From biorxiv.org
Global comparative structural analysis of responses to protein phosphorylation
2 2
Post-translational modifications (PTMs), particularly protein phosphorylation, are key regulators of cellular processes, impacting numerous aspects of protein activity. Despite widespread phosphorylation of eukaryotic proteomes, the function of most phosphosites remains unknown. Elucidating the...
#protein #bioinformatics #structuralbiology
18h ago
From biorxiv.org
1 1
Controllable gene circuits that respond to defined inputs are essential tools in synthetic biology. By leveraging regulatory mechanisms at either transcriptional or translational levels, synthetic responsive systems have been engineered to recognize diverse signals, such as small molecules...
2h ago
From biorxiv.org
1 1
Surfactants and film-forming polymers are common ingredients in consumer spray products such as cleaning products, hair care products, and anti-perspirants. Spraying eases application by creating aerosolised droplets of the product that can distribute evenly over the treated surface. However,...
7h ago
From biorxiv.org
Cooperative motility emerges in crowds of T cells but not neutrophils
1 1
T cells are among the most motile immune cells in the body, and their migration into and within tissues is key to their function. Remarkably, T cells can maintain their motility even in highly crowded environments like the densely packed T cell areas of lymphoid organs, but how they do so...
7h ago
From biorxiv.org
Decipher Fundamental Atomic Interactions to Unify Generative Molecular Docking and Design
1 1
Atomic interactions are fundamental to molecular structures and functions. We constructed PocketXMol, an all-atom AI model, to learn these interactions for general pocket-interacting molecular generative tasks. PocketXMol unified distinct molecular tasks under a single computational framework...
7h ago
From biorxiv.org
miR-210 locus deletion disrupts cellular homeostasis; an integrated genetic study
1 1
MiR-210 is widely recognized as the quintessential hypoxia-responsive miRNA and thought to fine-tune various facets of cellular homeostasis. We hereby present an integrative appraisal of phenotypic and molecular repercussions of disrupting the corresponding locus in human and mouse cells using...
18h ago
From biorxiv.org
1 1
ISG15's dual role in cancer biology still remains unclear. One major area requiring further investigation is the molecular mechanisms underlying ISG15's pro- and anti-tumorigenic roles in different cancer types. In this study, we try to find the probable pathways that could be influenced by...
22h ago
From biorxiv.org
Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature
1 1
Transgenerational epigenetic inheritance (TEI) mediated by transposable elements (TEs) is well established in plants. However, the molecular determinants and functional impact of this additional system of inheritance are poorly characterized. Through comprehensive analyses of severe DNA...
on Mon, 8AM
From biorxiv.org
1 1
The opportunistic pathogen Pseudomonas aeruginosa counts on a large collection of two-component regulatory systems (TCSs) to sense and adapt to changing environments. Among them, the Roc (Regulation of cup) system is a one-of-a-kind network of branched TCSs, composed of two histidine kinases...
on Mon, 8AM
From biorxiv.org
1 1
The dynamic nature of mitochondria makes live cell imaging an important tool in mitochondrial research. Although imaging using fluorescent probes is the golden standard in studying mitochondrial morphology, these probes might introduce a-specific features. In this study, live cell fluorescent...
on Sep 6
From biorxiv.org
1 2
The recent emergence of SARS-CoV-2 variants KP.2 and KP.3 has been marked by mutations F456L/R346T and F456L/Q493E, respectively, which significantly impact the virus’s interaction with human ACE2 and its resistance to neutralizing antibodies. KP.3, featuring F456L and Q493E, exhibits a markedly...
on Sep 6
From biorxiv.org
1 1
The field of crosslinking mass spectrometry has seen substantial advancements over the past decades, enabling the structural analysis of proteins and protein-complexes and serving as a powerful tool in protein-protein interaction studies. However, data analysis of large non-cleavable crosslink...
on Sep 6
From biorxiv.org
Mapping the ultrastructural topology of the corynebacterial cell surface
1 1
Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids....
on Sep 6
From biorxiv.org
Spatiotemporal dynamics of locomotor decisions in Drosophila melanogaster
1 1
Decision-making in animals often involves choosing actions while navigating the environment, a process markedly different from static decision paradigms commonly studied in laboratory settings. Even in decision-making assays in which animals can freely locomote, decision outcomes are often...
