Optical Tweezers to Study Viruses.

A virus is a complex molecular machine that propagates by channeling its genetic information from cell to cell. Unlike macroscopic engines, it operates in a nanoscopic world under continuous thermal agitation. Viruses have developed efficient passive and active strategies to pack and release nucleic acids.

Underlying drivers of coral reef vulnerability to bleaching in the Mesoamerican Reef.

Coral bleaching, a consequence of stressed symbiotic relationships between corals and algae, has escalated due to intensified heat stress events driven by climate change. Despite global efforts, current early warning systems lack local precision. Our study, spanning 2015-2017 in the Mesoamerican Reef, revealed prevalent intermediate bleaching, peaking in 2017.

Multiplexed vortex beam-based optical tweezers generated with spiral phase mask.

The design and implementation of a multiplexed spiral phase mask in an experimental optical tweezers setup are presented. This diffractive optical element allows the generation of multiple concentric vortex beams with independent topological charges and without amplitude modulation. The generalization of the phase mask for multiple concentric vortices is also shown.

A decade of population genetics studies of scleractinian corals: A systematic review.

Coral reefs are the most diverse marine ecosystems. However, coral cover has decreased worldwide due to natural disturbances, climate change, and local anthropogenic drivers. In recent decades, various genetic methods and molecular markers have been developed to assess genetic diversity, structure, and connectivity in different coral species to determine the vulnerability of their populations.

Fluctuation relations for irreversible emergence of information.

Information theory and Thermodynamics have developed closer in the last years, with a growing application palette in which the formal equivalence between the Shannon and Gibbs entropies is exploited. The main barrier to connect both disciplines is the fact that information does not imply a dynamics, whereas thermodynamic systems unfold with time, often away from equilibrium. Here, we analyze chain-like systems comprising linear sequences of physical objects carrying symbolic meaning.

Biological trade-offs underpin coral reef ecosystem functioning.

Human impact increasingly alters global ecosystems, often reducing biodiversity and disrupting the provision of essential ecosystem services to humanity. Therefore, preserving ecosystem functioning is a critical challenge of the twenty-first century. Coral reefs are declining worldwide due to the pervasive effects of climate change and intensive fishing, and although research on coral reef ecosystem functioning has gained momentum, most studies rely on simplified proxies, such as fish biomass.

Conservation actions and ecological context: optimizing coral reef local management in the Dominican Republic.

Over the past few decades, coral reef ecosystems have been lost at accelerated rates as a result of global climate change and local stressors. Local management schemes can help improve the condition of coral reefs by enhancing their ecosystem recovery capacity. Caribbean conservation efforts include mitigation of local anthropogenic stressors, and integrating social participation.

Drivers of coral bleaching in a Marine Protected Area of the Southern Gulf of Mexico during the 2015 event.

Here we report the bleached coral cover and its drivers observed at Alacranes Reef in 2015. Our results show that 2015 was an unprecedented heat stress event. However, we observed low coral bleaching, with the most substantial impact on sites with a 10-20% of coral cover with bleaching.

Coral reef restoration efforts in Latin American countries and territories.

Coral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, coral bleaching, and diseases. In areas where the natural recovery of an ecosystem is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions.

Genetic connectivity of lionfish () in marine protected areas of the Gulf of Mexico and Caribbean Sea.

Lionfish () have rapidly invaded the tropical Atlantic and spread across the wider Caribbean in a relatively short period of time. Because of its high invasion capacity, we used it as a model to identify the connectivity among nine marine protected areas (MPAs) situated in four countries in the Gulf of Mexico and the Caribbean Sea. This study provides evidence of local genetic differentiation of in the Gulf of Mexico and the Caribbean Sea.

Assessing and genotyping threatened staghorn coral nurseries during restoration in southeast Dominican Republic.

is a structurally and functionally important Caribbean coral species. Since the 1980s, it has suffered drastic population losses with no signs of recovery and has been classified as a critically endangered species. Its rapid growth rate makes it an excellent candidate for coral restoration programs.

Heat Generation in Single Magnetic Nanoparticles under Near-Infrared Irradiation.

