PubReading
346 episodes - English - Latest episode: 10 months ago -Researchers would love if they can expand time to fit in that publication, article, or review of their topic of interest; if that were true, however, there is no end to bottomless scrolling and missing the important details. PubReading would read out the abstract, results, and discussions to allow hassle-free information and a chance to create connections with like-minded individuals.
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Episodes
PubReading [244] - The long and short of it - L. Passmore & T. Tang
December 16, 2022 12:00 - 6 minutes - 9.55 MBLonger poly(A) tails improve translation in early development, but not in mature cells that have higher levels of the protein PABPC. DOI: https://doi.org/10.7554/eLife.70757 - 2021
PubReading [243] - Liquid biopsies for residual disease and recurrence - J. Chee Ming Wan, N. Rosenfeld et al.
December 15, 2022 12:00 - 47 minutes - 65.1 MBDetection of minimal residual disease in patients with cancer, who are in complete remission with no cancer cells detectable, has the potential to improve recurrence-free survival through treatment selection. Studies analyzing circulating tumor DNA (ctDNA) in patients with solid tumors suggest the potential to accurately predict and detect relapse, enabling treatment strategies that may improve clinical outcomes. Over the past decade, assays for ctDNA detection in plasma samples have steadil...
PubReading [242] - Single-particle cryo-EM at atomic resolution - T. Nakane, S. Scheres et al.
December 14, 2022 12:00 - 26 minutes - 36.7 MBThe three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years. However, it has proved difficult to obtain cryo-EM recons...
PubReading [241] - The neurons that restore walking after paralysis - C. Kathe, G. Courtine et al
December 13, 2022 12:00 - 32 minutes - 44.9 MBA spinal cord injury interrupts pathways from the brain and brainstem that project to the lumbar spinal cord, leading to paralysis. Here we show that spatiotemporal epidural electrical stimulation (EES) of the lumbar spinal cord applied during neurorehabilitation (EESREHAB) restored walking in nine individuals with chronic spinal cord injury. This recovery involved a reduction in neuronal activity in the lumbar spinal cord of humans during walking. We hypothesized that this unexpected reduct...
PubReading [240] - Is my paper relevant for an international audience? - F. Fernandez-llimos
December 12, 2022 12:00 - 12 minutes - 17.7 MBThis is the first question one should consider before submitting a paper to an international journal. The answer is simple: If researchers or practitioners from another country can learn something from your paper that can influence a practice or a research they are involved in, then your paper is relevant for an international audience. There are many elements that can influence in this cross-border transferability. One could think that having a big “n”, or performing complex statistical calc...
PubReading [239] - Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH - D. Rusling
December 09, 2022 12:00 - 40 minutes - 56.3 MBThe sequence-specific recognition of duplex DNA by unmodified parallel triplex-forming oligonucleotides is restricted to low pH conditions due to a necessity for cytosine protonation in the third strand. This has severely restricted their use as gene-targeting agents, as well as for the detection and/or functionalisation of synthetic or genomic DNA. Here I report that the nucleobase 6-amino-5-nitropyridin- 2-one (Z) finally overcomes this constraint by acting as an uncharged mimic of protona...
PubReading [238] - Heart regeneration using pluripotent stem cells - S. Kadota, Y. Tanaka, Y. Shiba
December 08, 2022 12:00 - 24 minutes - 33.7 MBPluripotent stem cells (PSCs), which include embryonic and induced pluripotent stem cells (ESCs and iPSCs, respectively), have great potential in regenerative medicine for heart diseases due to their virtually unlimited cardiogenic capacity. Many preclinical studies have described the functional benefits after transplantation of PSC-derived cardiomyocytes (PSC-CMs). However, transient ventricular arrhythmias were detected after injection into non-human primates and swine ischemic hearts; as ...
PubReading [237] - Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer - J. Niño, S. Bullman et al.