#sensory #Drosophila #drosophilamelanogaster
on Sep 5
From biorxiv.org
0 0
Correlative light and electron microscopy is a scientific method that encompasses several technologies and workflows. One of the pioneering workflows consisted in vitrifying by high pressure freezing a sample, shortly after live observation. Despite its extraordinary potential, it did not turn...
7h ago
From biorxiv.org
Stability vs flexibility: reshaping monolayer and bilayer archaeal membranes in silico
0 0
Across the tree of life, distinct designs of cellular membranes have evolved that are both stable and flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids that self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess both...
on Mon, 12AM
From biorxiv.org
0 1
Selection and application of protein inference algorithms can have a significant impact on the data output from tandem mass spectrometry (MS/MS) experiments, yet its use is often an afterthought in proteomics research due to the inability to apply different inference algorithms in existing...
on Sun, 6PM
From biorxiv.org
inTRACKtive - A Web-Based Tool for Interactive Cell Tracking Visualization
0 1
We introduce inTRACKtive, an innovative web-based tool for interactive visualization and sharing of large 3D cell tracking datasets, eliminating the need for software installations or data downloads. Built with modern web technologies, inTRACKtive enables researchers to explore cell-tracking...
on Sun, 6PM
From biorxiv.org
0 1
This study uses nonlinear analysis techniques to distinguish between mind wandering (MW) and focused attention (FA) states using EEG data. EEG recordings from 21 sessions were segmented into intervals of 2, 3, 5, 6, 10, and 15 seconds, and seven nonlinear features were extracted to capture the...
on Sun, 5PM
From biorxiv.org
0 1
Making accurate decisions in noisy or otherwise uncertain environments requires integrating evidence over time. Using simple tasks requiring rapid evaluation of a stationary sensory feature, two human neurophysiological signals have been found to evolve with similar integration dynamics, with...
on Sun, 5PM
From biorxiv.org
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
0 1
A pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many...
on Sun, 10AM
From biorxiv.org
0 1
Amyloid fibril formation is a hallmark of several protein misfolding diseases, including systemic hereditary amyloidosis (SHA), in which lysozyme aggregates into plaques, causing inflammation in various tissues. SHA is a rare disease with no current drug treatment options. In our efforts to...
on Sun, 10AM
From biorxiv.org
0 1
In today's fast-evolving landscape of omics research, tandem mass spectrometry has become a cornerstone for uncovering the complexities of biological systems. Yet, despite its essential role, the technology remains bound by the inherent limitations of quadrupole filters, which throw away up to...
on Sun, 9AM
From biorxiv.org
Non-lytic spread of poliovirus requires the nonstructural protein 3CD
0 1
Non-enveloped viruses like poliovirus (PV) have evolved the capacity to spread by non-lytic mechanisms. For PV, this mechanism exploits the host secretory autophagy pathway. Virions are selectively incorporated into autophagosomes, double-membrane vesicles that travel to the plasma membrane,...
on Sun, 7AM
From biorxiv.org
Tet Transgene Activation is Disrupted in Lipogenic Triple Negative Breast Cancer Cells
0 1
An important challenge for mammalian cell engineering is the unexpected response of transgenes to native transcriptional regulation pathways. One transgene can show different levels of expression at different genomic sites, in different cell types, and under different growth conditions....
on Sun, 7AM
From biorxiv.org
New assessment of teichoic acids in the cell envelope of Streptococcus pneumoniae
0 1
Teichoic acids are important phospho-saccharidic polymers of the envelope of Gram-positive bacteria, bound to the peptidoglycan (wall teichoic acids, WTA) or to the membrane (lipoteichoic acids, LTA). TA composition varies but their presence is conserved, hinting at a fundamental function...
