronounced seasonal variation for humpback, sperm and southern right whales than for Bryde’s whales. Southern right whales occurred closer to shore during winter, humpback whales were more likely to occur along the east coast in winter and the west coast in summer, and sperm whales were more concentrated off the shelf in winter. Our study shows that ensemble models using historical, incidental and scientific data, in conjunction with modern environmental variables, can provide baseline knowledge on important environmental drivers of cetacean distribution for conservation purposes. Results of this study can further be used to help develop marine spatial plans and identify important marine mammal areas.
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Ge, Shuyun, Haiwen Zhou, Zengtong Zhou, Lin Liu, and Jianing Lou. "Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry." PeerJ 9 (January 4, 2021): e10619. http://dx.doi.org/10.7717/peerj.10619.
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Background Oral cancer progresses from hyperplastic epithelial lesions through dysplasia to invasive carcinoma. The critical needs in oral cancer treatment are expanding our knowledge of malignant tumour progression and the development of useful approaches to prevent dysplastic lesions. This study was designed to gain insights into the underlying metabolic transformations that occur during the process of oral carcinogenesis. Methods We used gas chromatography-mass spectrometry (GC-MS) in conjunction with multivariate statistical techniques to observe alterations in serum metabolites in a 4-Nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis model. Thirty-eight male rats were randomly divided into two groups, including the 4NQO-induced model group of 30 rats and the healthy control group of five rats. Animals were sacrificed at weeks 9, 13, 20, 24, and 32, post-4NQO treatment. Tissue samples were collected for histopathological examinations and blood samples were collected for metabolomic analysis. Partial least squares discriminate analysis (PLS-DA) models generated from GC-MS metabolic profile data showed robust discrimination from rats with oral premalignant and malignant lesions induced by 4NQO, and normal controls. Results The results found 16 metabolites associated with 4NQO-induced rat tongue carcinogenesis. Dysregulated arachidonic acid, fatty acid, and glycine metabolism, as well as disturbed tricarboxylic acid (TCA) cycle and mitochondrial respiratory chains were observed in the animal model. The PLS-DA models of metabolomic results demonstrated good separations between the 4NQO-induced model group and the normal control group. Conclusion We found several metabolites modulated by 4NQO and provide a good reference for further study of early diagnosis in oral cancer.
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Buehler, Deborah M., and Theunis Piersma. "Travelling on a budget: predictions and ecological evidence for bottlenecks in the annual cycle of long-distance migrants." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1490 (July 18, 2007): 247–66. http://dx.doi.org/10.1098/rstb.2007.2138.
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Long-distance migration, and the study of the migrants who undertake these journeys, has fascinated generations of biologists. However, many aspects of the annual cycles of these migrants remain a mystery as do many of the driving forces behind the evolution and maintenance of the migrations themselves. In this article we discuss nutritional, energetic, temporal and disease - risk bottlenecks in the annual cycle of long-distance migrants, taking a sandpiper, the red knot Calidris canutus , as a focal species. Red knots have six recognized subspecies each with different migratory routes, well-known patterns of connectivity and contrasting annual cycles. The diversity of red knot annual cycles allows us to discuss the existence and the effects of bottlenecks in a comparative framework. We examine the evidence for bottlenecks focusing on the quality of breeding plumage and the timing of moult as indicators in the six subspecies. In terms of breeding plumage coloration, quality and timing of prealternate body moult (from non-breeding into breeding plumage), the longest migrating knot subspecies, Calidris canutus rogersi and Calidris canutus rufa , show the greatest impact of bottlenecking. The same is true in terms of prebasic body moult (from breeding into non-breeding plumage) which in case of both C. c. rogersi and C. c. rufa overlaps with southward migration and may even commence in the breeding grounds. To close our discussion of bottlenecks in long-distance migrants, we make predictions about how migrants might be impacted via physiological ‘trade-offs’ throughout the annual cycle, using investment in immune function as an example. We also predict how bottlenecks may affect the distribution of mortality throughout the annual cycle. We hope that this framework will be applicable to other species and types of migrants, thus expanding the comparative database for the future evaluation of seasonal selection pressures and the evolution of annual cycles in long-distance migrants. Furthermore, we hope that this synthesis of recent advancements in the knowledge of red knot annual cycles will prove useful in the ongoing attempts to model annual cycles in migratory birds.