December 07, 2022 12:00 - 40 minutes - 56.1 MBThe tumour-associated microbiota is an intrinsic component of the tumour microenvironment across human cancer types1,2. Intratumoral host–microbiota studies have so far largely relied on bulk tissue analysis1–3, which obscures the spatial distribution and localized effect of the microbiota within tumours. Here, by applying in situ spatial-profiling technologies4 and single-cell RNA sequencing5 to oral squamous cell carcinoma and colorectal cancer, we reveal spatial, cellular and molecular ho...
PubReading [236] - BioSimulators- a central registry of simulation engines and services for recommending specific tools - B. Shaikh, J. Karr et al.
December 06, 2022 13:00 - 33 minutes - 46.4 MBComputational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central reg...
PubReading [235] - How to...write a good research question - K. Mattick, J. Johnston and A. de la Croix
December 05, 2022 12:00 - 13 minutes - 19.1 MBThis paper, on writing research questions, is the first in a series that aims to support novice researchers within clinical education, particularly those undertaking their first qualitative study. Put simply, a research question is a question that a research project sets out to answer. Most research questions will lead to a project that aims to generate new insights, but the target audience and the methodology will vary widely. The term ‘evaluation question’ is used less commonly, but the sa...
PubReading [234] - The importance of synthetic chemistry in the pharmaceutical industry - K. Campos, E. Parmee et al.
December 02, 2022 12:00 - 46 minutes - 63.8 MBInnovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matter. We identify s...
PubReading [233] - The importance of synthetic chemistry in the pharmaceutical industry - K. Campos, E. Parmee et al.
December 01, 2022 12:01 - 8 minutes - 11 MBREVIEW SUMMARY Innovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matte...
PubReading [232] - The multiple flavors of GoU pairs in RNA - E. Westhof, M. Yusupov, G. Yusupova
November 30, 2022 12:00 - 21 minutes - 29.3 MBWobble GU pairs (or GoU) occur frequently within double‐stranded RNA helices interspersed within the standard G═C and A─U Watson‐Crick pairs. However, other types of GoU pairs interacting on their Watson‐Crick edges have been observed. The structural and functional roles of such alternative GoU pairs are surprisingly diverse and reflect the various pairings G and U can form by exploiting all the subtleties of their electronic configurations. Here, the structural characteristics of the GoU pa...
PubReading [231] - Light-activated communication in synthetic tissues - M. Booth, H. Bayley et al.
November 29, 2022 12:00 - 18 minutes - 25.4 MBWe have previously used three-dimensional (3D) printing to prepare tissue-like materials in which picoliter aqueous compartments are separated by lipid bilayers. These printed droplets are elaborated into synthetic cells by using a tightly regulated in vitro transcription/translation system. A light-activated DNA promoter has been developed that can be used to turn on the expression of any gene within the synthetic cells. We used light activation to express protein pores in 3D-printed patter...
PubReading [230] - Does a Graphical Abstract Bring More Visibility to Your Paper? - E. Pferschy-Wenzig, A. Atanasov et al.
November 28, 2022 12:00 - 12 minutes - 16.7 MBA graphical abstract (GA) represents a piece of artwork that is intended to summarize the main findings of an article for readers at a single glance. Many publishers currently encourage authors to supplement their articles with GAs, in the hope that such a convenient visual summary will facilitate readers with a clearer outline of papers that are of interest and will result in improved overall visibility of the respective publication. To test this assumption, we statistically compared public...
PubReading [229] - RNA-Puzzles toolkit- a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools - M. Magnus, Z. Miao et al.
November 25, 2022 12:00 - 46 minutes - 63.9 MBSignificant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systema...
PubReading [228] - Data, data, burning deep, in the forests of the net - E. Westhof
November 24, 2022 12:00 - 17 minutes - 23.8 MBContinuous and imaginative technological developments are leading to a massive accumulation of various types of data in all areas of biological research. As a result, the central importance of databases is increasing. Databases related to biology must not only be structured using controlled vocabularies, but also be fully integrated into the whole biological domain. To achieve this goal, they must be systematically grounded in biological evolution and exploit the available tools of evolution...
