Genetic interaction network of quantitative trait genes for heading date in rice.

Several quantitative trait genes (QTGs) related to rice heading date, a key factor for crop development and yield, have been identified, along with complex interactions among genes. However, a comprehensive genetic interaction network for these QTGs has not yet been established. In this study, we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date.

Tunable elliptical cylinders for rotational mechanical studies of single DNA molecules.

The angular optical trap (AOT) is a powerful technique for measuring the DNA topology and rotational mechanics of fundamental biological processes. Realizing the full potential of the AOT requires rapid torsional control of these processes. However, existing AOT quartz cylinders are limited in their ability to meet the high rotation rate requirement while minimizing laser-induced photodamage.

Chromatin Buffers Torsional Stress During Transcription.

Transcription through chromatin under torsion represents a fundamental problem in biology. Pol II must overcome nucleosome obstacles and, because of the DNA helical structure, must also rotate relative to the DNA, generating torsional stress. However, there is a limited understanding of how Pol II transcribes through nucleosomes while supercoiling DNA.

Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation.

The inherent helical structure of DNA dictates that a replisome must rotate relative to DNA during replication, presenting inevitable topological challenges to replication. However, little is known about how the replisome progresses against torsional stress. Here, we developed a label-free, high-resolution, real-time assay to monitor replisome movement under torsion.

Torsional Mechanics of Circular DNA.

Circular DNA found in the cell is actively regulated to an underwound state, with their superhelical density close to . While this underwound state is essential to life, how it impacts the torsional mechanical properties of DNA is not fully understood. In this work, we performed simulations to understand the torsional mechanics of circular DNA and validated our results with single-molecule measurements and analytical theory.

Geometry of Braided DNA Dictates Supercoiling Partition.

During DNA replication, the replisome must rotate relative to the DNA substrate, generating supercoiling that must be partitioned in front of or behind the replisome. Supercoiling partitioned behind the replisome may intertwine (or braid) daughter DNA molecules and restrict chromosome segregation. Supercoiling partitioning and torsional resistance at the replisome should depend on the geometry of the two daughter DNA molecules, determined by their end separations.

Tunable Elliptical Cylinders for Rotational Mechanical Studies of Single DNA Molecules.

The angular optical trap (AOT) is a powerful technique for measuring the DNA topology and rotational mechanics of fundamental biological processes. Realizing the full potential of the AOT requires rapid torsional control of these processes. However, existing AOT quartz cylinders are limited in their ability to meet the high rotation rate requirement while minimizing laser-induced photodamage.

Optical torque calculations and measurements for DNA torsional studies.

The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of these aberrations on torque measurements is not fully understood experimentally, partly due to a lack of theoretical guidance.

Optical Torque Calculations and Measurements for DNA Torsional Studies.

Unlabelled: The angular optical trap (AOT) is a powerful instrument for measuring the torsional and rotational properties of a biological molecule. Thus far, AOT studies of DNA torsional mechanics have been carried out using a high numerical aperture oil-immersion objective, which permits strong trapping, but inevitably introduces spherical aberrations due to the glass-aqueous interface. However, the impact of these aberrations on torque measurements is not fully understood experimentally, partly due to a lack of theoretical guidance.

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs.

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models.

Chromatinization modulates topoisomerase II processivity.

Type IIA topoisomerases are essential DNA processing enzymes that must robustly and reliably relax DNA torsional stress. While cellular processes constantly create varying torsional stress, how this variation impacts type IIA topoisomerase function remains obscure. Using multiple single-molecule approaches, we examined the torsional dependence of eukaryotic topoisomerase II (topo II) activity on naked DNA and chromatin.

Chromatinization Modulates Topoisomerase II Processivity.

Type IIA topoisomerases are essential DNA processing enzymes that must robustly and reliably relax DNA torsional stress . While cellular processes constantly create different degrees of torsional stress, how this stress feeds back to control type IIA topoisomerase function remains obscure. Using a suite of single-molecule approaches, we examined the torsional impact on supercoiling relaxation of both naked DNA and chromatin by eukaryotic topoisomerase II (topo II).

Water turbidity dynamics using random forest in the Yangtze River Delta Region, China.

