Shows
PubReadingPubReading [99] - MicroED: conception, practice and future opportunities - M. Clabbers, A. Shiriaevaa and T. GonenThis article documents a keynote seminar presented at the IUCr Congress in Prague, 2021. The cryo-EM method microcrystal electron diffraction is described and put in the context of macromolecular electron crystallography from its origins in 2D crystals of membrane proteins to today’s application to 3D crystals a millionth the size of that needed for X-ray crystallography. Milestones in method development and applications are described with an outlook to the future. - doi.org/10.1107/S2052252521013063 - 2022
2022-04-0343 minPubReadingPubReading [89] - Immunotherapy and prevention of pancreatic cancer - A. Morrison, K. Byrne and R. VonderheidePancreatic cancer is the third leading cause of cancer mortality in the United States, recently surpassing breast cancer. A key component of pancreatic cancer’s lethality is its acquired immune privilege, which is driven by an immunosuppressive microenvironment, poor T-cell infiltration, and a low mutational burden. Although immunotherapies such as checkpoint blockade or engineered T cells have yet to demonstrate efficacy, a growing body of evidence suggests that orthogonal combinations of these and other strategies could unlock immunotherapy in pancreatic cancer. In this review, we will discuss promising immunotherapies currently under investigation in pancreatic cancer and provide a roadmap fo...
2022-04-0142 minPubReadingPubReading [97] - Ultra-High Dose Rate (FLASH) Radiotherapy: Silver Bullet or Fool’s Gold? - J. Wilson, K. Petersson et al.Radiotherapy is a cornerstone of both curative and palliative cancer care. However, radiotherapy is severely limited by radiation-induced toxicities. If these toxicities could be reduced, a greater dose of radiation could be given therefore facilitating a better tumor response. Initial pre-clinical studies have shown that irradiation at dose rates far exceeding those currently used in clinical contexts reduce radiation-induced toxicities whilst maintaining an equivalent tumor response. This is known as the FLASH effect. To date, a single patient has been subjected to FLASH radiotherapy for the treatment of subcutaneous T-cell lymphoma resulting in complete response and minimal toxicities. The...
2022-03-311h 01PubReadingPubReading [96] - Highly accurate protein structure prediction for the human proteome - K. Tunyasuvunakool, D. Hassabis et al.Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally determined structure1. Here we markedly expand the structural coverage of the proteome by applying the state-of-the-art machine learning method, AlphaFold2, at a scale that covers almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. We introduce several metrics...
2022-03-3030 minPubReadingPubReading [95] - A safe lithium mimetic for bipolar disorder - N. Singh, G. Churchill et al.Lithium is the most effective mood stabilizer for the treatment of bipolar disorder, but it is toxic at only twice the therapeutic dosage and has many undesirable side effects. It is likely that a small molecule could be found with lithium-like efficacy but without toxicity through target-based drug discovery; however, therapeutic target of lithium remains equivocal. Inositol monophosphatase is a possible target but no bioavailable inhibitors exist. Here we report that the antioxidant ebselen inhibits inositol monophosphatase and induces lithium-like effects on mouse behaviour, which are reversed with inositol, consistent with a mechanism involving inhibition of inositol recycling. Ebselen...
2022-03-2923 minPubReadingPubReading [94] - Tissue architecture in tumor initiation and progression - J. Almagro, A. BehrensThe 3D architecture of tissues bearing tumors impacts on the mechanical microenvironment of cancer, the accessibility of stromal cells, and the routes of invasion. A myriad of intrinsic and extrinsic forces exerted by the cancer cells, the host tissue, and the molecular and cellular microenvironment modulate the morphology of the tumor and its malignant potential through mechanical, biochemical, genetic, and epigenetic cues. Recent studies have investigated how tissue architecture influences cancer biology from tumor initiation and progression to distant metastatic seeding and response to therapy. With a focus on carcinoma, the most common type of cancer, this review discusses...
2022-03-2842 min
PubReadingPubReading [98] - Immunotherapy and prevention of pancreatic cancer - A. Morrison, K. Byrne, and R. VonderheidePancreatic cancer is the third leading cause of cancer mortality in the United States, recently surpassing breast cancer. A key component of pancreatic cancer’s lethality is its acquired immune privilege, which is driven by an immunosuppressive microenvironment, poor T-cell infiltration, and a low mutational burden. Although immunotherapies such as checkpoint blockade or engineered T cells have yet to demonstrate efficacy, a growing body of evidence suggests that orthogonal combinations of these and other strategies could unlock immunotherapy in pancreatic cancer. In this review, we will discuss promising immunotherapies currently under investigation in pancreatic cancer and provide a roadmap fo...
2022-03-2742 minPubReadingPubReading [93] - Neuroprotective Actions of Dietary Choline - J. Blusztajn, B. Slack and T. MellottCholine is an essential nutrient for humans. It is a precursor of membrane phospholipids (e.g., phosphatidylcholine (PC)), the neurotransmitter acetylcholine, and via betaine, the methyl group donor S-adenosylmethionine. High choline intake during gestation and early postnatal development in rat and mouse models improves cognitive function in adulthood, prevents age-related memory decline, and protects the brain from the neuropathological changes associated with Alzheimer’s disease (AD), and neurological damage associated with epilepsy, fetal alcohol syndrome, and inherited conditions such as Down and Rett syndromes. These effects of choline are correlated with modifications in histone and DNA methylation in brain, an...
2022-03-2553 minPubReadingPubReading [92] - Progress toward understanding chromosome silencing by Xist RNA - N. Brockdorff, J. Bowness, and G. WeiThe X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify under-lying chromatin and silence X-linked genes in cis. Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between...
2022-03-2455 minPubReadingPubReading [91] - Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes - M. Vorlickova, J. Kypr et alNucleic acids bear the genetic information and participate in its expression and evolution during replication, repair, recombination, transcription, and translation. These phenomena are mostly based on recognition of nucleic acids by proteins. The major factor enabling the specific recognition is structure. Circular dichroism (CD) spectroscopy is very useful to study secondary structures of nucleic acids, in general, and DNA, in particular. CD sensitively reflects isomerizations among distinct conformational states. The isomerizations may operate as molecular switches regulating various physiological or pathological processes. Here, we review CD spectra of nucleic acids, beginning with early studies on natural DNA molecules through...
2022-03-2323 minPubReadingPubReading [90] - Functional enzyme–polymer complexes - C. Waltman, M. Olvera de la CruzEngineered and native enzymes are poised to solve challenges in medicine, bioremediation, and biotechnology. One important goal is the possibility of upcycling polymers using enzymes. However, enzymes are often inactive in industrial, nonbiological conditions. It is particularly difficult to protect water-soluble enzymes at elevated temperatures by methods that preserve their functionality. Through atomistic and coarse-grained molecular dynamics simulations that capture protein conformational change, we show that an enzyme, PETase (polyethylene terephthalate [PET]), can be stabilized at elevated temperatures by complexation with random copolymers into nanoscale aggregates that do not precipitate into macroscopic phases. We demonstrated the efficiency of the...
2022-03-2232 minPubReadingPubReading [89] - Novel Therapeutic Target(s) for Psoriatic Disease - V. Thakur and R. MahajanPsoriasis and psoriatic arthritis, together known as psoriatic disease, is highly prevalent chronic relapsing inflammatory disease affecting skin, joints or both and is associated with several comorbidities such as cardiovascular, metabolic, psychiatric, renal disease etc. The etiopathogenesis of psoriasis is complex and mainly driven by aberrant immune response owing to the genetic susceptibility and various environmental factors such as trauma, infections and drugs. Recent advances in understanding molecular and cellular pathways have identified tumor necrosis factor-α (TNF-α), interleukin-17 (IL-17), IL-23, IL-22 as major contributors in psoriasis pathogenesis. Advances in the knowledge of pathophysiology, the interaction of autoinflammation and clinical ph...
