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Mars probes : robots explore the red planet
\"In 1976, Viking 1 became the first spacecraft from Earth to land on Mars. For the first time, scientists were able to see the surface of the red planet. Since then, NASA and other space organizations have sent other probes to Mars and have learned a lot. Readers find out all about the robots created especially for the task of exploring Mars through detailed diagrams, full-color photographs, and interesting main content. Including information about STEM careers and the background of planning a space mission using robots, this book engages readers with exciting STEM content and careers.\"-- Provided by publisher.
Book
Quantitative measurement of exchange dynamics in proteins via ^sup 13^C relaxation dispersion of ^sup 13^CHD^sub 2^-labeled samples
Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit 13CH3- or 13CHD2-labeling in otherwise highly deuterated proteins. The 13CHD2 label offers the unique advantage of providing 13C, 1H and 2H spin probes, however a disadvantage has been the lack of an experiment to record 13C Carr-Purcell-Meiboom-Gill relaxation dispersion that monitors millisecond time-scale dynamics, implicated in a wide range of biological processes. Herein we develop an experiment that eliminates artifacts that would normally result from the scalar coupling between 13C and 2H spins that has limited applications in the past. The utility of the approach is established with a number of applications, including measurement of ms dynamics of a disease mutant of a 320 kDa p97 complex.
Journal Article
Ring current shifts in ^sup 19^F-NMR of membrane proteins
Fluorine-19 NMR markers are attractive reporter groups for use in studies of complex biomacromolecular systems, in particular also for studies of function-related conformational equilibria and rate processes in membrane proteins. Advantages of 19F-NMR probes include high sensitivity of the 19F chemical shifts to variations in the non-covalent environment. Nonetheless, in studies of G protein-coupled receptors (GPCR) we encountered situations where 19F chemical shifts were not responsive to conformational changes that had been implicated by other methods. This prompted us to examine possible effects of aromatic ring current fields on the chemical shifts of 19F-NMR probes used in GPCRs. Analysis of previously reported 19F-NMR data on the [beta]2-adrenergic receptor and mammalian rhodopsin showed that all 19F-labeling sites which manifested conformational changes are located near aromatic residues. Although ring current effects are small when compared to other known non-covalent effects on 19F chemical shifts, there is thus an indication that their contributions are significant when studying activation processes in GPCRs, since the observed activation-related 19F-NMR chemical shifts are comparable in size to the calculated ring current shifts. Considering the impact of ring current shifts may thus be helpful in identifying promising indigenous or engineered labeling sites for future 19F-NMR studies of GPCR activation, and novel information may be obtained on the nature of conformational rearrangements near the 19F-labels. It will then also be interesting to see if the presently indicated role of ring current shifts in membrane protein studies with 19F-NMR markers can be substantiated by a more extensive data base resulting from future studies.
Journal Article
Voyager probes : robots on an interstellar mission
Describes the Voyager 1 and Voyager 2 robotic probes that were launched in 1977, discussing the data they have sent back and plans for their future use.
Book
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications.
Journal Article
Dreams of other worlds : the amazing story of unmanned space exploration
Dreams of Other Worlds describes the unmanned space missions that have opened new windows on distant worlds. Spanning four decades of dramatic advances in astronomy and planetary science, Impey and Henry tell the story of eleven iconic exploratory missions and how they have fundamentally transformed our scientific and cultural perspectives on the universe and our place in it.
Book
DNA probes that store mechanical information reveal transient piconewton forces applied by T cells
The advent of molecular tension probes for real-time mapping of piconewton forces in living systems has had a major impact on mechanobiology. For example, DNA-based tension probes have revealed roles for mechanics in platelet, B cell, T cell, and fibroblast function. Nonetheless, imaging short-lived forces transmitted by low-abundance receptors remains a challenge. This is a particular problem for mechanoimmunology where ligand–receptor bindings are short lived, and a few antigens are sufficient for cell triggering. Herein, we present a mechanoselection strategy that uses locking oligonucleotides to preferentially and irreversibly bind DNA probes that are mechanically strained over probes at rest. Thus, infrequent and short-lived mechanical events are tagged. This strategy allows for integration and storage of mechanical information into a map of molecular tension history. Upon addition of unlocking oligonucleotides that drive toehold-mediated strand displacement, the probes reset to the real-time state, thereby erasing stored mechanical information. As a proof of concept, we applied this strategy to study OT-1 T cells, revealing that the T cell receptor (TCR) mechanically samples antigens carrying single amino acid mutations. Such events are not detectable using conventional tension probes. Each mutant peptide ligand displayed a different level of mechanical sampling and spatial scanning by the TCR that strongly correlated with its functional potency. Finally, we show evidence that T cells transmit pN forces through the programmed cell death receptor-1 (PD1), a major target in cancer immunotherapy. We anticipate that mechanical information storage will be broadly useful in studying the mechanobiology of the immune system.
Journal Article
Journey through our solar system
\"This book takes readers on a tour of our solar system\"--Provided by publisher.
Book
Comparative evaluation of DNA and RNA probes for capture-based mitochondrial DNA next-generation sequencing
Background
Probe-based liquid-phase hybridization capture is a powerful and commonly used approach for next-generation sequencing (NGS) of mitochondrial DNA (mtDNA). However, the performance difference between DNA and RNA probe-based capture strategies for mtDNA NGS remains to be determined, leading to the irrational interchangeable use in numerous studies.
Results
We custom-designed DNA and RNA probes targeting the double-stranded mtDNA and optimized their hybridization conditions for capture-based mtDNA NGS in fresh tissue and plasma samples. Under optimal conditions, we systematically compared the performance of DNA and RNA probes in mtDNA detection. RNA probes demonstrated superior mtDNA enrichment efficiency, characterized by higher mtDNA mapping rates and greater average mtDNA depth per gigabyte of sequencing data. However, DNA probes were more effective at reducing artifacts caused by nuclear mitochondrial DNA segments (NUMTs) in mtDNA mutation detection at both the read and mutation levels. Additionally, RNA probes captured a broader fragment size distribution and higher prevalence of longer fragments in plasma cell-free mtDNA.
Conclusions
The systematic evaluation of DNA and RNA probes in capture-based mtDNA NGS provides valuable insights into their performance differences. These findings advocate for informed probe selection tailored to the specific experimental and clinical needs, ultimately advancing the field of mtDNA characterization and its applications in genomics and diagnostics.
Journal Article