Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean.

Non-CG DNA methylation, a plant-specific epigenetic mark mainly regulated by chromomethylase (CMT), is known to play important roles in Arabidopsis thaliana. However, whether and to what extent non-CG DNA methylation modulates agronomic traits in crops remain to be explored. Here, we describe the consequences of non-CG DNA hypomethylation on development, seed composition, and yield in soybean (Glycine max). We created a Gmcmt mutant line lacking function of all four CMT genes. This line exhibited substantial hypomethylation of non-CG (CHG and CHH) sites. Non-CG hypomethylation enhanced chromatin accessibility and promoted or repressed the expression of hundreds of functionally relevant genes, including upregulation of GOLDEN-LIKE 10 (GmGLK10), which led to enhanced photosynthesis and, unexpectedly, improved nitrogen fixation efficiency. The Gmcmt line produced larger seeds with increased protein content. This study provides insights into the mechanisms of non-CG methylation-based epigenetic regulation of soybean development and suggests viable epigenetic strategies for improving soybean yield and nutritional value.

From synthesis to applications of biomolecule-protected luminescent gold nanoclusters.

Gold nanoclusters (AuNCs) are a class of novel luminescent nanomaterials that exhibit unique properties of ultra-small size, featuring strong anti-photo-bleaching ability, substantial Stokes shift, good biocompatibility, and low toxicity. Various biomolecules have been developed as templates or ligands to protect AuNCs with enhanced stability and luminescent properties for biomedical applications. In this review, the synthesis of AuNCs based on biomolecules including amino acids, peptides, proteins and DNA are summarized. Owing to the advantages of biomolecule-protected AuNCs, they have been employed extensively for diverse applications. The biological applications, particularly in bioimaging, biosensing, disease therapy and biocatalysis have been described in detail herein. Finally, current challenges and future potential prospects of bio-templated AuNCs in biological research are briefly discussed.

Activation of G protein-coupled receptor 39 alleviates neuropathic pain and chronic inflammation.

Neuropathic pain (NP) is mainly caused by lesions or diseases of the somatosensory nervous system and triggers severe physical burdens to patients. It is claimed that activated microglia-mediated neuroinflammation participates in the development of NP, which is regulated by p38 mitogen-activated protein kinase (MAPK)/nuclear factor-κappa B (NF-κB) p65 signaling. G protein-coupled receptor 39 (GPR39) is a trans-membrane protein involved in the activation of cellular transduction pathways, and TC-G 1008, a GPR39 agonist, is believed to have inhibitory effects on neuroinflammation. Our study will explore the possible alleviatory function of TC-G 1008 on NP in a rat model. GPR39 was found markedly downregulated in the spinal dorsal horn of chronic constriction injury (CCI)-stimulated rats. Rats were treated with CCI, followed by intranasal administration with 7.5 and 15 mg/kg TC-G 1008 at 1, 25, 49, and 73 h postmodeling, respectively. Drastically lowered values of paw withdrawal threshold and paw withdrawal latency, upregulated ionized calcium-binding adapter molecule 1, increased release of inflammatory cytokines, elevated spinal malondialdehyde levels, and reduced spinal glutathione peroxidase levels were observed in CCI-stimulated rats, all of which were markedly alleviated and rescued by TC-G 1008. Furthermore, the levels of p-p38/p38 and p-NF-κB p65 were found signally repressed in the spinal dorsal horn of CCI-stimulated rats, which was notably reversed by TC-G 1008. Collectively, TC-G 1008 markedly alleviated NP and neuroinflammation in CCI-treated rats. Our findings provide an attractive future direction for the treatment of NP.

Simple DFS and AOA simultaneous measurement scheme without directional ambiguity with co-frequency self-interference signal cancellation.

A photonic method based on a dual-polarization dual-parallel Mach-Zehnder modulator (DPol-DPMZM) for the simultaneous measurement of the Doppler frequency shift (DFS) and angle of arrival (AOA) of microwave signals is proposed and demonstrated by simulation. The upper arm of each sub-DPMZM is driven by the echo and self-interference signals from the antenna, while the lower arm is driven by the reference signal 1 and reference signal 2. The phase and amplitude of the reference signal 1 are adjusted to match the interference signals for achieving the self-interference cancellation (SIC). At the central office (CO), the DFS and AOA can be acquired in real time without directional ambiguity by processing the two downconverted low-frequency tones in the photocurrent. The simulation results show that the presence of the SI signal will seriously interfere with the observation of the SOI frequency and waveform, and the self-interference cancellation depth of about 42 dB can be obtained after the SIC. The measurement errors of the DFS without direction ambiguity are within 0.2 Hz. After the Hilbert transformation of the intermediate frequency (IF) signal, the AOA can be measured from -87.31∘ to +87.31∘ with errors less than 3.9°. The system has a large bandwidth, excellent real-time performance, and better invisibility, and is expected to be used in modern electronic warfare systems.

