A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes.

Single-cell genomics (SCG) methods provide a unique opportunity to analyse whole genome information at the resolution of an individual cell. While SCG has been extensively used to investigate bacterial and archaeal genomes, the technique has been rarely used to access the genetic makeup of uncultivated microbial eukaryotes. In this regard, the use of SCG can provide a wealth of information; not only do the methods allow exploration of the genome, they can also help elucidate the relationship between the cell and intracellular entities extant in nearly all eukaryotes. SCG enables the study of total eukaryotic cellular DNA, which in turn allows us to better understand the evolutionary history and diversity of life, and the physiological interactions that define complex organisms. This article is part of a discussion meeting issue 'Single cell ecology'

Out-of-plane Characterization of Silicon-on-insulator Multiuser MEMS Processes-based Tri-axis Accelerometer

In this paper, we discuss the analysis of out-of-plane characterization of a capacitive tri-axis accelerometer fabricated using SOI MUMPS (Silicon-on Insulator Multi user MEMS Processes) process flow and the results are compared with simulated results. The device is designed with wide operational 3 dB bandwidth suitable for measuring vibrations in industrial applications. The wide operating range is obtained by optimizing serpentine flexures at the four corners of the proof mass. The accelerometer structure was simulated using COMSOL Multiphysics and the displacement sensitivity was observed as 1.2978 nm/g along z-axis. The simulated resonant frequency of the device was found to be 13 kHz along z axis. The dynamic characterization of the fabricated tri-axis accelerometer produces the out-of-plane vibration mode frequency as 13 kHz which is same as the simulated result obtained in z-axis

A Perspective Around Cephalopods and Their Parasites, and Suggestions on How to Increase Knowledge in the Field

Although interest in several areas of cephalopod research has emerged over the last decades (e.g., neurobiology, aquaculture, genetics, and welfare), especially following their 2010 inclusion in the EU Directive on the use of animals for experimental purposes, knowledge regarding the parasites of cephalopods is lacking. Cephalopods can be intermediate, paratenic, or definitive hosts to a range of parasites with a wide variety of life cycle strategies. Here, we briefly review the current knowledge in cephalopod parasitological research, summarizing the main parasite groups that affect these animals. We also emphasize some topics that, in our view, should be addressed in future research, including: (i) better understanding of life cycles and transmission pathways of common cephalopod parasites; (ii) improve knowledge of all phases of the life cycle (i.e., paralarvae, juveniles, adults and senescent animals) and on species from polar deep sea regions; (iii) exploration of the potential of using cephalopod-parasite specificity to assess population boundaries of both, hosts and parasites; (iv) risk evaluation of the potential of standard aquacultural practices to result in parasite outbreaks; (v) evaluation and description of the physiological and behavioral effects of parasites on their cephalopod hosts; (vi) standardization of the methods for accurate parasite sampling and identification; (vii) implementation of the latest molecular methods to facilitate and enable research in above mentioned areas; (viii) sharing of information and samples among researchers and aquaculturists. In our view, addressing these topics would allow us to better understand complex host-parasite interactions, yield insights into cephalopod life history, and help improve the rearing and welfare of these animals in captivity

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.[Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.[Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.The work (proposal: 10.46936/10.25585/60000940) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. RS, MB, JL, and TW are supported by NIH grant R01AI168993. The John Templeton Foundation (grant nos. 51250 and 60973) supported TT and SVD, and the Gordon and Betty Moore Foundation grants (GBMF7617 and GBMF9340) supported SVD. MD is supported by the Generalitat Valenciana program GenT grant number CDEIGENT/2021/008. SPE is supported by a FPU grant from the Spanish Ministry of Universities (Reference: FPU20/05756).Peer reviewe

Diversity, phylogeny and phylogeography of free-living amoebae

This thesis consists of seven published papers on free-living amoebae (FLA), members of Amoebozoa, Excavata: Heterolobosea, and Cercozoa, and covers three main topics: (i) FLA as potential fish pathogens, (ii) diversity and phylogeography of FLA, and (iii) FLA as hosts of prokaryotic organisms. Diverse methodological approaches were used including culture-dependent techniques for isolation and identification of free-living amoebae, molecular phylogenetics, fluorescent in situ hybridization, and transmission electron microscopy

Ciliates from gills of marine fish simultaneously colonized with amphizoic amoebae

Ciliates isolated from gills of marine fish (colonized simultaneously with amphizoic amoebae) were characterized on the basis of their morphology. A strain isolated from Psetta maxima Linnaeus, 1758 was assigned to the genus Uronema Dujardin, 1841. Another two strains, from Salmo salar Linnaues, 1758 and Balistes polylepis Steindachner, 1896, were assigned to Pseudocohnilembus Evans et Thompson, 1964. Repeated clonal procedures and long-lasting culturing proved that Cohnilembus reniformis (strain obtained from UK National Culture Collection) is a polymorphic species. New data were obtained on cell structure of ciliates under study: rows of tubules found in the close vicinity of mitochondria of the Uronema strain; structures slightly protruding on the surface of oral cilia of C. reniformis

A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes.

Single-cell genomics (SCG) methods provide a unique opportunity to analyse whole genome information at the resolution of an individual cell. While SCG has been extensively used to investigate bacterial and archaeal genomes, the technique has been rarely used to access the genetic makeup of uncultivated microbial eukaryotes. In this regard, the use of SCG can provide a wealth of information; not only do the methods allow exploration of the genome, they can also help elucidate the relationship between the cell and intracellular entities extant in nearly all eukaryotes. SCG enables the study of total eukaryotic cellular DNA, which in turn allows us to better understand the evolutionary history and diversity of life, and the physiological interactions that define complex organisms. This article is part of a discussion meeting issue 'Single cell ecology'