Molecular Mechanism of TRP Channels

PubMed Central

Zheng, Jie

2013-01-01

Transient receptor potential (TRP) channels are cellular sensors for a wide spectrum of physical and chemical stimuli. They are involved in the formation of sight, hearing, touch, smell, taste, temperature, and pain sensation. TRP channels also play fundamental roles in cell signaling and allow the host cell to respond to benign or harmful environmental changes. As TRP channel activation is controlled by very diverse processes and, in many cases, exhibits complex polymodal properties, understanding how each TRP channel responds to its unique forms of activation energy is both crucial and challenging. The past two decades witnessed significant advances in understanding the molecular mechanisms that underlie TRP channels activation. This review focuses on our current understanding of the molecular determinants for TRP channel activation. PMID:23720286

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sotomayor, Marcos

Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictionsmore » must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.« less

Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress.

PubMed

Ren, Jing; Mao, Juan; Zuo, Cunwu; Calderón-Urrea, Alejandro; Dawuda, Mohammed Mujitaba; Zhao, Xin; Li, Xinwen; Chen, Baihong

2017-12-01

Drought stress is a major problem around the world and there is still little molecular mechanism about how fruit crops deal with moderate drought stress. Here, the physiological and phosphoproteomic responses of drought-sensitive genotype (M26) and drought-tolerant genotype (MBB) under moderate drought stress were investigated. Our results of the physiology analysis indicated that the MBB genotype could produce more osmosis-regulating substances. Furthermore, phosphoproteins from leaves of both genotypes under moderate drought stress were analyzed using the isobaric tags for relative and absolute quantification technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites, and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Five and thirty-five phosphoproteins with the phosphorylation levels significantly changed (PLSC) were identified in M26 and MBB, respectively. Among these, four PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlap of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins represent a unique combination of metabolism, transcription, translation, and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new and unique homeostasis of major cellular processes. The basic trend was an increase in protein and organic molecules abundance related to drought. These increases were higher in MBB than in M26. Our study is the first to address the phosphoproteome of apple rootstocks in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

NASA Astrophysics Data System (ADS)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

Ciona intestinalis notochord as a new model to investigate the cellular and molecular mechanisms of tubulogenesis.

PubMed

Denker, Elsa; Jiang, Di

2012-05-01

Biological tubes are a prevalent structural design across living organisms. They provide essential functions during the development and adult life of an organism. Increasing progress has been made recently in delineating the cellular and molecular mechanisms underlying tubulogenesis. This review aims to introduce ascidian notochord morphogenesis as an interesting model system to study the cell biology of tube formation, to a wider cell and developmental biology community. We present fundamental morphological and cellular events involved in notochord morphogenesis, compare and contrast them with other more established tubulogenesis model systems, and point out some unique features, including bipolarity of the notochord cells, and using cell shape changes and cell rearrangement to connect lumens. We highlight some initial findings in the molecular mechanisms of notochord morphogenesis. Based on these findings, we present intriguing problems and put forth hypotheses that can be addressed in future studies. Copyright © 2012 Elsevier Ltd. All rights reserved.

Revealing a steroid receptor ligand as a unique PPAR[gamma] agonist

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Shengchen; Han, Ying; Shi, Yuzhe

2012-06-28

Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPAR{gamma} agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPAR{gamma} target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPAR{gamma} ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination ofmore » RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPAR{gamma} ligands in the treatment of insulin resistance.« less

Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy

PubMed Central

Gibbons, Don L.; Pricl, Sabrina; Posocco, Paola; Laurini, Erik; Fermeglia, Maurizio; Sun, Hanshi; Talpaz, Moshe; Donato, Nicholas; Quintás-Cardama, Alfonso

2014-01-01

The acquisition of mutations within the BCR-ABL1 kinase domain is frequently associated with tyrosine kinase inhibitor (TKI) failure in chronic myeloid leukemia. Sensitive sequencing techniques have revealed a high prevalence of compound BCR-ABL1 mutations (polymutants) in patients failing TKI therapy. To investigate the molecular consequences of such complex mutant proteins with regards to TKI resistance, we determined by cloning techniques the presence of polymutants in a cohort of chronic-phase patients receiving imatinib followed by dasatinib therapy. The analysis revealed a high frequency of polymutant BCR-ABL1 alleles even after failure of frontline imatinib, and also the progressive exhaustion of the pool of unmutated BCR-ABL1 alleles over the course of sequential TKI therapy. Molecular dynamics analyses of the most frequent polymutants in complex with TKIs revealed the basis of TKI resistance. Modeling of BCR-ABL1 in complex with the potent pan-BCR-ABL1 TKI ponatinib highlighted potentially effective therapeutic strategies for patients carrying these recalcitrant and complex BCR-ABL1 mutant proteins while unveiling unique mechanisms of escape to ponatinib therapy. PMID:24550512

Comparative advantages of mechanical biosensors.

PubMed

Arlett, J L; Myers, E B; Roukes, M L

2011-04-01

Mechanical interactions are fundamental to biology. Mechanical forces of chemical origin determine motility and adhesion on the cellular scale, and govern transport and affinity on the molecular scale. Biological sensing in the mechanical domain provides unique opportunities to measure forces, displacements and mass changes from cellular and subcellular processes. Nanomechanical systems are particularly well matched in size with molecular interactions, and provide a basis for biological probes with single-molecule sensitivity. Here we review micro- and nanoscale biosensors, with a particular focus on fast mechanical biosensing in fluid by mass- and force-based methods, and the challenges presented by non-specific interactions. We explain the general issues that will be critical to the success of any type of next-generation mechanical biosensor, such as the need to improve intrinsic device performance, fabrication reproducibility and system integration. We also discuss the need for a greater understanding of analyte-sensor interactions on the nanoscale and of stochastic processes in the sensing environment.

Review: Animal model and the current understanding of molecule dynamics of adipogenesis.

PubMed

Campos, C F; Duarte, M S; Guimarães, S E F; Verardo, L L; Wei, S; Du, M; Jiang, Z; Bergen, W G; Hausman, G J; Fernyhough-Culver, M; Albrecht, E; Dodson, M V

2016-06-01

Among several potential animal models that can be used for adipogenic studies, Wagyu cattle is the one that presents unique molecular mechanisms underlying the deposit of substantial amounts of intramuscular fat. As such, this review is focused on current knowledge of such mechanisms related to adipose tissue deposition using Wagyu cattle as model. So abundant is the lipid accumulation in the skeletal muscles of these animals that in many cases, the muscle cross-sectional area appears more white (adipose tissue) than red (muscle fibers). This enhanced marbling accumulation is morphologically similar to that seen in numerous skeletal muscle dysfunctions, disease states and myopathies; this might indicate cross-similar mechanisms between such dysfunctions and fat deposition in Wagyu breed. Animal models can be used not only for a better understanding of fat deposition in livestock, but also as models to an increased comprehension on molecular mechanisms behind human conditions. This revision underlies some of the complex molecular processes of fat deposition in animals.

Molecular mechanism underlying ethanol activation of G-protein–gated inwardly rectifying potassium channels

PubMed Central

Bodhinathan, Karthik; Slesinger, Paul A.

2013-01-01

Alcohol (ethanol) produces a wide range of pharmacological effects on the nervous system through its actions on ion channels. The molecular mechanism underlying ethanol modulation of ion channels is poorly understood. Here we used a unique method of alcohol-tagging to demonstrate that alcohol activation of a G-protein–gated inwardly rectifying potassium (GIRK or Kir3) channel is mediated by a defined alcohol pocket through changes in affinity for the membrane phospholipid signaling molecule phosphatidylinositol 4,5-bisphosphate. Surprisingly, hydrophobicity and size, but not the canonical hydroxyl, were important determinants of alcohol-dependent activation. Altering levels of G protein Gβγ subunits, conversely, did not affect alcohol-dependent activation, suggesting a fundamental distinction between receptor and alcohol gating of GIRK channels. The chemical properties of the alcohol pocket revealed here might extend to other alcohol-sensitive proteins, revealing a unique protein microdomain for targeting alcohol-selective therapeutics in the treatment of alcoholism and addiction. PMID:24145411

Glioblastoma: new therapeutic strategies to address cellular and genomic complexity

PubMed Central

Cai, Xue; Sughrue, Michael E.

2018-01-01

Glioblastoma (GBM) is the most invasive and devastating primary brain tumor with a median overall survival rate about 18 months with aggressive multimodality therapy. Its unique characteristics of heterogeneity, invasion, clonal populations maintaining stem cell-like cells and recurrence, have limited responses to a variety of therapeutic approaches, and have made GBM the most difficult brain cancer to treat. A great effort and progress has been made to reveal promising molecular mechanisms to target therapeutically. Especially with the emerging of new technologies, the mechanisms underlying the pathology of GBM are becoming more clear. The purpose of this review is to summarize the current knowledge of molecular mechanisms of GBM and highlight the novel strategies and concepts for the treatment of GBM. PMID:29507709

Molecular mechanisms of magnetosome formation.

PubMed

Komeili, Arash

2007-01-01

Magnetotactic bacteria are a diverse group of microorganisms with the ability to use geomagnetic fields for direction sensing. This unique feat is accomplished with the help of magnetosomes, nanometer-sized magnetic crystals surrounded by a lipid bilayer membrane and organized into chains via a dedicated cytoskeleton within the cell. Because of the special properties of these magnetic crystals, magnetotactic bacteria have been exploited for a variety of applications in diverse disciplines from geobiology to biotechnology. In addition, magnetosomes have served as a powerful model system for the study of biomineralization and cell biology in bacteria. This review focuses on recent advances in understanding the molecular mechanisms of magnetosome formation and magnetite biomineralization.

Engineering the vibrational coherence of vision into a synthetic molecular device.

PubMed

Gueye, Moussa; Manathunga, Madushanka; Agathangelou, Damianos; Orozco, Yoelvis; Paolino, Marco; Fusi, Stefania; Haacke, Stefan; Olivucci, Massimo; Léonard, Jérémie

2018-01-22

The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the reactant excited state to the primary photoproduct ground state. The engineering of such an energy-funnelling function in synthetic compounds would pave the way towards biomimetic molecular machines capable of achieving optimum light-to-mechanical energy conversion. Here we use resonance and off-resonance vibrational coherence spectroscopy to demonstrate that a rhodopsin-like isomerization operates in a biomimetic molecular switch in solution. Furthermore, by using quantum chemical simulations, we show why the observed coherent nuclear motion critically depends on minor chemical modifications capable to induce specific geometric and electronic effects. This finding provides a strategy for engineering vibrationally coherent motions in other synthetic systems.