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Balmford, Andrew, Peter Crane, Andy Dobson, Rhys E. Green, and Georgina M. Mace. "The 2010 challenge: data availability, information needs and extraterrestrial insights." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1454 (February 28, 2005): 221–28. http://dx.doi.org/10.1098/rstb.2004.1599.
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At the 2002 Johannesburg World Summit on Sustainable Development, 190 countries endorsed a commitment to achieve, by 2010, a significant reduction of the current rate of biodiversity loss at the global, regional and national levels. A wide range of approaches is available to the monitoring of progress towards this objective. The strengths and weaknesses of many of these approaches are considered, with special attention being given to the proposed and existing indicators described in the other papers in this issue. Recommendations are made about the development of indicators. Most existing and proposed indicators use data collected for other purposes, which may be unrepresentative. In the short term, much remains to be done in expanding the databases and improving the statistical techniques that underpin these indicators to minimize potential biases. In the longer term, indicators based on unrepresentative data should be replaced with equivalents based on carefully designed sampling programmes. Many proposed and existing indicators do not connect clearly with human welfare and they are unlikely to engage the interest of governments, businesses and the public until they do so. The extent to which the indicators already proposed by parties to the Convention on Biological Diversity are sufficient is explored by reference to the advice an imaginary scientific consultant from another planet might give. This exercise reveals that the range of taxa and biomes covered by existing indicators is incomplete compared with the knowledge we need to protect our interests. More fundamentally, our understanding of the mechanisms linking together the status of biodiversity, Earth system processes, human decisions and actions, and ecosystem services impacting human welfare is still too crude to allow us to infer reliably that actions taken to conserve biodiversity and protect ecosystem services are well chosen and effectively implemented. The involvement of social and Earth system scientists, as well as biologists, in collaborative research programmes to build and parameterize models of the Earth system to elucidate these mechanisms is a high priority.
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Bondarchuk, E. Yu, A. A. Tsygichko, and F. M. Asaturova. "METHODOLOGICAL APPROACHES TO THE ASSESSMENT OF THE ENTOMOPATHOGENIC ACTIVITY OF MICROORGANISMS AGAINST INSECT PESTS IN VITRO (REVIEW)." TAURIDA HERALD OF THE AGRARIAN SCIENCES 3 (27) (2021): 20–34. http://dx.doi.org/10.33952/2542-0720-2021-3-27-20-34.
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Excessive application of chemical insecticides in agriculture has led to some serious problems that threaten the environment and human health. One of the possible ways to overcome the situation is to shift to environmentally-friendly preparations based on entomopathogenic bioagents. The purpose of this review was to search for and systematize methodological approaches to determine the entomopathogenic activity of microorganisms of various taxonomic groups in laboratory conditions. The expediency of choosing the necessary method when studying a particular phenomenon or process is an important point both in the fundamental and applied field of research. The primary assessment of the entomopathogenic activity of microorganisms in vitro is the basis for expanding the spectrum of their action, introducing new strains into collections. It also contributes to the replenishment of knowledge about the already known properties of various types of microorganisms. All this, certainly, is connected with the further choice of them as biological agents. Each of the presented groups of entomopathogens has its distinctive features of the mechanisms of action determined by the target insect. Concerning the choice of methodological approaches for assessing the entomopathogenic effect of fungi, the authors relied on the physiological characteristics of the insect and its stage of harmfulness. The researchers were guided by methodological approaches of oral infection of insects using an infected food source to study the activity of bacterial strains. Pathological changes in the cellular structure, as well as deformations of intestinal elements, were noted. The most common way to assess the effect of entomopathogenic viruses in the laboratory is the method of surface infection of the food source of the tested insect, taking into account the high specialization of the agent. When studying the mechanisms of action of fungal, bacterial and viral agents, researchers injected a suspension of the pathogen into the insect’s body. The search and systematization of relevant methodological approaches to assess entomopathogenic microorganisms depending on the taxonomic affiliation is an important part of the work directly related to the development of a high-quality and effective bioinsecticide.