on Sat, 5PM
From biorxiv.org
The genital tract microbiota of IVF patients and oocyte donors: a comparative analysis
0 1
Recent studies have observed an association between genital tract microbiota and reproductive outcomes in patients undergoing in vitro fertilization (IVF). This finding could be caused by ascending dysbiosis from the vagina to the endometrium. The main objective of this study was to compare the...
on Sat, 4PM
From biorxiv.org
Multiplexed phosphoproteomics of low cell numbers using SPARCE
0 1
Understanding cellular diversity and disease mechanisms requires global analysis of proteins and their modifications. While next-generation sequencing has advanced our understanding of cellular heterogeneity, it fails to capture downstream signalling networks. Ultrasensitive mass...
on Sat, 11AM
From biorxiv.org
0 1
Kaposi's sarcoma-associated herpesvirus (KSHV) is a γ-herpesvirus that has a tropism for endothelial cells and leads to the development of Kaposi's sarcoma, especially in people living with HIV. KSHV induces spindling in endothelial cells. The present study aimed to quantify morphological and...
on Sat, 8AM
From biorxiv.org
Collective dynamics of Escherichia coli growth under near-lethal acid stress
0 1
Many neutralophilic bacteria, including Escherichia coli, can withstand acidic conditions due to the action of several protective mechanisms. While the survival of E. coli under growth-inhibitory extreme acid stress is well understood, less is known about the physiology of E. coli growth under...
on Sat, 8AM
From biorxiv.org
0 1
Defining the substrates of Resistance-Nodulation-Division (RND) systems is often complicated by the presence of multiple systems in a single bacterial species. Using a major efflux knockout strain, we developed a Pseudomonas aeruginosa system that enables controlled expression of MexXY-OprM in...
on Sat, 7AM
From biorxiv.org
Coarse-Grained Dynamic Simulation of Cytoskeletal Microtubule Twist
0 0
Microtubule, a key component of the cytoskeleton, plays a crucial role in cell mitosis. Modeling and dynamic simulation of microtubules at the micrometer scale remain a significant challenge. In this study, we developed the helix-based ultra-coarse-grained (HB-UCG) model for the dynamic...
on Sat, 1AM
From biorxiv.org
Jasmonic acid signaling and glutathione coordinate plant recovery from high light stress
0 0
High light-induced chloroplast retrograde signaling originates from the photosynthetic apparatus and regulates nuclear gene expression to enhance photoprotection and coordination of cell metabolism. Here, we analyzed the transcript profiles and accumulation of ROS, stress hormones and small...
on Sat, 1AM
From biorxiv.org
0 1
Spastin is a microtubule-severing AAA+ ATPase that is highly expressed in neuronal cells and plays a crucial role in axonal growth, branching, and regeneration. This machine oligomerizes into hexamers in the presence of ATP and the microtubule carboxy-terminal tails (CTTs). Conformational...
on Fri, 3PM
From biorxiv.org
Benchmarking Generative Models for Antibody Design
0 1
Generative models trained on antibody sequences and structures have shown great potential in advancing machine learning-assisted antibody engineering and drug discovery. Current state-of-the-art models are primarily evaluated using two categories of in silico metrics: sequence-based metrics,...
on Fri, 3PM
From biorxiv.org
0 1
Protists are major functional players in the oceans. Time-resolved epipelagic protist successions remain poorly described in subtropical ecosystems, limiting current understanding of food web dynamics and responses to environmental changes in these major world-ocean regions. Here, we used...
on Fri, 2PM
From biorxiv.org
0 1
Glioblastoma (GBM) is one of the most debilitating and extremely aggressive tumors, with a median survival of less than a year. GBMs have high metastatic potential and frequently acquire chemoresistance. The current multimodal treatment approaches for GBM include surgical tumor resurrection,...
on Fri, 2PM
From biorxiv.org
0 2
Despite decades of reports of weak magnetic field effects in biology across the tree of life and on a broad range of cell types, the evidence to date remains met with skepticism. To remedy this, we present open-data, large scale, and varied morphological evidence that Xenopus laevis embryo...
