| 1. |
- Ahi, Ehsan Pashay, et al.
(författare)
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Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids
- 2020
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Ingår i: PeerJ. - : PEERJ INC. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorodgenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts.
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| 2. |
- Ahsan, Hajra, et al.
(författare)
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Photocatalysis and adsorption kinetics of azo dyes by nanoparticles of nickel oxide and copper oxide and their nanocomposite in an aqueous medium
- 2022
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Azo dyes are recalcitrant organic pollutants present in textile industry effluents. Conventional treatment methods to remove them come with a range of disadvantages. Nanoparticles and their nanocomposites offer more efficient, less expensive and easy to handle wastewater treatment alternative. Methods. In this study, nanoparticles of nickel oxide (NiO-NPs), copper oxide (CuO-NPs) and their nanocomposite (NiO/CuO-NC) were synthesized using co- precipitation method. The functional groups present on the surface of synthesized nanomaterials were verified using Fourier-transform infrared spectroscopy (FTIR). Surface morphology was assessed using scanning electron microscopy (SEM) whereas purity, shape and size of the crystallite were determined using X-ray diffraction (XRD) technique. The potential of these nanomaterials to degrade three dyes i.e., Reactive Red-2 (RR-2), Reactive Black-5 (RB-5) and Orange II sodium salt (OII) azo dyes, was determined in an aqueous medium under visible light (photocatalysis). The photodegradation effectiveness of all nanomaterials was evaluated under different factors like nanomaterial dose (0.02-0.1 g 10 mL-1), concentration of dyes (20-100 mg L-1), and irradiation time (60-120 min). They were also assessed for their potential to adsorb RR-2 and OII dyes. Results. Results revealed that at optimum concentration (60 mgL-1) of RR-2, RB-5, and OII dyes, NiO-NPs degraded 90, 82 and 83%, CuO-NPs degraded 49, 34, and 44%, whereas the nanocomposite NiO/CuO-NC degraded 92, 93, and 96% of the said dyes respectively. The nanomaterials were categorized as the efficient degraders of the dyes in the order: NiO/CuO-NC > NiO-NPs > CuO-NPs. The highest degradation potential shown by the nanocomposite was attributed to its large surface area, small particles size, and quick reactions which were proved by advance analytical techniques. The equilibrium and kinetic adsorption of RR-2 and OII on NiO-NPs, CuO-NPs, and NiO/CuO-NC were well explained with Langmuir and Pseudo second order model, respectively (R2 ≥0.96). The maximum RR-2 adsorption (103 mg/g) was obtained with NiO/CuO-NC. It is concluded that nanocomposites are more efficient and promising for the dyes degradation from industrial wastewater as compared with dyes adsorption onto individual NPs. Thus, the nanocomposite NiO/CuO-NC can be an excellent candidate for photodegradation as well as the adsorption of the dyes in aqueous media.
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| 3. |
- Angell, IL, et al.
(författare)
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De novo species identification using 16S rRNA gene nanopore sequencing
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8, s. e10029-
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Tidskriftsartikel (refereegranskat)abstract
- Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
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| 4. |
- Anikin, Andrey
(författare)
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The honest sound of physical effort
- 2023
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Ingår i: PeerJ. - 2167-8359. ; 11:e14944
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Tidskriftsartikel (refereegranskat)abstract
- Acoustic correlates of physical effort are still poorly understood, even though effort is vocally communicated in a variety of contexts with crucial fitness consequences, including both confrontational and reproductive social interactions. In this study 33 lay participants spoke during a brief, but intense isometric hold (L-sit), first without any voice-related instructions, and then asked either to conceal their effort or to imitate it without actually performing the exercise. Listeners in two perceptual experiments then rated 383 recordings on perceived level of effort (n = 39 listeners) or categorized them as relaxed speech, actual effort, pretended effort, or concealed effort (n = 102 listeners). As expected, vocal effort increased compared to baseline, but the accompanying acoustic changes (increased loudness, pitch, and tense voice quality) were under voluntary control, so that they could be largely suppressed or imitated at will. In contrast, vocal tremor at approximately 10 Hz was most pronounced under actual load, and its experimental addition to relaxed baseline recordings created the impression of concealed effort. In sum, a brief episode of intense physical effort causes pronounced vocal changes, some of which are difficult to control. Listeners can thus estimate the true level of exertion, whether to judge the condition of their opponent in a fight or to monitor a partner’s investment into cooperative physical activities.
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| 5. |
- Bakker, F. T., et al.
(författare)
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The Global Museum: natural history collections and the future of evolutionary science and public education
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.