PubReading [227] - Artificial intelligence in chemistry and drug design - N. Brown, N. Schneider et al
November 23, 2022 12:00 - 29 minutes - 40.2 MBThe discovery of molecular structures with desired properties for applications in drug discovery, crop protection, or chemical biology is among the most impactful scientific challenges. However, given the complexity of biological systems and the associated cost for experiments and trials, molecular design is also scientifically very challenging, prone to failure, inherently expensive and time consuming. To improve our odds and the timelines in this process, and to identify good starting poin...
PubReading [226] - The threat of programmed DNA damage to neuronal genome integrity and plasticity - K. Caldecott, M. Ward and A. Nussenzweig
November 22, 2022 12:01 - 26 minutes - 36.6 MBThe neuronal genome is particularly sensitive to loss or attenuation of DNA repair, and many neurological diseases ensue when DNA repair is impaired. It is well-established that the neuronal genome is subjected to stochastic DNA damage, most likely because of extensive oxidative stress in the brain. However, recent studies have identified unexpected high levels of ‘programmed’ DNA breakage in neurons, which we propose arise during physiological DNA metabolic processes intrinsic to neuronal d...
PubReading [225] - A brief guide to the science and art of writing manuscripts in biomedicine - Di. Forero, S. Lopez-Leon, G. Perry
November 21, 2022 12:00 - 28 minutes - 39.7 MBPublishing articles in international scientific journals is the primary method for the communication of validated research findings and ideas. Journal articles are commonly used as a major input for evaluations of researchers and institutions. Few articles have been published previously about the different aspects needed for writing high-quality articles. In this manuscript, we provide an updated and brief guide for the multiple dimensions needed for writing manuscripts in the health and bio...
PubReading [224] - Drug Design- Where We Are and Future Prospects - G. Zagotto and M. Bortoli
November 18, 2022 12:00 - 34 minutes - 47.8 MBMedicinal chemistry is facing new challenges in approaching precision medicine. Several powerful new tools or improvements of already used tools are now available to medicinal chemists to help in the process of drug discovery, from a hit molecule to a clinically used drug. Among the new tools, the possibility of considering folding intermediates or the catalytic process of a protein as a target for discovering new hits has emerged. In addition, machine learning is a new valuable approach hel...
PubReading [223] - The Discovery of the DNA Double Helix - A. Klung
November 17, 2022 12:01 - 54 minutes - 75.4 MBFifty years ago, on 25th April 1953, there appeared three papers in the journal, Nature, which changed our view of the world. The structure of the DNA double helix, with its complementary base-pairing, is one of the greatest discoveries in biology in the 20th Century. It was also most dramatic, since, quite unexpectedly, the structure itself pointed to the way in which a DNA molecule might replicate itself, and hence revealed the “secret of life”. The structure was solved in the Cavendish La...
PubReading [222] - Click Chemistry Enables Rapid Amplification of Full-Length Reverse Transcripts for Long-Read Third Generation Sequencing - E. Schönegger, T. Frischmuth
November 16, 2022 13:00 - 20 minutes - 28.6 MBHere we describe the development of a novel click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA, while avoiding the need for problematic template-switching (TS) reactions. Compared with prior efforts, our method involves neither random priming nor stochastic cDNA termination, thus enabling amplification of transcripts that were previously inaccessible via related click chemistry-based RNA sequencing techniques. A key modification inv...
PubReading [221] - Hairpin-like siRNA-Based Spherical Nucleic Acids - M. Vasher, G. Yamankurt, C. Mirkin
November 15, 2022 12:00 - 26 minutes - 36.6 MBThe therapeutic use of small interfering RNAs (siRNAs) as gene regulation agents has been limited by their poor stability and delivery. Although arranging siRNAs into a spherical nucleic acid (SNA) architecture to form siRNA-SNAs increases their stability and uptake, prototypical siRNA-SNAs consist of a hybridized architecture that causes guide strand dissociation from passenger strands, which limits the delivery of active siRNA duplexes. In this study, a new SNA design that directly attache...
