A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters.

Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.

Quantum illumination based on cavity-optomagnonics system with Kerr nonlinearity.

Quantum illumination is a quantum optical sensing technique, which employs an entangled source to detect low-reflectivity object immersed in a bright thermal background. Hybrid cavity-optomagnonics system promises to work as quantum illumination because a yttrium iron garnet (YIG) sphere can couple to microwave field and optical field. In this paper, we propose a scheme to enhance the entanglement between the output fields of the microwave and optical cavities by considering the intrinsic Kerr nonlinearity of the YIG. We investigate the difference between intrinsic Kerr nonlinearity and optomagnonical parametric-type coupling on improving entanglement. Our result show that the large value optomagnonical parametric-type coupling does not mean the large entanglement, nevertheless, the large value of Kerr nonlinearity does monotonously improve the entanglement for our group of parameters. Consequently, under feasible parameters of current experiment, the signal-to-noise ratio and probability of detection error can be improved after considering the magnon Kerr nonlinearity.

An Improved Recombineering Toolset for Plants.

Gene functional studies often rely on the expression of a gene of interest as transcriptional and translational fusions with specialized tags. Ideally, this is done in the native chromosomal contexts to avoid potential misexpression artifacts. Although recent improvements in genome editing have made it possible to directly modify the target genes in their native chromosomal locations, classical transgenesis is still the preferred experimental approach chosen in most gene tagging studies because of its time efficiency and accessibility. We have developed a recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the results obtained by direct chromosomal tagging using genome-editing strategies. These simple, scalable, customizable recombineering toolsets and protocols allow a variety of genetic modifications to be generated. In addition, we developed a highly efficient recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana). We demonstrated the utility of this system by generating more than 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes and characterizing the translational reporter expression patterns for 14 auxin biosynthesis genes.

Improving mechanical cooling by using magnetic thermal noise in a cavity-magnomechanical system.

The cavity-magnomechanical system is a significant platform for studying quantum information. In this paper, a scheme to realize the ground-state cooling of the mechanical phonon mode in a cavity-magnomechanical system is proposed. In the general cooling method, the system is usually driven by a strong pumping field, and the Hamiltonian of the system needs to be linearized. Different from this cooling method, in a cavity-magnomechanical tripartite interaction system, we consider the magnetic thermal noise as an incoherent drive to facilitate cooling, where the thermal magnon number can enhance the effective coupling between the photon and phonon modes. The mechanical mode can be cooled to its ground state when the magnon thermal number is increased.

Simultaneous ground-state cooling of identical mechanical oscillators by Lyapunov control.

The simultaneous cooling of multiple mechanical oscillators in the cavity optomechanical system has aroused people's attention and may be applicable in the quantum information process. In this paper, a scheme to realize the simultaneous ground-state cooling of two identical mechanical oscillators is proposed, where the frequency of one of the oscillators is designed according to Lyapunov control. By this method, the dark mode can effectively couple with the bright mode so that the two identical oscillators can be simultaneously cooled to their ground state. Extending this scheme into multiple identical mechanical oscillators, we show that simultaneous cooling can also be achieved.

Unidirectional amplification in optomechanical system coupling with a structured bath.

Nonreciprocity plays an indispensable role in quantum information transmission. We theoretically study the unidirectional amplification in the non-Markovian regime, in which a nanosphere surrounded by a structured bath is trapped in a single (dual)-mode cavity. The global mechanical response function of the nanosphere is markedly altered by the non-Markovian structured bath through shifting the effective frequency and magnifying the response function. Consequently, when there is a small difference in the transmission rate within the regime of Markovian, the unidirectional amplification is achieved in the super-Ohmic spectral environment. In the double-optomechanical coupling system, the phase difference between two optomechanical couplings can reverse the transmission direction. Meanwhile, the non-Markovian bath still can amplify the signal because of the XX-type coupling between nanosphere and its bath.

Simulating topological phases with atom arrays in an optical waveguide.

