Engineered fluorescent protein (FP) chimeras that modulate their fluorescence in response to changes in calcium ion (Ca²⁺) concentration are powerful tools for visualizing intracellular signaling ...activity. However, despite a decade of availability, the palette of single FP-based Ca²⁺ indicators has remained limited to a single green hue. We have expanded this palette by developing blue, improved green, and red intensiometric indicators, as well as an emission ratiometric indicator with an 11,000% ratio change. This series enables improved single-color Ca²⁺ imaging in neurons and transgenic Caenorhabditis elegans. In HeLa cells, Ca²⁺ was imaged in three subcellular compartments, and, in conjunction with a cyan FP—yellow FP—based indicator, Ca²⁺ and adenosine 5′-triphosphate were simultaneously imaged. This palette of indicators paints the way to a colorful new era of Ca²⁺ imaging.
Recent studies demonstrated that warming and elevated carbon dioxide (CO
) indirectly affect the soil microbial community structure via plant root exudates. However, there is no direct evidence for ...how the root exudates affect soil microbes and how the compositions of root exudates respond to climate change.
The results showed that warming directly decreased biomass of soil-borne bacteria and fungi for Acacia mearnsii De Willd but it did not impact soil microbial community for Eucalyptus urophylla S.T. Blake. In contrast, elevated CO
had strong direct effect on increasing soil microbial biomass for both plant species. However, plant roots could significantly increase the secretion of antibacterial chemicals (most probable organic acids), which inhibited the growth of bacteria and fungi in elevated CO
environment. This inhibitory effect neutralized the facilitation from increasing CO
concentration on microbial growth.
We concluded that climate change can directly affect microorganisms, and indirectly affect the soil microbial community structure by changes in composition and content of plant root exudates.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Heavy metals are widespread toxic environmental pollutants that can generate enormous health and public concern. Iron (oxyhydr)oxides are ubiquitous in both natural and engineered environments and ...have great retention capacity of heavy metals due to their high surface areas and reactivity. The sequestration of heavy metal by iron (oxyhydr)oxides is one of the most vital geochemical/chemical processes controlling their environmental fate, transport, and bioavailability. In this review, some of the common iron (oxyhydr)oxides are introduced in detail in terms of their formation, occurrence, structure characteristics and interaction with heavy metals. Moreover, the retention mechanisms of metal cations (e.g., Pb, Cu, Cd, Ni, Zn), metal oxyanions (e.g., As, Sb, Cr), and coexisting multiple metals on various iron (oxyhydr)oxides are fully reviewed. Principal mechanisms of surface complexation, surface precipitation and structural incorporation are responsible for heavy metal retention on iron (oxyhydr)oxides, and greatly dependent on mineral species, metal ion species, reacting conditions (i.e., pH, heavy metal concentration, ionic strength, etc.) and chemical process (i.e., adsorption, coprecipitaton and mineral phase transformation process). The retention mechanisms summarized in this review would be helpful for remediating heavy metal contamination and predicting the long-term behavior of heavy metal in natural and engineered environments.
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•Iron (oxyhydr)oxides characteristics and interaction with heavy metals are outlined.•Microscopic heavy metal retention mechanism by iron (oxyhydr)oxides is reviewed.•Retention mechanisms are controlled by mineral species, reacting conditions and chemical process.•Knowledge gaps and research needs of heavy metal retention mechanism are proposed.
Fluorogenic aptamers can potentially show minimal photobleaching during continuous irradiation since any photobleached fluorophore can exchange with fluorescent dyes in the media. However, ...fluorophores have not been designed to maximize “fluorophore recycling.” Here we describe TBI, a novel fluorophore for the Broccoli fluorogenic aptamer. Previous fluorophores either fail to rapidly dissociate when they undergo photobleaching via cis–trans isomerization, or bind slowly, resulting in extended periods after dissociation of the photobleached fluorophore when no fluorophore is bound. By contrast, photobleached TBI dissociates rapidly from Broccoli, and TBI from the media rapidly replaces dissociated photobleached fluorophore. Using TBI, Broccoli exhibits markedly enhanced fluorescence in cells during continuous imaging. These data show that designing fluorophores to optimize fluorophore recycling can lead to enhanced fluorescence of fluorogenic aptamers.