PubReading [220] - Interbase FRET in RNA: from A to Z - A. Fuechtbauer, M. Wilhelmsson et al.
November 14, 2022 12:00 - 25 minutes - 35.7 MBInterbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tCO and the non-emissive acceptor tCnitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA str...
PubReading [219] - An integrated workflow for crosslinking mass spectrometry - M. Mendes, J. Rappsilber et al
November 11, 2022 13:00 - 29 minutes - 40 MBWe present a concise workflow to enhance the mass spectrometric detection of crosslinked peptides by introducing sequential digestion and the crosslink identification software xiSEARCH. Sequential digestion enhances peptide detection by selective shortening of long tryptic peptides. We demonstrate our simple 12-fraction protocol for crosslinked multi-protein complexes and cell lysates, quantitative analysis, and high-density crosslinking, without requiring specific crosslinker features. This...
PubReading [218] - Covalent labeling of immune cells - L. Rösner, C. Konken, D. Depke, A. Rentmeister, M. Schäfers
November 10, 2022 12:00 - 23 minutes - 32.8 MBInflammation is a common, fast, and innate response of the immune system to sterile or infectious tissue damage or autoimmune triggers. It aims at minimizing tissue destruction and maintaining organ function, hence is vital to life. Therefore, the immune system comprises the concerted action of a variety of different immune cells with specific tasks in the initiation, maintenance, and termination of inflammation. Visualizing their localization, trafficking, and interaction is of utmost impor...
PubReading [217] - Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies - C. Bettegowda, L. Diaz Jr et al
November 09, 2022 12:00 - 46 minutes - 63.6 MBThe development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less t...
PubReading [216] - Bottom-Up Assembly of Synthetic Cells with a DNA Cytoskeleton - K. Jahnke, K. Göpfrich et al
November 08, 2022 12:00 - 28 minutes - 38.5 MBCytoskeletal elements, like actin and myosin, have been reconstituted inside lipid vesicles toward the vision to reconstruct cells from the bottom up. Here, we realize the de novo assembly of entirely artificial DNA-based cytoskeletons with programmed multifunctionality inside synthetic cells. Giant unilamellar lipid vesicles (GUVs) serve as cell-like compartments, in which the DNA cytoskeletons are repeatedly and reversibly assembled and disassembled with light using the cis–trans isomeriza...
PubReading [115] - Therapeutic application of sequence-specific binding molecules for novel genome editing tools - J. Nakao, T. Yamamoto and A. Yamayoshi
November 07, 2022 12:01 - 29 minutes - 41.1 MBGenome editing has been expected to widely increase the available treatment options for various diseases and permit pharmaceutical interventions in previously untreatable conditions. The availability of genome editing tools was dramatically increased by the development of the CRISPR-Cas9 system. However, a number of issues limit the use of the CRISPR-Cas9 system and other gene-editing tools in the clinical treatment of diseases. This review summarized the history and types of genome editing ...
PubReading [214] - Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance - A. Bowden, S. Jackson et al.
November 04, 2022 21:00 - 20 minutes - 28.3 MBCRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR- Cas9 screens using TP53 wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and TP53 knockout human re...
PubReading [213] - Stabilisation of self-assembled DNA crystals by triplex-directed photo-cross-linking - H. Abdallah, N. Seeman et al.
November 03, 2022 21:00 - 18 minutes - 25.4 MBThe tensegrity triangle is a robust DNA motif that can self-assemble to generate macroscopic three-dimensional crystals. However, the stability of these crystals is dependent on the high ionic conditions used for crystal growth. Here we demonstrate that a triplex-forming oligonucleotide can be used to direct the specific intercalation, and subsequent photo-cross-linking, of 4,5′,8-trimethylpsoralen to single or multiple loci within or between the tiles of the crystal. Cross-linking between t...