New Directions in Phthalocyanine Pigments

NASA Technical Reports Server (NTRS)

Vandemark, Michael R.

1992-01-01

The objectives were the following: (1) investigation of the synthesis of new phthalocyanines; (2) characterization of the new phthalocyanines synthesized; (3) investigate the properties of the newly synthesized phthalocyanines with emphasis on UV protection of plastics and coatings; and (4) utilize quantum mechanics to evaluate the structural relationships with possible properties and synthetic approaches. The proposed research targeted the synthesis of phthalocyanines containing an aromatic bridge between two phthalocyanine rings. The goal was to synthesize pigments which would protect plastics when exposed to the photodegradation effects of the sun in space. The stability and extended conjugation of the phthalocyanines offer a unique opportunity for energy absorption and numerous radiative and non-radiative energy loss mechanisms. Although the original targeted phthalocyanines were changed early in the project, several new and unique phthalocyanine compounds were prepared. The basic goals of this work were met and some unique and unexpected outcomes of the work were the result of the integral use of quantum mechanics and molecular modeling with the synthetic effort.

Phosphoenolpyruvate carboxylase: a new era of structural biology.

PubMed

Izui, Katsura; Matsumura, Hiroyoshi; Furumoto, Tsuyoshi; Kai, Yasushi

2004-01-01

There have been remarkable advances in our knowledge of this important enzyme in the last decade. This review focuses on three recent topics: the three-dimensional structure of the protein, molecular mechanisms of catalytic and regulatory functions, and the molecular cloning and characterization of PEPC kinases, which are Ser/Thr kinases involved specifically in regulatory phosphorylation of vascular plant PEPC. Analysis by X-ray crystallography and site-directed mutagenesis for E. coli and maize PEPC identified the catalytic site and allosteric effector binding sites, and revealed the functional importance of mobile loops. We present the reaction mechanism of PEPC in which we assign the roles of individual amino acid residues. We discuss the unique molecular property of PEPC kinase and its possible regulation at the post-translational level.

Mesothelioma: Identification of the Key Molecular Events Triggered by BAP1

DTIC Science & Technology

2014-09-01

amounts of asbestos that would normally not cause MM in the population at large. In order to study the mechanism(s), we assembled a unique cohort and...BAP1 status regulate NF-kB activity and HMGB1 release, and we also found that monoallelic BAP1 loss increases susceptibility to low doses of asbestos ...by using a mouse model. 15. SUBJECT TERMS mesothelioma, BAP1, asbestos , mechanisms 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18

Mechanical Properties of Organic Semiconductors for Stretchable, Highly Flexible, and Mechanically Robust Electronics.

PubMed

Root, Samuel E; Savagatrup, Suchol; Printz, Adam D; Rodriquez, Daniel; Lipomi, Darren J

2017-05-10

Mechanical deformability underpins many of the advantages of organic semiconductors. The mechanical properties of these materials are, however, diverse, and the molecular characteristics that permit charge transport can render the materials stiff and brittle. This review is a comprehensive description of the molecular and morphological parameters that govern the mechanical properties of organic semiconductors. Particular attention is paid to ways in which mechanical deformability and electronic performance can coexist. The review begins with a discussion of flexible and stretchable devices of all types, and in particular the unique characteristics of organic semiconductors. It then discusses the mechanical properties most relevant to deformable devices. In particular, it describes how low modulus, good adhesion, and absolute extensibility prior to fracture enable robust performance, along with mechanical "imperceptibility" if worn on the skin. A description of techniques of metrology precedes a discussion of the mechanical properties of three classes of organic semiconductors: π-conjugated polymers, small molecules, and composites. The discussion of each class of materials focuses on molecular structure and how this structure (and postdeposition processing) influences the solid-state packing structure and thus the mechanical properties. The review concludes with applications of organic semiconductor devices in which every component is intrinsically stretchable or highly flexible.

Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction.

PubMed

Sotomayor, Marcos; Weihofen, Wilhelm A; Gaudet, Rachelle; Corey, David P

2012-12-06

Hearing and balance use hair cells in the inner ear to transform mechanical stimuli into electrical signals. Mechanical force from sound waves or head movements is conveyed to hair-cell transduction channels by tip links, fine filaments formed by two atypical cadherins known as protocadherin 15 and cadherin 23 (refs 4, 5). These two proteins are involved in inherited deafness and feature long extracellular domains that interact tip-to-tip in a Ca(2+)-dependent manner. However, the molecular architecture of this complex is unknown. Here we combine crystallography, molecular dynamics simulations and binding experiments to characterize the protocadherin 15-cadherin 23 bond. We find a unique cadherin interaction mechanism, in which the two most amino-terminal cadherin repeats (extracellular cadherin repeats 1 and 2) of each protein interact to form an overlapped, antiparallel heterodimer. Simulations predict that this tip-link bond is mechanically strong enough to resist forces in hair cells. In addition, the complex is shown to become unstable in response to Ca(2+) removal owing to increased flexure of Ca(2+)-free cadherin repeats. Finally, we use structures and biochemical measurements to study the molecular mechanisms by which deafness mutations disrupt tip-link function. Overall, our results shed light on the molecular mechanics of hair-cell sensory transduction and on new interaction mechanisms for cadherins, a large protein family implicated in tissue and organ morphogenesis, neural connectivity and cancer.

The SOLA Team: A Star Formation Project To Study the Soul of Lupus with ALMA

NASA Astrophysics Data System (ADS)

De Gregorio-Monsalvo, Itziar; Saito, M.; Rodon, J.; Takahashi, S.

2017-06-01

The SOLA team is a multi-national and multi-wavelength collaboration composed by scientists with technical expertise in ALMA and in infrared and optical techniques. The aim of the team is to establish a low-mass star formation scenario based on the Lupus molecular clouds. In this talk I will present our unique catalog of pre-stellar and proto-stellar cores toward Lupus molecular clouds, the results on our latest studies in protoplanetary disks, as well as our ALMA Cycle 3 data aiming at testing the formation mechanism of sub-stellar objects in Lupus molecular clouds.

Kinemage of action - Proposed reaction mechanism of glutamate-1-semialdehyde aminomutase at an atomic level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sorensen, John L., E-mail: John_Sorensen@umanitoba.ca; Stetefeld, Joerg, E-mail: stetefel@cc.umanitoba.ca

2011-10-07

Highlights: {yields} Inhibitors of tetrapyrrole cofactor biosynthesis may be useful antibiotics. {yields} Mechanism of critical enzyme, glutamate-1-semialdehyde aminomutase, is presented. {yields} Unique vitamin B6-dependant enzyme traps intermediate in active site. {yields} Molecular dynamics show that a re-orientation of the substrate is required. -- Abstract: Glutamate-1-semialdehyde aminomutase (GSAM), a key enzyme in tetrapyrrole cofactor biosynthesis, performs a unique transamination on a single substrate. The substrate, glutamate-1-semialdehyde (GSA), undergoes a reaction that exchanges the position of an amine and a carbonyl group to produce 5-aminolevulinic acid (ALA). This transamination reaction is unique in the fact that is does not require an externalmore » cofactor to act as a nitrogen donor or acceptor in this transamination reaction. One of the other remarkable features of the catalytic mechanism is the release free in the enzyme active site of the intermediate 4,5-diaminovaleric acid (DAVA). The action of a gating loop prevents the escape of DAVA from the active site. In a MD simulation approach, using snapshots provided by X-ray crystallography and protein crystal absorption spectrometry data, the individual catalytic steps in this unique intramolecular transamination have been elucidated.« less

Variational Identification of Markovian Transition States

NASA Astrophysics Data System (ADS)

Martini, Linda; Kells, Adam; Covino, Roberto; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

2017-07-01

We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5 , and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

A tale of two approaches: complementary mechanisms of cytotoxic and targeted therapy resistance may inform next-generation cancer treatments

PubMed Central

Masui, Kenta; Gini, Beatrice; Wykosky, Jill; Zanca, Ciro; Cavenee, Webster K.

2013-01-01

Chemotherapy and molecularly targeted approaches represent two very different modes of cancer treatment and each is associated with unique benefits and limitations. Both types of therapy share the overarching limitation of the emergence of drug resistance, which prevents these drugs from eliciting lasting clinical benefit. This review will provide an overview of the various mechanisms of resistance to each of these classes of drugs and examples of drug combinations that have been tested clinically. This analysis supports the contention that understanding modes of resistance to both chemotherapy and molecularly targeted therapies may be very useful in selecting those drugs of each class that will have complementing mechanisms of sensitivity and thereby represent reasonable combination therapies. PMID:23455378

Single molecule detection, thermal fluctuation and life

PubMed Central

YANAGIDA, Toshio; ISHII, Yoshiharu

2017-01-01

Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

Asymmetric hydrogenation of α,β-unsaturated phosphonates with Rh-BisP* and Rh-MiniPHOS catalysts: Scope and mechanism of the reaction

PubMed Central

Gridnev, Ilya D.; Yasutake, Masaya; Imamoto, Tsuneo; Beletskaya, Irina P.

2004-01-01

Optically active 1,2-bis(alkylmethylphosphino)ethanes and bis(alkylmethylphosphino)methanes are unique diphosphine ligands combining the simple molecular structure and P-stereogenic asymmetric environment. This work shows that these ligands exhibit excellent enantioselectivity in rhodium-catalyzed asymmetric hydrogenation of α,β-unsaturated phosphonic acid derivatives. The enantioselective hydrogenation mechanism elucidated by NMR study is also described. PMID:15024119

Exploring the molecular aspects associated with testicular germ cell tumors: a review

PubMed Central

Facchini, Gaetano; Rossetti, Sabrina; Cavaliere, Carla; D’Aniello, Carmine; Di Franco, Rossella; Iovane, Gelsomina; Grimaldi, Giovanni; Piscitelli, Raffaele; Muto, Paolo; Botti, Gerardo; Perdonà, Sisto; Veneziani, Bianca Maria; Berretta, Massimiliano; Montanari, Micaela

2018-01-01

Testicular germ cell tumors (TGCTs) represent the most common solid tumors affecting young men. They constitute a distinct entity because of their embryonic origin and their unique biological behavior. Recent preclinical data regarding biological signaling machinery as well as genetic and epigenetic mechanisms associated with molecular patterns of tumors have contribute to explain the pathogenesis and the differentiation of TGCTs and to understand the mechanisms responsible for the development of resistance to treatment. In this review, we discuss the main genetic and epigenetic events associated with TGCTs development in order to better define their role in the pathogenesis of these tumors and in cisplatin-acquired resistance. PMID:29416701

Building better water models using the shape of the charge distribution of a water molecule

NASA Astrophysics Data System (ADS)

Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2017-11-01

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

Leigh syndrome: neuropathology and pathogenesis.

