| 1. |
- Jonsson, Per R., 1957, et al.
(författare)
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The Barnacle Balanus improvisus as a Marine Model - Culturing and Gene Expression
- 2018
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Ingår i: Jove-Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :138
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Tidskriftsartikel (refereegranskat)abstract
- Barnacles are marine crustaceans with a sessile adult and free-swimming, planktonic larvae. The barnacle Balanus (Amphibalanus) improvisus is particularly relevant as a model for the studies of osmoregulatory mechanisms because of its extreme tolerance to low salinity. It is also widely used as a model of settling biology, in particular in relation to antifouling research. However, natural seasonal spawning yields an unpredictable supply of cyprid larvae for studies. A protocol for the all-year-round culturing of B. improvisus has been developed and a detailed description of all steps in the production line is outlined (i.e., the establishment of adult cultures on panels, the collection and rearing of barnacle larvae, and the administration of feed for adults and larvae). The description also provides guidance on troubleshooting and discusses critical parameters (e.g., the removal of contamination, the production of high-quality feed, the manpower needed, and the importance of high-quality seawater). Each batch from the culturing system maximally yields roughly 12,000 nauplii and can deliver four batches in a week, so up to almost 50,000 larvae per week can be produced. The method used to culture B. improvisus is, probably, to a large extent also applicable to other marine invertebrates with free-swimming-larvae. Protocols are presented for the dissection of various tissues from adults as well as the production of high-quality RNA for studies on gene expression. It is also described how cultured adults and reared cyprids can be utilized in a wide array of experimental designs for examining gene expression in relation to external factors. The use of cultured barnacles in gene expression is illustrated with studies of possible osmoregulatory roles of Na+/K+ ATPase and aquaporins.
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| 2. |
- Abramova, Anna, 1990, et al.
(författare)
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A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments
- 2023
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Ingår i: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Tidskriftsartikel (refereegranskat)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 3. |
- Abramova, Anna, 1990, et al.
(författare)
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CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
- 2021
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059. ; 37:1, s. 121-122
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Tidskriftsartikel (refereegranskat)abstract
- Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.
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| 4. |
- Abramova, Anna, 1990, et al.
(författare)
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Meta-analysis reveals the global picture of antibiotic resistance gene prevalence across environments
- 2022
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Ingår i: bioRXIV. - : Cold Spring Harbor Laboratory.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, current AMR monitoring initiatives lack comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish the typical baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey across 2516 scientific papers, 150 of which contained relevant qPCR data on antibiotic resistance genes (ARGs) in environments associated with potential routes of AMR dissemination. The collected data include 1487 samples distributed across 30 different countries and 17 environmental types, in a time span from 2005 to 2018. More than 330 different genes were identified from the collected studies. Most surveyed environments contained a diverse set of ARGs, but generally at low abundances. We used linear mixed models and overrepresentation analysis to identify time trends and associations between ARGs and specific environments. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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| 5. |
- Abramova, Anna, 1990
(författare)
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Molecular biology of barnacle Balanus improvisus settlement
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this thesis was to investigate molecular mechanisms of various aspects of barnacle settlement, using the acorn barnacle Balanus improvisus. This barnacle is a common fouling species and a model organism for studies in settlement biology, in particular in relation to antifouling research. In order to facilitate the development of genomic resources in this species, we conducted a pilot study for the sequencing of the B. improvisus genome and performed an initial genomic characterization. The analysis revealed that B. improvisus genome has an extremely high genetic diversity, with about 5% nucleotide diversity in coding regions. In addition, we experimentally estimated the B. improvisus genome size, based on DNA staining and flow cytometry measurements, resulting in a haploid genome size of 738 Mbp. To investigate molecular changes during the settlement process, transcriptomes of four different settlement stages, ie free-swimming, closesearch, attached and juvenile, were compared. We identified several key genes involved in the hormonal regulation of molting and metamorphosis, including the broad complex, ecdysone receptor and retinoid X receptor, adding a new level of insight to the molecular mechanisms involved in settlement. Furthermore, we used two types of surfaces with different wettability to test if differences in surface preferences are reflected in gene expression. The results revealed that exploration of the “favourable” hydrophobic surface induced more genes and with larger changes in expression than on hydrophilic suggesting a stronger transcriptional response. We also investigated two specific aspects related to barnacle chemical communication during settlement - sensory receptors and pheromones. Analysis of the transcriptome of cyprid antennules resulted in the identification of two receptor classes, the chemosensory ionotropic receptors and mechanosensory receptors represented by several TRP subfamilies. We identified and characterized six homologs of the waterborne pheromone WSP in B. improvisus that showed differential expression during settlement. These results suggest the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components. With the aim to further establish B. improvisus into a potent marine model system, a detailed protocol was developed for an all-year-round culturing of B. improvisus and adapted at Tjärnö Marine Laboratory. Finally, I summarise current knowledge on the molecular mechanisms of barnacle settlement and outline new research directions to further improve our understanding of the settlement biology of this species.
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| 6. |
- Abramova, Anna, 1990, et al.
(författare)
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Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- - Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling. © 2019 Abramova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 7. |
- Abramova, Anna, 1990, et al.
(författare)
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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
- 2019
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Ingår i: Biofouling. - : Informa UK Limited. - 0892-7014 .- 1029-2454. ; 35:4, s. 416-428
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Tidskriftsartikel (refereegranskat)abstract
- A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in Balanus improvisus and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The B. improvisus WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the B. amphitrite WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.
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| 8. |
- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
- 2021
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Ingår i: Marine Biotechnology. - : Springer Science and Business Media LLC. - 1436-2228 .- 1436-2236. ; 23, s. 402-416
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Tidskriftsartikel (refereegranskat)abstract
- Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the baybarnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies. © 2021, The Author(s).
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| 9. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
- 2023
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Ingår i: Environment International. - 0160-4120 .- 1873-6750. ; 178
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Tidskriftsartikel (refereegranskat)abstract
- Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. How-ever, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the envi-ronment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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| 10. |
- Vishnyakova, I., et al.
(författare)
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Structure of freshwater zooplankton communities from tundra waterbodies in the Lena River Delta, Russian Arctic, with a discussion on new records of glacial relict copepods
- 2017
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Ingår i: Polar Biology. - : Springer Science and Business Media LLC. - 0722-4060 .- 1432-2056. ; 40:8, s. 1629-1643
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Tidskriftsartikel (refereegranskat)abstract
- We present new and more complete information than previously available on the pelagic fauna of the Lena River Delta, eastern Siberia. Zooplankton samples collected between 2000 and 2011 from 11 varied aquatic habitats on Samoylov Island have been examined and clear differences noted between the zooplankton communities in different types of tundra waterbody. Well-marked synchronism in the development of common species populations was, however, revealed by analysis of their life cycles. The pelagic fauna of the investigated aquatic ecosystems is heterogeneous in origin, consisting mainly of aboriginal Arctic species but also including invasive species from more temperate latitudes and relicts of ice-age fauna. One hundred and twenty-five zooplankton taxa belonging to Rotifera (67) and Arthropoda (58) phyla were identified. Five Copepoda species and seven Cladocera species were recorded for the first time in the Lena River Delta; the presence of most of these species in the delta's aquatic ecosystems is associated with Lena River water influx during spring flood. Two calanoid copepods, Eurytemora arctica Wilson and Tash and Eurytemora foveola Johnson, are new species to Palearctic pelagic fauna, previously known only from the Nearctic. The data obtained provide new confirmation that the last glaciation had a marked influence on microcrustacean distributions within the Arctic.
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