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scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data
Gapless dispersive continuum in a modulated quantum kagome antiferromagnet
Correlated fermionic-bosonic insulating states in twisted hetero-trilayer semiconductors
CLAVATA signalling shapes barley inflorescence by controlling activity and determinacy of shoot meristem and rachilla
Abstract The large variety of inflorescence architectures evolved in grasses depends on shape, longevity and determinacy of meristems directing growth of the main and lateral axes. The CLAVATA pathway is known to regulate meristem size and inflorescence architecture in grasses. However, how individual meristem activities are determined and integrated to generate specific inflorescences is not yet understood. We found that activity of distinct meristems in the barley inflorescence is controlled by a signalling pathway comprising the receptor-like kinase Hordeum vulgare CLAVATA1 (HvCLV1) and the secreted CLAVATA3/EMBRYO-SURROUNDING REGION RELATED (CLE)-family peptide FON2-LIKE CLE PROTEIN1 (HvFCP1). HvFCP1 and HvCLV1 interact to promote spikelet formation, but restrict inflorescence meristem and rachilla proliferation. Hvfcp1 or Hvclv1 mutants generate additional rows of spikelets and supernumerary florets from extended rachilla activity. HvFCP1/HvCLV1 signalling coordinates meristem activity through regulation of trehalose-6-phosphate levels. Our discoveries outline a path to engineer inflorescence architecture via specific regulation of distinct meristem activities.
Ultrasensitive detection of clinical pathogens through a target-amplification-free collateral-cleavage-enhancing CRISPR-CasΦ tool
Abstract Clinical pathogen diagnostics detect targets by qPCR (but with low sensitivity) or blood culturing (but time-consuming). Here we leverage a dual-stem-loop DNA amplifier to enhance non-specific collateral enzymatic cleavage of an oligonucleotide linker between a fluophore and its quencher by CRISPR-CasΦ, achieving ultrasensitive target detection. Specifically, the target pathogens are lysed to release DNA, which binds its complementary gRNA in CRISPR-CasΦ to activate the collateral DNA-cleavage capability of CasΦ, enabling CasΦ to cleave the stem-loops in the amplifier. The cleavage product binds its complementary gRNA in another CRISPR-CasΦ to activate more CasΦ. The activated CasΦ collaterally cleaves the linker, releasing the fluophore to recover its fluorescent signal. The cycle of stem-loop-cleavage/CasΦ-activation/fluorescence-recovery amplifies the detection signal. Our target amplification-free collateral-cleavage-enhancing CRISPR-CasΦ method (TCC), with a detection limit of 0.11 copies/μL, demonstrates enhanced sensitivity compared to qPCR. It can detect pathogenic bacteria as low as 1.2 CFU/mL in serum within 40 min.
A molecular framework for the GS2-SUG1 module-mediated control of grain size and weight in rice
Junctional force patterning drives both positional order and planar polarity in the auditory epithelia
Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter
Abstract Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.
Innovative biomass cogeneration system for a zero energy school building
Exploring quantum control landscape and solution space complexity through optimization algorithms and dimensionality reduction
Abstract Understanding the quantum control landscape (QCL) is important for designing effective quantum control strategies. In this study, we analyze the QCL for a single two-level quantum system (qubit) using various control strategies. We employ Principal Component Analysis (PCA), to visualize and analyze the QCL for higher dimensional control parameters. Our results indicate that dimensionality reduction techniques such as PCA, can play an important role in understanding the complex nature of quantum control in higher dimensions. Evaluations of traditional control techniques and machine learning algorithms reveal that Genetic Algorithms (GA) outperform Stochastic Gradient Descent (SGD), while Q-learning (QL) shows great promise compared to Deep Q-Networks (DQN) and Proximal Policy Optimization (PPO). Additionally, our experiments highlight the importance of reward function design in DQN and PPO demonstrating that using immediate reward results in improved performance rather than delayed rewards for systems with short time steps. A study of solution space complexity was conducted by using Cluster Density Index (CDI) as a key metric for analyzing the density of optimal solutions in the landscape. The CDI reflects cluster quality and helps determine whether a given algorithm generates regions of high fidelity or not. Our results provide insights into effective quantum control strategies, emphasizing the significance of parameter selection and algorithm optimization.
Comparative transcriptome analysis of bull X- and Y-spermatozoa
AI-based analysis of surgical outcomes in vitrectomy with and without cystotomy for refractory cystoid diabetic macular edema
Frailty, genetic predisposition, and incident chronic kidney disease
Crosstalk of lactate metabolism-related subtypes, establishment of a prognostic signature and immune infiltration characteristics in colon adenocarcinoma
Antibacterial and anti-virulence activity of eco-friendly resveratrol-loaded lipid nanocapsules against methicillin-resistant staphylococcus aureus
The effect of UVB radiation on the optical quality of rainbow trout eye-lenses
Amphistegina lessonii and Amphistegina lobifera shell microstructure, texture and twinning pattern reflect resilience to cadmium and lead
Abstract Biologically secreted carbonates are archives of environmental conditions, as shell and skeletal element minerals record chemical and physical signals of the ambient environment. We report the impact of Cd2+ and Pb2+ on foraminiferal shell crystal structural and organizational characteristics, such as microstructure, texture, crystal co-orientation strength and crystal twin formation for the rotaliid foraminifera Amphistegina lessonii and Amphistegina lobifera. The investigated species lived first in Cd2+- and Pb2+-free and, at a later growth stage, in Cd2+- and Pb2+-containing water. Enrichment in Cd2+ was increased 4 times relative to the ecological criteria maximum concentration (CMC) for both species. For Pb2+, it was increased 5 times for A. lobifera and 6 times for A. lessonii. Crystal organization was measured with Electron-Backscattered-Diffraction (EBSD), shell structure was imaged with FE-SEM. We detect that the Cd2+ and Pb2+ concentrations influence the degree of shell calcite twin formation. For A. lessonii the addition of Cd2+ to the water prevents crystal twin generation, Pb2+ induces decreased twinned calcite secretion. For A. lobifera, both Cd2+ and Pb2+ significantly decrease crystal twin formation. Our study indicates that crystal twin generation by Rotaliida can be developed as a structural indicator for environmental pollution with heavy toxic elements.