In this paper, we employ the atomic arrays in one-dimensional optical waveguides to simulate topological phases, where the waveguide is modeled as a one-dimensional infinitely long coupled cavity array. Under the Markov approximation, the coherent and dissipative coupling between atoms is established by eliminating waveguide modes. When the detuning between atoms and cavity fields lies in the band gap, the dynamics of the system is completely dominated by the coherent interaction. Under this condition, we designed three atomic arrays with different geometries and show that the topologically trivial and non-trivial phases of atomic arrays can be simulated. Furthermore, by introducing periodic atomic driving, the topological phase transition can be induced by adjusting the driving parameters. Finally, we investigate the effect of next-nearest neighbor interactions on topological state transfer and find that the next-nearest neighbor interactions break the degenerated bandgap state and establish a topological state transfer channel.

R233H mutation in patients with tyrosine hydroxylase deficiency and corresponding phenotypes: a study of four cases and literature review.

Owing to the small number of patients with tyrosine hydroxylase (TH) deficiency, no genotype-phenotype correlations have yet been identified. To investigate the genotype-phenotype correlation of R233H mutation in TH deficiency, we analyzed the clinical manifestations and treatment responses of four patients with the R233H homozygous mutation. Thirty-eight additional patients, available from the literature, known to be homozygous or heterozygous for the R233H mutation, were combined with the four cases from our hospital. Data for a total of 42 patients were retrieved. Our four patients showed clinical presentation consistent with Type A TH deficiency, and responded well to levodopa therapy, with an improvement in clinical symptoms within 1-2 weeks. In the 42 patients, 20 of 42 patients (48%) were homozygous and 22 (52%) were heterozygous for the R233H mutation. Of the 20 patients who were homozygous for the R233H mutation, a majority (80%) suffered from Type A TH deficiency. Of the 8 patients that were heterozygous for the R233H/the mutation located downstream of exon 11, 7 patients (86%) suffered from Type B TH deficiency. Of the 7 patients who were heterozygous for the R233H/nonsense mutation, 6 (86%) suffered from Type B TH deficiency. Genotype-phenotype correlation of R233H mutation was observed in TH deficiency. The homozygous R233H mutation frequently manifests as Type A TH deficiency, whereas R233H/nonsense mutation or any mutation located downstream of exon 11 manifests as Type B TH deficiency.

Improving few-photon optomechanical effects with coherent feedback.

Few-photon effects such as photon blockade and tunneling have potential applications in modern quantum technology. To enhance the few-photon effects in an optomechanical system, we introduce a coherent feedback loop to cavity mode theoretically. By studying the second-order correlation function, we show that the photon blockade effect can be improved with feedback. Under appropriate parameters, the photon blockade effect exists even when cavity decay rate is larger than the single-photon optomechanical coupling coefficient, which may reduce the difficulty of realizing single-photon source in experiments. Through further study of the third-order correlation function, we show that the tunneling effect can also be enhanced by feedback. In addition, we discuss the application of feedback on Schrödinger-cat state generation in an optomechanical system. The result shows that the fidelity of cat state generation can be improved in the presence of feedback loop.

Nonlinearity enhancement and photon blockade in hybrid optomechanical systems.

The nonlinear optomechanical coupling is an attracting characteristic in the field of optomechanics. However, the strength of single photon optomechanical coupling is still within weak coupling regime. Using the optomechanical coupling to achieve strong nonlinear interaction between photons is still a challenge. In this paper, we propose a scheme by employing optomechanical and spin-mechanical interactions to enhance the nonlinearity of photons. An effective Hamiltonian is derived, which shows that the self-Kerr and cross-Kerr nonlinearity strengths can be enhanced by adjusting the classical pumping or enhancing the spin-mechanical coupling strength. In addition, we investigate the potential usage of the nonlinearity in the photon blockade. We demonstrate that the single and two photon blockades can occur in two super modes.

Detailed characterization of the UMAMIT proteins provides insight into their evolution, amino acid transport properties, and role in the plant.

