SIMcheck:A toolbox for successful super-resolution structured illumination microscopy

Three-dimensional structured illumination microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-SIM data and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms and will promote routine application of super-resolution SIM imaging in cell biology

Strategic and practical guidelines for successful structured illumination microscopy

Linear 2D- or 3D-structured illumination microscopy (SIM or3D-SIM, respectively) enables multicolor volumetric imaging of fixed and live specimens with subdiffraction resolution in all spatial dimensions. However, the reliance of SIM on algorithmic post-processing renders it particularly sensitive to artifacts that may reduce resolution, compromise data and its interpretations, and drain resources in terms of money and time spent. Here we present a protocol that allows users to generate high-quality SIM data while accounting and correcting for common artifacts. The protocol details preparation of calibration bead slides designed for SIM-based experiments, the acquisition of calibration data, the documentation of typically encountered SIM artifacts and corrective measures that should be taken to reduce them. It also includes a conceptual overview and checklist for experimental design and calibration decisions, and is applicable to any commercially available or custom platform. This protocol, plus accompanying guidelines, allows researchers from students to imaging professionals to create an optimal SIM imaging environment regardless of specimen type or structure of interest. The calibration sample preparation and system calibration protocol can be executed within 1-2 d

Thermal Properties of Graphene, Carbon Nanotubes and Nanostructured Carbon Materials

Recent years witnessed a rapid growth of interest of scientific and engineering communities to thermal properties of materials. Carbon allotropes and derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range - of over five orders of magnitude - from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. I review thermal and thermoelectric properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. A special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe prospects of applications of graphene and carbon materials for thermal management of electronics.Comment: Review Paper; 37 manuscript pages; 4 figures and 2 boxe

Phenotypic Variation and Bistable Switching in Bacteria

Microbial research generally focuses on clonal populations. However, bacterial cells with identical genotypes frequently display different phenotypes under identical conditions. This microbial cell individuality is receiving increasing attention in the literature because of its impact on cellular differentiation, survival under selective conditions, and the interaction of pathogens with their hosts. It is becoming clear that stochasticity in gene expression in conjunction with the architecture of the gene network that underlies the cellular processes can generate phenotypic variation. An important regulatory mechanism is the so-called positive feedback, in which a system reinforces its own response, for instance by stimulating the production of an activator. Bistability is an interesting and relevant phenomenon, in which two distinct subpopulations of cells showing discrete levels of gene expression coexist in a single culture. In this chapter, we address techniques and approaches used to establish phenotypic variation, and relate three well-characterized examples of bistability to the molecular mechanisms that govern these processes, with a focus on positive feedback.

Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies

Expansion microscopy (ExM) enables imaging of preserved specimens with nanoscale precision on diffraction-limited instead of specialized super-resolution microscopes. ExM works by physically separating fluorescent probes after anchoring them to a swellable gel. The first ExM method did not result in the retention of native proteins in the gel and relied on custom-made reagents that are not widely available. Here we describe protein retention ExM (proExM), a variant of ExM in which proteins are anchored to the swellable gel, allowing the use of conventional fluorescently labeled antibodies and streptavidin, and fluorescent proteins. We validated and demonstrated the utility of proExM for multicolor super-resolution (~70 nm) imaging of cells and mammalian tissues on conventional microscopes.United States. National Institutes of Health (1R01GM104948)United States. National Institutes of Health (1DP1NS087724)United States. National Institutes of Health ( NIH 1R01EY023173)United States. National Institutes of Health (1U01MH106011

Incentivando o vínculo mãe-filho em situação de prematuridade: as intervenções de enfermagem no Hospital das Clínicas de Ribeirão Preto

This study aims at describing nursing actions performed in the high-risk neonatal units at a university hospital of the University of São Paulo at Ribeirão Preto so as to favor mother-child attachment in prematurity situations. The nurse accompanies parents in their first visit, giving them support as well as information concerning the equipment surrounding the newborn and encouraging skin-to-skin contact, touching and talking. Parents' access to and staying with high-risk newborns is permanently allowed. A visiting program by grandparents and siblings of pre-term newborns was implemented, even when under intensive care, which encourages family contact. Parents participate in a support group with other parents who experienced the situation of having their pre-term children in serious conditions and hospitalized. We consider that our experience has favored the establishment of mother-child and family attachment, observing greater interaction between the family and the newborn, particular involving the mother. Greater interest in learning about care as well as satisfaction concerning the assistance received have also been expressed by families.El objetivo de este estudio es describir las acciones de enfermería realizadas en las unidades neonatales de riesgo de un hospital-escuela de la ciudad de Ribeirão Preto - USP, en el sentido de favorecer el vinculo y apego madre-hijo en situación de prematuridad. La enfermera acompaña los padres en la primera visita, procurando apoyarlos e informar sobre los equipos que cercan al recién-nacido, incentivando el contacto piel a piel, el toque y habla. El acceso y permanencia de los padres junto a los bebes de riesgo son permitidos. Implantamos un programa de visitas de los abuelos y hermanos del prematuro, aunque estén en cuidado intensivo, con el objetivo de incentivar el contacto familiar. Los padres participan en un grupo de apoyo, conjuntamente con otros padres que pasan por la experiencia de tener sus hijos prematuros en estado grave y hospitalizados. Consideramos que nuestra experiencia favoreció el establecimiento del vinculo y apego madre-hijo y familia, resultando en una mayor interacción de la familia con el bebe, en especial, de la madre, y mayor interés en el aprendizaje de sus cuidados, además de la satisfacción manifestada por la atención recibida.O objetivo deste estudo é descrever as ações da enfermagem realizadas nas unidades neonatais de risco de um hospital-escola de Ribeirão Preto-USP, no sentido de favorecer o vínculo e apego mãe-filho em situação de prematuridade. A enfermeira acompanha os pais na primeira visita, procurando apoiá-los e informando-os sobre os equipamentos que cercam o recém-nascido, incentivando o contato pele-a-pele, o toque e a fala. O acesso e permanência dos pais junto aos bebês de risco são liberados.Foi implantado programa de visitas dos avós e irmãos do prematuro aos bebês, mesmo quando em cuidado intensivo, incentivando o contato familiar. Os pais participam de um grupo de apoio, juntamente com outros pais que passam pela experiência de terem seus filhos prematuros em estado grave e hospitalizados. Consideramos que a nossa experiência tem favorecido o estabelecimento do vínculo e apego mãe-filho e família, observando-se maior interação da família com o bebê, em especial da mãe, e maior interesse no aprendizado de seus cuidados, além da satisfação manifestada pela assistência recebida

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant

Brazilian Consensus on Photoprotection

Brazil is a country of continental dimensions with a large heterogeneity of climates and massive mixing of the population. Almost the entire national territory is located between the Equator and the Tropic of Capricorn, and the Earth axial tilt to the south certainly makes Brazil one of the countries of the world with greater extent of land in proximity to the sun. The Brazilian coastline, where most of its population lives, is more than 8,500 km long. Due to geographic characteristics and cultural trends, Brazilians are among the peoples with the highest annual exposure to the sun. Epidemiological data show a continuing increase in the incidence of nonmelanoma and melanoma skin cancers. Photoprotection can be understood as a set of measures aimed at reducing sun exposure and at preventing the development of acute and chronic actinic damage. Due to the peculiarities of Brazilian territory and culture, it would not be advisable to replicate the concepts of photoprotection from other developed countries, places with completely different climates and populations. Thus the Brazilian Society of Dermatology has developed the Brazilian Consensus on Photoprotection, the first official document on photoprotection developed in Brazil for Brazilians, with recommendations on matters involving photoprotection