Heat generation by pointlike structures is an appealing concept for its implications in nanotechnology and biomedicine. The way to pump energy that excites heat locally and the synthesis of nanostructures that absorb such energy are key issues in this endeavor. High-frequency alternating magnetic or near-infrared optical fields are used to induce heat in iron oxide nanoparticles, a combined solution that is being exploited in hyperthermia treatments.

Three decades of heat stress exposure in Caribbean coral reefs: a new regional delineation to enhance conservation.

Increasing heat stress due to global climate change is causing coral reef decline, and the Caribbean has been one of the most vulnerable regions. Here, we assessed three decades (1985-2017) of heat stress exposure in the wider Caribbean at ecoregional and local scales using remote sensing. We found a high spatial and temporal variability of heat stress, emphasizing an observed increase in heat exposure over time in most ecoregions, especially from 2003 identified as a temporal change point in heat stress.

Photoluminescence Activation of Organic Dyes via Optically Trapped Quantum Dots.

Laser tweezers afford quantum dot (QD) manipulation for use as localized emitters. Here, we demonstrate fluorescence by radiative energy transfer from optically trapped colloidal QDs (donors) to fluorescent dyes (acceptors). To this end, we synthesized silica-coated QDs of different compositions and triggered their luminescence by simultaneous trapping and two-photon excitation in a microfluidic chamber filled with dyes.

Writing, Proofreading and Editing in Information Theory.

Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains.

Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA.

TERRA is an RNA molecule transcribed from human subtelomeric regions toward chromosome ends potentially involved in regulation of heterochromatin stability, semiconservative replication, and telomerase inhibition, among others. TERRA contains tandem repeats of the sequence GGGUUA, with a strong tendency to fold into a four-stranded arrangement known as a parallel G-quadruplex. Here, we demonstrate by using single-molecule force spectroscopy that this potential is limited by the inherent capacity of RNA to self-associate randomly and further condense into entropically more favorable structures.

[Distribution and abundance of the lionfish Pterois volitans (Scorpaeniformes: Scorpaenidae) and associated native species in Parque Marino Cayos de San Felipe, Cuba].

The first lionfish sighting at the National Park "Cayos de San Felipe" was in 2009 and could be a threat to its marine ecosystem diversity and their capacity to generate services. To analyze the incidence of the lionfish invasion in the area, an annual sampling was conducted between 2013 and 2015. Lionfish abundance and size was investigated on mangroves through visual census on ten transects of 30x2 m/station, and on coral reefs (15 and 25 m deep) with stereo video on six transects of 50x2 m/station.

Thermodynamic framework for information in nanoscale systems with memory.

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory.

Mesoscopic model for DNA G-quadruplex unfolding.

Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been reported to date by all-atom simulations, which cannot dissect the major physical interactions responsible for their cohesion. Here, we propose a mesoscopic model to describe both the mechanical and thermal stability of DNA G-quadruplexes, where each nucleotide of the structure, as well as each central cation located at the inner channel, is mapped onto a single bead.

A DNA-centered explanation of the DNA polymerase translocation mechanism.

DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle.

DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein.

Single-stranded DNA-binding proteins (SSBs) play a key role in genome maintenance, binding and organizing single-stranded DNA (ssDNA) intermediates. Multimeric SSBs, such as the human mitochondrial SSB (HmtSSB), present multiple sites to interact with ssDNA, which has been shown in vitro to enable them to bind a variable number of single-stranded nucleotides depending on the salt and protein concentration. It has long been suggested that different binding modes might be used selectively for different functions.

A coral-algal phase shift in Mesoamerica not driven by changes in herbivorous fish abundance.

Coral-algal phase shifts in which coral cover declines to low levels and is replaced by algae have often been documented on coral reefs worldwide. This has motivated coral reef management responses that include restriction and regulation of fishing, e.g.

Information management in DNA replication modeled by directional, stochastic chains with memory.

Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors.

[Influence of sediments and tungsten traces on the skeletal structure of Pseudodiploria: a reef building scleractinian coral from the Veracruz Reef System National Park, Mexico].

Coral reefs are under intense conditions of stress caused by the anthropogenic activities in coastal areas and the increase of human population. Water effluents from urban and industrial areas carry large amounts of sediments and pollutants affecting corals populations, inducing bioerosion, increasing diseases and promoting the development of algae that compete for space with corals. In the Veracruz Reef System National Park (VRSNP) coral reefs are strongly affected by human activities carried out in the area.