Ribocentre-switch: a database of riboswitches.

Riboswitches are regulatory elements found in the untranslated regions (UTRs) of certain mRNA molecules. They typically comprise two distinct domains: an aptamer domain that can bind to specific small molecules, and an expression platform that controls gene expression. Riboswitches work by undergoing a conformational change upon binding to their specific ligand, thus activating or repressing the genes downstream. This mechanism allows gene expression regulation in response to metabolites or small molecules. To systematically summarise riboswitch structures and their related ligand binding functions, we present Ribocentre-switch, a comprehensive database of riboswitches, including the information as follows: sequences, structures, functions, ligand binding pockets and biological applications. It encompasses 56 riboswitches and 26 orphan riboswitches from over 430 references, with a total of 89 591 sequences. It serves as a good resource for comparing different riboswitches and facilitating the identification of potential riboswitch candidates. Therefore, it may facilitate the understanding of RNA structural conformational changes in response to ligand signaling. The database is publicly available at https://riboswitch.ribocentre.org.

Structure and ion-dependent folding of k-junctions.

k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.

Ribocentre: a database of ribozymes.

Ribozymes are excellent systems in which to study 'sequence - structure - function' relationships in RNA molecules. Understanding these relationships may greatly help structural modeling and design of functional RNA structures and some functional structural modules could be repurposed in molecular design. At present, there is no comprehensive database summarising all the natural ribozyme families. We have therefore created Ribocentre, a database that collects together sequence, structure and mechanistic data on 21 ribozyme families. This includes available information on timelines, sequence families, secondary and tertiary structures, catalytic mechanisms, applications of the ribozymes together with key publications. The database is publicly available at https://www.ribocentre.org.

Structure and mechanism of a methyltransferase ribozyme.

Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 Å, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry.

Effect of plant species on wastewater treatment performance of a subsurface vertical-flow constructed wetland with step-feeding at low temperature.

To improve the treatment performance of constructed wetlands under low-temperature conditions, this study investigated the effects of plant species on wastewater treatment performance at low temperature and the associated microbiological characteristics in a subsurface vertical-flow constructed wetland (VFCW) with step-feeding. The results showed that the redox microenvironment in the VFCW filter with step-feeding could be restored and optimized by planting appropriate species that can tolerate low temperature, ensuring a high nitrification performance for the system. Correspondingly, the abundance and activity of three functional microbes (namely nitrifiers, denitrifiers, and anammox bacteria) increased to different degrees in the system, eventually ensuring ideal nitrogen removal by the VFCW. Compared with the VFCW planted with Phragmites australis and Acorus gramineus, the operation performance of the VFCW planted with Iris wilsonii could be recovered at low temperature, and its chemical oxygen demand, total phosphorus, total nitrogen, and ammonium nitrate removal rates could respectively reach 95.7%, 99.2%, 93.0%, and 94.4%, respectively. Moreover, nitrogen removal in the system relied on the nitrification/denitrification and partial denitrification - anaerobic ammonium oxidation processes. Nitrosomonas, Nitrospira, Thauera, and Candidatus Brocadia were the four dominant bacterial genera in the filter layer.

Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.

k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence.

Measuring a frequency spectrum for single-molecule interactions with a confined nanopore.

Nanopore analysis is a powerful technique for single molecule analysis by virtue of its electrochemically confined effects. As a single molecule translocates through the nanopore, the featured ionic current pattern on the time scale contains single molecule characteristics including volume, charge, and conformational properties. Although the characteristics of a single molecule in a nanopore have been written to the featured ionic current, extracting the dynamic information from a complex current trace is still a big challenge. Here, we present an applicable nanopore analysis method employing the Hilbert-Huang Transform (HHT) to study the vibrational features and interactions of a single molecule during the dynamic translocation process through the confined space of a nanopore. The HHT method is specially developed for analyzing nonlinear and non-stationary data that is highly compatible with nanopore data with a high frequency resolution. To provide proof-of-concept, we applied HHT to measure the frequency response for the wild-type (WT) aerolysin and mutant K238E aerolysin nanopores with and without the presence of poly(dA)4, respectively. The energy-frequency-time distribution spectra demonstrate that the biological nanopore contributes greatly to the characteristics of the high frequency component (>2 kHz) in the current recording. Our results suggest that poly(dA)4 undergoes relatively more consistent and confined interactions with K238E than WT, leading to a prolonging of the duration time. Therefore, the characteristics in frequency analysis could be regarded as an "single-molecule ionic spectrum" inside the nanopore, which encodes the detailed behaviours of single-molecule weak interactions.