Amino acid transporters play a critical role in distributing amino acids within the cell compartments and between plant organs. Despite this importance, relatively few amino acid transporter genes have been characterized and their role elucidated with certainty. Two main families of proteins encode amino acid transporters in plants: the amino acid-polyamine-organocation superfamily, containing mostly importers, and the UMAMIT (usually multiple acids move in and out transporter) family, apparently encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively. Knowledge of UMAMITs is scarce, based on six Arabidopsis genes and a handful of genes from other species. To gain insight into the role of the members of this family and provide data to be used for future characterization, we studied the evolution of the UMAMITs in plants, and determined the functional properties, the structure, and localization of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are essentially localized at the tonoplast or the plasma membrane, and that most of them are able to export amino acids from the cytosol, confirming a role in intra- and intercellular amino acid transport. As an example, this set of data was used to hypothesize the role of a few AtUMAMITs in the plant and the cell.

Force sensing in a dual-mode optomechanical system with linear-quadratic coupling and modulated photon hopping.

A weak force sensor scheme is presented in an optomechanical system, in which the two cavity modes couple to a mechanical mode with linear and quadratic coupling. Due to introducing time-dependent hopping, the linear and quadratic coupling terms coexist under the rotating-wave approximation in the interaction picture. Compared with the quantum non-demolition measurement (ignoring the quadratic optomechanical coupling), the current scheme can decrease the additional noise to a lower level. Our proposal provides a promising platform for improving the detection of a weak force.

DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa.

DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) from snapdragon (Antirrhinum majus) is a MYB/SANT protein that interacts with related MYB/SANT proteins, RADIALIS and DIVARICATA, through its N-terminal MYB/SANT domain. In addition to the MYB/SANT domain, DRIF contains a C-terminal domain of unknown function (DUF3755). Here we describe novel protein-protein interactions involving a poplar (Populus trichocarpa) homolog of DRIF, PtrDRIF1. In addition to interacting with poplar homologs of RADIALIS (PtrRAD1) and DIVARICATA (PtrDIV4), PtrDRIF1 interacted with members of other families within the homeodomain-like superfamily, including PtrWOX13c, a WUSCHEL-RELATED HOMEOBOX protein, and PtrKNAT7, a KNOTTED1-LIKE HOMEOBOX protein. PtrRAD1 and PtrDIV4 interacted with the MYB/SANT-containing N-terminal portion of PtrDRIF1, whereas DUF3755 was both necessary and sufficient for interactions with PtrWOX13c and PtrKNAT7. Of the two MYB/SANT domains present in PtrDIV4, only the N-terminal MYB/SANT domain interacted with PtrDRIF1. GFP-PtrDRIF1 expressed alone or with PtrRAD1 localized to the cytoplasm, whereas co-expression of GFP-PtrDRIF1 with PtrDIV4, PtrWOX13c or PtrKNAT7 resulted in nuclear localization of GFP-PtrDRIF1. Modified yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiments using PtrDRIF1 as a bridge protein revealed that PtrDRIF1 simultaneously interacted with PtrRAD1 and PtrWOX13c, but could not form a heterotrimeric complex when PtrDIV4 was substituted for PtrRAD1. Moreover, a Y2H competition assay indicated that PtrKNAT7 inhibits the interaction between PtrRAD1 and PtrDRIF1. The discovery of an additional protein-protein interaction domain in DRIF proteins, DUF3755, and its ability to form heterodimers and heterotrimers involving MYB/SANT and wood-associated homeodomain proteins, implicates DRIF proteins as mediators of a broader array of processes than previously reported.

Multifaceted plant responses to circumvent Phe hyperaccumulation by downregulation of flux through the shikimate pathway and by vacuolar Phe sequestration.