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Marques da Silva, Wanderson, Nubia Seyffert, Artur Silva, and Vasco Azevedo. "A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome." PeerJ 9 (December 23, 2021): e12456. http://dx.doi.org/10.7717/peerj.12456.
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Background Corynebacterium pseudotuberculosis is a Gram-positive facultative intracellular pathogen and the etiologic agent of illnesses like caseous lymphadenitis in small ruminants, mastitis in dairy cattle, ulcerative lymphangitis in equines, and oedematous skin disease in buffalos. With the growing advance in high-throughput technologies, genomic studies have been carried out to explore the molecular basis of its virulence and pathogenicity. However, data large-scale functional genomics studies are necessary to complement genomics data and better understating the molecular basis of a given organism. Here we summarize, MS-based proteomics techniques and bioinformatics tools incorporated in genomic functional studies of C. pseudotuberculosis to discover the different patterns of protein modulation under distinct environmental conditions, and antigenic and drugs targets. Methodology In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of C. pseudotuberculosis at the protein level. Results Here, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of C. pseudotuberculosis at the protein level. The implementation and use of protocols, strategies, and proteomics approach to characterize the different subcellular fractions of the proteome of this pathogen. In addition, we have discussed the immunoproteomics, immunoinformatics and genetic tools employed to identify targets for immunoassays, drugs, and vaccines against C. pseudotuberculosis infection. Conclusion In this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the C. pseudotuberculosis genome. Together, all information generated from these proteomics studies allowed expanding our knowledge about factors related to the pathophysiology of this pathogen.
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Caspar, Kai R., Larissa Mader, Fabian Pallasdies, Miriam Lindenmeier, and Sabine Begall. "Captive gibbons (Hylobatidae) use different referential cues in an object-choice task: insights into lesser ape cognition and manual laterality." PeerJ 6 (August 6, 2018): e5348. http://dx.doi.org/10.7717/peerj.5348.
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Background Utilization of visual referential cues by non-human primates is a subject of constant scientific interest. However, only few primate species, mostly great apes, have been studied thoroughly in that regard, rendering the understanding of phylogenetic influences on the underlying cognitive patterns difficult. Methods We tested six species of captive gibbons in an object-choice task (n = 11) for their ability to interpret two different pointing gestures, a combination of body orientation and gaze direction as well as glancing as referential cues. Hand preferences were tested in the object-choice task and in a bimanual tube task (n = 18). Results We found positive responses to all signals except for the glancing cue at the individual as well as at the group level. The gibbons’ success rates partially exceed results reported for great apes in comparable tests and appear to be similarly influenced by prior exposure to human communicative cues. Hand preferences exhibited by the gibbons in the object-choice task as well as in a bimanual tube task suggest that crested gibbons (Nomascus sp.) are strongly lateralized at individual but not at population level for tasks involving object manipulation. Discussion Based on the available data, it can be assumed that the cognitive foundations to utilize different visual cues essential to human communication are conserved in extant hominoids and can be traced back at least to the common ancestor of great and lesser apes. However, future studies have to further investigate how the social environment of gibbons influences their ability to exploit referential signals. Gibbons’ manual laterality patterns appear to differ in several aspects from the situation found in great apes. While not extensive enough to allow for general conclusions about the evolution of hand preferences in gibbons or apes in general, our results add to the expanding knowledge on manual lateralization in the Hylobatidae.