PubMed

Lake, Nicole J; Bird, Matthew J; Isohanni, Pirjo; Paetau, Anders

2015-06-01

Leigh syndrome (LS) is the most common pediatric presentation of a defined mitochondrial disease. This progressive encephalopathy is characterized pathologically by the development of bilateral symmetrical lesions in the brainstem and basal ganglia that show gliosis, vacuolation, capillary proliferation, relative neuronal preservation, and by hyperlacticacidemia in the blood and/or cerebrospinal fluid. Understanding the molecular mechanisms underlying this unique pathology has been challenging, particularly in view of the heterogeneous and not yet fully determined genetic basis of LS. Moreover, animal models that mimic features of LS have only been created relatively recently. Here, we review the pathology of LS and consider what might be the molecular mechanisms underlying its pathogenesis. Data from a wide range of sources, including patient samples, animal models, and studies of hypoxic-ischemic encephalopathy (a condition that shares features with LS), were used to provide insight into the pathogenic mechanisms that may drive lesion development. Based on current data, we suggest that severe ATP depletion, gliosis, hyperlacticacidemia, reactive oxygen species, and potentially excitotoxicity cumulatively contribute to the neuropathogenesis of LS. An intimate understanding of the molecular mechanisms causing LS is required to accelerate the development of LS treatments.

Identification of Characteristic Macromolecules of Escherichia coli Genotypes by Atomic Force Microscope Nanoscale Mechanical Mapping

NASA Astrophysics Data System (ADS)

Chang, Alice Chinghsuan; Liu, Bernard Haochih

2018-02-01

The categorization of microbial strains is conventionally based on the molecular method, and seldom are the morphological characteristics in the bacterial strains studied. In this research, we revealed the macromolecular structures of the bacterial surface via AFM mechanical mapping, whose resolution was not only determined by the nanoscale tip size but also the mechanical properties of the specimen. This technique enabled the nanoscale study of membranous structures of microbial strains with simple specimen preparation and flexible working environments, which overcame the multiple restrictions in electron microscopy and label-enable biochemical analytical methods. The characteristic macromolecules located among cellular surface were considered as surface layer proteins and were found to be specific to the Escherichia coli genotypes, from which the averaged molecular sizes were characterized with diameters ranging from 38 to 66 nm, and the molecular shapes were kidney-like or round. In conclusion, the surface macromolecular structures have unique characteristics that link to the E. coli genotype, which suggests that the genomic effects on cellular morphologies can be rapidly identified using AFM mechanical mapping. [Figure not available: see fulltext.

Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic.

PubMed

Santiago, Marina; Lee, Wonsik; Fayad, Antoine Abou; Coe, Kathryn A; Rajagopal, Mithila; Do, Truc; Hennessen, Fabienne; Srisuknimit, Veerasak; Müller, Rolf; Meredith, Timothy C; Walker, Suzanne

2018-06-01

Identifying targets of antibacterial compounds remains a challenging step in the development of antibiotics. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures identified from directional biases in insertions revealed known molecular targets and resistance mechanisms for the majority of these. Because single-gene upregulation does not always confer resistance, we used a complementary machine-learning approach to predict the mechanism from inactivation mutant fitness profiles. This approach suggested the cell wall precursor Lipid II as the molecular target of the lysocins, a mechanism we have confirmed. We conclude that docking to membrane-anchored Lipid II precedes the selective bacteriolysis that distinguishes these lytic natural products, showing the utility of our approach for nominating the antibiotic mechanism of action.

When biomolecules meet graphene: from molecular level interactions to material design and applications.

PubMed

Li, Dapeng; Zhang, Wensi; Yu, Xiaoqing; Wang, Zhenping; Su, Zhiqiang; Wei, Gang

2016-12-01

Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses. The different interactions between graphene and biomolecules at the molecular level are demonstrated and discussed in detail. In addition, the potential applications of the created graphene-biomolecule nanohybrids in drug delivery, cancer treatment, tissue engineering, biosensors, bioimaging, energy materials, and other nanotechnological applications are presented. This review will be helpful to know the modification of graphene with biomolecules, understand the interactions between graphene and biomolecules at the molecular level, and design functional graphene-based nanomaterials with unique properties for various applications.

The role of the hydrophobic phase in the unique rheological properties of saponin adsorption layers.

PubMed

Golemanov, Konstantin; Tcholakova, Slavka; Denkov, Nikolai; Pelan, Eddie; Stoyanov, Simeon D

2014-09-28

Saponins are a diverse class of natural, plant derived surfactants, with peculiar molecular structure consisting of a hydrophobic scaffold and one or several hydrophilic oligosaccharide chains. Saponins have strong surface activity and are used as natural emulsifiers and foaming agents in food and beverage, pharmaceutical, ore processing, and other industries. Many saponins form adsorption layers at the air-water interface with extremely high surface elasticity and viscosity. The molecular origin of the observed unique interfacial visco-elasticity of saponin adsorption layers is of great interest from both scientific and application viewpoints. In the current study we demonstrate that the hydrophobic phase in contact with water has a very strong effect on the interfacial properties of saponins and that the interfacial elasticity and viscosity of the saponin adsorption layers decrease in the order: air > hexadecane ≫ tricaprylin. The molecular mechanisms behind these trends are analyzed and discussed in the context of the general structure of the surfactant adsorption layers at various nonpolar phase-water interfaces.

An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants

USDA-ARS?s Scientific Manuscript database

Phosphorus (P) is one of the most limiting macronutrients in soils for plant growth and development. However, the whole genome molecular mechanisms contributing to plant acclimation to Pi-deficiency remains largely unknown. White lupin (Lupinus albus L.) has evolved unique adaptation systems for gro...

Evolutionary diversification of TTX-resistant sodium channels in a predator-prey interaction.

PubMed

Geffeney, Shana L; Fujimoto, Esther; Brodie, Edmund D; Brodie, Edmund D; Ruben, Peter C

2005-04-07

Understanding the molecular genetic basis of adaptations provides incomparable insight into the genetic mechanisms by which evolutionary diversification takes place. Whether the evolution of common traits in different lineages proceeds by similar or unique mutations, and the degree to which phenotypic evolution is controlled by changes in gene regulation as opposed to gene function, are fundamental questions in evolutionary biology that require such an understanding of genetic mechanisms. Here we identify novel changes in the molecular structure of a sodium channel expressed in snake skeletal muscle, tsNa(V)1.4, that are responsible for differences in tetrodotoxin (TTX) resistance among garter snake populations coevolving with toxic newts. By the functional expression of tsNa(V)1.4, we show how differences in the amino-acid sequence of the channel affect TTX binding and impart different levels of resistance in four snake populations. These results indicate that the evolution of a physiological trait has occurred through a series of unique functional changes in a gene that is otherwise highly conserved among vertebrates.

Between destiny and disease: genetics and molecular pathways of human central nervous system aging.

PubMed

Glorioso, Christin; Sibille, Etienne

2011-02-01

Aging of the human brain is associated with "normal" functional, structural, and molecular changes that underlie alterations in cognition, memory, mood and motor function, amongst other processes. Normal aging also imposes a robust constraint on the onset of many neurological diseases, ranging from late onset neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's diseases (PD), to early onset psychiatric disorders, such as bipolar disorder (BPD) and schizophrenia (SCZ). The molecular mechanisms and genetic underpinnings of age-related changes in the brain are understudied, and, while they share some overlap with peripheral mechanisms of aging, many are unique to the largely non-mitotic brain. Hence, understanding mechanisms of brain aging and identifying associated modulators may have profound consequences for the prevention and treatment of age-related impairments and diseases. Here we review current knowledge on age-related functional and structural changes, their molecular and genetic underpinnings, and discuss how these pathways may contribute to the vulnerability to develop age-related neurological diseases. We highlight recent findings from human post-mortem brain microarray studies, which we hypothesize, point to a potential genetically controlled transcriptional program underlying molecular changes and age-gating of neurological diseases. Finally, we discuss the implications of this model for understanding basic mechanisms of brain aging and for the future investigation of therapeutic approaches. Copyright © 2010 Elsevier Ltd. All rights reserved.

Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II.

PubMed

Cheng, Cheng; Kamiya, Motoshi; Uchida, Yoshihiro; Hayashi, Shigehiko

2015-10-21

Color variants of human cellular retinol binding protein II (hCRBPII) created by protein engineering were recently shown to exhibit anomalously wide photoabsorption spectral shifts over ∼200 nm across the visible region. The remarkable phenomenon provides a unique opportunity to gain insight into the molecular basis of the color tuning of retinal binding proteins for understanding of color vision as well as for engineering of novel color variants of retinal binding photoreceptor proteins employed in optogenetics. Here, we report a theoretical investigation of the molecular mechanism underlying the anomalously wide spectral shifts of the color variants of hCRBPII. Computational modeling of the color variants with hybrid molecular simulations of free energy geometry optimization succeeded in reproducing the experimentally observed wide spectral shifts, and revealed that protein flexibility, through which the active site structure of the protein and bound water molecules is altered by remote mutations, plays a significant role in inducing the large spectral shifts.

Splanchnic vein thrombosis in myeloproliferative neoplasms: pathophysiology and molecular mechanisms of disease

PubMed Central

How, Joan; Zhou, Amy; Oh, Stephen T.

2016-01-01

Myeloproliferative neoplasms (MPNs) are the most common underlying prothrombotic disorder found in patients with splanchnic vein thrombosis (SVT). Clinical risk factors for MPN-associated SVTs include younger age, female sex, concomitant hypercoagulable disorders, and the JAK2 V617F mutation. These risk factors are distinct from those associated with arterial or deep venous thrombosis (DVT) in MPN patients, suggesting disparate disease mechanisms. The pathophysiology of SVT is thought to derive from local interactions between activated blood cells and the unique splanchnic endothelial environment. Other mutations commonly found in MPNs, including CALR and MPL, are rare in MPN-associated SVT. The purpose of this article is to review the clinical and molecular risk factors for MPN-associated SVT, with particular focus on the possible mechanisms of SVT formation in MPN patients. PMID:28246554

Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs.

PubMed

Lan, DaoLiang; Xiong, XianRong; Ji, WenHui; Li, Jian; Mipam, Tserang-Donko; Ai, Yi; Chai, ZhiXin

2018-04-01

The yak (Bos grunniens), which is a unique bovine breed that is distributed mainly in the Qinghai-Tibetan Plateau, is considered a good model for studying plateau adaptability in mammals. The lungs are important functional organs that enable animals to adapt to their external environment. However, the genetic mechanism underlying the adaptability of yak lungs to harsh plateau environments remains unknown. To explore the unique evolutionary process and genetic mechanism of yak adaptation to plateau environments, we performed transcriptome sequencing of yak and cattle (Bos taurus) lungs using RNA-Seq technology and a subsequent comparison analysis to identify the positively selected genes in the yak. After deep sequencing, a normal transcriptome profile of yak lung that containing a total of 16,815 expressed genes was obtained, and the characteristics of yak lungs transcriptome was described by functional analysis. Furthermore, Ka/Ks comparison statistics result showed that 39 strong positively selected genes are identified from yak lungs. Further GO and KEGG analysis was conducted for the functional annotation of these genes. The results of this study provide valuable data for further explorations of the unique evolutionary process of high-altitude hypoxia adaptation in yaks in the Tibetan Plateau and the genetic mechanism at the molecular level.

Chromophobe hepatocellular carcinoma with abrupt anaplasia: a proposal for a new subtype of hepatocellular carcinoma with unique morphological and molecular features

PubMed Central

Wood, Laura D; Heaphy, Christopher M; Daniel, Hubert Darius-J; Naini, Bita V; Lassman, Charles R; Arroyo, May R; Kamel, Ihab R; Cosgrove, David P; Boitnott, John K; Meeker, Alan K; Torbenson, Michael S

2014-01-01

Hepatocellular carcinomas exhibit heterogeneous morphologies by routine light microscopy. Although some morphologies represent insignificant variations in growth patterns, others may represent unrecognized subtypes of hepatocellular carcinoma. Identification of these subtypes could lead to separation of hepatocellular carcinomas into discrete groups with unique underlying genetic changes, prognosis, or therapeutic responses. In order to identify potential subtypes, two pathologists independently screened a cohort of 219 unselected hepatocellular carcinoma resection specimens and divided cases into potential subtypes. One of these promising candidate subtypes was further evaluated using histological and molecular techniques. This subtype was characterized by a unique and consistent set of histological features: smooth chromophobic cytoplasm, abrupt focal nuclear anaplasia (small clusters of tumor cells with marked nuclear anaplasia in a background of tumor cells with bland nuclear cytology), and scattered microscopic pseudocysts—we designate this variant as ‘chromophobe hepatocellular carcinoma with abrupt anaplasia’. Thirteen cases were identified (6% of all hepatocellular carcinomas), including 6 men and 7 women with an average age of 61 years. Six cases occurred in cirrhotic livers. Serum AFP was elevated in 6 out of 10 cases. There were a variety of underlying liver diseases, but cases were enrichment for chronic hepatitis B, P = 0.006. Interestingly, at the molecular level, this variant was strongly associated with the alternative lengthening of telomere (ALT) phenotype by telomere FISH. ALT is a telomerase-independent mechanism of telomere maintenance and is found in approximately 8% of unselected hepatocellular carcinomas. In contrast, 11/12 (92%) of the cases of chromophobe hepatocellular carcinoma with abrupt anaplasia were ALT-positive. In summary, we propose that chromophobe hepatocellular carcinoma with abrupt anaplasia represents a new subtype of hepatocellular carcinoma with unique morphological and molecular features. PMID:23640129

Chromophobe hepatocellular carcinoma with abrupt anaplasia: a proposal for a new subtype of hepatocellular carcinoma with unique morphological and molecular features.

PubMed

Wood, Laura D; Heaphy, Christopher M; Daniel, Hubert Darius-J; Naini, Bita V; Lassman, Charles R; Arroyo, May R; Kamel, Ihab R; Cosgrove, David P; Boitnott, John K; Meeker, Alan K; Torbenson, Michael S

2013-12-01

Hepatocellular carcinomas exhibit heterogeneous morphologies by routine light microscopy. Although some morphologies represent insignificant variations in growth patterns, others may represent unrecognized subtypes of hepatocellular carcinoma. Identification of these subtypes could lead to separation of hepatocellular carcinomas into discrete groups with unique underlying genetic changes, prognosis, or therapeutic responses. In order to identify potential subtypes, two pathologists independently screened a cohort of 219 unselected hepatocellular carcinoma resection specimens and divided cases into potential subtypes. One of these promising candidate subtypes was further evaluated using histological and molecular techniques. This subtype was characterized by a unique and consistent set of histological features: smooth chromophobic cytoplasm, abrupt focal nuclear anaplasia (small clusters of tumor cells with marked nuclear anaplasia in a background of tumor cells with bland nuclear cytology), and scattered microscopic pseudocysts--we designate this variant as 'chromophobe hepatocellular carcinoma with abrupt anaplasia'. Thirteen cases were identified (6% of all hepatocellular carcinomas), including 6 men and 7 women with an average age of 61 years. Six cases occurred in cirrhotic livers. Serum AFP was elevated in 6 out of 10 cases. There were a variety of underlying liver diseases, but cases were enrichment for chronic hepatitis B, P=0.006. Interestingly, at the molecular level, this variant was strongly associated with the alternative lengthening of telomere (ALT) phenotype by telomere FISH. ALT is a telomerase-independent mechanism of telomere maintenance and is found in approximately 8% of unselected hepatocellular carcinomas. In contrast, 11/12 (92%) of the cases of chromophobe hepatocellular carcinoma with abrupt anaplasia were ALT-positive. In summary, we propose that chromophobe hepatocellular carcinoma with abrupt anaplasia represents a new subtype of hepatocellular carcinoma with unique morphological and molecular features.

Role of motor unit structure in defining function

NASA Technical Reports Server (NTRS)

Monti, R. J.; Roy, R. R.; Edgerton, V. R.

2001-01-01

Motor units, defined as a motoneuron and all of its associated muscle fibers, are the basic functional units of skeletal muscle. Their activity represents the final output of the central nervous system, and their role in motor control has been widely studied. However, there has been relatively little work focused on the mechanical significance of recruiting variable numbers of motor units during different motor tasks. This review focuses on factors ranging from molecular to macroanatomical components that influence the mechanical output of a motor unit in the context of the whole muscle. These factors range from the mechanical properties of different muscle fiber types to the unique morphology of the muscle fibers constituting a motor unit of a given type and to the arrangement of those motor unit fibers in three dimensions within the muscle. We suggest that as a result of the integration of multiple levels of structural and physiological levels of organization, unique mechanical properties of motor units are likely to emerge. Copyright 2001 John Wiley & Sons, Inc.

New insights into the targeting of a sub-set of tail-anchored proteins to the outer mitochondrial membrane

USDA-ARS?s Scientific Manuscript database

Tail-anchored (TA) proteins are a unique class of functionally diverse membrane proteins that are defined by their single C-terminal membrane-spanning domain and their ability to insert post-translationally into specific organelles with an Nout-Cin orientation. The molecular mechanisms by which TA p...

"ICT-not-quenching" near infrared ratiometric fluorescent detection of picric acid in aqueous media.

PubMed

Xu, Yongqian; Li, Benhao; Li, Weiwei; Zhao, Jie; Sun, Shiguo; Pang, Yi

2013-05-25

The first "off-on" and ratiometric fluorescent method based on ICT mechanism for picric acid (PA) recognition in the near infrared region was constructed. Key advantages of the unique molecular architecture can fulfil the ratiometric response to electron-deficient featured PA which inclines to quench fluorescence of all reported sensors for PA.

'Drawing' a Molecular Portrait of CIN and Cervical Cancer: a Review of Genome-Wide Molecular Profiling Data.

PubMed

Kurmyshkina, Olga V; Kovchur, Pavel I; Volkova, Tatyana O

2015-01-01

In this review we summarize the results of studies employing high-throughput methods of profiling of HPV-associated cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancers at key intracellular regulatory levels to demonstrate the unique identity of the landscape of molecular changes underlying this oncopathology, and to show how these changes are related to the 'natural history' of cervical cancer progression and the formation of clinically significant properties of tumors. A step-wise character of cervical cancer progression is a morphologically well-described fact and, as evidenced by genome-wide screenings, it is indeed the consistent change of the molecular profiles of HPV-infected epithelial cells through which they progressively acquire the phenotypic hallmarks of cancerous cells. In this sense, CIN/cervical cancer is a unique model for studying the driving forces and mechanisms of carcinogenesis. Recent research has allowed definition of the whole-genome spectrum of both random and regular molecular alterations, as well as changes either common to processes of carcinogenesis or specific for cervical cancer. Despite the existence of questions that are still to be investigated, these findings are of great value for the future development of approaches for the diagnostics and treatment of cervical neoplasms.

Comparative proteomics lends insight into genotype-specific pathogenicity.

PubMed

Guarnieri, Michael T

2013-09-01

Comparative proteomic analyses have emerged as a powerful tool for the identification of unique biomarkers and mechanisms of pathogenesis. In this issue of Proteomics, Murugaiyan et al. utilize difference gel electrophoresis (DIGE) to examine differential protein expression between nonpathogenic and pathogenic genotypes of Prototheca zopfii, a causative agent in bovine enteritis and mastitis. Their findings provide insights into molecular mechanisms of infection and evolutionary adaptation of pathogenic genotypes, demonstrating the power of comparative proteomic analyses. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A review of the evolution of viviparity in squamate reptiles: the past, present and future role of molecular biology and genomics.

PubMed

Murphy, Bridget F; Thompson, Michael B

2011-07-01

Squamate reptiles (lizards and snakes) offer a unique model system for testing hypotheses about the evolutionary transition from oviparity (egg-laying) to viviparity (live-bearing) in amniote vertebrates. The evolution of squamate viviparity has occurred remarkably frequently (>108 times) and has resulted in major changes in reproductive physiology. Such frequent changes in reproductive strategy pose two questions: (1) what are the molecular mechanisms responsible for the evolution of squamate viviparity? (2) Are these molecular mechanisms the same for separate origins of viviparity? Molecular approaches, such as RT-PCR, in situ hybridisation, Western blotting and immunofluorescence, have been invaluable for identifying genes and proteins that are involved in squamate placental development, materno-foetal immunotolerance, placental transport, placental angiogenesis, hormone synthesis and hormone receptor expression. However, the candidate-gene or -protein approach that has been used until now does not allow for de novo gene/protein discovery; results to date suggest that the reproductive physiologies of mammals and squamate reptiles are very similar, but this conclusion may simply be due to a limited capacity to study the subset of genes and proteins that are unique to reptiles. Progress has also been slowed by the lack of appropriate molecular and genomic resources for squamate reptiles. The advent of next-generation sequencing provides a relatively inexpensive way to conduct rapid high-throughput sequencing of genomes and transcriptomes. We discuss the potential use of next-generation sequencing technologies to analyse differences in gene expression between oviparous and viviparous squamates, provide important sequence information for reptiles, and generate testable hypotheses for the evolution of viviparity.

