Controlling magnetotactic bacteria through an integrated nanofabricated metallic island and optical microscope approach.
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ABSTRACT:
SUBMITTER: Gonzalez LM
PROVIDER: S-EPMC3930094 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In this report, we describe the selective cloning of large DNA fragments from magnetotactic metagenomes from various aquatic habitats. This was achieved by a two-step magnetic enrichment which allowed the mass collection of environmental magnetotactic bacteria (MTB) virtually free of nonmagnetic contaminants. Four fosmid libraries were constructed and screened by end sequencing and hybridization analysis using heterologous magnetosome gene probes. A total of 14 fosmids were fully sequenced. We identified and characterized two fosmids, most likely originating from two different alphaproteobacterial strains of MTB that contain several putative operons with homology to the magnetosome island (MAI) of cultivated MTB. This is the first evidence that uncultivated MTB exhibit similar yet differing organizations of the MAI, which may account for the diversity in biomineralization and magnetotaxis observed in MTB from various environments.
| S-EPMC2698345 | biostudies-literature
Project description:PurposeWe develop and assess the impact of depth-based, motion-stabilized colorization (color) of microscope-integrated optical coherence tomography (MIOCT) volumes on microsurgical performance and ability to interpret surgical volumes.MethodsColor was applied in real-time as gradients indicating axial position and stabilized based on calculated center of mass. In a test comparing colorization versus grayscale visualizations of prerecorded intraoperative volumes from human surgery, ophthalmologists (N = 7) were asked to identify retinal membranes, the presence of an instrument, its contact with tissue, and associated deformation of the retina. In a separate controlled trial, trainees (N = 15) performed microsurgical skills without conventional optical visualization and compared colorized versus grayscale MIOCT visualization on a stereoptic screen. Skills included thickness identification, instrument placement, and object manipulation, and were assessed based on time, performance metrics, and confidence.ResultsIn intraoperative volume testing, colorization improved ability to differentiate membrane from retina (P < 0.01), correctly identify instrument contact with membrane (P = 0.03), and retinal deformation (P = 0.01). In model microsurgical skills testing, trainees working with colorized volumes were faster (P < 0.01) and more correct (P < 0.01) in assessments of thickness for recessed and elevated objects, were less likely to inadvertently contact a surface when approaching with an instrument (P < 0.01), and uniformly more confident (P < 0.01 for each) in conducting each skill.ConclusionsDepth-based colorization enables effective identification of retinal membranes and tissue deformation. In microsurgical skill testing, it improves user efficiency, and confidence in microscope-independent, OCT-guided model surgical maneuvers.Translational relevanceNovel depth-based colorization and stabilization technology improves the use of intraoperative MIOCT.
| S-EPMC6218157 | biostudies-literature
Project description:Purpose:To evaluate the potential value of microscope-integrated optical coherence tomography (MI-OCT) in anterior segment surgical maneuvers. Methods:Twenty-four ophthalmology residents, who were randomly and evenly divided into two groups, performed four anterior segment surgical maneuvers (corneal tunnel, scleral tunnel, simple corneal suture, and corneal laceration repair) on porcine eyes with (group B) or without (group A) real-time MI-OCT feedback. All residents performed the maneuvers again without MI-OCT. Results:Compared with group A, group B (with MI-OCT) showed better accuracy in the length/depth of the corneal tunnel and the length of the scleral tunnel. However, both groups showed similar performances in the depth of both the simple corneal suture and the corneal laceration suture. When both groups performed the maneuvers again without MI-OCT, group B still showed better results than group A for the length of both the corneal and scleral tunnels. Conclusions:Primary results suggest that real-time MI-OCT images are valuable for some anterior segment surgical maneuvers and could be helpful in surgical training. Translational Relevance:MI-OCT systems can be valuable in improving accuracy and decision making during anterior segment surgery and will be useful in surgical training.
| S-EPMC7414702 | biostudies-literature
Project description:We describe the implementation of an OPT plate to perform optical projection tomography (OPT) on a commercial wide-field inverted microscope, using our open-source hardware and software. The OPT plate includes a tilt adjustment for alignment and a stepper motor for sample rotation as required by standard projection tomography. Depending on magnification requirements, three methods of performing OPT are detailed using this adaptor plate: a conventional direct OPT method requiring only the addition of a limiting aperture behind the objective lens; an external optical-relay method allowing conventional OPT to be performed at magnifications >4x; a remote focal scanning and region-of-interest method for improved spatial resolution OPT (up to ~1.6 μm). All three methods use the microscope's existing incoherent light source (i.e. arc-lamp) and all of its inherent functionality is maintained for day-to-day use. OPT acquisitions are performed on in vivo zebrafish embryos to demonstrate the implementations' viability.
| S-EPMC5507440 | biostudies-literature
Project description:Both magnetic collection and "race track" purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the Alphaproteobacteria. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the Nitrospira phylum, displaying 91% 16S rRNA sequence similarity to "Magnetobacterium bavaricum." In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus Magnetospirillum which had not routinely been isolated in pure culture before were obtained.