A novel fluorescent probe based on rhodamine hydrazone derivatives bearing a thiophene group for Al³âº.

In the present work, a novel 5-methyl-thiophene-carbaldehyde-functionalized rhodamine 6G Schiff base (RA) was designed and easily prepared as an Al(3+) fluorescent and colorimetric probe, which could selectively and sensitively detect Al(3+) by showing enhanced fluorescence emission. Meanwhile distinct color variation from colorless to pink also provided 'naked eye' detection of Al(3+), due to the ring spirolactam opening of the rhodamine derivative. Other metal ions (including K(+), Mg(2+), Na(+), Ba(2+), Mn(2+), Cd(2+), Fe(2+), Ni(2+), Pb(2+), Zn(2+), Hg(2+), Co(2+), Li(+), Sr(2+) and Cu(2+)) could only induce limited interference. The detection limit of the fluorescent probe was estimated to be 4.17 × 10(-6) M, the binding constant of the RA-Al(3+) complex was 1.4 × 10(6) M(-1). Moreover, this fluorescent probe RA possessed high reversibility. As aluminum is a ubiquitous metal in nature and plays vital roles in many biological processes, this chemosensor could be explored for biological study applications.

Bibliometric and literature review of the development of mineral fertilizers.

Mineral fertilizers are a new type of sustainable fertilizers, containing natural ores as the primary raw material with various nutrients and organic matters. This study combines two methods of bibliometric analysis to comprehensively review the progress of mineral fertilizers from 2000 to 2021. The results showed that the research on mineral fertilizers has increased in the past 21 years, especially after 2014. Developed countries studied mineral fertilizers more extensively than developing countries, but some developing countries, such as China and India, are also paying attention to this area in recent years. Chinese Academic of Sciences, Agriculture and Agri-Food Canada, and Chinese Academy of Agricultural Sciences were the main publishing institutions. Nutrient elements, changes in soil properties, and the effects on promoting crop growth were the main contents of the research. Still, such issues as bioremediation, soil environment improvement, and crop resistance are becoming hot spots. The field of mineral fertilizers showed a strong interdisciplinary nature and an increasingly comprehensive research perspective. The goal is that this synthesis will be used as a starting point for a broader study on responsible environmental management and research on improving fertilizer use efficiency.

A Universal Coulombic Efficiency Compensation Strategy for Zinc-Based Flow Batteries.

Alkaline zinc-iron flow batteries (AZIFBs) are well suited for energy storage because of their good safety, high cell voltage, and low cost. However, the occurrence of irreversible anodic parasitic reactions results in a diminished coulombic efficiency (CE), unbalanced charge state of catholyte/anolyte and subsequently, a poor cycling performance. Here, a universal CE compensation strategy centered around the oxygen evolution reaction (OER) on the cathodic side, is reported. This strategy aims to equalize the charge state of the [Fe(CN)6]3-/4--based catholyte and counteract pH fluctuations. The OER process can be implemented either directly on the electrode through electrochemical reaction or in an external catalytic reactor column via a redox-mediated process. This innovative approach effectively mitigates the gradual accumulation of [Fe(CN)6]3- in discharged catholyte and [Zn(OH)4]2- in charged anolyte by consuming the extra OH- during a continuous cycling process. As a result, AZIFBs demonstrate exceptional cycling performance with an extremely low capacity fading rate of 0.0128%/day (or 0.0005%/cycle) over 600 cycles at 80% state of charge (SOC). The proposed CE compensation strategy not only provides an effective way to address the CE loss issue for AZIFBs, but also can be applied to diverse battery technologies encountering CE loss caused by water/oxygen-induced parasitic reactions.

Advance in the role of chemokines/chemokine receptors in carcinogenesis: Focus on pancreatic cancer.