2022-03-2133 minPubReadingPubReading [88] - Factors influencing self-harm thoughts and behaviours over the first year of the COVID-19 pandemic in the UK: longitudinal analysis of 49 324 adults - E. Paul and D. FancourtThere is concern that the COVID-19 pandemic and its aftermath will result in excess suicides by increasing known risk factors such as self-harm, but evidence on how pandemic-related risk factors contribute to changes in these outcomes is lacking.In total, 26.1% and 7.9% of respondents reported self-harm thoughts and behaviours respectively at least once over the study period. The number of adverse experiences was more strongly related to outcomes than the number of worries. The largest specific adversity contributing to increases in both outcomes was having experienced physical or psychological abuse. Financial worries increased the likelihood of both outcomes...
2022-03-1733 minPubReadingPubReading [87] - Adipocytes, Innate Immunity and Obesity: A Mini-Review - A.Blaszczak, A. Jalilvand and W. HsuehThe role of adipose tissue (AT) inflammation in obesity and its multiple related- complications is a rapidly expanding area of scientific interest. Within the last 30 years, the role of the adipocyte as an endocrine and immunologic cell has been progressively established. Like the macrophage, the adipocyte is capable of linking the innate and adaptive immune system through the secretion of adipokines and cytokines; exosome release of lipids, hormones, and microRNAs; and contact interaction with other immune cells. Key innate immune cells in AT include adipocytes, macrophages, neutrophils, and innate lymphoid cells type 2 (ILC2s). The role of the innate...
2022-03-1533 minPubReadingPubReading [86] - What is the structural chemistry of the living organism at its temperature and pressure? - J. HelliwellThe three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature...
2022-03-1437 minPubReadingPubReading [85] - Low-dose metformin targets the lysosomal AMPK pathway through PEN2 - T. Ma, S. LinMetformin, the most prescribed antidiabetic medicine, has shown other benefits such as anti-ageing and anticancer effects1–4. For clinical doses of metformin, AMP-activated protein kinase (AMPK) has a major role in its mechanism of action4,5; however, the direct molecular target of metformin remains unknown. Here we show that clinically relevant concentrations of metformin inhibit the lysosomal proton pump v-ATPase, which is a central node for AMPK activation following glucose starvation6. We synthesize a photoactive metformin probe and identify PEN2, a subunit of γ-secretase7, as a binding partner of metformin with a dissociation constant at micromolar levels. Metformin-bound PEN2 forms a com...
2022-03-0700 minPubReadingPubReading [85] - Low-dose metformin targets the lysosomal AMPK pathway through PEN2 - T. Ma, S. LinMetformin, the most prescribed antidiabetic medicine, has shown other benefits such as anti-ageing and anticancer effects1–4. For clinical doses of metformin, AMP-activated protein kinase (AMPK) has a major role in its mechanism of action4,5; however, the direct molecular target of metformin remains unknown. Here we show that clinically relevant concentrations of metformin inhibit the lysosomal proton pump v-ATPase, which is a central node for AMPK activation following glucose starvation6. We synthesize a photoactive metformin probe and identify PEN2, a subunit of γ-secretase7, as a binding partner of metformin with a dissociation constant at micromolar levels. Metformin-bound PEN2 forms a com...
2022-03-0735 minPubReadingPubReading [84] - Neurotrauma and Repair Research: Traumatic Brain Injury (TBI) and its Treatments - H. Algattas and J. HuangTraumatic brain injury (TBI) affects a growing portion of the population and continues to take national spotlight with advances in imaging technology and understanding of long-term effects. However, there is large variance in TBI treatment protocols due to injury variability and lack of both mechanistic understanding and strong treatment recommendations. Recent practice suggests three disparate treatment approaches, all which aim at promoting neuroprotection after TBI, show promise: immediate hypothermia, hyper- baric oxygen, and progesterone supplementation. The research is controversial at times, yet there are abundant opportunities to develop the technology behind hypothermia and hyperbaric oxygen treatments which would surely...
2022-03-0126 minPubReadingPubReading [83] - CAR T cells produced in vivo to treat cardiac injury - J. Rurik, J. Epstein et al.Fibrosis affects millions of people with cardiac disease. We developed a therapeutic approach to generate transient antifibrotic chimeric antigen receptor (CAR) T cells in vivo by delivering modified messenger RNA (mRNA) in T cell–targeted lipid nanoparticles (LNPs). The efficacy of these in vivo–reprogrammed CAR T cells was evaluated by injecting CD5-targeted LNPs into a mouse model of heart failure. Efficient delivery of modified mRNA encoding the CAR to T lymphocytes was observed, which produced transient, effective CAR T cells in vivo. Antifibrotic CAR T cells exhibited trogocytosis and retained the target antigen as they accumulated in the...
2022-01-1321 minPubReadingPubReading [82] - How to Write a Systematic Review - R. Wright, K. Spindler et al.Evidence-based medicine (EBM) is the combination of the best available research evidence with clinical experience and patient needs. The concept of EBM as a part of clinical decision making has become increasingly popular over the last decade. In the hierarchy of studies meta-analysis and systematic reviews occupy the highest levels. A systematic review of a clinical question can be performed by following a relatively standard form. These techniques as described here can be performed without formal training. Systematic reviews conducted in this fashion can be used as a higher form of current concepts or as review articles and replace...
2022-01-1234 minPubReadingPubReading [80] - Exercise plasma boosts memory and dampens brain inflammation via clusterin - Z. De Miguel, T. Wyss-Coray et al.Physical exercise is generally beneficial to all aspects of human and animal health, slowing cognitive ageing and neurodegeneration1. The cognitive benefits of physical exercise are tied to an increased plasticity and reduced inflammation within the hippocampus2–4, yet little is known about the factors and mechanisms that mediate these effects. Here we show that ‘runner plasma’, collected from voluntarily running mice and infused into sedentary mice, reduces baseline neuroinflammatory gene expression and experimentally induced brain inflammation. Plasma proteomic analysis revealed a concerted increase in complement cascade inhibitors including clusterin (CLU). Intravenously injected CLU binds to brain endothelial cells and reduces neuroi...
2021-12-2126 minPubReadingPubReading [81] - The N-terminal cysteine is a dual sensor of oxygen and oxidative stress - A. Jung Heo, Y. Tae Kwon et al.Cellular homeostasis requires the sensing of and adaptation to intracellular oxygen (O2) and reactive oxygen species (ROS). The Arg/N-degron pathway targets proteins that bear destabilizing N-terminal residues for degradation by the proteasome or via autophagy. Under normoxic conditions, the N-terminal Cys (Nt-Cys) residues of specific substrates can be oxidized by dioxygenases such as plant cysteine oxidases and cysteamine (2-aminoethane- thiol) dioxygenases and arginylated by ATE1 R-transferases to generate Arg-CysO2(H) (R-CO2). Proteins bearing the R-CO2 N-degron are targeted via Lys48 (K48)–linked ubiquitylation by UBR1/UBR2 N-recognins for proteasomal degradation. During acute hypoxia, such proteins are partially stabilized, ow...
2021-12-2050 minPubReadingPubReading [79] - Nanopore sequencing technology, bioinformatics and applications - Y. Wang, K. Fai Au et al.Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored...
2021-12-201h 11PubReadingPubReading [78] - Megahertz serial crystallography - Max Wiedorn et al.The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase f...
