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. We observed that topo II is ~50-fold more processive on buckled DNA than previously estimated. We further discovered that topo II relaxes supercoiled DNA prior to plectoneme formation, but with processivity reduced by ~100-fold. This relaxation decreases with diminishing torsion, consistent with topo II capturing transient DNA loops. Topo II retains high processivity on buckled chromatin (~10,000 turns) and becomes highly processive even on chromatin under low torsional stress (~1000 turns), consistent with chromatin's predisposition to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function.

Chromatinization Modulates Topoisomerase II Processivity.

Type IIA topoisomerases are essential DNA processing enzymes that must robustly and reliably relax DNA torsional stress in vivo. 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). We observed that topo II was at least ~ 50-fold more processive on plectonemic DNA than previously estimated, capable of relaxing > 6000 turns. We further discovered that topo II could relax supercoiled DNA prior to plectoneme formation, but with a ~100-fold reduction in processivity; strikingly, the relaxation rate in this regime decreased with diminishing torsion in a manner consistent with the capture of transient DNA loops by topo II. Chromatinization preserved the high processivity of the enzyme under high torsional stress. Interestingly, topo II was still highly processive (~ 1000 turns) even under low torsional stress, consistent with the predisposition of chromatin to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function, capable of enhancing function even under low torsional stress.

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. The results show that the turbidity trend differed from -1.3 NTU/yr to 0.7 NTU/yr in different water surfaces. Turbidity decreased significantly in the mainstream of the Yangtze River (MYR), aquaculture ponds (AP) and other water bodies, whilst increasing significantly in the medium lakes (ML) and mainstream of the Qiantang River (MQR). Meanwhile, no significant changes in turbidity were observed in the great lakes (GL) and small lakes (SL). Rather than climatic factors, urbanisation and decreasing wastewater discharge were the dominant drivers of turbidity trends during the study period. In addition, ecological engineering in AP increased water transparency. The Three Gorges Dam also decreased turbidity in MYR. Increasing turbidity in the downstream of MQR was driven by increasing seasonal water surfaces and reclamation projects near Hangzhou Bay. GL faced no significant increase in turbidity due to the offset of afforestation to urbanisation-induced turbidity increase. These findings provide important information for government decision-making for subsequent aquatic environmental protection and restoration in the YRDR.

Selectively gas-filled anti-resonant hollow-core fibers for broadband high-purity LP11 mode guidance.

An anti-resonant hollow-core fiber capable of propagating the LP11 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 2.7 m, the fabricated fiber shows a mode extinction ratio of over 40 dB at 1550 nm and above 30 dB in a wavelength range of 150 nm. The loss of the LP11 mode is measured to be 2.46 dB/m at 1550 nm. We discuss the potential application of such fibers in high-fidelity high-dimensional quantum state transmission.

A non-Newtonian fluid quasi-solid electrolyte designed for long life and high safety Li-O2 batteries.

The Li dendrite growth and the liquid electrolyte volatilization under semi-open architecture are intrinsic issues for Li-O2 battery. In this work, we propose a non-Newtonian fluid quasi-solid electrolyte (NNFQSE) SiO2-SO3Li/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. Furthermore, NNFQSE exhibits shear-thinning property to eliminate the stress of dendrite growth during repeated cycling. Meanwhile, when the force suddenly increases, such as a high current rate, the NNFQSE may dynamically turn shear-thickening to respond and mechanically stiffen to inhibit the lithium dendrite penetration. By coupling with the NNFQSE, the lithium symmetrical battery can run over 2000 h under 1 mA cm-2 at room temperature, and the quasi-solid Li-O2 battery actualizes long life above 5000 h at 100 mA g-1.

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 (∂ß2/∂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 0.1 ps2/km and 2 × 10-3 ps2/km, respectively, and validate our model. Consistent with our model, a pronounced negative ∂ß2/∂p is observed experimentally for the first time, to our knowledge. Our model can also be extended to other HCFs with cladding resonances in predicting ∂ß2/∂p, such as in photonic bandgap types of HCF.

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 1.8 × 10-5 are demonstrated. This achieved loss is more than one order of magnitude lower than the previously reported birefringent AR-HCF and the bandwidth is one order of magnitude broader than the reported birefringent photonic bandgap hollow-core fiber (PBG-HCF) with the same loss level. The polarization extinction ratio (PER) reaches the ∼20 dB level in a 90 m-long fiber under >25 cm bending radius. Combined with the single mode and low dispersion features, the developed semi-tube AR-HCF may find a variety of applications in frequency metrology, interferometric fiber gyroscopes, and long-baseline stellar interferometry.

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. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

Genome-Wide Association Study Reveals Novel QTLs and Candidate Genes for Grain Number in Rice.