Fluorogenic RNA aptamers bind to and activate the fluorescence of otherwise nonfluorescent dyes. Here we show an approach to maximize their fluorescence by reducing the impact of photobleaching. We engineered TBI, a fluorophore that rapidly dissociates upon photobleaching and can be rapidly replaced by TBI in the media. By maximizing “fluorophore recycling”, we achieve higher fluorescence and enable long‐term fluorescence imaging.
Abstract
Grid-connection of new energy is highly important in promoting the use of clean and renewable energy. However, it will bring huge risks to the power grid operation security, such as ...frequency stability, voltage stability, small signal stability, and transient stability, etc.,. In the study, SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis has been employed to construct 24 kinds of internal and external evaluation factors and 8 kinds of improvement strategies, for assessing operation security prospective with new energy power system of HM in China. The weights of SWOT factors are determined with the fuzzy-AHP method. Moreover, the fuzzy-MARCOS approach is used to select the most suitable strategies for power system operation security effective implementation. The reported research reveals that new energy in HM area not only has an ample potential for full development and generating electricity, but also brings operation security problems due to large-scale grid connection. Therefore, 8 kinds of improvement strategies are suggested to encourage the government to exploit and develop new resources, improve the investment pay, power generation and transmission technologies to mitigate the current energy crisis, and increase the energy security for sustainable development of the country. The methodology proposed herein is applicable with a case study concerning the operation security prospective of HM power grid, and all phases of the comparative analysis and sensitivity analysis illustrate the validity of MARCOS method. Furthermore, the ranked order of strategies is obtained as
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, i.e., “improving the technical establishment to encourage efficient and cheap electricity production”, “strive to build local permanent load, and reduce the risk of long-distance and high-capacity transmission”, “taking advantage of government incentives and investment to modify the irrational energy policies and energy planning”, respectively.
The corneal wound healing response, including the development of stromal opacity in some eyes, is a process that often leads to scarring that occurs after injury, surgery or infection to the cornea. ...Immediately after epithelial and stromal injury, a complex sequence of processes contributes to wound repair and regeneration of normal corneal structure and function. In some corneas, however, often depending on the type and extent of injury, the response may also lead to the development of mature vimentin+ α-smooth muscle actin+ desmin+ myofibroblasts. Myofibroblasts are specialized fibroblastic cells generated in the cornea from keratocyte-derived or bone marrow-derived precursor cells. The disorganized extracellular matrix components secreted by myofibroblasts, in addition to decreased expression of corneal crystallins in these cells, are central biological processes that result in corneal stromal fibrosis associated with opacity or “haze”. Several factors are associated with myofibroblast generation and haze development after PRK surgery in rabbits, a reproducible model of scarring, including the amount of tissue ablated, which may relate to the extent of keratocyte apoptosis in the early response to injury, irregularity of stromal surface after surgery, and changes in corneal stromal proteoglycans, but normal regeneration of the epithelial basement membrane (EBM) appears to be a critical factor determining whether a cornea heals with relative transparency or vision-limiting stromal opacity. Structural and functional abnormalities of the regenerated EBM facilitate prolonged entry of epithelium-derived growth factors such as transforming growth factor β (TGF-β) and platelet-derived growth factor (PDGF) into the stroma that both drive development of mature myofibroblasts from precursor cells and lead to persistence of the cells in the anterior stroma. A major discovery that has contributed to our understanding of haze development is that keratocytes and corneal fibroblasts produce critical EBM components, such as nidogen-1, nidogen-2 and perlecan, that are essential for complete regeneration of a normal EBM once laminin secreted by epithelial cells self-polymerizes into a nascent EBM. Mature myofibroblasts that become established in the anterior stroma are a barrier to keratocyte/corneal fibroblast contributions to the nascent EBM. These myofibroblasts, and the opacity they produce, often persist for months or years after the injury. Transparency is subsequently restored when the EBM is completely regenerated, myofibroblasts are deprived of TGFβ and undergo apoptosis, and the keratocytes re-occupy the anterior stroma and reabsorb disordered extracellular matrix. The aim of this review is to highlight factors involved in the generation of stromal haze and its subsequent removal.
•The level of keratocyte apoptosis is important in corneal opacity.•Keratocytes produce key corneal epithelial basement membrane components.•Competition between myofibroblasts and keratocytes is critical in haze development.