Detrimental effects of hyperaccumulation of the aromatic amino acid phenylalanine (Phe) in animals, known as phenylketonuria, are mitigated by excretion of Phe derivatives; however, how plants endure Phe accumulating conditions in the absence of an excretion system is currently unknown. To achieve Phe hyperaccumulation in a plant system, we simultaneously decreased in petunia flowers expression of all three Phe ammonia lyase (PAL) isoforms that catalyze the non-oxidative deamination of Phe to trans-cinnamic acid, the committed step for the major pathway of Phe metabolism. A total decrease in PAL activity by 81-94% led to an 18-fold expansion of the internal Phe pool. Phe accumulation had multifaceted intercompartmental effects on aromatic amino acid metabolism. It resulted in a decrease in the overall flux through the shikimate pathway, and a redirection of carbon flux toward the shikimate-derived aromatic amino acids tyrosine and tryptophan. Accumulation of Phe did not lead to an increase in flux toward phenylacetaldehyde, for which Phe is a direct precursor. Metabolic flux analysis revealed this to be due to the presence of a distinct metabolically inactive pool of Phe, likely localized in the vacuole. We have identified a vacuolar cationic amino acid transporter (PhCAT2) that contributes to sequestering excess of Phe in the vacuole. In vitro assays confirmed PhCAT2 can transport Phe, and decreased PhCAT2 expression in PAL-RNAi transgenic plants resulted in 1.6-fold increase in phenylacetaldehyde emission. These results demonstrate mechanisms by which plants maintain intercompartmental aromatic amino acid homeostasis, and provide critical insight for future phenylpropanoid metabolic engineering strategies.

Arabidopsis UMAMIT24 and 25 are amino acid exporters involved in seed loading.

Phloem-derived amino acids are the major source of nitrogen supplied to developing seeds. Amino acid transfer from the maternal to the filial tissue requires at least one cellular export step from the maternal tissue prior to the import into the symplasmically isolated embryo. Some members of UMAMIT (usually multiple acids move in an out transporter) family (UMAMIT11, 14, 18, 28, and 29) have previously been implicated in this process. Here we show that additional members of the UMAMIT family, UMAMIT24 and UMAMIT25, also function in amino acid transfer in developing seeds. Using a recently published yeast-based assay allowing detection of amino acid secretion, we showed that UMAMIT24 and UMAMIT25 promote export of a broad range of amino acids in yeast. In plants, UMAMIT24 and UMAMIT25 are expressed in distinct tissues within developing seeds; UMAMIT24 is mainly expressed in the chalazal seed coat and localized on the tonoplast, whereas the plasma membrane-localized UMAMIT25 is expressed in endosperm cells. Seed amino acid contents of umamit24 and umamit25 knockout lines were both decreased during embryogenesis compared with the wild type, but recovered in the mature seeds without any deleterious effect on yield. The results suggest that UMAMIT24 and 25 play different roles in amino acid translocation from the maternal to filial tissue; UMAMIT24 could have a role in temporary storage of amino acids in the chalaza, while UMAMIT25 would mediate amino acid export from the endosperm, the last step before amino acids are taken up by the developing embryo.

XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED.

The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C-terminal region containing linear motifs (CKII-acidic, LXCXE, E2FTD -like and LXCXE-mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA-RELATED (RBR). Protein-protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR-interaction motifs. Deletion of either the LXCXE or the LXCXE-mimic motif reduced both the XND1-RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C-terminal domain could be partially replaced by RBR fused to the N-terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR-interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm-specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem-specific pathway for inhibition of differentiation.

UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots.

Amino acids are the main form of nitrogen transported between the plant organs. Transport of amino acids across membranes is mediated by specialized proteins: importers, exporters, and facilitators. Unlike amino acid importers, amino acid exporters have not been thoroughly studied, partly due to a lack of high-throughput techniques enabling their isolation. Usually Multiple Acids Move In and out Transporters 14 (UMAMIT14) from Arabidopsis shares sequence similarity to the amino acid facilitator Silique Are Red1 (UMAMIT18), and has been shown to be involved in amino acid transfer to the seeds. We show here that UMAMIT14 is also expressed in root pericycle and phloem cells and mediates export of a broad range of amino acids in yeast. Loss-of-function of UMAMIT14 leads to a reduced shoot-to-root and root-to-medium transfer of amino acids originating from the leaves. These fluxes were further reduced in an umamti14 umamit18 double loss-of-function mutant. This study suggests that UMAMIT14 is involved in phloem unloading of amino acids in roots, and that UMAMIT14 and UMAMIT18 are involved in the radial transport of amino acids in roots, which is essential for maintaining amino acid secretion to the soil.