Grain number per panicle (GNPP), determined mainly by panicle branching, is vital for rice yield. The dissection of the genetic basis underlying GNPP could help to improve rice yield. However, genetic resources, including quantitative trait loci (QTL) or genes for breeders to enhance rice GNPP, are still limited. Here, we conducted the genome-wide association study (GWAS) on the GNPP, primary branch number (PBN), and secondary branch number (SBN) of 468 rice accessions. We detected a total of 18 QTLs, including six for GNPP, six for PBN, and six for SBN, in the whole panel and the indica and japonica subpanels of 468 accessions. More importantly, qPSG1 was a common QTL for GNPP, PBN, and SBN and was demonstrated by chromosome segment substitution lines (CSSLs). Considering gene annotation, expression, and haplotype analysis, seven novel and strong GNPP-related candidate genes were mined from qPSG1. Our results provide clues to elucidate the molecular regulatory network of GNPP. The identified QTLs and candidate genes will contribute to the improvement of GNPP and rice yield via molecular marker-assisted selection (MAS) breeding and genetic engineering techniques.

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) (∼0.7 dB), and high PER (∼27 dB) are achieved, representing the first high-performance PM-HCF/SCF interconnections, to the best of our knowledge. This greatly facilitates the applications of PM-HCF in widespread fields such as precise metrologies, gyroscopes, and ultrafast/high-power laser deliveries.

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. To resolve these two issues, it is of importance to develop ultralow-loss and plug-and-play HCF interconnections. In this work, we report on HCF interconnections with the lowest-ever insertion losses (0.10 dB for HCF to standard single-mode fiber (SMF) and 0.13 dB for HCF to itself in the 1.5 µm waveband) and in a pluggable means. Two fiber mode-field adapters, one based on a graded-index multi-mode fiber (GIF) and the other utilizing a thermally expanded core (TEC) SMF, have been tested and compared. An extra insertion loss arising from imperfect refractive index distribution in a commercial GIF is observed. Our HCF interconnections also realize a back-reflection of <-35 dB over a 100 nm bandwidth as well as other critical metrics in favor of practical applications. Our technique is viable for any type of HCF.

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. The study data, including 124,941 records from 3,366 boars, were collected from seven boar AI centers in South China between 2010 and 2019. To evaluate alternative models, we compared different polynomial orders of fixed, additive, and permanent environment effects in total 216 models using Bayesian Information Criterions. The result indicated that the best model always has higher-order polynomials of permanent environment effect and lower-order polynomials of fixed effect and additive effect regression. In Landrace boars, the heritabilities ranged from 0.18 to 0.28, 0.06 to 0.43, 0.03 to 0.14, and 0.05 to 0.24 for semen volume, sperm motility, sperm concentration, and abnormal sperm percentage, respectively. In Large White boars, the heritabilities ranged from 0.20 to 0.26, 0.07 to 0.15, 0.10 to 0.23, and 0.06 to 0.34 for semen volume, sperm motility, sperm concentration, and abnormal sperm percentage, respectively.

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. This platform integrates a critically-coupled resonator design to the nSWAT and incorporates a novel trap reset scheme. The nSWAT can now perform standard single-molecule experiments, including stretching DNA molecules to measure their force-extension relations, unzipping DNA molecules, and disrupting and mapping protein-DNA interactions. These experiments have realized trapping forces on the order of 20 pN while demonstrating base-pair resolution with measurements performed on multiple molecules in parallel. Thus, the resonator-nSWAT platform now meets the benchmarks of a table-top precision optical trapping instrument in terms of force generation and resolution. This represents the first demonstration of a nanophotonic platform for such single-molecule experiments.

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. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96-15.02 Mb, SSC7: 97.18-98.18 Mb, SSC14: 128.29-131.15 Mb, SSC17: 15.39-17.27 Mb, and SSC17: 22.04-24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

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. We measured the twist persistence length of extended DNA to be 22 nm under an extremely low force (∼0.02 pN) and the twist persistence length of plectonemic DNA to be 24 nm. In addition, we implemented a rigorous data analysis scheme that bridged our measurements with existing theoretical models of DNA torsional behavior. This comprehensive set of torsional parameters demonstrates that at least 20% of DNA supercoiling is partitioned into twist for both extended DNA and plectonemic DNA. This work provides a new experimental methodology, as well as an analytical and interpretational framework, which will enable, expand, and enhance future studies of DNA torsional properties.

Confidentiality-enhanced chaotic optical communication system with variable RF amplifier gain.

To solve the security problem of information transmission, we add a more complex key of variable RF amplifier gain to enhance the confidentiality of the chaotic optical communication system. In the system, the RF amplifier gain is variable. The numerical results indicate that the bit error rate of the eavesdropper is much higher than that of the authorized receiver. And the eavesdropper cannot decrease the BER by decreasing the mismatch of other parameters in the electro-optic oscillator gain. Such system can be used to realize communication with high level of privacy in the future.