The chemokines/chemokine receptors pathway significantly influences cell migration, particularly in recruiting immune cells to the tumor microenvironment (TME), impacting tumor progression and treatment outcomes. Emerging research emphasizes the involvement of chemokines in drug resistance across various tumor therapies, including immunotherapy, chemotherapy, and targeted therapy. This review focuses on the role of chemokines/chemokine receptors in pancreatic cancer (PC) development, highlighting their impact on TME remodeling, immunotherapy, and relevant signaling pathways. The unique immunosuppressive microenvironment formed by the interaction of tumor cells, stromal cells and immune cells plays an important role in the tumor proliferation, invasion, migration and therapeutic resistance. Chemokines/chemokine receptors, such as chemokine ligand (CCL) 2, CCL3, CCL5, CCL20, CCL21, C-X-C motif chemokine ligand (CXCL) 1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL8, CXCL9, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL16, CXCL17, and C-X3-C motif chemokine ligand (CX3CL)1, derived mainly from leukocyte cells, cancer-related fibroblasts (CAFs), pancreatic stellate cells (PSCs), and tumor-associated macrophages (TAMs), contribute to PC progression and treatment resistance. Chemokines recruit myeloid-derived suppressor cells (MDSC), regulatory T cells (Tregs), and M2 macrophages, inhibiting the anti-tumor activity of immune cells. Simultaneously, they enhance pathways like epithelial-mesenchymal transition (EMT), Akt serine/threonine kinase (AKT), extracellular regulated protein kinases (ERK) 1/2, and nuclear factor kappa-B (NF-κB), etc., elevating the risk of PC metastasis and compromising the efficacy of radiotherapy, chemotherapy, and anti-PD-1/PD-L1 immunotherapy. Notably, the CCLx-CCR2 and CXCLx-CXCR2/4 axis emerge as potential therapeutic targets in PC. This review integrates recent findings on chemokines and receptors in PC treatment, offering valuable insights for innovative therapeutic approaches.

A Natural Casein-Based Separator with Brick-and-Mortar Structure for Stable, High-Rate Proton Batteries.

Rechargeable aqueous proton batteries with small organic molecule anodes are currently considered promising candidates for large-scale energy storage due to their low cost, stable safety, and environmental friendliness. However, the practical application is limited by the poor cycling stability caused by the shuttling of soluble organic molecules between electrodes. Herein, a cell separator is modified by a GO-casein-Cu2+ layer with a brick-and-mortar structure to inhibit the shuttling of small organic molecules. Experimental and calculation results indicate that, attributed to the synergistic effect of physical blocking of casein molecular chains and electrostatic and coordination interactions of Cu2+, bulk dissolution and shuttling of multiple small molecules can be inhibited simultaneously, while H+ transfer across the separators is not almost affected. With the protection of the GO-casein-Cu2+ separator, soluble small molecules, such as diquinoxalino[2,3-a:2',3'-c]phenazine,2,3,8,9,14,15-hexacyano (6CN-DQPZ) exhibit a high reversible capacity of 262.6 mA h g-1 and amazing stability (capacity retention of 92.9% after 1000 cycles at 1 A g-1). In addition, this strategy is also proved available to other active conjugated small molecules, such as indanthrone (IDT), providing a general green sustainable strategy for advancing the use of small organic molecule electrodes in proton cells.

Steric hindrance modulation of hexaazatribenzanthraquinone isomers for high-capacity and wide-temperature-range aqueous proton battery.

Organic materials with rich active sites are good candidates of high-capacity anodes in aqueous batteries, but commonly low utilization of active sites limits their capacity. Herein, two isomers, symmetric and asymmetric hexaazatribenzanthraquinone (s-HATBAQ and a-HATBAQ), with rich active sites have been synthesized in a controllable manner. It has been revealed for the first time that a sulfuric acid catalyst can facilitate the stereoselective formation of s-HATBAQ. Attributed to the reduced steric hindrance in favor of proton insertion as well as the amorphous structure conducive to electrochemical dynamics, s-HATBAQ exhibits 1.5 times larger specific capacity than a-HATBAQ. Consequently, the electrode of s-HATBAQ with 50% reduced graphene oxide (s-HATBAQ-50%rGO) delivers a record high specific capacity of 405 mAh g-1 in H2SO4 electrolyte. Moreover, the assembled MnO2//s-HATBAQ-50%rGO aqueous proton full batteries show an exceptional cycling stability at 25°C and can maintain ∼92% capacity after 1000 cycles at 0.5 A g-1 at -80°C. This work demonstrates the controllable synthesis of isomers, showcases a wide-temperature-range prototype proton battery and highlights the significance of precise molecular structure modulation in organic energy storage.

Picosecond dissipative soliton generation from an ytterbium-doped fiber laser based on a BP/SnSe2-PVA mixture saturable absorber.