Aerial vehicle detection has significant applications in aerial surveillance and traffic control. The pictures captured by the UAV are characterized by many tiny objects and vehicles obscuring each ...other, significantly increasing the detection challenge. In the research of detecting vehicles in aerial images, there is a widespread problem of missed and false detections. Therefore, we customize a model based on YOLOv5 to be more suitable for detecting vehicles in aerial images. Firstly, we add one additional prediction head to detect smaller-scale objects. Furthermore, to keep the original features involved in the training process of the model, we introduce a Bidirectional Feature Pyramid Network (BiFPN) to fuse the feature information from various scales. Lastly, Soft-NMS (soft non-maximum suppression) is employed as a prediction frame filtering method, alleviating the missed detection due to the close alignment of vehicles. The experimental findings on the self-made dataset in this research indicate that compared with YOLOv5s, the mAP@0.5 and mAP@0.5:0.95 of YOLOv5-VTO increase by 3.7% and 4.7%, respectively, and the two indexes of accuracy and recall are also improved.
Sequenced Protein-Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating ...the design of novel therapeutic interventions. Conventional methods for extracting features through experimental processes have proven to be both costly and exceedingly complex. In light of these challenges, the scientific community has turned to computational approaches, particularly those grounded in deep learning methodologies. Despite the progress achieved by current deep learning technologies, their effectiveness diminishes when applied to larger, unfamiliar datasets.
In this study, the paper introduces a novel deep learning framework, termed DL-PPI, for predicting PPIs based on sequence data. The proposed framework comprises two key components aimed at improving the accuracy of feature extraction from individual protein sequences and capturing relationships between proteins in unfamiliar datasets. 1. Protein Node Feature Extraction Module: To enhance the accuracy of feature extraction from individual protein sequences and facilitate the understanding of relationships between proteins in unknown datasets, the paper devised a novel protein node feature extraction module utilizing the Inception method. This module efficiently captures relevant patterns and representations within protein sequences, enabling more informative feature extraction. 2. Feature-Relational Reasoning Network (FRN): In the Global Feature Extraction module of our model, the paper developed a novel FRN that leveraged Graph Neural Networks to determine interactions between pairs of input proteins. The FRN effectively captures the underlying relational information between proteins, contributing to improved PPI predictions. DL-PPI framework demonstrates state-of-the-art performance in the realm of sequence-based PPI prediction.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, ...these techniques suffer from inherent limitations such as time consumption and high costs. To address these challenges, the field of bioinformatics has increasingly turned to deep learning technologies for analyzing gene sequences. Nevertheless, the pursuit of improved experimental results has led to the inclusion of numerous complex analysis function modules, resulting in models with a growing number of parameters. To overcome these limitations, it is proposed a novel approach for analyzing DNA transcription factor sequences, which is named as DeepCAC. This method leverages deep convolutional neural networks with a multi-head self-attention mechanism. By employing convolutional neural networks, it can effectively capture local hidden features in the sequences. Simultaneously, the multi-head self-attention mechanism enhances the identification of hidden features with long-distant dependencies. This approach reduces the overall number of parameters in the model while harnessing the computational power of sequence data from multi-head self-attention. Through training with labeled data, experiments demonstrate that this approach significantly improves performance while requiring fewer parameters compared to existing methods. Additionally, the effectiveness of our approach is validated in accurately predicting DNA transcription factor sequences.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A new type of deacetylated cellulose acetate (DA)@polydopamine (PDA) composite nanofiber membrane was fabricated by electrospinning and surface modification. The membrane was applied as a highly ...efficient adsorbent for removing methylene blue (MB) from an aqueous solution. The morphology, surface chemistry, surface wettability, and effects of operating conditions on MB adsorption ability, as well as the equilibrium, kinetics, thermodynamics, and mechanism of adsorption, were systematically studied. The results demonstrated that a uniform PDA coating layer was successfully developed on the surface of DA nanofibers. The adsorption capacity of the DA@PDA nanofiber membrane reached up to 88.2 mg/g at a temperature of 25 °C and a pH of 6.5 after adsorption for 30 h, which is about 8.6 times higher than that of DA nanofibers. The experimental results showed that the adsorption behavior of DA@PDA composite nanofibers followed the Weber’s intraparticle diffusion model, pseudo-second-order model, and Langmuir isothermal model. A thermodynamic analysis indicated that endothermic, spontaneous, and physisorption processes occurred. Based on the experimental results, the adsorption mechanism of DA@PDA composite nanofibers was also demonstrated.
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