2021-12-1429 minPubReadingPubReading [77] - Engineering transplantable jejunal mucosal grafts using patient- derived organoids from children with intestinal failure - M. Laween, V. Li et al.Intestinal failure (IF), following extensive anatomical or functional loss of small intestine (SI), has debilitating long-term consequences on children1. The priority of patient care is to increase the length of functional intestine, particularly the jejunum, to promote nutritional independence2. Here we construct autologous jejunal mucosal grafts using pediatric patient biomaterials and show that patient-derived organoids (PDO) can be expanded efficiently in vitro. In parallel, we generate decellularized human intestinal matrix with intact nanotopography, that forms biological scaffolds. Proteomic and Raman spectroscopy analyses reveal highly analogous biochemical profiles of human SI and colon scaffolds, indicating that they can be used...
2021-12-1331 minPubReadingPubReading [76] - The Catalytic Asymmetric Intermolecular Prins Reaction - D. Díaz-Oviedo, R. Maji, and B. ListDespite their significant potential, catalytic asymmetric reactions of olefins with formaldehyde are rare and metal-free approaches have not been previously disclosed. Here we describe an enantioselective intermolecular Prins reaction of styrenes and paraformaldehyde to form 1,3-dioxanes, using confined imino-imidodiphosphate (iIDP) Brønsted acid catalysts. Isotope labeling experiments and computations suggest a concerted, highly asynchronous addition of an acid-activated formaldehyde oligomer to the olefin. The enantioenriched 1,3-dioxanes can be transformed into the corresponding optically active 1,3-diols, which are valuable synthetic building blocks. - https://doi.org/10.1021/jacs.1c10245 - 2021
2021-12-1021 minPubReadingPubReading [74] - Sodium/glucose cotransporter 2 (SGLT2) inhibitors improve cardiac function by reducing JunD expression in human diabetic hearts - R. Marfella, G. Paolisso et al. Background: The pathogenesis of experimental diabetic cardiomyopathy may involve the activator protein 1 (AP-1) member, JunD. Using non-diabetic heart transplant (HTX) in recipients with diabetes, we examined the effects of the diabetic milieu (hyperglycemia and insulin resistance) on cardiac JunD expression over 12 months. Because sodium/glucose cotransporter-2 inhibitors (SGLT2i) significantly reverse high glucose-induced AP-1 binding in the proximal tubular cell, we investigated JunD expression in a subgroup of type 2 diabetic recipients receiving SGLT2i treatment.Methods: We evaluated 77 first HTX recipients (40 and 37 patients with and without diabetes, respectively). Among the recipients with diabetes, 17 (45.9%) were receiving SGLT2i...
2021-12-0928 minPubReadingPubReading [73] - Electronic health records and polygenic risk scores for predicting disease risk - R. Li, J. Moore et al.Accurate prediction of disease risk based on the genetic make-up of an individual is essential for effective prevention and personalized treatment. Nevertheless, to date, individual genetic variants from genome-wide association studies have achieved only moderate prediction of disease risk. The aggregation of genetic variants under a polygenic model shows promising improvements in prediction accuracies. Increasingly, electronic health records (EHRs) are being linked to patient genetic data in biobanks, which provides new opportunities for developing and applying polygenic risk scores in the clinic, to systematically examine and evaluate patient susceptibilities to disease. However, the heterogeneous nature of EHR data brings...
2021-12-0852 minPubReadingPubReading [72] - Delivery strategies for macromolecular drugs in cancer therapy - Q. Guo, C. Jiang et al.With the development of biotherapy, biomacromolecular drugs have gained tremendous attention recently, especially in drug development field due to the sophisticated functions in vivo. Over the past few years, a motley variety of drug delivery strategies have been developed for bio- macromolecular drugs to overcome the difficulties in the druggability, e.g., the instability and easily restricted by physiologic barriers. The application of novel delivery systems to deliver bio- macromolecular drugs can usually prolong the half-life, increase the bioavailability, or improve patient compliance, which greatly improves the efficacy and potentiality for clinical use of biomacromolecular drugs. In this review...
2021-12-0735 minPubReadingPubReading [71] - Optical Microscopy and Electron Microscopy for the Morphological Evaluation of Tendons: A Mini Review - M. Xu, B. Liu et al.The morphological characteristics of tendons have been thoroughly evaluated via microscopy. Optical microscopy and electron microscopy are the most commonly used techniques for tendon tissue observation. According to the principles of both microscopy types, preparation and evaluation methods vary. Simple optical microscopy is commonly used in the observation of cells and extracellular matrix, and many stains, including hematoxylineosin, Van Gieson, Prussian blue, Alcian blue, and toluidine blue, are used for evaluating cells, collagen fiber arrangement, and non-collagenous proteins. Histological scoring systems have been used in many studies for semi-quantification. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) are...
2021-12-0624 minPubReadingPubReading [70] - Flavonoids as Anticancer Agents - D. Kopustinskiene, J. Bernatoniene et alFlavonoids are polyphenolic compounds subdivided into 6 groups: isoflavonoids, flavanones, flavanols, flavonols, flavones and anthocyanidins found in a variety of plants. Fruits, vegetables, plant-derived beverages such as green tea, wine and cocoa-based products are the main dietary sources of flavonoids. Flavonoids have been shown to possess a wide variety of anticancer effects: they modulate reactive oxygen species (ROS)-scavenging enzyme activities, participate in arresting the cell cycle, induce apoptosis, autophagy, and suppress cancer cell proliferation and invasiveness. Flavonoids have dual action regarding ROS homeostasis—they act as antioxidants under normal conditions and are potent pro-oxidants in cancer cells triggering the ap...
2021-12-0454 minPubReadingPubReading [69]- Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection - A. Di Pietro, K. Good-Jacobson et al Ineffective antibody-mediated responses are a key characteristic of chronic viral infection. However, our understanding of the intrinsic mechanisms that drive this dysregulation are unclear. Here, we identify that targeting the epigenetic modifier BMI-1 in mice improves humoral responses to chronic lymphocytic choriomeningitis virus. BMI-1 was upregulated by germinal center B cells in chronic viral infection, correlating with changes to the accessible chromatin landscape, compared to acute infection. B cell-intrinsic deletion of Bmi1 accelerated viral clearance, reduced splenomegaly and restored splenic architecture. Deletion of Bmi1 restored c-Myc expression in B cells, concomitant with improved quality of antibody and coupled with...
2021-12-0356 minPubReadingPubReading [68] - Omega-3 fatty acids attenuate dendritic cell function via NF-κB independent of PPARγ - E. Draper and H. RocheLong-chain n-3 polyunsaturated fatty acids (n-3 PUFA) have been shown to modulate the immune response and have therapeutic effects in inflammatory disorders. PUFA are also peroxisome proliferators-activator receptor-gamma (PPARγ) ligands; a family of ligand-activated transcription factors, which when activated antagonise the pro-inflammatory capability of nuclear factor κB (NF-κB). PPARγ plays a role in dendritic cell (DC) maturation and n-3 PUFA have been shown to affect DC maturation by decreasing activation of NF-κB. While n-3 PUFA can function as PPAR ligands, it is not known whether the NF-κB-mediated immunomodulatory properties of n-3 PUFA are PPARγ-dependent. In this st...
2021-12-0231 minPubReadingPubReading [67] - DNA methylation in human sperm: a systematic review - F. Asenius, A. Danson and S. MarziBACKGROUND: Studies in non-human mammals suggest that environmental factors can influence spermatozoal DNA methylation, and some research suggests that spermatozoal DNA methylation is also implicated in conditions such as subfertility and imprinting disorders in the offspring. Together with an increased availability of cost-effective methods of interrogating DNA methylation, this premise has led to an increasing number of studies investigating the DNA methylation landscape of human spermatozoa. However, how the human spermatozoal DNA methylome is influenced by environmental factors is still unclear, as is the role of human spermatozoal DNA methylation in subfertility and in influencing offspring health....
2021-12-011h 09PubReadingPubReading [66] - The 2021 Nucleic Acids Research database issue and the online molecular biology database collection - D. Rigden and X. FernandezThe 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV- 2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In...