Crystallization of Dimensional Isomers in Covalent Organic Frameworks.

Dimensional isomers, defined in reticular chemistry as frameworks consisting of identical molecular building blocks but extended in two or three dimensions (2D or 3D), are an important type of framework isomers that have never been isolated. Herein, we report the crystallization of dimensional isomers in covalent organic frameworks (COFs) for the first time. By polymerization of the same molecular building blocks at different temperatures, both 2D and 3D COFs were successfully constructed due to the temperature-induced conformational changes of precursors from planar to tetrahedral. In addition, the non-fluorescent 2D COF can be gradually converted into the fluorescent 3D COF by increasing the temperature under solvothermal conditions. Therefore, it is reasonable to crystallize the dimensional isomers of reticular materials by controlling the conformation of molecular building blocks, and more examples can be expected. Since the obtained dimensional isomers show different properties and functions, this work will definitely motivate us to design reticular materials for target applications in the future.

One-Stop Extraction and In Situ RT-qPCR for Ultrasensitive Detection of Highly Diluted SARS-CoV-2 in Large-Volume Samples from Aquatic Environments.

Surveillance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in aquatic environments attracted attention due to its considerable impacts on human health and ecology, especially in countries with poor sanitation standards. Based on a strategy of one-stop extraction and in situ amplification, we developed an ultrasensitive method that uses a polyacrylamide derivative-modified filter disc (PAD-FD), in which highly diluted RNA can be efficiently concentrated onto the filter disc and directly used for amplification. A newly designed spin column with a cup-like filter base facilitated the non-contact transfer of the affinity filter disc from the column to a PCR tube. The limit of detection of the PAD-FD coupled with RT-qPCR is 10 copies/mL. Using 32 suspected SARS-CoV-2 samples, we demonstrated that the detection rate of our method (62.5%, 20/32) was triple the rate of the commercial kit (18.8%, 6/32). Using a PAD-FD, 56.3% (18/32) and 40.6% (13/32) of the 10-fold-dilution samples with river and tap water, respectively, were detected. Even when diluted 100-fold, 28.1% (9/32) and 37.5% (12/32) were still detected in river and tap water, respectively. We believe that the PAD-FD method offers an accurate testing tool for monitoring viral RNA in aquatic environments, contributing to the forewarning of the SARS-CoV-2 outbreak and the breaking of the transmission chain.

Identification and mapping of a recessive allele, dt3, specifying semideterminate stem growth habit in soybean.

KEY MESSAGE: A locus, dt3, modulating semideterminancy in soybean, was discovered by a combination of genome-wide association studies and linkage mapping with multiple distinct biparental populations. Stem growth habit is a key architectural trait in many plants that contributes to plant productivity and environmental adaptation. In soybean, stem growth habit is classified as indeterminate, semideterminate, or determinate, of which semideterminacy is often considered as a counterpart of the "Green Revolution" trait in cereals that significantly increased grain yields. It has been demonstrated that semideterminacy in soybean is modulated by epistatic interaction between two loci, Dt1 on chromosome 19 and Dt2 on chromosome 18, with the latter as a negative regulator of the former. Here, we report the discovery of a third locus, Dt3, modulating soybean stem growth habit, which was delineated to a ~ 196-kb region on chromosome 10 by a combination of allelic and haplotypic analysis of the Dt1 and Dt2 loci in the USDA soybean Germplasm Collection, genome-wide association studies with three subsets of the collection, and linkage mapping with four biparental populations derived from crosses between one of two elite indeterminate cultivars and each of four semideterminate varieties possessing neither Dt2 nor dt1. These four semideterminate varieties are recessive mutants (i.e., dt3/dt3) in the Dt1/Dt1;dt2/dt2 background. As the semideterminacy modulated by the Dt2 allele has unfavorable pleotropic effects such as sensitivity to drought stress, dt3 may be an ideal alternative for use to develop semideterminate cultivars that are more resilient to such an environmental stress. This study enhances our understanding of the genetic factors underlying semideterminacy and enables more accurate marker-assisted selection for stem growth habit in soybean breeding.