Radiation-induced mismatch effect on performances of space chaos laser communication systems.

Chaotic modulation serves as an excellent scheme to enhance the confidentiality of space laser communication systems. Considering radiation and intensity scintillation, we establish bit error rate (BER) computation models for both an inter-satellite chaos laser communication system and a satellite-to-ground chaos laser communication system. Based on such models, numerical simulations are conducted to investigate the mismatch effect on BER performance of these two typical systems. For an inter-satellite system, radiation can induce great parameter mismatches. For a satellite-to-ground system, the BER only slightly rises due to intensity scintillation being a more dominant deterioration effect than radiation. Our work has good reference value for the practical design of space chaos laser communication systems.

Effect of controllable parameter synchronization on the ensemble average bit error rate of space-to-ground downlink chaos laser communication system.

Chaotic modulation is a scheme used to enhance the information security through the configuration parameter synchronization. When chaotic modulation is adopted in the space-to-ground laser communication system, the traditional bit error rate (BER) calculation model for fiber-based chaos communication system is no longer available to depict the long-term communication performance. To solve this problem, we established a new ensemble average BER calculation model under the effects of intensity scintillation and pointing error. Based on this model, we conduct a simulation to research such a system, and our numerical results indicate that space-to-ground chaos laser communication system has a great anti-interference against these two effects when the detector mismatch approaches zero. Our results display the advantages of chaotic modulation and also reflect the characteristics of space-to-ground chaos laser communication system.

Compression Induced Chondrogenic Differentiation of Embryonic Stem Cells in Three-Dimensional Polydimethylsiloxane Scaffolds.

Embryonic stem cells (ESCs) are an ideal source for chondrogenic progenitors for the repair of damaged cartilage tissue. It is currently difficult to induce uniform and scalable ESC differentiation in vitro, a process required for stem cell therapy. This is partly because stem cell fate is determined by complex interactions with the native microenvironment and mechanical properties of the extracellular matrix. Mechanical signaling is considered to be one of the major factors regulating the proliferation and differentiation of chondrogenic cells both in vitro and in vivo. We used biocompatible and elastic polydimethylsiloxane (PDMS) scaffolds, capable of transducing mechanical signals, including compressive stress in vitro. ESCs seeded into the PDMS scaffolds and subjected to mechanical loading resulted in induction of differentiation. Differentiated ESC derivatives in three-dimensional (3-D) PDMS scaffolds exhibited elongated single cell rather than round clonal ESC morphology. They expressed chondrogenic marker, Col2, with concomitant reduction in the expression of pluripotent marker, Oct4. Immunocytochemical analysis also showed that the expression of COL2 protein was significantly higher in ESCs in 3-D scaffolds subjected to compressive stress. Further analysis showed that compressive stress also resulted in expression of early chondrogenic makers, Sox9 and Acan, but not hypertrophic chondrogenic markers, Runx2, Col10, and Mmp13. Compressive stress induced differentiation caused a reduction in the expression of ß-Catenin and an increase in the expression of genes, Rhoa, Yap, and Taz, which are known to be affected by mechanosignaling. The chondroinductive role of RhoA was confirmed by its downregulation with simultaneous decrease in the transcriptional and translational expression of early chondrogenic markers, SOX9, COL2, and ACAN, when ESCs in PDMS scaffolds were subjected to compressive stress and treated with RhoA inhibitor, CCG-1432. Based on these observations, a model for compression induced chondrogenic differentiation of ESCs in 3-D scaffolds was proposed.

Conjugation of basic fibroblast growth factor on a heparin gradient for regulating the migration of different types of cells.

Regulation of cell migration by cell growth factors is critical in tissue regeneration such as angiogenesis, wound healing, and bone formation. In this work, basic fibroblast growth factor (bFGF) with a density varying between 0 and 295 ng/cm2 was conjugated on heparinized glass slides. The amount of conjugated bFGF was determined by immunofluorescent staining. The mobility of vascular smooth muscle cells (VSMCs) was largely dominated by the bFGF density, whereas that of mesenchymal stem cells (MSCs) and endothelial cells (ECs) was slightly influenced. The migration rate of VSMCs increased initially and then decreased along with the increase of bFGF density. The fastest rate (22 µm/h) was found on the bFGF surface with a density of 83 ng/cm2. The intrinsic mechanisms of the diverse migration behaviors of the VSMCs, MSCs, and ECs were revealed by studying the expression of bFGF receptors and migration-related proteins. The results show that the cell mobility is regulated by complex and synergetic intracellular signals in a cell type-dependent manner.