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| 6. |
- Baranowski, Bartosz, et al.
(författare)
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Protein family neighborhood analyzer-ProFaNA
- 2023
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Ingår i: PeerJ. - 2167-8359. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Functionally related genes are well known to be often grouped in close vicinity in the genomes, particularly in prokaryotes. Notwithstanding the diverse evolutionary mechanisms leading to this phenomenon, it can be used to predict functions of uncharacterized genes. Methods: Here, we provide a simple but robust statistical approach that leverages the vast amounts of genomic data available today. Considering a protein domain as a functional unit, one can explore other functional units (domains) that significantly often occur within the genomic neighborhoods of the queried domain. This analysis can be performed across different taxonomic levels. Provisions can also be made to correct for the uneven sampling of the taxonomic space by genomic sequencing projects that often focus on large numbers of very closely related strains, e.g., pathogenic ones. To this end, an optional procedure for averaging occurrences within subtaxa is available. Results: Several examples show this approach can provide useful functional predictions for uncharacterized gene families, and how to combine this information with other approaches. The method is made available as a web server at http://bioinfo.sggw.edu.pl/neighborhood_analysis.
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| 7. |
- Beckmann, Lara Maleen, 1993, et al.
(författare)
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Odd family reunion: DNA barcoding reveals unexpected relationship between three hydrozoan species
- 2023
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Ingår i: PeerJ. - 2167-8359. ; 11:e15118
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of life histories is crucial for understanding ecological and evolutionary processes, but for many hydrozoan species only incomplete life cycles have been described due to challenges in linking hydromedusae with their polyp stages. Using a combination of DNA barcoding, morphology, and ecological information, we describe for the first time the polyp stage of Halopsis ocellata Agassiz, 1865 and re-describe that of Mitrocomella polydiademata (Romanes, 1876). Campanulinid hydroids referable to Lafoeina tenuis Sars, 1874 and collected in the same biogeographic region as the type locality of this species are shown to be the polyp stage of these two mitrocomid hydromedusae. The nominal species L. tenuis thus is a species complex that includes the polyp stage of medusae belonging to at least two genera currently placed in a different family. Consistent morphological and ecological differences were found between the polyps linked to each of these two hydromedusae, but molecular results suggest that yet other species may have morphologically similar hydroids. Polyps morphologically identified to L. tenuis are therefore better referred to as Lafoeina tenuis-type until further associations are resolved, particularly when occurring outside of the area of distribution of H. ocellata and M. polydiademata. Molecular identification integrated with traditional taxonomy is confirmed as an effective approach to link inconspicuous stages of marine invertebrates with hitherto unknown life cycles, especially in often-overlooked taxa. Disentangling the relationships between L. tenuis, H. ocellata, and M. polydiademata lays the ground for future research aimed at resolving the taxonomy and systematics of the enigmatic families Mitrocomidae and Campanulinidae.
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| 8. |
- Belle, Simon
(författare)
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Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background. This study aimed to assess whether ecological inferences from isotopic functional indices (IFIs) are impacted by changes in isotopic baselines in aquatic food webs. We used sudden CO2-outgassing and associated shifts in DIC- delta C-13 brought by waterfalls as an excellent natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inferences from IFIs.Methods. Carbon (delta C-13) and nitrogen (delta N-15) stable isotopic ratios of invertebrate communities sharing similar structure were measured at above- and below-waterfall sampling sites from five rivers and streams in Southern Quebec (Canada). For each sampled invertebrate community, the six Laymans IFIs were then calculated in the delta-space (delta C-13 vs. delta N-15).Results. As expected, isotopic functional richness indices, measuring the overall extent of community trophic space, were strongly sensitive to changes in isotopic baselines unlike other IFIs. Indeed, other IFIs were calculated based on the distribution of species within delta-space and were not strongly impacted by changes in the vertical or horizontal distribution of specimens in the delta-space. Our results highlighted that IFIs exhibited different sensitivities to changes in isotopic baselines, leading to potential misinterpretations of IFIs in river studies where isotopic baselines generally show high temporal and spatial variabilities. The identification of isotopic baselines and their associated variability, and the use of independent trophic tracers to identify the actual energy pathways through food webs must be a prerequisite to IFIs-based studies to strengthen the reliability of ecological inferences of food web structural properties.
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| 9. |
- Benjamin, Bolduc, et al.
(författare)
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The IsoGenie database : an interdisciplinary data management solution for ecosystems biology and environmental research
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.
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| 10. |
- Bensch, Hanna, et al.
(författare)
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Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
- 2022
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature.Methods: In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction.Results: We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
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