Signature properties of water: Their molecular electronic origins

PubMed Central

Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

2015-01-01

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

Unique catalytic activities and scaffolding of p21 activated kinase-1 in cardiovascular signaling.

PubMed

Ke, Yunbo; Lei, Ming; Wang, Xin; Solaro, R John

2013-09-27

P21 activated kinase-1 (Pak1) has diverse functions in mammalian cells. Although a large number of phosphoproteins have been designated as Pak1 substrates from in vitro studies, emerging evidence has indicated that Pak1 may function as a signaling molecule through a unique molecular mechanism - scaffolding. By scaffolding, Pak1 delivers signals through an auto-phosphorylation-induced conformational change without transfer of a phosphate group to its immediate downstream effector(s). Here we review evidence for this regulatory mechanism based on structural and functional studies of Pak1 in different cell types and research models as well as in vitro biochemical assays. We also discuss the implications of Pak1 scaffolding in disease-related signaling processes and the potential in cardiovascular drug development.

Genetic and cellular mechanisms of the formation of Esophageal Atresia and Tracheoesophageal Fistula

PubMed Central

Jacobs, Ian J.; Que, Jianwen

2015-01-01

Foregut separation involves dynamic changes in the activities of signaling pathways and transcription factors. Recent mouse genetic studies demonstrate that some of these pathways interact with each other to form a complex network, leading to a unique dorsal-ventral patterning in the early foregut. In this review we will discuss how this unique dorsal-ventral patterning is set prior to the foregut separation and how disruption of this patterning affects the separation process. We will further discuss the roles of downstream targets of these pathways in regulating separation at cellular and molecular levels. Understanding the mechanism of normal separation process will provide us insights into the pathobiology of a relatively common birth defect Esophageal Atresia (EA) with/without Tracheo-esophageal Fistula (TEF). PMID:23679023

Computational analysis of hydrogenated graphyne folding

NASA Astrophysics Data System (ADS)

Lenear, Christopher; Becton, Matthew; Wang, Xianqiao

2016-02-01

This letter employs molecular mechanics simulations to analyze the geometric changes of foreign-atom-doped graphyne. Simulation results show that higher the density of dopant and the greater area covered by the dopant correlates to a greater folding angle of the graphyne sheet. Compared to graphene, graphyne folding could prove to be more effective for various nanodevices based on its unique band gap, especially when doped, and its tunable interactions with and absorption of foreign molecules. Therefore, our findings may offer unique perspectives into the development of novel graphyne-based nanodevices and stimulate the community's research interest in graphene-related origami.

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.

PubMed

Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M; Ray, David A; Gilbert, M Thomas P; Myers, Eugene

2018-02-15

Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

Molecular Cogs: Interplay between Circadian Clock and Cell Cycle.

PubMed

Gaucher, Jonathan; Montellier, Emilie; Sassone-Corsi, Paolo

2018-05-01

The cell cycle and the circadian clock operate as biological oscillators whose timed functions are tightly regulated. Accumulating evidence illustrates the presence of molecular links between these two oscillators. This mutual interplay utilizes various coupling mechanisms, such as the use of common regulators. The connection between these two cyclic systems has unique interest in the context of aberrant cell proliferation since both of these oscillators are frequently misregulated in cancer cells. Further studies will provide deeper understanding of the detailed molecular connections between the cell cycle and the circadian clock and may also serve as a basis for the design of innovative therapeutic strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Plants that attack plants: molecular elucidation of plant parasitism.

PubMed

Yoshida, Satoko; Shirasu, Ken

2012-12-01

Obligate parasitic plants in the family Orobanchaceae, such as Striga and Orobanche (including Phelipanche) spp., parasitize important crops and cause severe agricultural damage. Recent molecular studies have begun to reveal how these parasites have adapted to hosts in a parasitic lifecycle. The parasites detect nearby host roots and germinate by a mechanism that seems to have evolved from a conserved germination system found in non-parasites. The development of a specialized infecting organ called a haustorium is a unique feature of plant parasites and is triggered by host compounds and redox signals. Newly developed genomic and genetic resources will facilitate more rapid progress toward a molecular understanding of plant parasitism. Copyright © 2012 Elsevier Ltd. All rights reserved.

Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures

NASA Astrophysics Data System (ADS)

Lu, George J.; Farhadi, Arash; Szablowski, Jerzy O.; Lee-Gosselin, Audrey; Barnes, Samuel R.; Lakshmanan, Anupama; Bourdeau, Raymond W.; Shapiro, Mikhail G.

2018-05-01

Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or mechanical phenotypes, allow multiplexed imaging using parametric MRI and differential acoustic sensitivity. Additionally, clustering-induced changes in MRI contrast enable the design of dynamic molecular sensors. By coupling the complementary physics of MRI and ultrasound, this nanomaterial gives rise to a distinct modality for molecular imaging with unique advantages and capabilities.

Exploring possible mechanisms of action for the nanotoxicity and protein binding of decorated nanotubes: interpretation of physicochemical properties from optimal QSAR models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esposito, Emilio Xavier, E-mail: emilio@exeResearch.com; The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045; Hopfinger, Anton J., E-mail: hopfingr@gmail.com

2015-10-01

Carbon nanotubes have become widely used in a variety of applications including biosensors and drug carriers. Therefore, the issue of carbon nanotube toxicity is increasingly an area of focus and concern. While previous studies have focused on the gross mechanisms of action relating to nanomaterials interacting with biological entities, this study proposes detailed mechanisms of action, relating to nanotoxicity, for a series of decorated (functionalized) carbon nanotube complexes based on previously reported QSAR models. Possible mechanisms of nanotoxicity for six endpoints (bovine serum albumin, carbonic anhydrase, chymotrypsin, hemoglobin along with cell viability and nitrogen oxide production) have been extracted frommore » the corresponding optimized QSAR models. The molecular features relevant to each of the endpoint respective mechanism of action for the decorated nanotubes are also discussed. Based on the molecular information contained within the optimal QSAR models for each nanotoxicity endpoint, either the decorator attached to the nanotube is directly responsible for the expression of a particular activity, irrespective of the decorator's 3D-geometry and independent of the nanotube, or those decorators having structures that place the functional groups of the decorators as far as possible from the nanotube surface most strongly influence the biological activity. These molecular descriptors are further used to hypothesize specific interactions involved in the expression of each of the six biological endpoints. - Highlights: • Proposed toxicity mechanism of action for decorated nanotubes complexes • Discussion of the key molecular features for each endpoint's mechanism of action • Unique mechanisms of action for each of the six biological systems • Hypothesized mechanisms of action based on QSAR/QNAR predictive models.« less

Molecular System for the Division of Self-Propelled Oil Droplets by Component Feeding.

PubMed

Banno, Taisuke; Toyota, Taro

2015-06-30

Unique dynamics using inanimate molecular assemblies have drawn a great amount of attention for demonstrating prebiomimetic molecular systems. For the construction of an organized logic combining two fundamental dynamics of life, we demonstrate here a molecular system that exhibits both division and self-propelled motion using oil droplets. The key molecule of this molecular system is a novel cationic surfactant containing a five-membered acetal moiety, and the molecular system can feed the self-propelled oil droplet composed of a benzaldehyde derivative and an alkanol. The division dynamics of the self-propelled oil droplets were observed through the hydrolysis of the cationic surfactant in bulk solution. The mechanism of the current dynamics is argued to be based on the supply of "fresh" oil components in the moving oil droplets, which is induced by the Marangoni instability. We consider this molecular system to be a prototype of self-reproducing inanimate molecular assembly exhibiting self-propelled motion.

Atmospheric pressure ionization of chlorinated ethanes in ion mobility spectrometry and mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ewing, Robert G.; Atkinson, David A.; Benson, Michael T.

2015-05-16

This study investigates the APCI mechanisms associated with chlorinated ethanes in an attempt to define conditions under which unique pseudo-molecular adducts, in addition to chloride ion, can be produced for analytical measurements using IMS and MS. The ionization chemistry of chlorinated compounds typically leads to the detection of only the halide ions. Using molecular modeling, which provides insights into the ion formation and relative binding energies, predictions for the formation of pseudo-molecular adducts are postulated. Predicted structures of the chloride ion with multiple hydrogens on the ethane backbone was supported by the observation of specific pseudo-molecular adducts in IMS andmore » MS spectra. With the proper instrumental conditions, such as short reaction times and low temp.« less

Molecular Innovations Toward Theranostics of Aggressive Prostate Cancer

DTIC Science & Technology

2015-09-01

therapeutic agents assisted with new imaging probe is expect to bring a new frontier for prostate cancer management. Our objective is to develop dendrimer ...selective dendrimer nanoparticle platform with both targeted imaging and drug delivery capabilities to target metastatic PCa. Using this unique...constructing dendrimer conjugated with therapeutic peptide, determining the mechanism of action and preparing chelator for conjugating PET tracer and

Membrane-Based Gas Separation Accelerated by Hollow Nanosphere Architectures

DOE PAGES

Zhang, Jinshui; Schott, Jennifer Ann; Univ. of Tennessee, Knoxville, TN; ...

2016-11-15

We report that the coupling of hollow carbon nanospheres with triblock copolymers is a promising strategy to fabricate mixed-matrix membranes, because the symmetric microporous shells combine with the hollow space to promote gas transport and the unique soft-rigid molecular structure of triblock copolymers can accommodate a high loading of fillers without a significant loss of mechanical strength.

Mechanism of the dielectric enhancement in polymer-alumina nano-particle composites

NASA Astrophysics Data System (ADS)

Jacob, Rebecca; Jacob, Anne Pavitra; Mainwaring, David E.

2009-09-01

Polymer-alumina nano-composites with enhanced dielectric properties as a possibility to enable the miniaturization of devices have been reported. The enhancement of dielectric properties was found to be unique to the polymer. In the present work, the mechanism of the dielectric enhancement is established by performing ab initio molecular orbital calculations in order to study the molecular interactions in the interfacial region between the alumina-nano-particle surface and the polymer medium. The calculations predict the existence of strong electrostatic attraction between the positive charge on the aluminium of the alumina clusters and the negative charge of the oxygens of the polymer at the polymer-nano-particle interface resulting in an increase in the dipole moment and the polarization of the system leading to enhanced dielectric properties. The oxygen thus plays a dual role by involving in covalent bonding with the polymer chain and electrostatic bonding interactions with the alumina nano-particles. The unique structure of the polymer provides the highly electronegative oxygens, as carbonyl groups or ether linkages in conjugation with aromatic rings in an extended polymer chain system, facilitating this type of bonding at the interface.

Chlorella vulgaris: A Multifunctional Dietary Supplement with Diverse Medicinal Properties.

PubMed

Panahi, Yunes; Darvishi, Behrad; Jowzi, Narges; Beiraghdar, Fatemeh; Sahebkar, Amirhossein

2016-01-01

Chlorella vulgaris is a green unicellular microalgae with biological and pharmacological properties important for human health. C. vulgaris has a long history of use as a food source and contains a unique and diverse composition of functional macro- and micro-nutrients including proteinsChlorella vulgaris is a green unicellular microalgae with biological and pharmacological properties important for human health. C. vulgaris has a long history of use as a food source and contains a unique and diverse composition of functional macro- and micro-nutrients including proteins, omega-3 polyunsaturated fatty acids, polysaccharides, vitamins and minerals. Clinical trials have suggested that supplementation with C. vulgaris can ameliorate amelioration hyperlipidemia and hyperglycemia, and protect against oxidative stress, cancer and chronic obstructive pulmonary disease. In this review, we summarize the findings on the health benefits of Chlorella supplementation and the molecular mechanisms underlying these effects., omega-3 polyunsaturated fatty acids, polysaccharides, vitamins and minerals. Clinical trials have suggested that supplementation with C. vulgaris can ameliorate amelioration hyperlipidemia and hyperglycemia, and protect against oxidative stress, cancer and chronic obstructive pulmonary disease. In this review, we summarize the findings on the health benefits of Chlorella supplementation and the molecular mechanisms underlying these effects.

Molecularly organic/inorganic hybrid hollow mesoporous organosilica nanocapsules with tumor-specific biodegradability and enhanced chemotherapeutic functionality.

PubMed

Huang, Ping; Chen, Yu; Lin, Han; Yu, Luodan; Zhang, Linlin; Wang, Liying; Zhu, Yufang; Shi, Jianlin

2017-05-01

Based on the intrinsic features of high stability and unique multifunctionality, inorganic nanoparticles have shown remarkable potentials in combating cancer, but their biodegradability and biocompatibility are still under debate. As a paradigm, this work successfully demonstrates that framework organic-inorganic hybridization can endow the inorganic mesoporous silica nanocarriers with unique tumor-sensitive biodegradability and high biocompatibility. Based on a "chemical homology" mechanism, molecularly organic-inorganic hybridized hollow mesoporous organosilica nanocapsules (HMONs) with high dispersity and sub-50 nm particle dimension were constructed in mass production. A physiologically active disulfide bond (SS) was directly incorporated into the silica framework, which could break up upon contacting the reducing microenvironment of tumor tissue and biodegrade accordingly. Such a tumor-specific biodegradability is also responsible for the tumor-responsive drug releasing by the fast biodegradation and disintegration of the framework. The ultrasmall particle size of HMONs guarantees their high accumulation into tumor tissue, thus causing the high chemotherapeutic outcome. This research provides a paradigm that framework organic-inorganic hybridization can endow the inorganic nanocarrier with unique biological effects suitable for biomedical application, benefiting the development of novel nanosystems with the unique bio-functionality and performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Fish interferon response and its molecular regulation: a review].

PubMed

Zhang, Yibing; Gui, Jianfang

2011-05-01

Interferon response is the first line of host defense against virus infection. Recent years have witnessed tremendous progress in understanding of fish innate response to virus infection, especially in fish interferon antiviral response. A line of fish genes involved in interferon antiviral response have been identified and functional studies further reveal that fish possess an IFN antiviral system similar to mammals. However, fish virus-induced interferon genes contain introns similar to mammalian type III interferon genes although they encode proteins similar to type I interferons, which makes it hard to understand the evolution of vertebrate interferon genes directly resulting in a debate on nomenclature of fish interferon genes. Actually, fish display some unique mechanisms underlying interferon antiviral response. This review documents the recent progress on fish interferon response and its molecular mechanism.

Neurogenesis in the Developing and Adult Brain—Similarities and Key Differences

PubMed Central

Götz, Magdalena; Nakafuku, Masato; Petrik, David

2017-01-01

Adult neurogenesis in the mammalian brain is often viewed as a continuation of neurogenesis at earlier, developmental stages. Here, we will critically review the extent to which this is the case highlighting similarities as well as key differences. Although many transcriptional regulators are shared in neurogenesis at embryonic and adult stages, recent findings on the molecular mechanisms by which these neuronal fate determinants control fate acquisition and maintenance have revealed profound differences between development and adulthood. Importantly, adult neurogenesis occurs in a gliogenic environment, hence requiring adult-specific additional and unique mechanisms of neuronal fate specification and maintenance. Thus, a better understanding of the molecular logic for continuous adult neurogenesis provides important clues to develop strategies to manipulate endogenous stem cells for the purpose of repair. PMID:27235475

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.

PubMed

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Ying; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tom Tang, Y; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lu, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhongjian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

2014-12-02

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.

Ultra-High Molecular Weight Polyethylene: Influence of the Chemical, Physical and Mechanical Properties on the Wear Behavior. A Review

PubMed Central

Bellare, Anuj; Bistolfi, Alessandro

2017-01-01

Ultra-high molecular weight polyethylene (UHMWPE) is the most common bearing material in total joint arthroplasty due to its unique combination of superior mechanical properties and wear resistance over other polymers. A great deal of research in recent decades has focused on further improving its performances, in order to provide durable implants in young and active patients. From “historical”, gamma-air sterilized polyethylenes, to the so-called first and second generation of highly crosslinked materials, a variety of different formulations have progressively appeared in the market. This paper reviews the structure–properties relationship of these materials, with a particular emphasis on the in vitro and in vivo wear performances, through an analysis of the existing literature. PMID:28773153

Latent memory facilitates relearning through molecular signaling mechanisms that are distinct from original learning.

PubMed

Menges, Steven A; Riepe, Joshua R; Philips, Gary T

2015-09-01

A highly conserved feature of memory is that it can exist in a latent, non-expressed state which is revealed during subsequent learning by its ability to significantly facilitate (savings) or inhibit (latent inhibition) subsequent memory formation. Despite the ubiquitous nature of latent memory, the mechanistic nature of the latent memory trace and its ability to influence subsequent learning remains unclear. The model organism Aplysia californica provides the unique opportunity to make strong links between behavior and underlying cellular and molecular mechanisms. Using Aplysia, we have studied the mechanisms of savings due to latent memory for a prior, forgotten experience. We previously reported savings in the induction of three distinct temporal domains of memory: short-term (10min), intermediate-term (2h) and long-term (24h). Here we report that savings memory formation utilizes molecular signaling pathways that are distinct from original learning: whereas the induction of both original intermediate- and long-term memory in naïve animals requires mitogen activated protein kinase (MAPK) activation and ongoing protein synthesis, 2h savings memory is not disrupted by inhibitors of MAPK or protein synthesis, and 24h savings memory is not dependent on MAPK activation. Collectively, these findings reveal that during forgetting, latent memory for the original experience can facilitate relearning through molecular signaling mechanisms that are distinct from original learning. Copyright © 2015 Elsevier Inc. All rights reserved.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Regulation of bone by the adaptive immune system in arthritis

PubMed Central

2011-01-01

Studies on the immune regulation of osteoclasts in rheumatoid arthritis have promoted the new research field of 'osteoimmunology', which investigates the interplay between the skeletal and immune systems at the molecular level. Accumulating evidence lends support to the theory that bone destruction associated with rheumatoid arthritis is caused by the enhanced activity of osteoclasts, resulting from the activation of a unique helper T cell subset, 'Th17 cells'. Understanding the interaction between osteoclasts and the adaptive immune system in rheumatoid arthritis and the molecular mechanisms of Th17 development will lead to the development of potentially effective therapeutic strategies. PMID:21635718

Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

PubMed

Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

2016-03-01

Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

Transcriptomics exposes the uniqueness of parasitic plants.

PubMed

Ichihashi, Yasunori; Mutuku, J Musembi; Yoshida, Satoko; Shirasu, Ken

2015-07-01

Parasitic plants have the ability to obtain nutrients directly from other plants, and several species are serious biological threats to agriculture by parasitizing crops of high economic importance. The uniqueness of parasitic plants is characterized by the presence of a multicellular organ called a haustorium, which facilitates plant-plant interactions, and shutting down or reducing their own photosynthesis. Current technical advances in next-generation sequencing and bioinformatics have allowed us to dissect the molecular mechanisms behind the uniqueness of parasitic plants at the genome-wide level. In this review, we summarize recent key findings mainly in transcriptomics that will give us insights into the future direction of parasitic plant research. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Aero-Thermo-Dynamic Mass Analysis

NASA Astrophysics Data System (ADS)

Shiba, Kota; Yoshikawa, Genki

2016-07-01

Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis.

Virology and Molecular Pathogenesis of Human Papillomavirus (HPV)-Associated Oropharyngeal Squamous Cell Carcinoma

PubMed Central

Miller, Daniel L.; Puricelli, Michael D.; Stack, M. Sharon

2012-01-01

Current literature fully supports HPV-associated oropharyngeal squamous cell carcinoma (OPSCC) as a unique clinical entity. It affects an unambiguous patient population with defined risk factors, has a genetic expression pattern more similar to cervical squamous cell carcinoma than non-HPV-associated head and neck squamous cell carcinoma (HNSCC), and may warrant divergent clinical management compared to HNSCC associated with traditional risk factors. However, a detailed understanding of the molecular mechanisms driving these differences and the ability to exploit this knowledge to improve clinical management of OPSCC has not yet come to fruition. This review summarizes the etiology of HPV positive (HPV+) OPSCC and provides a detailed overview of HPV virology and molecular pathogenesis relevant to infection of oropharyngeal tissues. Methods of detection and differential gene expression analyses are also summarized. Future research into mechanisms that mediate tropism of HPV to oropharyngeal tissues, improved detection strategies, and the pathophysiologic significance of altered gene and microRNA expression profiles is warranted. PMID:22452816

Janus effect of antifreeze proteins on ice nucleation.

PubMed

Liu, Kai; Wang, Chunlei; Ma, Ji; Shi, Guosheng; Yao, Xi; Fang, Haiping; Song, Yanlin; Wang, Jianjun

2016-12-20

The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non-ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation.

Janus effect of antifreeze proteins on ice nucleation

PubMed Central

Liu, Kai; Wang, Chunlei; Ma, Ji; Shi, Guosheng; Yao, Xi; Fang, Haiping; Song, Yanlin; Wang, Jianjun

2016-01-01

The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non–ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water. The generality of this Janus effect is verified by investigating three representative AFPs. Molecular dynamics simulation analysis shows that the Janus effect can be established by the distinct structures of the hydration layer around IBF and NIBF. Our work greatly enhances the understanding of the mechanism of AFPs at the molecular level and brings insights to the fundamentals of heterogeneous ice nucleation. PMID:27930318

Harnessing Preclinical Molecular Imaging to Inform Advances in Personalized Cancer Medicine.

PubMed

Clark, Peter M; Ebiana, Victoria A; Gosa, Laura; Cloughesy, Timothy F; Nathanson, David A

2017-05-01

Comprehensive molecular analysis of individual tumors provides great potential for personalized cancer therapy. However, the presence of a particular genetic alteration is often insufficient to predict therapeutic efficacy. Drugs with distinct mechanisms of action can affect the biology of tumors in specific and unique ways. Therefore, assays that can measure drug-induced perturbations of defined functional tumor properties can be highly complementary to genomic analysis. PET provides the capacity to noninvasively measure the dynamics of various tumor biologic processes in vivo. Here, we review the underlying biochemical and biologic basis for a variety of PET tracers and how they may be used to better optimize cancer therapy. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Hepatitis A virus: host interactions, molecular epidemiology and evolution.

PubMed

Vaughan, Gilberto; Goncalves Rossi, Livia Maria; Forbi, Joseph C; de Paula, Vanessa S; Purdy, Michael A; Xia, Guoliang; Khudyakov, Yury E

2014-01-01

Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions. Published by Elsevier B.V.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling.

PubMed

Tan, Jianjun; Yuan, Hongling; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin

2016-04-01

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

From "seahorse" to "molecular Recording"

NASA Astrophysics Data System (ADS)

Gao, Hong-Jun

2002-08-01

We will first present unique dendritic "seahorse" patterns observed when we study structural features in functional C60-TCNQ complex thin films, and their formation mechanism. Then we report a new process for ultrahigh density, erasable data storage, based on the molecular electrical bistability of an organic charge transfer complex, 3-nitrobenzal malononitrile and 1,4-phenylenediamine (NBMN-pDA). Switched by a voltage pulse from a scanning tunneling microscope (STM), we demonstrate a data density exceeding 1013 bits/cm2. The experiment results and theoretical ab initio calculations show the writing and erasing mechanism to be a conductance transition of the organic compound due to a structural change from crystalline to noncrystalline. The ultimate bit density appears limited only by the size of the organic complex, less than 1 nm in our case, corresponding to 1014 bits/cm2.

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

PubMed Central

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Ying; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tom Tang, Y.; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lu, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhongjian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L.; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

2014-01-01

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates. PMID:25463417

Hsp100/ClpB Chaperone Function and Mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vierling, Elizabeth

2015-01-27

The supported research investigated the mechanism of action of a unique class of molecular chaperones in higher plants, the Hsp100/ClpB proteins, with the ultimate goal of defining how these chaperones influence plant growth, development, stress tolerance and productivity. Molecular chaperones are essential effectors of cellular “protein quality control”, which comprises processes that ensure the proper folding, localization, activation and turnover of proteins. Hsp100/ClpB proteins are required for temperature acclimation in plants, optimal seed yield, and proper chloroplast development. The model plant Arabidopsis thaliana and genetic and molecular approaches were used to investigate two of the three members of the Hsp100/ClpBmore » proteins in plants, cytosolic AtHsp101 and chloroplast-localized AtClpB-p. Investigating the chaperone activity of the Hsp100/ClpB proteins addresses DOE goals in that this activity impacts how “plants generate and assemble components” as well as “allowing for their self repair”. Additionally, Hsp100/ClpB protein function in plants is directly required for optimal “utilization of biological energy” and is involved in “mechanisms that control the architecture of energy transduction systems”.« less

Transient Binding and Viscous Dissipation in Semi-flexible Polymer Networks

NASA Astrophysics Data System (ADS)

Lieleg, Oliver; Claessens, Mireille; Bausch, Andreas

2008-03-01

Nature specifically chooses from a myriad of actin binding proteins (ABPs) to tailor the cytoskeletal microstructure. Herein, cells rely on the dynamics of the cytoskeleton as its structural and mechanical adaptability is crucial to allow for dynamic processes. A molecular understanding of such biological complexity calls for an in vitro system with well-defined structural rearrangements and cross-linker dynamics to elucidate the physical origin of the unique viscoelastic properties of cells. As we present here, the frequency-dependent viscoelastic response of cross-linked in vitro actin networks is determined by the binding kinetics of cross-linking molecules. Independent from the particular network structure, the viscous dissipation (loss modulus) exhibits a pronounced minimum in an intermediate frequency which is dominated by elasticity. We show that in this frequency regime the molecular origin of the viscoelastic response is given by the non-static nature of actin/ABP bonds as they are subjugated to chemical on/off kinetics. The time scale of the resulting stress release is set by the lifetime distribution of the cross-linking molecule and therefore can be tuned independently from other relaxation mechanisms. We speculate that unbinding of distinct cross-links might be the molecular mechanism employed by cells for mechanosensing.

Atomistic investigation of the structural, transport, and mechanical properties of Cu-Zr metallic glasses

NASA Astrophysics Data System (ADS)

Kumar, Mohit

The unique set of mechanical and magnetic properties possessed by metallic glasses has attracted a lot of recent scientific and technological interest. The development of new metallic glass alloys with improved manufacturability, enhanced properties and higher ductility relies on the fundamental understanding of the interconnections between their atomic structure, glass forming ability (GFA), transport properties, and elastic and plastic deformation mechanisms. This thesis is focused on finding these atomic structure-property relationships in Cu-Zr BMGs using molecular dynamics simulations. In the first study described herein, molecular dynamics simulations of the rapid solidification process over the Cu-Zr compositional domain were conducted to explore inter-dependencies of atomic transport and fragility, elasticity and structural ordering, and GFA. The second study investigated the atomic origins of serration events, which is the characteristic plastic deformation behaviour in BMGs. The combined results of this work suggest that GFA and ductility of metallic glasses could be compositionally tuned.

Mechanisms by Which Dietary Fatty Acids Regulate Mitochondrial Structure-Function in Health and Disease.

PubMed

Sullivan, E Madison; Pennington, Edward Ross; Green, William D; Beck, Melinda A; Brown, David A; Shaikh, Saame Raza

2018-05-01

Mitochondria are the energy-producing organelles within a cell. Furthermore, mitochondria have a role in maintaining cellular homeostasis and proper calcium concentrations, building critical components of hormones and other signaling molecules, and controlling apoptosis. Structurally, mitochondria are unique because they have 2 membranes that allow for compartmentalization. The composition and molecular organization of these membranes are crucial to the maintenance and function of mitochondria. In this review, we first present a general overview of mitochondrial membrane biochemistry and biophysics followed by the role of different dietary saturated and unsaturated fatty acids in modulating mitochondrial membrane structure-function. We focus extensively on long-chain n-3 (ω-3) polyunsaturated fatty acids and their underlying mechanisms of action. Finally, we discuss implications of understanding molecular mechanisms by which dietary n-3 fatty acids target mitochondrial structure-function in metabolic diseases such as obesity, cardiac-ischemia reperfusion injury, obesity, type 2 diabetes, nonalcoholic fatty liver disease, and select cancers.

Polyvinylpyrrolidone-induced anisotropic growth of gold nanoprisms in plasmon-driven synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Yueming; DuChene, Joseph S.; Wang, Yi-Chung

After more than a decade, it is still unknown whether the plasmon-mediated growth of silver nanostructures can be extended to the synthesis of other noble metals, as the molecular mechanisms governing the growth process remain elusive. Herein, we demonstrate the plasmon-driven synthesis of gold nanoprisms and elucidate the details of the photochemical growth mechanism at the single-nanoparticle level. Our investigation reveals that the surfactant polyvinylpyrrolidone preferentially adsorbs along the nanoprism perimeter and serves as a photochemical relay to direct the anisotropic growth of gold nanoprisms. This discovery confers a unique function to polyvinylpyrrolidone that is fundamentally diferent from its widelymore » accepted role as a crystal-face-blocking ligand. Additionally, we find that nanocrystal twinning exerts a profound influence on the kinetics of this photochemical process by controlling the transport of plasmon-generated hot electrons to polyvinylpyrrolidone. These insights establish a molecular-level description of the underlying mechanisms regulating the plasmon-driven synthesis of gold nanoprisms.« less

Polyvinylpyrrolidone-induced anisotropic growth of gold nanoprisms in plasmon-driven synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Yueming; DuChene, Joseph S.; Wang, Yi-Chung

After more than a decade, it is still unknown whether the plasmon-mediated growth of silver nanostructures can be extended to the synthesis of other noble metals, as the molecular mechanisms governing the growth process remain elusive. In this paper, we demonstrate the plasmon-driven synthesis of gold nanoprisms and elucidate the details of the photochemical growth mechanism at the single-nanoparticle level. Our investigation reveals that the surfactant polyvinylpyrrolidone preferentially adsorbs along the nanoprism perimeter and serves as a photochemical relay to direct the anisotropic growth of gold nanoprisms. This discovery confers a unique function to polyvinylpyrrolidone that is fundamentally different frommore » its widely accepted role as a crystal-face-blocking ligand. Additionally, we find that nanocrystal twinning exerts a profound influence on the kinetics of this photochemical process by controlling the transport of plasmon-generated hot electrons to polyvinylpyrrolidone. Finally, these insights establish a molecular-level description of the underlying mechanisms regulating the plasmon-driven synthesis of gold nanoprisms.« less

Polyvinylpyrrolidone-induced anisotropic growth of gold nanoprisms in plasmon-driven synthesis

DOE PAGES

Zhai, Yueming; DuChene, Joseph S.; Wang, Yi-Chung; ...

