Fluorescent oxide nanoparticles adapted to active tips for near-field optics

We present a new kind of fluorescent oxide nanoparticles with properties well suited to active-tip based near-field optics. These particles with an average diameter in the range 5-10 nm are produced by Low Energy Cluster Beam Deposition (LECBD) from a YAG:Ce3+ target. They are studied by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), classical photoluminescence, cathodoluminescence and near-field scanning optical microscopy (NSOM). Particles of extreme photo-stability as small as 10 nm in size are observed. These emitters are validated as building blocks of active NSOM tips by coating a standard optical tip with a 10 nm thick layer of YAG:Ce3+ particles directly in the LECBD reactor and by subsequently performing NSOM imaging of test surfaces.Comment: Changes made following Referee's comments; added references; one added figure. See story on this article at: http://nanotechweb.org/cws/article/tech/3606

Imaging Gold Nanoparticles in Living Cells Environments using Heterodyne Digital Holographic Microscopy

This paper describes an imaging microscopic technique based on heterodyne digital holography where subwavelength-sized gold colloids can be imaged in cell environment. Surface cellular receptors of 3T3 mouse fibroblasts are labeled with 40 nm gold nanoparticles, and the biological specimen is imaged in a total internal reflection configuration with holographic microscopy. Due to a higher scattering efficiency of the gold nanoparticles versus that of cellular structures, accurate localization of a gold marker is obtained within a 3D mapping of the entire sample's scattered field, with a lateral precision of 5 nm and 100 nm in the x,y and in the z directions respectively, demonstrating the ability of holographic microscopy to locate nanoparticles in living cells environments

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm

A robust, scanning quantum system for nanoscale sensing and imaging

Controllable atomic-scale quantum systems hold great potential as sensitive tools for nanoscale imaging and metrology. Possible applications range from nanoscale electric and magnetic field sensing to single photon microscopy, quantum information processing, and bioimaging. At the heart of such schemes is the ability to scan and accurately position a robust sensor within a few nanometers of a sample of interest, while preserving the sensor's quantum coherence and readout fidelity. These combined requirements remain a challenge for all existing approaches that rely on direct grafting of individual solid state quantum systems or single molecules onto scanning-probe tips. Here, we demonstrate the fabrication and room temperature operation of a robust and isolated atomic-scale quantum sensor for scanning probe microscopy. Specifically, we employ a high-purity, single-crystalline diamond nanopillar probe containing a single Nitrogen-Vacancy (NV) color center. We illustrate the versatility and performance of our scanning NV sensor by conducting quantitative nanoscale magnetic field imaging and near-field single-photon fluorescence quenching microscopy. In both cases, we obtain imaging resolution in the range of 20 nm and sensitivity unprecedented in scanning quantum probe microscopy

Optical phase conjugation for turbidity suppression in biological samples

Elastic optical scattering, the dominant light-interaction process in biological tissues, prevents tissues from being transparent. Although scattering may appear stochastic, it is in fact deterministic in nature. We show that, despite experimental imperfections, optical phase conjugation (λ = 532 nm) can force a transmitted light field to retrace its trajectory through a biological target and recover the original light field. For a 0.69-mm-thick chicken breast tissue section, we can enhance point-source light return by a factor of ~5 x 10^3 and achieve a light transmission enhancement factor of 3.8 within a collection angle of 29°. Additionally, we find that the reconstruction's quality, measured by the width of the reconstructed point source, is independent of tissue thickness (up to a thickness of 0.69 mm). This phenomenon may be used to enhance light transmission through tissue, enable measurement of small tissue movements, and form the basis of new tissue imaging techniques

Organizações sociais e agroecologia: construção de identidades e transformações sociais.

No presente trabalho, procuramos discutir as transformações ocorridas no espaço da agricultura familiar pós-Revolução Verde, especialmente a partir do movimento contestatório engendrado por organizações sociais que defendem o ideário agroecológico. Inicialmente, procurou-se compreender como a identidade a e realidade social são construídas e reconstruídas socialmente. Utilizou-se uma abordagem fenomenológica para investigar como se dá a ruptura com a realidade convencional e a transição para a agroecologia. Com base nas evidências empíricas, é possível dizer que a agroecologia participa da ressignificação positiva da identidade social dos agricultores. Entretanto, o reconhecimento da nova identidade passa pelo questionamento da realidade dominante a partir de crises vividas pelos agricultores. Sua manutenção requer partilhá-la intersubjetivamente com um grupo ou organização

HAMLET Binding to α-Actinin Facilitates Tumor Cell Detachment

Cell adhesion is tightly regulated by specific molecular interactions and detachment from the extracellular matrix modifies proliferation and survival. HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) is a protein-lipid complex with tumoricidal activity that also triggers tumor cell detachment in vitro and in vivo, suggesting that molecular interactions defining detachment are perturbed in cancer cells. To identify such interactions, cell membrane extracts were used in Far-western blots and HAMLET was shown to bind α-actinins; major F-actin cross-linking proteins and focal adhesion constituents. Synthetic peptide mapping revealed that HAMLET binds to the N-terminal actin-binding domain as well as the integrin-binding domain of α-actinin-4. By co-immunoprecipitation of extracts from HAMLET-treated cancer cells, an interaction with α-actinin-1 and -4 was observed. Inhibition of α-actinin-1 and α-actinin-4 expression by siRNA transfection increased detachment, while α-actinin-4-GFP over-expression significantly delayed rounding up and detachment of tumor cells in response to HAMLET. In response to HAMLET, adherent tumor cells rounded up and detached, suggesting a loss of the actin cytoskeletal organization. These changes were accompanied by a reduction in β1 integrin staining and a decrease in FAK and ERK1/2 phosphorylation, consistent with a disruption of integrin-dependent cell adhesion signaling. Detachment per se did not increase cell death during the 22 hour experimental period, regardless of α-actinin-4 and α-actinin-1 expression levels but adherent cells with low α-actinin levels showed increased death in response to HAMLET. The results suggest that the interaction between HAMLET and α-actinins promotes tumor cell detachment. As α-actinins also associate with signaling molecules, cytoplasmic domains of transmembrane receptors and ion channels, additional α-actinin-dependent mechanisms are discussed

Perspectives on tracking data reuse across biodata resources

c The Author(s) 2024. Published by Oxford University Press.Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge. Results: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources