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Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA

Demonstration of gold nanorod systems for enhanced total efficiency: Experimental and numerical analysis

This study investigates the photothermal performance of gold nanorods engineered to exhibit longitudinal plasmon resonances at 695 nm, 780 nm, and 970 nm. The work combines synthesis, structural characterization, extinction measurements, numerical modeling, and controlled temperature experiments to quantify how nanorod geometry, resonance tuning, concentration, and chamber shape jointly influence heat generation. Transmission electron microscopy confirms that increasing nanorod aspect ratio systematically shifts the longitudinal plasmon peak toward the near-infrared region. Extinction measurements show strong agreement with theoretical predictions, validating the numerical model across two independent datasets. Three chamber geometries were tested under laser excitation at 640 nm, 808 nm, and 980 nm: an ascending stepped base, a flat base, and a descending stepped base. Without nanorods, the ascending geometry produced the highest efficiency due to enhanced natural convection. After introducing gold nanorods, all geometries exhibited substantial thermal enhancement, with total efficiencies exceeding 20%. The strongest improvement was obtained for nanorods resonant at 780 nm with a mass concentration of 4.6 mg/mL implemented on the descending stepped-base geometry. This performance resulted from the combined effect of spectral overlapping with the 808 nm laser, the highest nanorod concentration, and localized heat accumulation that intensified buoyancy-driven flow. The findings demonstrate that total efficiency is governed by a synergistic interplay between optical resonance, nanoparticle concentration, and macroscopic chamber design, revealing the system-level coupling between nanoscale plasmonic absorption and macroscale heat-transfer phenomena. The results provide a validated framework for tuning nanoscale plasmonic absorbers and optimizing thermal systems for applications requiring efficient light-to-heat conversion.

77 NANOSCIENCE AND NANOTECHNOLOGY

An enzyme-based approach for highly efficient self-replication of DNA origami dimers

Self-replication and exponential growth are essential to all living things, the driving force for Darwinian evolution, and potentially useful in nanotechnology for large-scale production of nanoscopic materials. An artificial (nonliving) self-replication system has been shown to exhibit exponential growth and selection using DNA monomer origami tiles templated on a dimer seed. That system purposefully avoided the use of enzymes to get a hint of how self-replication might have evolved in a prebiotic world by using CNV K and UV light to crosslink complementary DNA single strands. For further investigations into competition and extinction and for potential applications involving biocompatibility, we wanted to investigate enzymatic ligation to replace the chemical photo crosslinking step. Here, we present a system which uses thermotolerant T4 DNA ligase and no UV. This system has several additional advantages including a much faster cycling time, yielding 2,000,000 amplifications in 12 h. We also introduce competition to study the possibility of Darwinian-like evolution. Two pairs of DNA origami tiles compete for the same connection strands and show different growth rates under different connection strand concentrations. This system has the potential to combine with other enzymes, such as RNA polymerase to support feedback, allowing us to fine-tune replication dynamics and achieve sophisticated, life-like behaviors. The highly efficient self-replication and exponential growth of DNA origami dimers demonstrated in this work not only enhances our understanding of Darwinian evolution in nature but also opens the door to applications ranging from synthetic biology to smart materials.

Science & Technology - Other Topics

Studies of laser stimulated photodetachment from nanoparticles for particle charge measurements

Determining nanoparticle charge is more challenging than that for microparticles due to change in the particle size during the synthesis substantial plasma property variations, and difficulties in visualizing individual particles, rendering conventional microparticle charge diagnostics ineffective in dusty plasma. In this work, we utilized laser-stimulated photodetachment (LSPD) to deduce the mean charge of nanoparticles. Nanoparticles were grown in an Ar/C 2 H 2 mixture using a capacitively coupled RF discharge and the LSPD induced changes in the electron current monitored by a cylindrical Langmuir probe. LSPD signals were obtained and analyzed across different dust growth phases. The prolonged decay of electron current pulses was attributed to the presence of residual negative ions, caused by the effective electrostatic trapping of these ions and the potential post—LSPD re-formation of new ones. The particle charge was estimated by combining the laser-stimulated photodetachment signal from the probe with the dust density obtained from laser-light extinction using the measured nanoparticle size distribution. For a nanoparticles size range of approximately 100–250 nm and mean diameter of $d$ p ∼154.37 nm, the effective mean charge was estimated to be $\langle$$Q$$\rangle$ d $≈$ 37 elementary charge units. The measured charge values are lower than those predicted by orbital motion limited theory, which may be attributed to significant electron depletion in the nanodusty plasma. LSPD results in Ar/C 2 H 2 nano-dusty plasma confirm the applicability of this method for estimating individual nanoparticle charges. However, it has also been demonstrated that electron detachment from residual background negative ions can influence the detachment current decay and must be carefully considered.

dust particle charge

Evaluating Polymer Properties with Different Additives for Carbon Capture and Other Applications

Anthropogenic climate change is one of this generation’s most pressing concerns, with the potential to completely alter the delicate balance we’ve struck with nature. Already, global temperatures have risen 1.29°C, leading to disrupted weather systems, extinctions, increased risks of wildfires, and sea level rise, to name a few effects. Carbon dioxide emission from the combustion of fossil fuels and other industrial activity is a large driver of this phenomenon, as it absorbs heat before it can be radiated away from Earth, trapping it. Carbon dioxide has reached unprecedented levels in our atmosphere, showing a 50% increase from preindustrial averages to a whopping 430 ppm. Thus, reducing the amount of carbon dioxide via carbon capture technology is an important endeavor that serves to benefit everyone. The Microencapsulated CO 2 Sorbent (MECS) team at Lawrence Livermore National Laboratory (LLNL) has turned to microencapsulation to approach this endeavor. Microcapsules provide an attractive approach to carbon capture, combining large surface areas for more efficient mass transfer, regenerative abilities, reduced solvent loss, and improved handling. Additionally, while existing carbon capture technology relies on industrial plants, capsules could present a modular approach to carbon capture, reducing the need for extensive physical infrastructure. The MECS team’s design consists of a polymer membrane that contains a liquid carbon sequestering sorbent, aqueous sodium carbonate. The carbon capturing reaction occurs in three distinct steps, the first of which is the dissolution of carbon dioxide into the sorbent solution and its conversion into carbonic acid (H 2 CO 3 ), shown in equations 1 and 2 respectively. Because this step hinges upon the ability of carbon dioxide to reach the solution inside the capsule, it is necessary that the microcapsule shell is permeable to carbon dioxide gas. The MECS team produces these microcapsules using the in-air droplet encapsulation apparatus (IDEA) shown in figure 1, which can produce uniform micron-scale droplets at speeds much faster than traditional single-dispersal microfluidic-based techniques. The IDEA Is 100 times faster than these current techniques and can reach up to 1000 times their speed when incorporating a multi-nozzle design. Additionally, because droplets are produced in-air via vibration, IDEA can decrease post-processing times and material waste by 99% and can fabricate microgels that are 10 to 100 times more viscous than can be produced via traditional microfluidics. While this design represents a breakthrough in the throughput, efficiency, and tunability of microcapsule production, it imposes a major constraint on the microcapsule curing process. Because microcapsule shells are crosslinked with UV light while falling 30 cm through the air, this gives them a reaction window of approximately 0.2 seconds. Thus, the system and shell formulations must be optimized such that the shells can be fully crosslinked within this very narrow window, prompting investigations into curing behavior.

36 MATERIALS SCIENCE