| S-EPMC1087566 | biostudies-literature
Project description:We report the first use of swept-source microscope-integrated optical coherence tomography (SS-MIOCT) capable of live four-dimensional (4D) (three-dimensional across time) imaging intraoperatively to directly visualize tube shunt placement and trabeculectomy surgeries in two patients with severe open-angle glaucoma and elevated intraocular pressure (IOP) that was not adequately managed by medical intervention or prior surgery. We performed tube shunt placement and trabeculectomy surgery and used SS-MIOCT to visualize and record surgical steps that benefitted from the enhanced visualization. In the case of tube shunt placement, SS-MIOCT successfully visualized the scleral tunneling, tube shunt positioning in the anterior chamber, and tube shunt suturing. For the trabeculectomy, SS-MIOCT successfully visualized the scleral flap creation, sclerotomy, and iridectomy. Postoperatively, both patients did well, with IOPs decreasing to the target goal. We found the benefit of SS-MIOCT was greatest in surgical steps requiring depth-based assessments. This technology has the potential to improve clinical outcomes.
| S-EPMC5369296 | biostudies-literature
Project description:There are longstanding and ongoing controversies about the abiotic or biological origin of nanocrystals of magnetite. On Earth, magnetotactic bacteria perform biomineralization of intracellular magnetite nanoparticles under a controlled pathway. These bacteria are ubiquitous in modern natural environments. However, their identification in ancient geological material remains challenging. Together with physical and mineralogical properties, the chemical composition of magnetite was proposed as a promising tracer for bacterial magnetofossil identification, but this had never been explored quantitatively and systematically for many trace elements. Here, we determine the incorporation of 34 trace elements in magnetite in both cases of abiotic aqueous precipitation and of production by the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1. We show that, in biomagnetite, most elements are at least 100 times less concentrated than in abiotic magnetite and we provide a quantitative pattern of this depletion. Furthermore, we propose a previously unidentified method based on strontium and calcium incorporation to identify magnetite produced by magnetotactic bacteria in the geological record.
| S-EPMC4330721 | biostudies-literature
Project description:The authors report the use of swept-source microscope-integrated optical coherence tomography (SS-MIOCT), capable of live four-dimensional (three-dimensional across time) intraoperative imaging, to directly visualize suture depth during lateral rectus resection. Key surgical steps visualized in this report included needle depth during partial and full-thickness muscle passes along with scleral passes. [J Pediatr Ophthalmol Strabismus. 2017;54:e1-e5.].
| S-EPMC5963505 | biostudies-literature
Project description:Intra-operative optical coherence tomography (OCT) requires a display technology which allows surgeons to visualize OCT data without disrupting surgery. Previous research and commercial intrasurgical OCT systems have integrated heads-up display (HUD) systems into surgical microscopes to provide monoscopic viewing of OCT data through one microscope ocular. To take full advantage of our previously reported real-time volumetric microscope-integrated OCT (4D MIOCT) system, we describe a stereoscopic HUD which projects a stereo pair of OCT volume renderings into both oculars simultaneously. The stereoscopic HUD uses a novel optical design employing spatial multiplexing to project dual OCT volume renderings utilizing a single micro-display. The optical performance of the surgical microscope with the HUD was quantitatively characterized and the addition of the HUD was found not to substantially effect the resolution, field of view, or pincushion distortion of the operating microscope. In a pilot depth perception subject study, five ophthalmic surgeons completed a pre-set dexterity task with 50.0% (SD = 37.3%) higher success rate and in 35.0% (SD = 24.8%) less time on average with stereoscopic OCT vision compared to monoscopic OCT vision. Preliminary experience using the HUD in 40 vitreo-retinal human surgeries by five ophthalmic surgeons is reported, in which all surgeons reported that the HUD did not alter their normal view of surgery and that live surgical maneuvers were readily visible in displayed stereoscopic OCT volumes.
| S-EPMC4871076 | biostudies-other
Project description:Capable of forming magnetofossils similar to some magnetite nanocrystals observed in the Martian meteorite ALH84001, magnetotactic bacteria (MTB) once occupied a special position in the field of astrobiology during the 1990s and 2000s. This flourish of interest in putative Martian magnetofossils faded from all but the experts studying magnetosome formation, based on claims that abiotic processes could produce magnetosome-like magnetite crystals. Recently, the rapid growth in our knowledge of the extreme environments in which MTB thrive and their phylogenic heritage, leads us to advocate for a renaissance of MTB in astrobiology. In recent decades, magnetotactic members have been discovered alive in natural extreme environments with wide ranges of salinity (up to 90 g L-1), pH (1-10), and temperature (0-70 °C). Additionally, some MTB populations are found to be able to survive irradiated, desiccated, metal-rich, hypomagnetic, or microgravity conditions, and are capable of utilizing simple inorganic compounds such as sulfate and nitrate. Moreover, MTB likely emerged quite early in Earth's history, coinciding with a period when the Martian surface was covered with liquid water as well as a strong magnetic field. MTB are commonly discovered in suboxic or oxic-anoxic interfaces in aquatic environments or sediments similar to ancient crater lakes on Mars, such as Gale crater and Jezero crater. Taken together, MTB can be exemplary model microorganisms in astrobiology research, and putative ancient Martian life, if it ever occurred, could plausibly have included magnetotactic microorganisms. Furthermore, we summarize multiple typical biosignatures that can be applied for the detection of ancient MTB on Earth and extraterrestrial MTB-like life. We suggest transporting MTB to space stations and simulation chambers to further investigate their tolerance potential and distinctive biosignatures to aid in understanding the evolutionary history of MTB and the potential of magnetofossils as an extraterrestrial biomarker.
| S-EPMC10504353 | biostudies-literature