2021-11-3033 minPubReadingPubReading [65] - Cell Cycle Regulation of Stem Cells by MicroRNAs - M. Mens and M. GhanbariMicroRNAs (miRNAs) are a class of small non-coding RNA molecules involved in the regulation of gene expression. They are involved in the fine-tuning of fundamental biological processes such as proliferation, differentiation, survival and apoptosis in many cell types. Emerging evidence suggests that miRNAs regulate critical pathways involved in stem cell function. Several miRNAs have been suggested to target transcripts that directly or indirectly coordinate the cell cycle progression of stem cells. Moreover, previous studies have shown that altered expression levels of miRNAs can contribute to pathological conditions, such as cancer, due to the loss of cell cycle regulation. However...
2021-11-2956 minPubReadingPubReading [64] - Lysosome-targeting chimaeras for degradation of extracellular proteins - S. Banik, C. Bertozzi et alThe majority of therapies that target individual proteins rely on specific activity- modulating interactions with the target protein—for example, enzyme inhibition or ligand blocking. However, several major classes of therapeutically relevant proteins have unknown or inaccessible activity profiles and so cannot be targeted by such strategies. Protein-degradation platforms such as proteolysis-targeting chimaeras (PROTACs)1,2 and others (for example, dTAGs3, Trim-Away4, chaperone-mediated autophagy targeting5 and SNIPERs6) have been developed for proteins that are typically difficult to target; however, these methods involve the manipulation of intracellular protein degradation machinery and are therefore fundamentally limited to proteins that contain cytosolic domains to wh...
2021-11-2434 minPubReadingPubReading [63] - Integrated analysis of multimodal single-cell data -Y. Hao, R. SatijaThe simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce ‘‘weighted-nearest neighbor’’ analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and vali...
2021-11-231h 06PubReadingPubReading [62] - Molecular Printing with DNA Nanotechnology - F. Rizzuto, T. Trinh and H. SleimanDNA nanotechnology has generated a wealth of structures uniquely suited for nanoscale patterning; however, scalability, affordability, and recyclability are important preconditions for the industrial production and widespread use of DNA-based materials. In this perspective, we propose that ‘‘printing’’ programmed particles from transient DNA templates provides a practical pathway toward overcoming these hurdles. Just as a printing press transfers ink to paper in a cyclical process, DNA can translocate materials from one substrate to another while preserving spatial information. DNA printing decorates a particle with arbitrarily designed patterns that break its symmetry, enabling its autonomous assembly into complex structures. Printing thus org...
2021-11-2245 minPubReadingPubReading [61] - Discovery of a novel pseudo β-hairpin structure of N-truncated amyloid-β for use as a vaccine against Alzheimer’s disease - P. Bakrania, T. Bayer et alOne of the hallmarks of Alzheimer’s disease (AD) are deposits of amyloid-beta (Aβ) protein in amyloid plaques in the brain. The Aβ peptide exists in several forms, including full-length Aβ1-42 and Aβ1-40 – and the N-truncated species, pyroglutamate Aβ3-42 and Aβ4-42, which appear to play a major role in neurodegeneration. We previously identified a murine antibody (TAP01), which binds specifically to soluble, non-plaque N-truncated Aβ species. By solving crystal structures for TAP01 family antibodies bound to pyroglutamate Aβ3-14, we identified a novel pseudo β-hairpin structure in the N-terminal region of Aβ and show that this underpins...
2021-11-1835 minPubReadingPubReading [60] - DNA helicases in homologous recombination repair - D. Branzei and B. SzakalHelicases are in the spotlight of DNA metabolism and are critical for DNA repair in all domains of life. At their biochemical core, they bind and hydrolyze ATP, converting this energy to translocate unidirectionally, with different strand polarities and substrate binding specificities, along one strand of a nucleic acid. In doing so, DNA and RNA helicases separate duplex strands or remove nucleoprotein complexes, affecting DNA repair and the architecture of replication forks. In this review, we focus on recent advances on the roles and regulations of DNA helicases in homologous recombination repair, a critical pathway for mending damaged chromosomes...
2021-11-1730 minPubReadingPubReading [59] - Complexities of Viral Mutation Rates - K. Peck & A. LauringaMany viruses evolve rapidly. This is due, in part, to their high mutation rates. Mutation rate estimates for over 25 viruses are currently available. Here, we review the population genetics of virus mutation rates. We specifically cover the topics of mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent. - doi.org/10.1128/JVI .01031-17. - 2018
2021-11-1634 minPubReadingPubReading [58] - Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing - X. Xu, L. S. Qi et al.Compact and versatile CRISPR-Cas systems will enable genome engineering applications through high-efficiency delivery in a wide variety of contexts. Here, we create an efficient miniature Cas system (CasMINI) engineered from the type V-F Cas12f (Cas14) system by guide RNA and protein engineering, which is less than half the size of currently used CRISPR systems (Cas9 or Cas12a). We demonstrate that CasMINI can drive high levels of gene activation (up to thousands-fold increases), while the natural Cas12f system fails to function in mammalian cells. We show that the CasMINI system has comparable activities to Cas12a for...
2021-11-1545 minPubReadingPubReading [57] - Obesity and hypertension - G. Seravallea and G. GrassiObesity and in particular the excessive visceral fat distribution is accompanied by several alterations at hormonal, inflammatory and endothelial level. These alterations induce a stimulation of several other mechanisms that contribute to the hypertensive state and on the other side to increase the cardiovascular morbidity. In these chapter we will examine the main mechanisms of obesity and obesity-related hypertension and in particular the role of sympathetic nervous system, the alterations of the renal function and at the microvascular level. We will also depict the role of insulin resistance as factor stimulating and potentiating the other mechanisms. The second part...
2021-11-0931 minPubReadingPubReading [56] - Hypertension and cardiovascular risk: General aspects - S. E. KjeldsenHypertension is the strongest or one of the strongest risk factors for almost all different cardiovascular diseases acquired during life, including coronary disease, left ventricular hypertrophy and valvular heart diseases, cardiac arrhythmias including atrial fibrillation, cerebral stroke and renal failure. The continuous relationship between blood pressure and cardiovascular and renal events makes the distinction between high normal blood pressure and hypertension based on arbitrary cut-off values for blood pressures. Overall the prevalence of hypertension in different European countries appears to be around 30–45% of the general population, with a steep increase with ageing. The prevention of cardiovascular disease and treatment re...
2021-11-0823 minPubReadingPubReading [55] - Protein phase separation and determinants of in cell crystallization - C. N. Mudogo, C. BetzelLiquid-liquid phase separation (LLPS) in cells is known as a complex physicochemical process causing the formation of membrane-less organelles (MLOs). Cells have well-defined different membrane-surrounded organelles like mitochondria, endoplasmic reticulum, lysosomes, peroxisomes, etc., however, on demand they can create MLOs as stress granules, nucleoli and P bodies to cover vital functions and regulatory activities. However, the mechanism of intracellular molecule assembly into functional compartments within a living cell remains till now not fully understood. in vitro and in vivo investigations unveiled that MLOs emerge after preceding liquid-liquid, liquid gel, liquid-semi-crystalline, or liquid-crystalline phase separations. Liquid-liquid and liquid-gel MLOs form...
2021-11-0634 minPubReadingPubReading [54] - The Role of Inflammation in Diabetes: Current Concepts and Future Perspectives - S. Tsalamandris, D. Tousoulis et alDiabetes is a complex metabolic disorder affecting the glucose status of the human body. Chronic hyperglycaemia related to diabetes is associated with end organ failure. The clinical relationship between diabetes and atherosclerotic cardiovascular disease is well established. This makes therapeutic approaches that simultaneously target diabetes and atherosclerotic disease an attractive area for research. The majority of people with diabetes fall into two broad pathogenetic categories, type 1 or type 2 diabetes. The role of obesity, adipose tissue, gut microbiota and pancreatic beta cell function in diabetes are under intensive scrutiny with several clinical trials to have been completed while more are...