PubReading [212] - Glyoxal oxidases: their nature and properties - M. Daou and C.Faulds
November 02, 2022 21:00 - 38 minutes - 53 MBH2O2 has been found to be required for the activity of the main microbial enzymes responsible for lignin oxidative cleavage, peroxidases. Along with other small radicals, it is implicated in the early attack of plant biomass by fungi. Among the few extracellular H2O2-generating enzymes known are the glyoxal oxidases (GLOX). GLOX is a copper-containing enzyme, sharing high similarity at the level of active site structure and chemistry with galactose oxidase. Genes encoding GLOX enzymes are wi...
PubReading [211] - 3D DNA Crystals and Nanotechnology - P. Paukstelis and N. Seeman
November 01, 2022 12:00 - 41 minutes - 56.4 MBDNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in desig...
PubReading [210] - Interbase‐FRET binding assay for pre‐microRNAs - M. Bood, M. Wilhelmsson, M. Grøtli et al.
October 31, 2022 12:00 - 27 minutes - 38.4 MBThe aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small‐molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)‐labeled oligoribonucleotides of the precursor of the oncogenic miR‐21 (pre‐miR‐21) an...
PubReading [209] - Flipping the Switch: Innovations in Inducible Probes for Protein Profiling - S. McKenna, E. Fay and J. McGouran
October 28, 2022 11:00 - 52 minutes - 72.3 MBOver the past two decades, activity-based probes have enabled a range of discoveries, including the characterization of new enzymes and drug targets. However, their suitability in some labeling experiments can be limited by nonspecific reactivity, poor membrane permeability, or high toxicity. One method for overcoming these issues is through the development of “inducible” activity-based probes. These probes are added to samples in an unreactive state and require in situ transformation to the...
PubReading [208] - Cystatin C as a biomarker of chronic kidney disease: latest developments - S. Benoit, E. Ciccia, P. Devarajan
October 27, 2022 11:00 - 38 minutes - 52.9 MBChronic kidney disease (CKD) is common, occurring in over 10% of individuals globally, and is increasing in prevalence. The limitations of traditional biomarkers of renal dysfunction, such as serum creatinine, have been well-demonstrated in the literature. Therefore, augmenting clinical assessment with newer biomarkers, such as serum cystatin C, has the potential to improve disease monitoring and patient care. The present paper assesses the utility and limitations of serum cystatin C as a bi...
PubReading [207] - Holliday junction-resolving enzymes—structures and mechanisms - David Lilley
October 26, 2022 11:00 - 32 minutes - 44.3 MBHolliday junction-resolving enzymes are nucleases that are highly specific for the structure of the junction, to which they bind in dimeric form. Two symmetrically disposed cleavages are made. These are not simultaneous, but the second cleavage is accelerated relative to the first, so ensuring that bilateral cleavage occurs during the lifetime of the DNA–protein complex. In eukaryotic cells there are two known junction-resolving activities. GEN1 is similar to enzymes from lower organisms. A ...
PubReading [206] - The path for metal complexes to a DNA target - A. Komora and J. Barton
October 25, 2022 11:00 - 1 hour - 87.5 MBThe discovery of cisplatin as a therapeutic agent stimulated a new era in the application of transition metal complexes for therapeutic design. Here we describe recent results on a variety of transition metal complexes targeted to DNA to illustrate many of the issues involved in new therapeutic design. We describe first structural studies of complexes bound covalently and non-covalently to DNA to identify potential lesions within the cell. We then review the biological fates of these complex...
PubReading [205] - Targeting tumor cell senescence and polyploidy as potential therapeutic strategies - T. Saleh, D. Gewirtz et al.
October 24, 2022 11:00 - 41 minutes - 57.2 MBSenescence is a unique state of growth arrest that develops in response to a plethora of cellular stresses, including replicative exhaustion, oxidative injury, and genotoxic insults. Senescence has been implicated in the pathogenesis of multiple aging-related pathologies, including cancer. In cancer, senescence plays a dual role, initially acting as a barrier against tumor progression by enforcing a durable growth arrest in premalignant cells, but potentially promoting malignant transformati...
PubReading [204] - Antibody targeting of E3 ubiquitin ligases for receptor degradation - H. Marei, F. de Sousa e Melo et al.
