scholarly journals Visualization of the spontaneous emergence of a complex, dynamic, and autocatalytic system

2016 ◽  
Vol 113 (40) ◽  
pp. 11122-11126 ◽  
Author(s):  
Jaime Ortega-Arroyo ◽  
Andrew J. Bissette ◽  
Philipp Kukura ◽  
Stephen P. Fletcher
Keyword(s):  
De Novo ◽  
Label Free ◽  
Real Time Visualization ◽  
Nanoscale Imaging ◽  
Autocatalytic System ◽  
Aqueous Mixture ◽  
Reactive Interface ◽  
Life On Earth ◽  
Insight Into

Autocatalytic chemical reactions are widely studied as models of biological processes and to better understand the origins of life on Earth. Minimal self-reproducing amphiphiles have been developed in this context and as an approach to de novo “bottom–up” synthetic protocells. How chemicals come together to produce living systems, however, remains poorly understood, despite much experimentation and speculation. Here, we use ultrasensitive label-free optical microscopy to visualize the spontaneous emergence of an autocatalytic system from an aqueous mixture of two chemicals. Quantitative, in situ nanoscale imaging reveals heterogeneous self-reproducing aggregates and enables the real-time visualization of the synthesis of new aggregates at the reactive interface. The aggregates and reactivity patterns observed vary together with differences in the respective environment. This work demonstrates how imaging of chemistry at the nanoscale can provide direct insight into the dynamic evolution of nonequilibrium systems across molecular to microscopic length scales.

scholarly journals Nanoscale Imaging of Biomolecules using Molecule Anchorable Gel-enabled Nanoscale In-situ Fluorescence Microscopy

2021 ◽  
Author(s):  
Aleksandra Klimas ◽  
Brendan Gallagher ◽  
Piyumi Wijesekara ◽  
Sinda Fekir ◽  
Donna Stolz ◽  
...  
Keyword(s):  
Low Cost ◽  
Super Resolution ◽  
Human Kidney ◽  
Synaptic Proteins ◽  
Proteinase K ◽  
Objective Lens ◽  
Nanoscale Imaging ◽  
Imaging Strategy ◽  
Insight Into

Abstract Expansion microscopy (ExM) is a powerful imaging strategy that offers a low-cost solution for nanoimaging with conventional microscopes by physically and isotropically magnifying preserved biological specimens embedded in a cross-linked water-swellable hydrogel. Current ExM protocols require prior treatment with specialized reactive anchoring chemicals to link specific labels and biomolecule classes to the gel. In addition, most techniques reportedly use strong Proteinase K to digest endogenous epitopes to enable expansion and are limited by using mechanically fragile gel formulas to expand specimens by at most 4.5× linearly. Here we describe a new ExM framework, Molecule Anchorable Gel-enabled Nanoscale In-situ Fluorescence MicroscopY (MAGNIFY), that uses a mechanically sturdy gel that enables broad retention of nucleic acids, proteins, and lipids without the need for a separate anchoring step. MAGNIFY expands biological specimens up to 11× and facilitates imaging of cells and tissues with effectively ~25-nm-resolution using an ∼280-nm diffraction-limited objective lens on conventional optical microscopes or with ~13 nm-resolution if combined with Super-resolution Optical Fluctuation Imaging (SOFI). Further, MAGNIFY generalizes well across a broad range of biological specimens, providing insight into nanoscopic subcellular structures including synaptic proteins from mouse brain, podocyte foot processes in human kidney, and defects in cilia and basal bodies in drug-treated human lung organoids. MAGNIFY provides a novel advance that expands the precision, utility, accessibility, and generality of subcellular nanoscopy.

Nanomechanical Microcantilevers for In-Vitro Biomolecular Detection

2007 ◽  
Author(s):  
Kilho Eom ◽  
Tae Yun Kwon ◽  
Jinsung Park ◽  
Sungsoo Na ◽  
Dae Sung Yoon ◽  
...  
Keyword(s):  
Real Time ◽  
Biological Molecules ◽  
Label Free ◽  
Biomolecular Detection ◽  
Label Free Detection ◽  
Detection Of Biomolecules ◽  
Kinetics Of ◽  
Insight Into

Nanomechanical microcantilevers have enabled the sensitive label-free detection of chemical and/or biological molecules. In recent years, resonating microcantilevers have achieved the unprecedented sensitivity in detecting molecules. In this article, we review our current works on the label-free detection of biomolecules based on resonating microcantilevers. Our piezoelectric thick film microcantilevers exhibit the relatively high quality factor in a viscous liquid, indicating the potential of our cantilever to in situ biosensor applications for real-time detection of biomolecular interactions. It is shown that our microcantilevers allow the noise-free real-time monitoring of biomolecular recognitions, providing the insight into kinetics of biomolecular recognitions.