2021-11-0542 minPubReadingPubReading [53] - Molecular targeted therapy of glioblastoma - E. Le Rhun, M. Weller et al.Glioblastomas are intrinsic brain tumors thought to originate from neuroglial stem or progenitor cells. More than 90% of glioblastomas are isocitrate dehydrogenase (IDH)-wildtype tumors. Incidence increases with age, males are more often affected. Beyond rare instances of genetic predisposition and irradiation exposure, there are no known glioblastoma risk factors. Surgery as safely feasible followed by involved-field radiotherapy plus concomitant and maintenance temozolomide chemotherapy define the standard of care since 2005. Except for prolonged progression-free, but not overall survival afforded by the vascular endothelial growth factor antibody, bevacizumab, no pharmacological intervention has been demonstrated to alter the course of disease. Specifically...
2021-11-0437 minPubReadingPubReading [52] - Choosing the Method of Crystallization to Obtain Optimal Results - L. Govada and N. E. ChayenAnyone who has ever attempted to crystallise a protein or other biological macromolecule has encountered at least one, if not all of the following scenarios: No crystals at all, tiny low quality that do not diffract at all. In this paper, we review a number of simple ways to overcome such problems, which have worked well in our hands and in other laboratories. It brings together information that has been dispersed in various publications and lectures over the years and includes further information that has not been previously published. - doi:10.3390/cryst9020106 - 2019
2021-11-0320 minPubReadingPubReading [51] - p53, cancer and the immune response - J. Blagih, M. D. Buck and K. H. VousdenThe importance of cancer-cell-autonomous functions of the tumour suppressor p53 (encoded by TP53) has been established in many studies, but it is now clear that the p53 status of the cancer cell also has a profound impact on the immune response. Loss or mutation of p53 in cancers can affect the recruitment and activity of myeloid and T cells, allowing immune evasion and promoting cancer progression. p53 can also function in immune cells, resulting in various outcomes that can impede or support tumour development. Understanding the role of p53 in tumour and immune cells will help in the development...
2021-11-0153 minPubReadingPubReading [50] - Ki-67 gene expression - S. Uxa, K. EngelandKi-67 serves as a prominent cancer marker. We describe how expression of the MKI67 gene coding for Ki-67 is controlled during the cell cycle. MKI67 mRNA and Ki-67 protein are maximally expressed in G2 phase and mitosis. Expression is dependent on two CHR elements and one CDE site in the MKI67 promoter. DREAM transcriptional repressor complexes bind to both CHR sites and downregulate the expression in G0/G1 cells. Upregulation of MKI67 transcription coincides with binding of B-MYB-MuvB and FOXM1-MuvB complexes from S phase into G2/M. Importantly, binding of B-MYB to the two CHR elements correlates with...
2021-10-301h 02PubReadingPubReading [49] - Rationally designed ruthenium complexes for 1- and 2-photon photodynamic therapy - J. Karges, G. Gasser et al.The use of photodynamic therapy (PDT) against cancer has received increasing attention over recent years. However, the application of the currently approved photosensitizers (PSs) is limited by their poor aqueous solubility, aggregation, photobleaching and slow clearance from the body. To overcome these limitations, there is a need for the development of new classes of PSs with ruthenium(II) polypyridine complexes currently gaining momentum. However, these compounds generally lack significant absorption in the biological spectral window, limiting their application to treat deep-seated or large tumors. To overcome this drawback, ruthenium(II) polypyridine complexes designed in silico with (E,E′)-4,4′-bis...
2021-10-2927 minPubReadingPubReading [48] - Induction of ubiquitin C (UBC) gene transcription is mediated by HSF1: role of proteotoxic and oxidative stress - M. Bianchi, M. Magnani et al.The polyubiquitin gene ubiquitin C (UBC) is considered a stress protective gene and is upregulated under various stressful conditions, which is probably a consequence of an increased demand for ubiquitin in order to remove toxic misfolded proteins. We previously identified heat shock elements (HSEs) within the UBC promoter, which are responsible for heat shock factor (HSF)1-driven induction of the UBC gene and are activated by proteotoxic stress. Here, we determined the molecular players driving the UBC gene transcriptional response to arsenite treatment, mainly addressing the role of the nuclear factor-erythroid 2-related factor 2 (Nrf2)-mediated antioxidant pathway. Exposure of...
2021-10-2845 minPubReadingPubReading [47] - Renal artery aneurysms - D. M. Coleman and J. C. StanleyRenal artery aneurysms are rare in the general population, although the true incidence and natural history remain elusive. Controversy over criteria for repair persists across decades. Indications for repair presently include aneurysm size >2 cm, female gender within childbearing age, symptoms like pain and hematuria, medically refractory hypertension including that associated with functionally important renal artery stenosis, thromboembolism, dissection, and rupture. Conventional surgical reconstruction options are variable and continue to offer technically sound and durable results. Endovascular therapies with novel devices also offer technical success with few major adverse events, and are increasingly employed as indications for intervention broaden. This...
2021-10-2713 minPubReadingPubReading [46] - DNA-mediated engineering of multicomponent enzyme crystals - J. D. Brodina, C. A. Mirkin et al.The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein–protein interactions for DNA–DNA interactions to direct the assembly of two nucleic-acid–functionalized proteins with distinct surface chemstries into six unique...
2021-10-2627 minPubReadingPubReading [45] - Built-In Active Microneedle Patch with Enhanced Autonomous Drug Delivery - M.A. Lopez-Ramirez, J. Wang et al.The use of microneedles has facilitated the painless localized delivery of drugs across the skin. However, their efficacy has been limited by slow diffusion of molecules and often requires external triggers. Herein, an autonomous and degradable, active microneedle delivery platform is introduced, employing magnesium microparticles loaded within the microneedle patch, as the built-in engine for deeper and faster intradermal payload delivery. The magnesium particles react with the interstitial fluid, leading to an explosive-like rapid production of H2 bubbles, providing the necessary force to breach dermal barriers and enhance payload delivery. The release kinetics of active microneedles is evaluated in...
2021-10-2540 minPubReadingPubReading [44] - I-motif DNA structures are formed in the nuclei of human cells - M. Zeraati, D. Christ et al.Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such...
2021-10-2330 minPubReadingPubReading [43] - Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents - N. McStay, A. Kellett et al.Metallodrugs provide important first-line treatment against various forms of human cancer. To overcome chemotherapeutic resistance and widen treatment possibilities, new agents with improved or alternative modes of action are highly sought after. Here, we present a click chemistry strategy for developing DNA damaging metallodrugs. The approach in- volves the development of a series of polyamine ligands where three primary, secondary or tertiary alkyne-amines were selected and ‘clicked’ using the copper-catalysed azide-alkyne cycloaddition reac- tion to a 1,3,5-azide mesitylene core to produce a family of compounds we call the ‘Tri-Click’ (TC) se- ries. From the isolated library, one dominant ligand (TC1) eme...
2021-10-2259 minPubReadingPubReading [42] - Circulating tumoral DNA: Preanalytical validation and quality control in a diagnostic laboratory - S. Nikolaev, T. Nouspikel et al.We present the results of our technical validation process in establishing the analysis of circulating tumor DNA (ctDNA) as a diagnostic tool. Like most cells in our body, tumor cells shed DNA in the blood flow. Analysis of ctDNA mutational content can provide invaluable information on the genetic makeup of a tumor, and assist oncologists in deciding on therapy, or in following residual disease. However, low absolute amounts of circulating DNA and low tumor fraction constitute formidable analytical challenges. A key step is to avoid contamination with genomic DNA from cell lysis. Several brands of specialized blood collection tubes...