The genetic basis of shoot architecture in soybean.

Shoot architecture refers to the three-dimensional body plan of the above ground organs of the plant. The patterning of this body plan results from the tight genetic control of the size and maintenance of meristems, the initiation of axillary growth, and the timing of developmental phase transition. Variation in shoot architecture can result in dramatic differences in plant productivity and/or grain yield due to their effects on light interception, photosynthetic efficiency, response to agronomic inputs, and environmental adaptation. The fine-tuning of shoot architecture has consequently been of great interest to plant breeders, driving the need for deeper understanding of the genes and molecular mechanisms governing these traits. In soybean, the world's most important oil and protein crop, major components of shoot architecture include stem growth habit, plant height, branch angle, branch number, leaf petiole angle, and the size and shape of leaves. Key genes underlying some of these traits have been identified to integrate hormonal, developmental, and environmental signals modulating the growth and orientation of shoot organs. Here we summarize the current knowledge and recent advances in the understanding of the genetic control of these important architectural traits in soybean.

Photonic approach for Doppler-frequency-shift and angle-of-arrival measurement with direction unambiguity and high precision.

A novel, to the best of our knowledge, scheme based on a dual-drive Mach-Zehnder modulator (DDMZM) is proposed for Doppler-frequency-shift (DFS) and angle-of-arrival (AOA) measurement without direction ambiguity. The echo signal from one antenna is coupled with a local oscillator and then fed into the upper RF port of the DDMZM, and the echo signal from the other one is directly fed to its lower RF port. The generated two first-order optical sidebands are separated by an interleaver to form two channels and then detected by two identical low-speed photodiodes, and so both magnitude and orientation of the AOA and DFS can be deduced from the power and frequency of the beating signals. The AOA measurement without direction ambiguity can be achieved by comparing the power of beating signals from two channels. In addition, through operating the DDMZM at different transmission points for different AOA measurement ranges, the range of high-precision AOA measurement can be extended. The system has the low complexity and high stability because only a DDMZM is used. The simulation results demonstrate the measurement of the DFS in the range of 500 kHz with errors <0.05H z and the AOA from -90∘ to +90∘ with error <0.8∘.

Photonic instantaneous microwave frequency measurement based on frequency-phase mapping with high precision.

This paper presents an instantaneous microwave frequency measurement scheme based on a frequency-phase mapping technique. In our scheme, a low-frequency (LF) reference signal and two microwave signals with a relative time delay are modulated on the optical carriers via two dual-parallel Mach-Zehnder modulators. The generated electrical signal has the same frequency as that of the LF reference signal, but with a phase shift, which depends on the microwave signal frequency and the time delay. Therefore, a linear frequency-phase mapping function with a high slope is constructed, which improves the accuracy of the whole frequency measurement range. The scheme has a compact structure without an optical filter and polarization devices, which enhances the long-term stability of the system. The simulation shows that our scheme has a 4.1-40 GHz frequency measurement range with errors less than ±0.04 GHz.

Tri-comb generation with a dual-ring structure.

By introducing a third measurement comb with different repetition frequencies (Δ f r e p ), the tri-comb spectroscopy technique overcomes the ambiguity problem of the original dual-comb spectroscopy technique and eliminates physical delay stages in multidimensional coherent spectroscopy. Nowadays, tri-comb generation based on three frequency-stabilized comb lasers is overly complicated and costly for many potential applications. Previous research on single-cavity dual-combs inspired research on single-cavity tri-combs. However, the currently reported tri-comb structures cannot achieve independently controllable pulses. This paper shows a dual-ring tri-comb seed-source structure using wavelength-based multiplexing in one of the rings. The wavelength and power of the output pulse are independently controlled by using the dual-ring structure. The Δ f r e p of wavelength multiplexing-based dual-comb output can be tuned by adjusting the intra-ring polarization controller (PC). In the case of single-wavelength mode-locking, the PC can be adjusted to achieve a wavelength tuning range of nearly 20 nm. The tri-comb source could offer an attractive alternative solution as a low-complexity light source for field-deployable multi-comb metrology applications.

Locating Hydrogen Positions for COF-300 by Cryo-3D Electron Diffraction.

