Browsing Ciències Bàsiques by Subject "57"
Now showing items 1-20 of 21
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2P-111 Stochastic resonance in DNA hairpins(The 46th Annual Meeting of the Biophysical Society of Japan)
(Seibutsu Butsuri, 2008) -
The ADP-ribose hydrolase NUDT5 is important for DNA repair
(Cell Reports, 2022-12)DNA damage leads to rapid synthesis of poly(ADP-ribose) (pADPr), which is important for damage signaling and repair. pADPr chains are removed by poly(ADP-ribose) glycohydrolase (PARG), releasing free ... -
ADP-ribose–derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling
(Science, 2016)Key nuclear processes in eukaryotes, including DNA replication, repair, and gene regulation, require extensive chromatin remodeling catalyzed by energy-consuming enzymes. It remains unclear how the ATP ... -
Chronic full-band recordings with graphene microtransistors as neural interfaces for discrimination of brain states
(Nanoscale Horizons, 2024)Brain states such as sleep, anesthesia, wakefulness, or coma are characterized by specific patterns of cortical activity dynamics, from local circuits to full-brain emergent properties. We previously ... -
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
(Nucleic Acids Research, 2017)DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different ... -
Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes
(Journal of Statistical Mechanics: Theory and Experiment, 2009)We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive ... -
Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation
(Journal of Statistical Mechanics: Theory and Experiment, 2009)We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two-state manner under the action of mechanical force. We apply path thermodynamics to derive ... -
Engineering a genome-reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo
(Molecular Systems Biology, 2021)Bacteria present a promising delivery system for treating human diseases. Here, we engineered the genome-reduced human lung pathogen Mycoplasma pneumoniae as a live biotherapeutic to treat biofilm-associated ... -
Functional characterization of a novel non-coding mutation “Ghent +49A > G” in the iron-responsive element of L-ferritin causing hereditary hyperferritinaemia-cataract syndrome
(Scientific Reports, 2017)Hereditary hyperferritinaemia-cataract syndrome (HHCS) is a rare disorder usually caused by heterozygous mutations in the iron-responsive element (IRE) in the 5′ untranslated region (5′UTR) of the ... -
Hormone-induced repression of genes requires BRG1-mediated H1.2 deposition at target promoters
(The EMBO Journal, 2016)Eukaryotic gene regulation is associated with changes in chromatin compaction that modulate access to DNA regulatory sequences relevant for transcriptional activation or repression. Although much is ... -
Investigating the thermodynamics of small biosystems with optical tweezers
(Physica E: Low-dimensional Systems and Nanostructures, 2010)We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic ... -
Iron Regulation and the Cell Cycle: identification of an iron-responsive element in the 3′-untranslated region of human cell division cycle 14a mrna by a refined microarray-based screening strategy
(The Journal of Biological Chemistry, 2006)Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5′- or ... -
LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions
(Microbial Biotechnology, 2021)The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are ... -
Measurement of work in single-molecule pulling experiments
(The Journal of Chemical Physics, 2009)A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify ... -
Modeling cell adhesion and proliferation: a cellular-automata based approach
(Advanced Modeling and Simulation in Engineering Sciences, 2015)Background: Cell adhesion is a process that involves the interaction between the cell membrane and another surface, either a cell or a substrate. Unlike experimental tests, computer models can simulate ... -
New partners identified by mass spectrometry assay reveal functions of NCAM2 in neural cytoskeleton organization
(International Journal of Molecular Sciences, 2021)Neuronal cell adhesion molecule 2 (NCAM2) is a membrane protein with an important role in the morphological development of neurons. In the cortex and the hippocampus, NCAM2 is essential for proper ... -
Probing RNA structural landscapes across Candida yeast genomes
(Frontiers in Microbiology, 2024)Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress ... -
Single-molecule derivation of salt dependent base-pair free energies in DNA
(Proceedings of the National Academy of Sciences., 2010)Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in ... -
Statistical properties of metastable intermediates in DNA unzipping
(Physical Review Letters, 2009)We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes ... -
SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome
(Nucleic Acids Research, 2022)The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a ...