October 21, 2022 11:00 - 31 minutes - 42.9 MBMost current therapies that target plasma membrane receptors function by antagonizing ligand binding or enzymatic activities. However, typical mammalian proteins comprise multiple domains that execute discrete but coordinated activities. Thus, inhibition of one domain often incompletely suppresses the function of a protein. Indeed, targeted protein degradation technologies, including proteolysis-targeting chimeras1 (PROTACs), have highlighted clinically important advantages of target degrada...
PubReading [203] - The mechanism of replication stalling and recovery within repetitive DNA - C. Cases-Delucchi, M. Daza-Martin, S. Williams & G. Coster
October 20, 2022 11:00 - 57 minutes - 78.4 MBAccurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins. Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone rep...
PubReading [202] - Potentialities of Gene Therapy in Pediatric Endocrinology - G. Frontino. M. Stancampiano, A. Aiuti
October 19, 2022 11:01 - 47 minutes - 65.4 MBGene therapy has become an appealing therapeutic option in many pediatric fields, including endocrinology. Unlike traditional drugs based on molecules that require repeated and frequent burdensome administrations, a single genetic therapeutic intervention may allow durable and curative clinical benefits. Although this highly innovative technology holds a great promise for the treatment of monogenic diseases, its clinical applications in the field of endocrinology have been so far challenging...
PubReading [201] - The cryo-EM method microcrystal electron diffraction (MicroED) - B. Nannenga and T. Gone
October 18, 2022 20:00 - 39 minutes - 54.7 MBIn 2013 we established a cryo-electron microscopy (cryo-EM) technique called microcrystal electron diffraction (MicroED). Since that time, data collection and analysis schemes have been fine-tuned, and structures for more than 40 different proteins, oligopeptides and organic molecules have been determined. Here we review the MicroED technique and place it in context with other structure-determination methods. We showcase example structures solved by MicroED and provide practical advice to pr...
PubReading [200] - Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery - T. Baladi, M. Wilhelmsson et al
October 17, 2022 11:00 - 46 minutes - 63.6 MBMethods for tracking RNA inside living cells without perturbing their natural interactions and functions are critical within biology and, in particular, to facilitate studies of therapeutic RNA delivery. We present a stealth labeling approach that can efficiently, and with high fidelity, generate RNA transcripts, through enzymatic incorporation of the triphosphate of tCO, a fluorescent tricyclic cytosine analogue. We demonstrate this by incorporation of tCO in up to 100% of the natural cytos...
PubReading [199] - Live-seq enables temporal transcriptomic recording of single cells - W. Chen, B. Deplanke et al
October 14, 2022 11:00 - 47 minutes - 64.7 MBSingle-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell’s ground-state transcriptome to its downstream molecular or phenotypic...
PubReading [198] - Neutron crystallography: opportunities, challenges, and limitations - M. Blakeley, A. Podjarny et al
October 13, 2022 11:00 - 24 minutes - 34 MBNeutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of ad...
PubReading [197] - Nanopore microscope identifies RNA isoforms with structural colours - F. Bošković and U. Keyser
October 12, 2022 11:00 - 26 minutes - 36.7 MBIdentifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colours. Structural colours consist of DNA structures,...
PubReading [196] - Radiation damage to biological samples: still a pertinent issue - E. Garman and M. Weik
October 11, 2022 20:00 - 35 minutes - 48.2 MBAn understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques. For X-ray diffraction, an in-depth study of multi-crystal small-wedge data collection single-wavelength anomalous dispersion phasing protocols is presented, ...
PubReading [195] - Inflammatory and immune effects on tumor progression - K. Mehla and M. Hollingsworth
October 10, 2022 20:00 - 18 minutes - 25.3 MBTumor progression is known occur in a complex microenvironment that leads to genetic, cellular, and metabolic adaptations. Two articles from Martin et al. and Del Poggetto et al. enlighten us on the role of inflammation and the immune system in guiding the progression of preneoplastic cells to oncogenic transformation and on subsequent tumor evolution. doi.org/10.1016/j.it.2021.11.009 - 2022