Abstract Protein dynamics and related conformational changes are essential for their function but difficult to characterise and interpret. Amino acids in a protein behave according to their local ...energy landscape, which is determined by their local structural context and environmental conditions. The lowest energy state for a given residue can correspond to sharply defined conformations, e.g. in a stable helix, or can cover a wide range of conformations, e.g. in intrinsically disordered regions. A good definition of such low energy states is therefore important to describe the behaviour of a residue and how it changes with its environment. We propose a data-driven probabilistic definition of six low energy conformational states typically accessible for amino acid residues in proteins. This definition is based on solution NMR information of 1322 proteins through a combined analysis of structure ensembles with interpreted chemical shifts. We further introduce a conformational state variability parameter that captures, based on an ensemble of protein structures from molecular dynamics or other methods, how often a residue moves between these conformational states. The approach enables a different perspective on the local conformational behaviour of proteins that is complementary to their static interpretation from single structure models.
Abstract Biomedical research takes advantage of omic data, such as transcriptomics, to unravel the complexity of diseases. A conventional strategy identifies transcriptomic biomarkers characterized ...by expression patterns associated with a phenotype by relying on feature selection approaches. Hybrid ensemble feature selection (HEFS) has become increasingly popular as it ensures robustness of the selected features by performing data and functional perturbations. However, it remains difficult to make the best suited choices at each step when designing such approaches. We conducted an extensive analysis of four possible HEFS scenarios for the identification of Stage IV colorectal, Stage I kidney and lung and Stage III endometrial cancer biomarkers from transcriptomic data. These scenarios investigate the use of two types of feature reduction by filters (differentially expressed genes and variance) conjointly with two types of resampling strategies (repeated holdout by distribution-balanced stratified and random stratified) for downstream feature selection through an aggregation of thousands of wrapped machine learning models. Based on our results, we emphasize the advantages of using HEFS approaches to identify complex disease biomarkers, given their ability to produce generalizable and stable results to both data and functional perturbations. Finally, we highlight critical issues that need to be considered in the design of such strategies.
Abstract Human endogenous retroviruses (HERVs), the remnants of ancient germline retroviral integrations, comprise almost 8% of the human genome. The elucidation of their biological roles is hampered ...by our inability to link HERV mRNA and protein production with specific HERV loci. To solve the riddle of the integration-specific RNA expression of HERVs, several bioinformatics approaches have been proposed; however, no single process seems to yield optimal results due to the repetitiveness of HERV integrations. The performance of existing data-bioinformatics pipelines has been evaluated against real world datasets whose true expression profile is unknown, thus the accuracy of widely-used approaches remains unclear. Here, we simulated mRNA production from specific HERV integrations to evaluate second and third generation sequencing technologies along with widely used bioinformatic approaches to estimate the accuracy in describing integration-specific expression. We demonstrate that, while a HERV-family approach offers accurate results, per-integration analyses of HERV expression suffer from substantial expression bias, which is only partially mitigated by algorithms developed for calculating the per-integration HERV expression, and is more pronounced in recent integrations. Hence, this bias could erroneously result into biologically meaningful inferences. Finally, we demonstrate the merits of accurate long-read high-throughput sequencing technologies in the resolution of per-locus HERV expression.
Abstract Increased risk for the development of hepatocellular carcinoma (HCC) is driven by a number of etiological factors including hepatitis viral infection and dietary exposures to foods ...contaminated with aflatoxin-producing molds. Intracellular metabolic activation of aflatoxin B1 (AFB1) to a reactive epoxide generates highly mutagenic AFB1-Fapy-dG adducts. Previously, we demonstrated that repair of AFB1-Fapy-dG adducts can be initiated by the DNA glycosylase NEIL1 and that male Neil1−/− mice were significantly more susceptible to AFB1-induced HCC relative to wild-type mice. To investigate the mechanisms underlying this enhanced carcinogenesis, WT and Neil1−/− mice were challenged with a single, 4 mg/kg dose of AFB1 and frequencies and spectra of mutations were analyzed in liver DNAs 2.5 months post-injection using duplex sequencing. The analyses of DNAs from AFB1-challenged mice revealed highly elevated mutation frequencies in the nuclear genomes of both males and females, but not the mitochondrial genomes. In both WT and Neil1−/− mice, mutation spectra were highly similar to the AFB1-specific COSMIC signature SBS24. Relative to wild-type, the NEIL1 deficiency increased AFB1-induced mutagenesis with concomitant elevated HCCs in male Neil1−/− mice. Our data establish a critical role of NEIL1 in limiting AFB1-induced mutagenesis and ultimately carcinogenesis.
Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat multidrug-resistant bacterial infections.
, a pathogen responsible for various ...infections, harbors highly conserved DNA quadruplexes in genes linked to its pathogenesis. In this study, we introduce a novel approach to counter antibiotic resistance by stabilizing G-quadruplex structures within the open reading frames of key resistance-associated genes (
,
and
). We synthesized
, a bis-anthracene derivative, using Cu(I)-catalyzed azide-alkyne cycloaddition, which exhibited remarkable binding and stabilization of the G-quadruplex in the
gene responsible for drug efflux.
effectively permeated multidrug-resistant
strains, leading to a substantial 12.5-fold reduction in ciprofloxacin resistance. Furthermore,
downregulated
gene expression, enhancing drug retention within bacterial cells. Remarkably, the
G-quadruplex cloned into the pET28a(+) plasmid transformed into
BL21 cells can template Cu-free bio-orthogonal synthesis of
from its corresponding alkyne and azide fragments. This study presents a pioneering strategy to combat antibiotic resistance by genetically reducing drug efflux pump expression through G-quadruplex stabilization, offering promising avenues for addressing antibiotic resistance.
Abstract Antibiotic resistance rapidly develops against almost all available therapeutics. Therefore, searching for new antibiotics to overcome the problem of antibiotic resistance alone is ...insufficient. Given that antibiotic resistance can be driven by mutagenesis, an avenue for preventing it is the inhibition of mutagenic processes. We previously showed that the DNA translocase Mfd is mutagenic and accelerates antibiotic resistance development. Here, we present our discovery of a small molecule that inhibits Mfd-dependent mutagenesis, ARM-1 (anti-resistance molecule 1). We found ARM-1 using a high-throughput, small molecule, in vivo screen. Using biochemical assays, we characterized the mechanism by which ARM-1 inhibits Mfd. Critically, we found that ARM-1 reduces mutagenesis and significantly delays antibiotic resistance development across highly divergent bacterial pathogens. These results demonstrate that the mutagenic proteins accelerating evolution can be directly inhibited. Furthermore, our findings suggest that Mfd inhibition, alongside antibiotics, is a potentially effective approach for prevention of antibiotic resistance development during treatment of infections.
Hsp70 (70 kDa heat shock protein) performs molecular chaperone functions by assisting the folding of newly synthesized and misfolded proteins, thereby counteracting various cell stresses and ...preventing multiple diseases, including neurodegenerative disorders and cancers. It is well established that, immediately after heat shock, Hsp70 gene expression is mediated by a canonical mechanism of cap-dependent translation. However, the molecular mechanism of Hsp70 expression during heat shock remains elusive. Intriguingly, the 5' end of Hsp70 messenger RNA (mRNA) appears to form a compact structure with the potential to regulate protein expression in a cap-independent manner. Here, we determined the minimal length of the mHsp70 5'-terminal mRNA sequence that is required for RNA folding into a highly compact structure. This span of this RNA element was mapped and the secondary structure characterized by chemical probing, resulting in a secondary structural model that includes multiple stable stems, including one containing the canonical start codon. All of these components, including a short stretch of the 5' open reading frame (ORF), were shown to be vital for RNA folding. This work provides a structural basis for future investigations on the role of translational regulatory structures in the 5' untranslated region and ORF sequences of Hsp70 during heat shock.
In the century after the Civil War, an economic revolution improved the American standard of living in ways previously unimaginable. Electric lighting, indoor plumbing, motor vehicles, air travel, ...and television transformed households and workplaces. But has that era of unprecedented growth come to an end? Weaving together a vivid narrative, historical anecdotes, and economic analysis,The Rise and Fall of American Growthchallenges the view that economic growth will continue unabated, and demonstrates that the life-altering scale of innovations between 1870 and 1970 cannot be repeated. Robert Gordon contends that the nation's productivity growth will be further held back by the headwinds of rising inequality, stagnating education, an aging population, and the rising debt of college students and the federal government, and that we must find new solutions. A critical voice in the most pressing debates of our time,The Rise and Fall of American Growthis at once a tribute to a century of radical change and a harbinger of tougher times to come.