Covalent organic frameworks (COFs) have wide-ranging applications, and their host-guest interactions play an essential role in the achievement of COF functions. To investigate these host-guest interactions, it is necessary to locate all atoms, especially hydrogen atoms. However, it is difficult to determine the hydrogen atomic positions in COFs because of the complexities in synthesizing high-quality large single crystals. Three-dimensional electron diffraction (3D ED) has unique advantages for the structural determination of nanocrystals and identification of light atoms. In this study, it was demonstrated for the first time that the hydrogen atoms of a COF, not only on the framework but also on the guest molecule, can be located by 3D ED using continuous precession electron diffraction tomography (cPEDT) under cryogenic conditions. The host-guest interactions were clarified with the location of the hydrogen atoms. These findings provide novel insights into the investigation of COFs.

Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes.

In comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT-rich introns were retained in the TNP2-like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2-like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2-like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.

Rational Design of ZIF-8 for Constructing Luminescent Biosensors with Glucose Oxidase and AIE-Type Gold Nanoclusters.

The development of modern technologies has acclimatized biosensors to complicated applicable scenarios with integrated properties as a whole instead of the pursuit of a single-point breakthrough. Here, we targeted a few concerns in the development of enzyme-based biosensors, including stability, analyte enrichment, and signal transduction, and developed a general biosensing model utilizing enzymes, aggregation-induced emission (AIE) luminogens, and stimuli-responsive framework materials as the units. We propose such proof-of-concept of glucose biosensors by coencapsulating glucose oxidase and AIE-type gold nanoclusters into acid-sensitive zeolite imidazolate framework (ZIF)-8 nanocrystals. The acid-activated degradation of ZIF-8 bridges the molecular signals produced by the enzyme-catalytic reaction of glucose and the photon signals generated by ZIF-8-induced AIE effects of gold nanoclusters, resulting in the "turn-off" model nanoprobes for glucose detection with high selectivity. After embedding the nanoprobes into hollow-out tapes, the formed paper biosensors can conveniently detect glucose with the help of a smartphone.

Luminescent Covalent Organic Frameworks for Biosensing and Bioimaging Applications.

Luminescent covalent organic frameworks (LCOFs) have attracted significant attention due to their tunability of structures and photophysical properties at molecular level. LCOFs are built to highly ordered and periodic 2D or 3D framework structures through covalently assembling with various luminophore building blocks. Recently, the advantages of LCOFs including predesigned properties of structure, unique photoluminescence, hypotoxicity and good biocompatibility and tumor penetration, broaden their applications in biorelated fields, such as biosensing, bioimaging, and drug delivery. A specific review that analyses the advances of LCOFs in the field of biosensing and bioimaging is thus urged to emerge. Here the construction of LCOFs is reviewed first. The synthetic chemistry of LCOFs highlights the key role of chemical linkages, which not only concrete the building blocks but also affect the optical properties and even can act as the responsive sites for potential sensing applications. How to brighten LCOFs are clarified through description of structure managements. The ability to utilize the luminescence of LCOFs for applications in biosensing and bioimaging is discussed using state-of-the-art examples of varied practical goals. A prospect finally addresses opportunities and challenges the development of LCOFs facing from chemistry, physics to the applications, according to their current progress.

Identification and molecular mapping of a major quantitative trait locus underlying branch angle in soybean.

KEY MESSAGE: A major quantitative trait locus (QTL) modulating soybean (Glycine max) branch angle was identified by linkage analysis using two bi-parental mapping populations with and without pedigree from wild soybean (Glycine soja). Soybean branch angle is a critical architectural trait that affects many other traits of agronomic importance associated with the plant's productivity and grain yield and is thus a vital consideration in soybean breeding. However, the genetic basis for modulating this important trait in soybean and many other crops remain unknown. Previously, we developed a recombinant inbred line (RIL) population derived from a cross between a domesticated soybean (Glycine max) variety, Williams 82, and a wild soybean (Glycine soja) accession, PI 479,752, and observed drastic variation in plant architecture including branch angle among individual RILs. In this study, one of the RILs possessing extremely wide branch angle (WBA) was crossed with an elite soybean cultivar (LD00-3309) possessing narrow branch angle (NBA) to produce an F2 population composed of 147 plants and F2-derived F3 families for inheritance analysis and QTL mapping. We found that branch angle is controlled by a major QTL located on chromosome 19, designated qGmBa1 and that WBA-derived from the wild soybean accession-is dominant over NBA. This locus was also detected as a major one underlying branch angle by QTL mapping using a subset of the soybean nested association mapping (SoyNAM) population composed of 140 RILs, which were derived from a cross between a landrace, PI 437169B, possessing WBA and an elite variety, IA3023, possessing NBA. Molecular markers located in the QTL region defined by both mapping populations can be used for marker-assisted selection of branch angle in soybean breeding.