on Fri, 2PM
From biorxiv.org
Ductal pancreatic cancer interception by FGFR2 abrogation
0 1
Activating KRAS mutations are a key feature of pancreatic ductal adenocarcinoma (PDA) and drive tumor initiation and progression. However, mutant KRAS by itself is weakly oncogenic. The pathways that cooperate with mutant KRAS to induce tumorigenesis are less-defined. Analyzing organoids and...
on Fri, 1PM
From biorxiv.org
Fast and robust visual object recognition in young children
0 1
By adulthood, humans rapidly identify objects from sparse visual displays and across significant disruptions to their appearance. What are the minimal conditions needed to achieve robust recognition abilities and when might these abilities develop? To test this question, we investigated the...
on Fri, 1PM
From biorxiv.org
Searching for Sulfotyrosines (sY) in a HA(pY)STACK
0 0
Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is near-isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as...
on Fri, 12PM
From biorxiv.org
Nonlinear Singular Value Decomposition Beamforming for Ultrasound Imaging of Gas Vesicles
0 0
Ultrasound imaging holds significant promise for the observation of molecular and cellular phenomena through the utilization of acoustic contrast agents and acoustic reporter genes. Optimizing imaging methodologies for enhanced detection represents an imperative advancement in this field. Most...
on Fri, 12PM
From biorxiv.org
The First Comprehensive Description of the Platelet Single Cell Transcriptome
0 1
Platelets are derived from megakaryocytes, either in peripheral or pulmonic circulation. The transcriptome of megakaryocytes has been studied, while the platelet transcriptome is thought to be a reflection of their parent cells; it has not yet been investigated. Although platelets lack nuclei,...
on Fri, 10AM
From biorxiv.org
Human Topoisomerase IIα Promotes Chromatin Condensation Via a Phase Transition
0 1
Topoisomerase II (topo II) enzymes are essential enzymes known to resolve topological entanglements during DNA processing. Curiously, while yeast expresses a single topo II, humans express two topo II isozymes, topo IIα and topo IIβ, which share a similar catalytic domain but differ in their...
on Fri, 9AM
From biorxiv.org
0 0
Despite decades of reports of weak magnetic field effects in biology across the tree of life and on a broad range of cell types, the evidence to date remains met with skepticism. To remedy this, we present open-data, large-scale, and varied morphological evidence that Xenopus laevis embryo...
on Fri, 9AM
From biorxiv.org
0 0
Background: Immune checkpoint inhibitor (ICI) therapy efficacy varies among cancer patients, necessitating precise predictive biomarkers for optimized treatment strategies. Methods: We developed the Adaptive best subset selection algorithm and Genetic algorithm Aided Ensemble learning (AGAE)...
on Fri, 9AM
From biorxiv.org
Interpretable multi-omics integration with UMAP embeddings and density-based clustering
0 1
Integrating high-dimensional cellular multi-omics data is crucial for understanding various layers of biological control. Single ‘omic methods provide important insights, but often fall short in handling the complex relationships between genes, proteins, metabolites and beyond. Here, we present...
on Fri, 9AM
From biorxiv.org
Hydroxyurea induces ER stress and cytoplasmic protein aggregation
0 1
The endoplasmic reticulum (ER) lumen provides the proper redox environment for disulfide bond formation, which is required for the appropriate folding of proteins that enter the secretory pathway and constitute membranes. Defective protein folding in the ER activates proteostatic mechanisms that...
on Fri, 8AM
From biorxiv.org
A global resource constrained model to predict metabolic flux dynamics in fluctuating environments
0 1
Environmental changes often induce global variations on bacterial gene expression, frequently accompanied by alterations in growth rates. Integrating non-metabolic cellular processes, such as gene expression and macromolecule synthesis, with metabolic modeling remains a significant challenge in...
on Fri, 8AM
From biorxiv.org
Virological characteristics of the SARS-CoV-2 XEC variant
0 5
The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), arising from BA.2.86.1 with spike protein (S) substitution S:L455S, outcompeted the previously predominant XBB lineages by the beginning of 2024. Subsequently, JN.1 subvariants including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired...
on Fri, 5AM