2021-10-2127 minPubReadingPubReading [41] - Apoptosis: A Target for Anticancer Therapy - C. M. Pfeffer and A. T. K. SinghApoptosis, the cell’s natural mechanism for death, is a promising target for anticancer therapy. Both the intrinsic and extrinsic pathways use caspases to carry out apoptosis through the cleavage of hundreds of proteins. In cancer, the apoptotic pathway is typically inhibited through a wide variety of means including overexpression of antiapoptotic proteins and under-expression of proapoptotic proteins. Many of these changes cause intrinsic resistance to the most common anticancer therapy, chemotherapy. Promising new anticancer therapies are plant-derived compounds that exhibit anticancer activity through activating the apoptotic pathway. doi:10.3390/ijms19020448 - 2018
2021-10-2031 minPubReadingPubReading [40] - Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling - M. Tanzer, M. Mann et alTumor necrosis factor (TNF) is one of the few cytokines successfully targeted by therapies against inflammatory diseases. However, blocking this well studied and pleiotropic ligand can cause dramatic side-effects. Here, we reason that a systems-level proteomic analysis of TNF signaling could dissect its diverse functions and offer a base for developing more targeted therapies. Therefore, we combine phosphoproteomics time course experiments with sub-cellular localization and kinase inhibitor analysis to identify functional modules of protein phosphorylation. The majority of regulated phosphorylation events can be assigned to an upstream kinase by inhibiting master kinases. Spatial proteomics reveals phosphorylation- dependent translocations of...
2021-10-1953 minPubReadingPubReading [39] - Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane - R. L. Lieberman and A. C. RosenzweigParticulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8A ̊. The enzyme is a trimer with an a3b3g3 polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles c...
2021-10-1936 minPubReadingPubReading [38] - PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification - S. Feola, V. Cerullo et al.Identification of HLA class I ligands from the tumor surface (ligandome or immunopeptidome) is essential for designing T-cell mediated cancer therapeutic approaches. However, the sensitivity of the process for isolating MHC-I restricted tumor-specific peptides has been the major limiting factor for reliable tumor antigen characterization, making clear the need for technical improvement. Here, we describe our work from the fabrication and development of a microfluidic-based chip (PeptiCHIP) and its use to identify and characterize tumor-specific ligands on clinically relevant human samples. Specifically, we assessed the potential of immobilizing a pan-HLA antibody on solid surfaces via well-characterized streptavidin−biotin chemistry, ov...
2021-10-161h 04PubReadingPubReading [37] - High resolution single particle cryo-electron microscopy using beam-image shift - A. Cheng, B. Carragher et al.Automated data acquisition is used widely for single-particle reconstruction of three-dimensional (3D) volumes of biological complexes preserved in vitreous ice and imaged in a transmission electron microscope. Automation has become integral to this method because of the very large number of particle images required in order to overcome the typically low signal-to-noise ratio of these images. For optimal efficiency, automated data acquisition software packages typically employ some beam-image shift targeting as this method is both fast and accurate ( ± 0.1 μm). In contrast, using only stage movement, relocation to a targeted area under low-dose conditions can only be achieved in combination wi...
2021-10-1523 minPubReadingPubReading [36] - APE1: A skilled nucleic acid surgeon - A. Whitaker and B. FreudenthalBefore a deleterious DNA lesion can be replaced with its undamaged counterpart, the lesion must first be removed from the genome. This process of removing and replacing DNA lesions is accomplished by the careful coordination of several protein factors during DNA repair. One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). APE1 preforms AP site incision with surgical precision and skill, by sculpting the DNA to place the cleavage site in an optimal position for nucleophilic attack within its compact...
2021-10-1439 minPubReadingPubReading [35] - Oligonucleotide conjugated multi-functional adeno-associated viruses - D. Katrekar, P. Mali et al.Recombinant adeno-associated viruses (AAVs) are among the most commonly used vehicles for in vivo gene delivery. However, their tropism is limited, and additionally their efficacy can be negatively affected by prevalence of neutralizing antibodies in sera. Methodologies to systematically engineer AAV capsid properties would thus be of great relevance. In this regard, we develop here multi-functional AAVs by engineering precision tethering of oligonucleotides onto the AAV surface, and thereby enabling a spectrum of nucleic-acid programmable functionalities. Towards this, we engineered genetically encoded incorporation of unnatural amino acids (UAA) bearing bio-orthogonal chemical handles onto capsid proteins. Via these we enabled...
2021-10-1326 minPubReadingPubReading [34] - Replication protein A binds RNA and promotes R-Loop formation - O. Mazina, A. V. Mazin et al.Replication protein A (RPA), a major eukaryotic ssDNA- binding protein, is essential for all metabolic processes that involve ssDNA, including DNA replication, repair, and damage signaling. To perform its functions, RPA binds ssDNA tightly. In contrast, it was presumed that RPA binds RNA weakly. However, recent data suggest that RPA may play a role in RNA metabolism. RPA stimulates RNA-templated DNA repair in vitro and associates in vivo with R-loops, the three-stranded structures consisting of an RNA-DNA hybrid and the displaced ssDNA strand. R-loops are common in the genomes of pro- and eukaryotes, including humans, and may play an...
2021-10-1233 minPubReadingPubReading [33] - Oxidative DNA Cleavage with Clip-Phenanthroline Triplex-Forming Oligonucleotide Hybrids - A. Panattoni, M. Hocek et al. A systematic study of several new types of hybrids of Cu-chelated clamped phenanthroline artificial metallonuclease (AMN) with triplex-forming oligonucleotides (TFO) for sequence-specific cleavage of double-stranded DNA (dsDNA) is reported. The synthesis of these AMN–TFO hybrids is based on application of the alkyne–azide cycloaddition click reaction as the key step. The AMN was attached through different linkers at either the 5’- or 3’-ends or in the middle of the TFO stretch. The diverse hybrids efficiently formed triplexes with the target purine-rich sequence and their copper complexes were studied for their ability to cleave dsDNA in the presence of ascorbat...
2021-10-1139 minPubReadingPubReading [32] - Enhancing Protein Crystallization under a Magnetic Field - S. Young Ryu, H. Kyu Song et al.High-quality crystals are essential to ensure high-resolution structural information. Protein crystals are controlled by many factors, such as pH, temperature, and the ion concentration of crystalline solutions. We previously reported the development of a device dedicated to protein crystallization. In the current study, we have further modified and improved our device. Exposure to external magnetic field leads to alignment of the crystal toward a preferred direction depending on the magnetization energy. Each material has different magnetic susceptibilities depending on the individual direction of their unit crystal cells. One of the strategies to acquire a large crystal entails controlling the...
2021-10-0922 minPubReadingPubReading [31] - TLR8 Is a Sensor of RNase T2 Degradation Products - W. Greulic, T. Carell, V. Hornung et al.TLR8 is among the highest-expressed pattern-recognition receptors in the human myeloid compartment, yet its mode of action is poorly understood. TLR8 engages two distinct ligand binding sites to sense RNA degradation products, although it remains unclear how these ligands are formed in cellulo in the context of complex RNA molecule sensing. Here, we identified the lysosomal endoribonuclease RNase T2 as a non-redundant upstream component of TLR8- dependent RNA recognition. RNase T2 activity is required for rendering complex single-stranded, exogenous RNA molecules detectable for TLR8. This is due to RNase T2’s preferential cleavage of single-stranded RNA molecules between pu...
2021-10-0855 minPubReadingPubReading [30] - Cone-shaped HIV-1 capsids are transported through intact nuclear pores - V. Zila, M. Beck et al.Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids...
2021-10-0647 minPubReadingPubReading [29] - Using antibodies to control DNA-templated chemical reactions - L. B. Pellejero, F. Ricci, T. Brown Jr et al.DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be...