Stable picosecond dissipative soliton pulses were observed in an ytterbium-doped fiber laser employing a high-quality mixture of BP/SnSe2-PVA saturable absorber (SA). The modulation depth, saturation intensity, and non-saturable loss of the mixture of BP/SnSe2-PVA SA were measured with values of 5.98%, 18.37 MW/cm2, and 33%, respectively. Within the pump power range of 150-270 mW, stable dissipative soliton pulses were obtained with an output power of 1.68-4 mW. When the minimum pulse duration is 1.28 ps, a repetition rate of 0.903 MHz, center wavelength of 1064.38 nm and 3 dB bandwidth of 2 nm were obtained. The maximum pulse energy of 4.43 nJ and the signal-to-noise ratio up to 72 dB were achieved at pump power of 270 mW. The results suggest that the BP/SnSe2-PVA mixture SA has outstanding nonlinear saturable absorption characteristics and broad ultrafast laser applications.

An integrative analysis of lncRNAs and mRNAs highlights the potential roles of lncRNAs in the process of follicle selection in Taihang chickens.

Taihang chickens are a domestic breed distributed throughout Hebei province in the Taihang Mountains of China and are characterized by their high meat and egg quality. However, the relatively limited egg production by this breed constrains their more widespread commercial utilization. The follicle selection process is closely linked to oocyte development and ovulation, making it a key determinant of laying performance and fecundity in hens. To understand the biological basis for such follicle selection and to identify the associated regulatory pathways, we conducted a genome-wide analysis of long noncoding RNAs (lncRNAs) and mRNAs from the pre-hierarchical follicles and hierarchical follicles of Taihang laying hens. We identified 81 lncRNAs and 528 mRNAs that were differentially expressed during follicle selection, and integrated network analyses suggested that these RNAs were associated with the cell cycle, focal adhesion, oocyte meiosis, peroxisome proliferator-activated receptor signaling, and steroid hormone biosynthesis pathways. The identified lncRNAs were also predicted to influence a series of target genes in cis and trans, suggesting that they may be important regulators of ovarian follicular development. Overall, the present analysis of lncRNA and mRNA expression patterns associated with ovarian follicle development offers a new foundation for future studies of reproductive physiology in Taihang chickens, highlighting new opportunities to improve the laying performance of this important domestic breed.

miR-140-3p promotes follicle granulosa cell proliferation and steroid hormone synthesis via targeting AMH in chickens.

Granulosa cells (GCs) are the ovary's most critical cells since they undergo cell differentiation and hormone synthesis changes closely associated with follicle development. While micro RNA 140-3p (miRNA-140-3p) has an apparent cell signaling role, particularly in cell proliferation, its biological role in chicken ovarian follicle growth and development remains elusive. This study explored miR-140-3p's effects on chicken GC proliferation and steroid hormone synthesis. MiR-140-3p dramatically increased GC proliferation, prevented apoptosis, increased progesterone synthesis, and enhanced gene expression related to steroid hormone synthesis. In addition, the anti-Müllerian hormone (AMH) gene was identified as a direct miR-140-3p target. MiR-140-3p abundance correlated negatively with AMH mRNA and protein levels in GCs. Our findings show that miR-140-3p influences chicken GC proliferation and steroid hormone synthesis by suppressing AMH expression.

Sestrin 2 Deficiency Exacerbates Noise-Induced Cochlear Injury Through Inhibiting ULK1/Parkin-Mediated Mitophagy.

Aims: Noise damage to auditory hair cells is associated with oxidative stress and mitochondrial dysfunction. This study aimed to investigate the possible effect of sestrin 2 (SESN2), an endogenous antioxidant protein, on noise-induced hearing loss (NIHL) and the underlying mechanisms. Results: We identified SESN2 as a protective factor against oxidative stress in NIHL through activation of Parkin-mediated mitophagy. Consistently, SESN2 expression was increased and mitophagy was induced during the early stage after a temporary threshold shift due to noise exposure or hydrogen peroxide(H2O2) stimulation; conversely, SESN2 deficiency blocked mitophagy and exacerbated acoustic trauma. Mechanistically, SESN2 interacted with Unc-51-like protein kinase 1(ULK1), promoting ULK1 protein-level stabilization by interfering with its proteasomal degradation. This stabilization is essential for mitophagy initiation, since restoring ULK1 expression in SESN2-silenced cells rescued mitophagy defects. Innovation and Conclusion: Our results provide novel insights regarding SESN2 as a therapeutic target against noise-induced cochlear injury, possibly through improved mitophagy. Antioxid. Redox Signal. 38, 115-136.

Segmentation of retinal fluid based on deep learning: application of three-dimensional fully convolutional neural networks in optical coherence tomography images.