The
Chlorobiales
are anoxygenic phototrophs that produce solid, extracellular elemental sulfur globules as an intermediate step in the oxidation of sulfide to sulfate. These organisms must export ...sulfur while preventing cell encrustation during S
0
globule formation; during globule degradation they must find and mobilize the sulfur for intracellular oxidation to sulfate. To understand how the
Chlorobiales
address these challenges, we characterized the spatial relationships and physical dynamics of
Chlorobaculum tepidum
cells and S
0
globules by light and electron microscopy.
Cba. tepidum
commonly formed globules at a distance from cells. Soluble polysulfides detected during globule production may allow for remote nucleation of globules. Polysulfides were also detected during globule degradation, probably produced as an intermediate of sulfur oxidation by attached cells. Polysulfides could feed unattached cells, which made up over 80% of the population and had comparable growth rates to attached cells. Given that S
0
is formed remotely from cells, there is a question as to how cells are able to move toward S
0
in order to attach. Time-lapse microscopy shows that
Cba. tepidum
is in fact capable of twitching motility, a finding supported by the presence of genes encoding type IV pili. Our results show how
Cba. tepidum
is able to avoid mineral encrustation and benefit from globule degradation even when not attached. In the environment,
Cba. tepidum
may also benefit from soluble sulfur species produced by other sulfur-oxidizing or sulfur-reducing bacteria as these organisms interact with its biogenic S
0
globules.
Why did Europe experience industrialisation and modern economic growth before China, India or Japan? This is one of the most fundamental questions in Economic History and one that has provoked ...intense debate. The main concern of this book is to determine when the gap in living standards between the East and the West emerged. The established view, dating back to Adam Smith, is that the gap emerged long before the Industrial Revolution, perhaps thousands of years ago. While this view has been called into question - and many of the explanations for it greatly undermined - the issue demands much more empirical research than has yet been undertaken. How did the standard of living in Europe and Asia compare in the seventeenth and eighteenth centuries? The present book proposes an answer by considering evidence of three sorts. The first is economic, focusing on income, food production, wages, and prices. The second is demographic, comparing heights, life expectancy and other demographic indicators. The third combines the economic and demographic by investigating the demographic vulnerability to short-term economic stress. The contributions show the highly complex and diverse pattern of the standard of living in the pre-industrial period. The general picture emerging is not one of a great divergence between East and West, but instead one of considerable similarities. These similarities not only pertain to economic aspects of standard of living but also to demography and the sensitivity to economic fluctuations. In addition to these similarities, there were also pronounced regional differences within the East and within the West - regional differences that in many cases were larger than the average differences between Europe and Asia. This clearly highlights the importance of analysing several dimensions of the standard of living, as well as the danger of neglecting regional, social, and household specific differences when assessing the level of well-being in the past. Available in OSO: http://www.oxfordscholarship.com/oso/public/content/economicsfinance/0199280681/toc.html Contributors to this volume - Kenneth Pomeranz, University of California, Irvine Li Bozhong, Tsinghua University Osamu Saito, Hitotsubashi University Prasannan Parthasarathi, Boston College Robert C. Allen, Oxford University P. Hoffman, D. Jacks, P. Levin and P. Lindert, California Institute of Technology and University of California, Davis Jan Luiten van Zanden, IISG Jaime Reis, University of Lisbon Richard Steckel, Ohio State University Boris Mironov, St. Petersburg State University E. Hammel and A. Gullickson, University of California, Berkley and Columbia University Hans Christian Johansen, University of Southern Denmark M. Breschi, A. Fornasin, and G. Gonano, University of Udine T. Bengtsson and M. Dribe, Lund University M. Oris, G. Alter and M. Neven, University of Geneva, Indiana University and University of Liege C. Campbell and J. Lee, UCLA and University of Michigan N.Tsuya and S. Kurosu, Keio University and Keitaku University
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