2021-10-0534 minPubReadingPubReading [28] - DNA G‐quadruplexes in the human genome: detection, functions and therapeutic potential - R. Hänsel-Hertsch, M. Di Antonio and S. BalasubramanianSingle-stranded guanine-rich DNA sequences can fold into four-stranded DNA structures called G-quadruplexes (G4s) that arise from the self-stacking of two or more guanine quartets. There has been considerable recent progress in the detection and mapping of G4 structures in the human genome and in biologically relevant contexts. These advancements, many of which align with predictions made previously in computational studies, provide important new insights into the functions of G4 structures in, for example, the regulation of transcription and genome stability, and uncover their potential relevance for cancer therapy. - doi:10.1038/nrm.2017.3 - 2017
2021-10-0432 minPubReadingPubReading [27] - Rapid Generation of Long Noncoding RNA Knockout Mice Using CRISPR/Cas9 Technology - N. R. Hansmeier, J.W. Kornfeld et al.In recent years, long noncoding RNAs (lncRNAs) have emerged as multifaceted regulators of gene expression, controlling key developmental and disease pathogenesis processes. However, due to the paucity of lncRNA loss-of-function mouse models, key questions regarding the involvement of lncRNAs in organism homeostasis and (patho)-physiology remain difficult to address experimentally in vivo. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 platform provides a powerful genome-editing tool and has been successfully applied across model organisms to facilitate targeted genetic mutations, including Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Mus musculus. However, just a few lncRNA-deficient mouse lines have been...
2021-10-0224 minPubReadingPubReading [26] - Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review - A. J. Miles, Robert W. Janes and B. A. WallaceCircular dichroism (CD) spectroscopy is a widely-used method in biochemistry, structural biology and pharmaceutical chemistry. More than 24000 papers published in the past decade have included CD characterisations of proteins; many of those studies have also included other complementary chemical, biophysical, and computational chemistry methods. This tutorial review describes the background to the technique of CD spectroscopy and good practice methods for high quality data collection. It specifically focuses on both established and new methods and tools available for experimental design and interpretation, data processing, visualisation, analysis, validation, archiving, and accession, including tools developed to enhance the complementarity of this...
2021-09-291h 06PubReadingPubReading [25] - Brown adipose tissue monocytes support tissue expansion - A. Gallerand, L. Yvan-Charvet1 & S. Ivanov et al.Monocytes are part of the mononuclear phagocytic system. Monocytes play a central role during inflammatory conditions and a better understanding of their dynamics might open therapeutic opportunities. In the present study, we focused on the characterization and impact of monocytes on brown adipose tissue (BAT) functions during tissue remodeling. Single-cell RNA sequencing analysis of BAT immune cells uncovered a large diversity in monocyte and macrophage populations. Fate-mapping experiments demonstrated that the BAT macrophage pool requires constant replenishment from monocytes. Using a genetic model of BAT expansion, we found that brown fat monocyte numbers were selectively increased in this scenario...
2021-09-2847 minPubReadingPubReading [24] - Root of the Tree: The Significance, Evolution, and Origins of the Ribosome - J. C. Bowman, L. D. Williams et al.The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by...
2021-09-271h 38PubReadingPubReading [23] - Deformylation of 5-Formylcytidine in Different Cell Types - E. Korytiakovà and T. CarellEpigenetic programming of cells requires methylation of deoxycytidines (dC) to 5-methyl-dC (mdC) followed by oxidation to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). Subsequent transformation of fdC and cadC back to dC by various pathways establishes a chemical intra-genetic control circle. One of the discussed pathways involves the Tdg-independent deformylation of fdC directly to dC. Here we report the synthesis of a fluorinated fdC feeding probe (F-fdC) to study direct deformylation to F-dC. The synthesis was performed along a novel pathway that circumvents any F-dC as a reaction intermediate to avoid contamination interference. Feeding of F-fdC and observation of...
2021-09-0926 minPubReadingPubReading [22] - Shining Light on CRISPR Gene Editing - L. Taemaitree and T. BrownAdvanced spatiotemporal control of CRISPR-Cas9 activity is demonstrated through the use of chemically modified photoactivatable guide RNA. - doi.org/10.1021/acscentsci.0c00350 - 2020
2021-09-0709 minPubReadingPubReading [21] - DNA structure from A to B - R.Dickerson and HL. NgP. Shing Ho and his colleagues at Oregon State and Berkeley publish in this issue of PNAS an interesting study (1) of helical structure in the DNA hexamer GGCGCC, finding that various states that appear to be logical intermediates between A-DNA and B-DNA can be induced by methylation or bromination of cytosine or by crystal packing. Their results bear on three issues that have been argued over in the past: (i) the differences between A-DNA and B- DNA and transitions between them, (ii) the intrinsic sequence-dependent malleability of a DNA duplex, and (iii) the effects of local helix packing on...
2021-09-0714 minPubReadingPubReading [20] - Anatomy, Back, Cauda Equina - E. Berg, J. Ashurst.In 1595, French anatomist Andre du Laurens first described the structure of a rope-like tail of fibers at the caudal end of the spinal cord. This bundle of numerous axons was termed the cauda equina, from the Latin translation meaning “horse’s tail,” and it contains nerves which innervate both sensory and motor targets within lumbar, sacral, and coccygeal spinal cord levels. Epidemiologic assessments regard lesions to the cauda equina as uncommon, with a prevalence of 1 to 3 per 100,000 subjects. Typically caused by a herniated intervertebral disc at the L5-S1 levels, such lesions affect females as often as males and manife...
2021-09-0711 minPubReadingPubReading [19] - Hospitalization Length after Myocardial Infarction: Risk-Assessment-Based Time of Hospital Discharge vs. Real Life Practice - Michał Wegiel and Tomasz RakowskiAccording to guidelines, it is safe for low-risk patients with myocardial infarction (MI) to be discharged within 72 h of hospitalization. However, results coming from registries show that the hospital stay is often much longer in a real-life situation. Data on the length of the hospital stay (LOS) of MI patients in Polish centers are lacking. We enrolled 212 consecutive patients with acute MI. Low-risk patients were defined according to PAMI II criteria: age 45%, no persistent ventricular arrhythmia, and no multi-vessel disease (MVD). The median of the hospitalization length was eight days (Q1: 6; Q3: 9). In low-risk patients (25%), the median of LOS...
2021-09-0321 minPubReadingPubReading [18] - Controlling and enhancing CRISPR systems - H. Shivram, B. Cress, G. Knott, J. DoudnaMany bacterial and archaeal organisms use CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems to defend themselves from mobile genetic elements. These CRISPR-Cas systems are classified into six types based on their composition and mechanism. CRISPR-Cas enzymes are widely used for genome editing and offer immense therapeutic opportunity to treat genetic diseases. To realize their full potential, it is important to control the timing, duration, efficiency and specificity of CRISPR-Cas enzyme activities. In this review we discuss the mechanisms of natural CRISPR-Cas regulatory biomolecules that enhance or inhibit CRISPR-Cas immunity by altering enzyme function. We also discuss the...
2021-09-0248 minPubReadingPubReading [17] - Antisense, RNAi, and gene silencing strategies for therapy: Mission possible or impossible? - E. Rayburn and R. ZhangAntisense oligonucleotides can regulate gene expression in living cells. As such, they regulate cell function and division, and can modulate cellular responses to internal and external stresses and stimuli. Although encouraging results from preclinical and clinical studies have been obtained and significant progress has been made in developing these agents as drugs, they are not yet recognized as effective therapeutics. Several major hurdles remain to be overcome, including problems with efficacy, off-target effects, delivery and side effects. The lessons learned from antisense drug development can help in the development of other oligonucleotide-based therapeutics such as CpG oligonucleotides, RNAi and...