Turbidity is a water quality indicator that is essential for the sustainable development of aquatic ecosystems and the protection of biodiversity. The turbidity of different water surfaces and its response mechanisms to regional climatic factors and human activities in the Yangtze River Delta Region (YRDR), an important rapid economic development region in China, remain poorly understood. To enhance the knowledge of turbidity variations and dominant drivers of YRDR water surfaces, a complete long-term turbidity series was obtained using Landsat images from 1990 to 2020.

Selectively gas-filled anti-resonant hollow-core fibers for broadband high-purity LP mode guidance.

An anti-resonant hollow-core fiber capable of propagating the LP mode with high purity and over a wide wavelength range is proposed and demonstrated. The suppression of the fundamental mode relies on the resonant coupling with specific gas selectively filled into the cladding tubes. After a length of 2.

A non-Newtonian fluid quasi-solid electrolyte designed for long life and high safety Li-O batteries.

The Li dendrite growth and the liquid electrolyte volatilization under semi-open architecture are intrinsic issues for Li-O battery. In this work, we propose a non-Newtonian fluid quasi-solid electrolyte (NNFQSE) SiO-SOLi/PVDF-HFP, which has both shear-thinning and shear-thickening properties. The component interactions among the sulfonated silica nanoparticles, liquid electrolyte, and polymer network are beneficial for decent Li conductivity and high liquid electrolyte retention without volatilization.

Accurate modeling and measurement of pressure-induced group velocity dispersion variations in anti-resonant hollow-core fibers.

Precise control of group velocity dispersion (GVD) by pressure in a gas-filled hollow-core fiber (HCF) is of essential importance for many gas-based nonlinear optical applications. To accurately calculate the pressure-induced dispersion variations (∂β/∂p) in anti-resonant types of HCF, an analytical model combining the contribution of the gas material, capillary waveguide, and cladding resonances is developed, with an insightful physical picture. Broadband (∼1000 nm) GVD measurements in a single-shot manner realize accuracy and precision as low as 0.

Birefringent, low loss, and broadband semi-tube anti-resonant hollow-core fiber.

We report on the design, fabrication, and characterization of a low-loss birefringent semi-tube anti-resonant hollow-core fiber (AR-HCF). By optimizing the structure design and the stack-and-draw fabrication technique, a transmission loss of 4.8 dB/km at 1522 nm, a <10 dB/km bandwidth of 154 nm, and a phase birefringence of 1.

High extinction ratio and low backreflection polarization maintaining hollow-core to solid-core fiber interconnection.

We develop a hybrid cold/heat two-step splicing approach for low loss, low backreflection, and high polarization extinction ratio (PER) hollow-core to solid-core fiber interconnection. The employed hollow-core fiber (HCF) is our recently developed high-birefringence polarization-maintaining hollow-core fiber (PM-HCF) with a PER value of ∼30 dB, and the solid-core fiber (SCF) is a commercial Panda polarization-maintaining fiber (Panda fiber). Simultaneous low backreflection (<-35 dB), low insertion loss (IL) (∼0.

Connector-style hollow-core fiber interconnections.

To go beyond the fundamental limits imposed by latency, nonlinearity, and laser damage threshold in silica glass fibers, the hollow-core fiber (HCF) technique has been intensively investigated for decades. Recent breakthroughs in ultralow-loss HCF clearly imply that long-haul applications of HCF in communications and lasers are going to appear. Nevertheless, up to now, the HCF technique as a whole is still hampered by the limited length of a single span and the lack of HCF-based functional devices.

Estimates of Variance Components and Heritability Using Random Regression Models for Semen Traits in Boars.

It has been proven that the random regression model has a great advantage over the repeatability model in longitudinal data analysis. At present, the random regression model has been used as a standard analysis method in longitudinal data analysis. The aim of this study was to estimate the variance components and heritability of semen traits over the reproductive lifetime of boars.

Resonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement.

Nanophotonic tweezers represent emerging platforms with significant potential for parallel manipulation and measurements of single biological molecules on-chip. However, trapping force generation represents a substantial obstacle for their broader utility. Here, we present a resonator nanophotonic standing-wave array trap (resonator-nSWAT) that demonstrates significant force enhancement.

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs.

Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping.

Torsional Stiffness of Extended and Plectonemic DNA.

DNA torsional elastic properties play a crucial role in DNA structure, topology, and the regulation of motor protein progression. However, direct measurements of these parameters are experimentally challenging. Here, we present a constant-extension method integrated into an angular optical trap to directly measure torque during DNA supercoiling.