Sourcing DNA parts for synthetic biology applications in plants.

Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.

Serum sodium level fluctuations following the resection of childhood-onset craniopharyngioma.

BACKGROUND: Craniopharyngiomas are low-grade malignancies (WHO I) in the sellar region. Most cases of childhood-onset craniopharyngioma are adamantinomatous craniopharyngioma, and neurosurgery is the treatment of choice. Affected patients have postoperative complications, including water and electrolyte disturbances, because these malignancies develop near the hypothalamus and pituitary gland. Determining postoperative serum sodium fluctuation patterns in these patients can reduce postoperative mortality and improve prognosis. OBJECTIVE: To measure changes in serum sodium levels in pediatric patients who underwent craniopharyngioma surgery and identify influencing factors. METHODS: This retrospective study measured the serum sodium levels of 202 patients aged 0-18 years who underwent craniopharyngioma resection in Beijing Tiantan Hospital and Beijing Children's Hospital and identified predictors of severe hyponatremia and hypernatremia. RESULTS: The mean age of the cohort was 8.35 ± 4.35 years. The prevalence of hypernatremia, hyponatremia, and their severe forms (serum Na+  > 150 mmol/L and serum Na+  < 130 mmol/L) within 14 days after surgery was 66.3%, 72.8%, 37.1%, and 40.6%, respectively. The mean postoperative serum sodium level showed a triphasic pattern, characterized by two peaks separated by a nadir. Sodium levels peaked on days 2 (143.6 ± 7.6 mmol/L) and 14 (143.2 ± 6.7 mmol/L) and reached their lowest on day 6 (135.5 ± 7.5 mmol/L). A total of 31 (15.3%) patients met the diagnostic threshold for hyponatremia and hypernatremia of the triphase response, whereas 116 (57.4%) patients presented this pattern, regardless of met the diagnostic criteria or not. The prevalence of severe hyponatremia varied depending on preoperative endocrine hormone deficiency, tumor status (primary or recurrent), and surgical approach. CONCLUSIONS: Serum sodium levels after craniopharyngioma resection in children showed a triphasic pattern in most cases. The risk of postoperative hyponatremia varied depending on preoperative endocrine hormone deficiency, tumor status (primary or recurrent), and surgical approach.

Serum IL-17A and IL-6 in paediatric Mycoplasma pneumoniae pneumonia: implications for different endotypes.

Paediatric Mycoplasma pneumoniae pneumonia (MPP) is a heterogeneous disease with a diverse spectrum of clinical phenotypes. No studies have demonstrated the relationship between underlying endotypes and clinical phenotypes as well as prognosis about this disease. Thus, we conducted a multicentre prospective longitudinal study on children hospitalized for MPP between June 2021 and March 2023, with the end of follow-up in August 2023. Blood samples were collected and processed at multiple time points. Multiplex cytokine assay was performed to characterize serum cytokine profiles and their dynamic changes after admission. Cluster analysis based on different clinical phenotypes was conducted. Among the included 196 patients, the levels of serum IL-17A and IL-6 showed remarkable variabilities. Four cytokine clusters based on the two cytokines and four clinical groups were identified. Significant elevation of IL-17A mainly correlated with diffuse bronchiolitis and lobar lesion by airway mucus hypersecretions, while that of IL-6 was largely associated with lobar lesion which later developed into lung necrosis. Besides, glucocorticoid therapy failed to inhibit IL-17A, and markedly elevated IL-17A and IL-6 levels may correlate with lower airway obliterans. Our study provides critical relationship between molecular signatures (endotypes) and clustered clinical phenotypes in paediatric patients with MPP.