Stable Zinc(II) Coordination Polymer as a Rapid and Highly Sensitive Fluorescence Sensor for the Discriminative Sensing of Biomarker 2-(2-Methoxyethoxy) Acetic Acid.

A novel two-dimensional bilayer Zn-based luminescent coordination polymer (LCP) [Zn2(µ2-OH)(4-dptp)(3,4',5-bpt)] (LCP 1) [4-dptp = N3,N4-bis(pyridin-4-ylmethyl)thiophene-3,4-dicarboxamide and 3,4',5-H3bpt = biphenyl-3,4',5-tricarboxylic acid] was successfully prepared under hydrothermal conditions and characterized by single-crystal X-ray diffraction, IR spectroscopy, powder X-ray diffraction, and luminescence spectroscopy. LCP 1 displayed excellent fluorescence-quenching efficiency toward a biomarker 2-(2-methoxyethoxy) acetic acid (MEAA) with a high Ksv (5.153 × 104 M-1), a low limit of detection (0.244 µM), and a rapid response time (28 s). Additionally, LCP 1 can repeatedly detect MEAA at least eight times with excellent stability. The sensing mechanism was also carefully investigated through UV-vis absorption spectroscopy, density functional theory calculations, and fluorescence lifetime analysis.

Coronavirus Disease 2019 Patients in Earlier Stages Exhaled Millions of Severe Acute Respiratory Syndrome Coronavirus 2 Per Hour.

Coronavirus disease 2019 (COVID-19) patients exhaled millions of severe acute respiratory syndrome coronavirus 2 RNA copies per hour, which plays an important role in COVID-19 transmission. Exhaled breath had a higher positive rate (26.9%, n = 52) than surface (5.4%, n = 242) and air (3.8%, n = 26) samples.

A transposon-mediated reciprocal translocation promotes environmental adaptation but compromises domesticability of wild soybeans.

Large structural variations frequently occur in higher plants; however, the impact of such variations on plant diversification, adaptation and domestication remains elusive. Here, we mapped and characterised a reciprocal chromosomal translocation in soybeans and assessed its effects on diversification and adaptation of wild (Glycine soja) and semiwild (Glycine gracilis) soybeans, and domestication of cultivated soybean (Glycine max), by tracing the distribution of the translocation in the USDA Soybean Germplasm Collection and population genetics analysis. We demonstrate that the translocation occurred through CACTA transposon-mediated chromosomal breakage in wild soybean c. 0.34 Ma and is responsible for semisterility in translocation heterozygotes and reduces their reproductive fitness. The translocation has differentiated Continental (i.e. China and Russia) populations from Maritime (i.e. Korea and Japan) populations of G. soja and predominately adapted to cold and dry climates. Further analysis revealed that the divergence of G. max from G. soja predates the translocation event and that G. gracilis is an evolutionary intermediate between G. soja and G. max. Our results highlight the effects of a chromosome rearrangement on the processes leading to plant divergence and adaptation, and provides evidence that suggests G. gracilis, rather than G. soja, as the ancestor of cultivated soybean.

Identification and molecular mapping of Rps14, a gene conferring broad-spectrum resistance to Phytophthora sojae in soybean.

KEY MESSAGE: A soybean landrace carries broad-spectrum resistance to Phytophthora sojae, which is conferred by a single gene, designated Rps14, on the short arm of chromosome 3. Phytophthora sojae is the causative agent for Phytophthora root and stem rot in soybean [Glycine max (L.) Merr.] and can be managed by deployment of resistance to P. sojae (Rps) genes. PI 340,029 is a soybean landrace carrying broad-spectrum resistance to the pathogen. Analysis of an F2 population derived from a cross between PI 340,029 and a susceptible cultivar 'Williams' reveals that the resistance to P. sojae race 1 is conferred by a single gene, designated Rps14, which was initially mapped to a 4.5-cM region on the short arm of chromosome 3 by bulked segregant analysis (BSA), and subsequently narrowed to a 1.48 cM region corresponding to 229-kb in the Williams 82 reference genome (Wm82 v2.a1), using F3:4 families derived from the F2 population. Further analysis indicates that the broad-spectrum resistance carried by PI 340,029 is fully attributable to Rps14. The genomic sequences corresponding to the defined Rps14 region from a set of diverse soybean varieties exhibit drastic NBS-LRR gene copy number variation, ranging from 3 to 17 copies. Ultimate isolation of Rps14 would be critical for precise selection and deployment of the gene for soybean protection.