scholarly journals Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna M. Kotowska ◽  
Gustavo F. Trindade ◽  
Paula M. Mendes ◽  
Philip M. Williams ◽  
Jonathan W. Aylott ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Secondary Ion Mass Spectrometry ◽  
De Novo ◽  
Ion Beam ◽  
Peptide Sequencing ◽  
Protein Characterization ◽  
Label Free ◽  
Peptide Cleavage

AbstractLabel-free protein characterization at surfaces is commonly achieved using digestion and/or matrix application prior to mass spectrometry. We report the assignment of undigested proteins at surfaces in situ using secondary ion mass spectrometry (SIMS). Ballistic fragmentation of proteins induced by a gas cluster ion beam (GCIB) leads to peptide cleavage producing fragments for subsequent OrbitrapTM analysis. In this work we annotate 16 example proteins (up to 272 kDa) by de novo peptide sequencing and illustrate the advantages of this approach by characterizing a protein monolayer biochip and the depth distribution of proteins in human skin.

scholarly journals In situ nanoscale imaging of moiré superlattices in twisted van der Waals heterostructures

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yue Luo ◽  
Rebecca Engelke ◽  
Marios Mattheakis ◽  
Michele Tamagnone ◽  
Stephen Carr ◽  
...  
Keyword(s):  
Van Der Waals ◽  
Van Der Waals Heterostructures ◽  
Nanoscale Imaging

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Development of Fragility Curves for Piping and Slope Stability of River Levees

Water ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 738
Author(s):  
Nicola Rossi ◽  
Mario Bačić ◽  
Meho Saša Kovačević ◽  
Lovorka Librić
Keyword(s):  
Slope Stability ◽  
Fragility Curves ◽  
Safety Margin ◽  
Water Levels ◽  
Flood Event ◽  
Soil Parameters ◽  
Design Code ◽  
A Site ◽  
Insight Into

The design code Eurocode 7 relies on semi-probabilistic calculation procedures, through utilization of the soil parameters obtained by in situ and laboratory tests, or by the means of transformation models. To reach a prescribed safety margin, the inherent soil parameter variability is accounted for through the application of partial factors to either soil parameters directly or to the resistance. However, considering several sources of geotechnical uncertainty, including the inherent soil variability, measurement error and transformation uncertainty, full probabilistic analyses should be implemented to directly consider the site-specific variability. This paper presents the procedure of developing fragility curves for levee slope stability and piping as failure mechanisms that lead to larger breaches, where a direct influence of the flood event intensity on the probability of failure is calculated. A range of fragility curve sets is presented, considering the variability of levee material properties and varying durations of the flood event, thus providing crucial insight into the vulnerability of the levee exposed to rising water levels. The procedure is applied to the River Drava levee, a site which has shown a continuous trend of increased water levels in recent years.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

scholarly journals Associations between Amplification (1q) and Prior Cancer in a Real-World De Novo Myeloma Cohort

2021 ◽  
Author(s):  
Elizabeth B Lamont ◽  
Andrew J Yee ◽  
Stuart L Goldberg ◽  
David S Siegel ◽  
Andrew D Norden
Keyword(s):  
Real World ◽  
Fluorescent In Situ Hybridization ◽  
De Novo ◽  
Chromosome 1 ◽  
Second Malignancies ◽  
Cancer History ◽  
Screening Strategies ◽  
Cytogenetic Testing

Abstract Genomic biomarkers inform treatment in multiple myeloma (MM) making patient clinical data a potential window into MM biology. We evaluated de novo MM patients for associations between specific MM cytogenetic patterns and prior cancer history. Analyzing a MM real-world dataset (RWD), we identified a cohort of 1,769 patients with fluorescent in-situ hybridization (FISH) cytogenetic testing at diagnosis. Fully 241 patients (0.14) had histories of prior cancer(s). Amplification of the long arm of chromosome 1 [amp(1q)] varied by prior cancer history (0.31 with prior cancer vs 0.24 without; p = .02). No other MM translocations, amplifications, or deletions were associated with prior cancers. Amp(1q) and cancer history remained strongly associated in a logistic regression adjusting for patient demographic and disease attributes. The results merit follow-up regarding carcinogenic treatment effects and screening strategies for second malignancies. Broadly the findings suggest analyses of patient-level phenotypic-genomic RWD may accelerate cancer research through hypothesis generating studies.

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