2021-09-0136 minPubReadingPubReading [16] - Measuring cancer evolution from the genome - T. Graham and A. Sottoriva -The temporal dynamics of cancer evolution remain elusive, because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences made from a single point in time – the endpoint in the cancer’s evolution, when it is removed from the body and studied in the laboratory. Fortuitously however, the cancer genome, by virtue of ongoing mutations that uniquely mark clonal lineages within the tumour, provides a rich, yet surreptitious, record of cancer development. In this review, we describe how a cancer’s genome can be analysed to reveal the tempor...
2021-08-3041 minPubReadingPubReading [15] - Engineering antibody therapeutics - M. Chiu and G. GillilandThe successful introduction of antibody-based protein therapeutics into the arsenal of treatments for patients has within a few decades fostered intense innovation in the production and engineering of antibodies. Reviewed here are the methods currently used to produce antibodies along with how our knowledge of the structural and functional characterization of immunoglobulins has resulted in the engineering of antibodies to produce protein therapeutics with unique properties, both biological and biophysical, that are leading to novel therapeutic approaches. Antibody engineering includes the introduction of the antibody combining site (variable regions) into a host of architectures including bi and multi-specific formats...
2021-08-2443 minPubReadingPubReading [14] - Acute abdominal pain in patients with Crohn’s disease: What urgent imaging tests should be done? - P. García, A. López-Jurado, A. BártulosCrohn’s disease is an autoimmune disease that predominantly affects the gastrointestinal tract. Crohn’s disease is diagnosed at a young age and runs a chronic course with acute flare-ups. When patients with Crohn’s disease present with flare-ups at the emergency department, they are usually managed in a way similar to patients with acute abdomen; there is no consensus about the most appropriate imaging work-up for patients with flare-ups of Crohn’s disease. Thus, we decided to review the literature about the imaging tests indicated (whether related to their diagnostic performance or to lower exposure to ionizing radiation) for acut...
2021-08-2111 minPubReadingPubReading [13] - Herpesvirus capsid assembly and DNA packaging - J. Heming, J. Conway and F. HomaHerpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome. The capsid shell of HSV-1 is built from four structural proteins: a major capsid protein, VP5, which forms the capsomers (hexons...
2021-08-2051 minPubReadingPubReading [12] - Ruthenium Complexes as Anticancer Agents: A Brief History and Perspectives - S. Lee, C. Kim, T.G. NamPlatinum (Pt)-based anticancer drugs such as cisplatin have been used to treat various cancers. However, they have some limitations including poor selectivity and toxicity towards normal cells and increasing chemoresistance. Therefore, there is a need for novel metallo-anticancers, which has not been met for decades. Since the initial introduction of ruthenium (Ru) polypyridyl complex, a number of attempts at structural evolution have been conducted to improve efficacy. Among them, half-sandwich Ru-arene complexes have been the most prominent as an anticancer platform. Such complexes have clearly shown superior anticancer profiles such as increased selectivity toward cancer cells and ameliorating...
2021-08-1859 minPubReadingPubReading [11] - Outcomes of critically ill patients with acute kidney injury in COVID-19 infection: an observational study - Rodrigo Bezerra et al.Background: Early reports indicate that AKI is common during COVID-19 infection. Different mortality rates of AKI due to SARS-CoV-2 have been reported, based on the degree of organic dysfunction and varying from public to private hospitals. However, there is a lack of data about AKI among critically ill patients with COVID-19.Methods: We conducted a multicenter cohort study of 424 critically ill adults with severe acute respiratory syndrome (SARS) and AKI, both associated with SARS-CoV-2, admitted to six public ICUs in Brazil. We used multivariable logistic regression to identify risk factors for AKI severity and in-hospital mortality.
2021-08-1732 minPubReadingPubReading [9] - Principles of ubiquitin and SUMO modifications in DNA repair - S. Bergink, S. JentschWith the discovery in the late 1980s that the DNA-repair gene RAD6 encodes a ubiquitin-conjugating enzyme, it became clear that protein modification by ubiquitin conjugation has a much broader significance than had previously been assumed. Now, two decades later, ubiquitin and its cousin SUMO are implicated in a range of human diseases, including breast cancer and Fanconi anaemia, giving fresh momentum to studies focused on the relationships between ubiquitin, SUMO and DNA-repair pathways. - NATURE - 2009 -. doi:10.1038/nature07963
2021-08-1437 minPubReadingPubReading [10] - Recommendations on pre-hospital and early hospital management of acute heart failure - short version - Alexandre Mebazaa et al.Despite several critical steps forward in the management of chronic heart failure (CHF), the area of acute heart failure (AHF) has remained relatively stagnant. As stated in the updated ESC HF guidelines, clinicians responsible for managing patients with AHF must frequently make treatment decisions without adequate evidence, usually on the basis of expert opinion consensus.2 Specifically, the treatment of acute HF remains largely opinion-based with little good evidence to guide therapy. Acute heart failure is a syndrome in which emergency physicians, cardiologists, intensivists, nurses, and other healthcare providers have to cooperate to provide ‘rapid’ benefit to the patients. We here...
2021-08-1317 minPubReadingPubReading [8] - A Glimpse of Structural Biology through X-Ray Crystallography - Yigong ShiSince determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography—using as examples mechanistic understanding of protein kinases and integral membrane proteins—and comment on the impact of technological development and outlook of X-ray crystallography - dx.doi.org/10.1016/j.cell.2014.10.051 - 2014
2021-08-061h 23PubReadingPubReading [7] - Modified nucleic acids: replication, evolution, and next-generation therapeutics - K. Duffy, S. Arangundy-Franklin and P. HolligerModified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs. K. Duffy, S. Arangundy-Franklin and P. Holliger -doi.org/10.1186...
2021-08-0643 minPubReadingPubReading [6] Will CRISPR‐Cas9 Have Cards to Play Against Cancer? An Update on its Applications - P Daisy, K Shreyas, T. S. Anitha - Molecular Biotechnology Genome editing employs targeted nucleases as powerful tools to precisely alter the genome of target cells and regulate functional genes. Various strategies have been risen so far as the molecular scissors-mediated genome editing that includes zinc finger nuclease, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats—CRISPR-related protein 9. These tools allow researchers to understand the basics of manipulating the genome, create animal models to study human diseases, understand host–pathogen interactions and design disease targets. Targeted genome modification utilizing RNA-guided nucleases are of recent curiosity, as it is a fast and effective strategy that enables the rese...
2021-08-031h 06
PubReadingPubReading [5] G-Quadruplexes at Telomeres: Friend or Foe? - Tracy Bryan - MoleculesTelomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by...
2021-07-2951 minPubReadingPubReading [4] Triplex-forming oligonucleotides: a third strand for DNA nanotechnology - Arun Chandrasekaran, David Rusling - Nucleic Acids ResearchDNA self-assembly has proved to be a useful bottom- up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base-pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that diff...
2021-07-271h 30PubReadingPubReading [3] DNA Structure: A-, B- and Z-DNA Helix Families - David W Ussery - Encyclopedia Of Life ScienceThere are three major families of DNA helices: A-DNA, B-DNA and Z-DNA. The helicalstructure of DNA is variable and depends on the sequence as well as the environment. David W Ussery
2021-07-2326 minPubReadingPubReading [2] New Approaches Towards Recognition of Nucleic Acid Triple Helices - Dev P. Arya - Acc Chem ResWe show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the T·A·T triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (T·A·T and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson–Hoogsteen groove, making it the first molecule that s...
2021-07-2143 min
PubReadingPubReading [1] A structure for Deoxyribose Nucleic Acid - J. D. Watson, F. H. C. Crick - NatureMolecular Structure of Nucleic Acids - A structure for Deoxyribose Nucleic Acid - We wish to suggest astructure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest. J. D. Watson, F. H. C Crick.
2021-07-1707 min