AIM: To explore a segmentation algorithm based on deep learning to achieve accurate diagnosis and treatment of patients with retinal fluid. METHODS: A two-dimensional (2D) fully convolutional network for retinal segmentation was employed. In order to solve the category imbalance in retinal optical coherence tomography (OCT) images, the network parameters and loss function based on the 2D fully convolutional network were modified. For this network, the correlations of corresponding positions among adjacent images in space are ignored. Thus, we proposed a three-dimensional (3D) fully convolutional network for segmentation in the retinal OCT images. RESULTS: The algorithm was evaluated according to segmentation accuracy, Kappa coefficient, and F1 score. For the 3D fully convolutional network proposed in this paper, the overall segmentation accuracy rate is 99.56%, Kappa coefficient is 98.47%, and F1 score of retinal fluid is 95.50%. CONCLUSION: The OCT image segmentation algorithm based on deep learning is primarily founded on the 2D convolutional network. The 3D network architecture proposed in this paper reduces the influence of category imbalance, realizes end-to-end segmentation of volume images, and achieves optimal segmentation results. The segmentation maps are practically the same as the manual annotations of doctors, and can provide doctors with more accurate diagnostic data.

The Effectiveness of Acupuncture for Osteoporosis: A Systematic Review and Meta-Analysis.

To summarize the existing evidence and evaluate the efficacy of acupuncture as a clinical treatment for osteoporosis. Six English and four Chinese databases were searched from their inception to April 2017. Randomized controlled trials were included, in which warm acupuncture, needling or electroacupuncture were compared with sole Western medicine with osteoporosis. All the data were assessed and extracted by two authors independently. The bias risk assessment recommended by the Cochrane Collaboration's tool was used to assess the quality of the selected studies. This meta-analysis was conducted by using RevMan 5.3. Pooled analyses were calculated by standardized mean difference (SMD) and 95% confidence interval (CI). Heterogeneity was assessed by I2 test. Thirty-five studies involving 3014 patients were located. Meta-analysis showed that warm acupuncture could increase the bone mineral density of lumar (SMD [Formula: see text] 0.93, 95% CI [Formula: see text] 0.65, 1.21, [Formula: see text][Formula: see text]0.00001) and femur (MD[Formula: see text][Formula: see text][Formula: see text]0.11, 95% CI[Formula: see text][Formula: see text][Formula: see text]0.05, 0.16, P[Formula: see text][Formula: see text][Formula: see text]0.0002), the level of serum calcium (MD[Formula: see text][Formula: see text][Formula: see text]0.18, 95% CI[Formula: see text][Formula: see text][Formula: see text]0.13, 0.24, [Formula: see text][Formula: see text]0.00001) and estradiol (SMD[Formula: see text][Formula: see text][Formula: see text]0.65, 95% CI[Formula: see text][Formula: see text][Formula: see text]0.32, 0.98, P[Formula: see text][Formula: see text][Formula: see text]0.0001), relieve pain (MD[Formula: see text][Formula: see text][Formula: see text]-1.64, 95% CI[Formula: see text][Formula: see text][Formula: see text]-2.69, -0.59, P[Formula: see text][Formula: see text][Formula: see text]0.002), decrease the level of serum alkaline phosphatase (MD[Formula: see text][Formula: see text][Formula: see text]-7.8, 95% CI[Formula: see text][Formula: see text][Formula: see text]-14.17, -0.84, P [Formula: see text] 0.03) compared with sole Western medicine. Electroacupuncture could relieve pain (MD[Formula: see text][Formula: see text] -1.32, 95% CI[Formula: see text][Formula: see text][Formula: see text]-2.15, -0.48, P[Formula: see text][Formula: see text][Formula: see text]0.002), increase the level of serum calcium (MD[Formula: see text][Formula: see text][Formula: see text]-0.12, 95% CI [Formula: see text] -0.16,-0.09, [Formula: see text][Formula: see text]0.00001) and decrease the level of serum alkaline phosphatase (MD [Formula: see text] -3.63, 95% CI [Formula: see text] -6.60, -0.66, P [Formula: see text] 0.02) compared with sole Western medicine. Needling could relieve pain (MD [Formula: see text] -2.27, 95% CI [Formula: see text] -3.11, -1.43, [Formula: see text][Formula: see text]0.00001) compared with sole Western medicine. This present systematic review indicated that acupuncture could be an effective therapy for treating osteoporosis. Warm acupuncture seemed to more effective than electroacupuncture and needling for osteoporosis in comparison to sole Western medicine.