2016-07-04

After more than a decade, it is still unknown whether the plasmon-mediated growth of silver nanostructures can be extended to the synthesis of other noble metals, as the molecular mechanisms governing the growth process remain elusive. In this paper, we demonstrate the plasmon-driven synthesis of gold nanoprisms and elucidate the details of the photochemical growth mechanism at the single-nanoparticle level. Our investigation reveals that the surfactant polyvinylpyrrolidone preferentially adsorbs along the nanoprism perimeter and serves as a photochemical relay to direct the anisotropic growth of gold nanoprisms. This discovery confers a unique function to polyvinylpyrrolidone that is fundamentally different frommore » its widely accepted role as a crystal-face-blocking ligand. Additionally, we find that nanocrystal twinning exerts a profound influence on the kinetics of this photochemical process by controlling the transport of plasmon-generated hot electrons to polyvinylpyrrolidone. Finally, these insights establish a molecular-level description of the underlying mechanisms regulating the plasmon-driven synthesis of gold nanoprisms.« less

Effect of Molecular Weight on the Ion Transport Mechanism in Polymerized Ionic Liquids

DOE PAGES

Fan, Fei; Wang, Weiyu; Holt, Adam P.; ...

2016-06-07

The unique properties of ionic liquids (ILs) have made them promising candidates for electrochemical applications. Polymerization of the corresponding ILs results in a new class of materials called polymerized ionic liquids (PolyILs). Though PolyILs offer the possibility to combine the high conductivity of ILs and the high mechanical strength of polymers, their conductivities are typically much lower than that of the corresponding small molecule ILs. In this study, seven PolyILs were synthesized having degrees of polymerization ranging from 1 to 333, corresponding to molecular weights (MW) from 482 to 160 400 g/mol. Depolarized dynamic light scattering, broadband dielectric spectroscopy, rheology,more » and differential scanning calorimetry were employed to systematically study the influence of MW on the mechanism of ionic transport and segmental dynamics in these materials. Finally, the modified Walden plot analysis reveals that the ion conductivity transforms from being closely coupled with structural relaxation to being strongly decoupled from it as MW increases.« less

New insights into the mechanisms of mammalian erythroid chromatin condensation and enucleation.

PubMed

Ji, Peng

2015-01-01

A unique feature in mammalian erythropoiesis is the dramatic chromatin condensation followed by enucleation. This step-by-step process starts at the beginning of terminal erythropoiesis after the hematopoietic stem cells are committed to erythroid lineage. Although this phenomenon is known for decades, the mechanisms of chromatin condensation and enucleation remain elusive. Recent advances in cell and molecular biology have started to reveal the molecular pathways in the regulation of chromatin condensation, the establishment of nuclear polarity prior enucleation, and the rearrangement of actin cytoskeleton in enucleation. However, many challenging questions, especially whether and how the apoptotic mechanisms are involved in chromatin condensation and how to dissect the functions of many actin cytoskeleton proteins in cytokinesis and enucleation, remain to be answered. Here I review our current understanding of mammalian erythroid chromatin condensation and enucleation during terminal differentiation with a focus on more recent studies. I conclude with my perspective of future works in this rising topic in developmental and cell biology. Copyright © 2015 Elsevier Inc. All rights reserved.

Effect of Molecular Weight on the Ion Transport Mechanism in Polymerized Ionic Liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, Fei; Wang, Weiyu; Holt, Adam P.

The unique properties of ionic liquids (ILs) have made them promising candidates for electrochemical applications. Polymerization of the corresponding ILs results in a new class of materials called polymerized ionic liquids (PolyILs). Though PolyILs offer the possibility to combine the high conductivity of ILs and the high mechanical strength of polymers, their conductivities are typically much lower than that of the corresponding small molecule ILs. In this study, seven PolyILs were synthesized having degrees of polymerization ranging from 1 to 333, corresponding to molecular weights (MW) from 482 to 160 400 g/mol. Depolarized dynamic light scattering, broadband dielectric spectroscopy, rheology,more » and differential scanning calorimetry were employed to systematically study the influence of MW on the mechanism of ionic transport and segmental dynamics in these materials. Finally, the modified Walden plot analysis reveals that the ion conductivity transforms from being closely coupled with structural relaxation to being strongly decoupled from it as MW increases.« less

Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanematsu, Yusuke; Tachikawa, Masanori

2014-11-14

Multicomponent quantum mechanical (MC-QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC-QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC-QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC-QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O–H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solventmore » effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC-QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.« less

Update on the Mechanisms of Liver Regeneration.

PubMed

Preziosi, Morgan E; Monga, Satdarshan P

2017-05-01

Liver possesses many critical functions such as synthesis, detoxification, and metabolism. It continually receives nutrient-rich blood from gut, which incidentally is also toxin-rich. That may be why liver is uniquely bestowed with a capacity to regenerate. A commonly studied procedure to understand the cellular and molecular basis of liver regeneration is that of surgical resection. Removal of two-thirds of the liver in rodents or patients instigates alterations in hepatic homeostasis, which are sensed by the deficient organ to drive the restoration process. Although the exact mechanisms that initiate regeneration are unknown, alterations in hemodynamics and metabolism have been suspected as important effectors. Key signaling pathways are activated that drive cell proliferation in various hepatic cell types through autocrine and paracrine mechanisms. Once the prehepatectomy mass is regained, the process of regeneration is adequately terminated. This review highlights recent discoveries in the cellular and molecular basis of liver regeneration. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

[Methods of quantitative proteomics].

PubMed

Kopylov, A T; Zgoda, V G

2007-01-01

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

Anomalous charge transport in conjugated polymers reveals underlying mechanisms of trapping and percolation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mollinger, Sonya A.; Salleo, Alberto; Spakowitz, Andrew J.

While transport in conjugated polymers has many similarities to that in crystalline inorganic materials, several key differences reveal the unique relationship between the morphology of polymer films and the charge mobility. We develop a model that directly incorporates the molecular properties of the polymer film and correctly predicts these unique transport features. At low degree of polymerization, the increase of the mobility with the polymer chain length reveals trapping at chain ends, and saturation of the mobility at high degree of polymerization results from conformational traps within the chains. Similarly, the inverse field dependence of the mobility reveals that transportmore » on single polymer chains is characterized by the ability of the charge to navigate around kinks and loops in the chain. Lastly, these insights emphasize the connection between the polymer conformations and the transport and thereby offer a route to designing improved device morphologies through molecular design and materials processing.« less

Anomalous charge transport in conjugated polymers reveals underlying mechanisms of trapping and percolation

DOE PAGES

Mollinger, Sonya A.; Salleo, Alberto; Spakowitz, Andrew J.

2016-11-10

While transport in conjugated polymers has many similarities to that in crystalline inorganic materials, several key differences reveal the unique relationship between the morphology of polymer films and the charge mobility. We develop a model that directly incorporates the molecular properties of the polymer film and correctly predicts these unique transport features. At low degree of polymerization, the increase of the mobility with the polymer chain length reveals trapping at chain ends, and saturation of the mobility at high degree of polymerization results from conformational traps within the chains. Similarly, the inverse field dependence of the mobility reveals that transportmore » on single polymer chains is characterized by the ability of the charge to navigate around kinks and loops in the chain. Lastly, these insights emphasize the connection between the polymer conformations and the transport and thereby offer a route to designing improved device morphologies through molecular design and materials processing.« less

Genetics, Molecular, and Proteomics Advances in Filamentous Fungi.

PubMed

Sharma Ghimire, Prakriti; Jin, Cheng

2017-10-01

Filamentous fungi play a dynamic role in health and the environment. In addition, their unique and complex hyphal structures are involved in their morphogenesis, integrity, synthesis, and degradation, according to environmental and physiological conditions and resource availability. However, in biotechnology, it has a great value in the production of enzymes, pharmaceuticals, and food ingredients. The beginning of nomenclature of overall fungi started in early 1990 after which the categorization, interior and exterior mechanism, function, molecular and genetics study took pace. This mini-review has emphasized some of the important aspects of filamentous fungi, their pattern of life cycle, history, and development of different strategic methods applied to exploit this unique organism. New trends and concepts that have been applied to overcome obstacle because of their basic structure related to genomics and systems biology has been presented. Furthermore, the future aspects and challenges that need to be deciphered to get a bigger and better picture of filamentous fungi have been discussed.

Structure-property relation and relevance of beam theories for microtubules: a coupled molecular and continuum mechanics study.

PubMed

Li, Si; Wang, Chengyuan; Nithiarasu, Perumal

2018-04-01

Quasi-one-dimensional microtubules (MTs) in cells enjoy high axial rigidity but large transverse flexibility due to the inter-protofilament (PF) sliding. This study aims to explore the structure-property relation for MTs and examine the relevance of the beam theories to their unique features. A molecular structural mechanics (MSM) model was used to identify the origin of the inter-PF sliding and its role in bending and vibration of MTs. The beam models were then fitted to the MSM to reveal how they cope with the distinct mechanical responses induced by the inter-PF sliding. Clear evidence showed that the inter-PF sliding is due to the soft inter-PF bonds and leads to the length-dependent bending stiffness. The Euler beam theory is found to adequately describe MT deformation when the inter-PF sliding is largely prohibited. Nevertheless, neither shear deformation nor the nonlocal effect considered in the 'more accurate' beam theories can fully capture the effect of the inter-PF sliding. This reflects the distinct deformation mechanisms between an MT and its equivalent continuous body.

Nano-Sized Cyclodextrin-Based Molecularly Imprinted Polymer Adsorbents for Perfluorinated Compounds—A Mini-Review

PubMed Central

Karoyo, Abdalla H.; Wilson, Lee D.

2015-01-01

Recent efforts have been directed towards the design of efficient and contaminant selective remediation technology for the removal of perfluorinated compounds (PFCs) from soils, sediments, and aquatic environments. While there is a general consensus on adsorption-based processes as the most suitable methodology for the removal of PFCs from aquatic environments, challenges exist regarding the optimal materials design of sorbents for selective uptake of PFCs. This article reviews the sorptive uptake of PFCs using cyclodextrin (CD)-based polymer adsorbents with nano- to micron-sized structural attributes. The relationship between synthesis of adsorbent materials and their structure relate to the overall sorption properties. Hence, the adsorptive uptake properties of CD-based molecularly imprinted polymers (CD-MIPs) are reviewed and compared with conventional MIPs. Further comparison is made with non-imprinted polymers (NIPs) that are based on cross-linking of pre-polymer units such as chitosan with epichlorohydrin in the absence of a molecular template. In general, MIPs offer the advantage of selectivity, chemical tunability, high stability and mechanical strength, ease of regeneration, and overall lower cost compared to NIPs. In particular, CD-MIPs offer the added advantage of possessing multiple binding sites with unique physicochemical properties such as tunable surface properties and morphology that may vary considerably. This mini-review provides a rationale for the design of unique polymer adsorbent materials that employ an intrinsic porogen via incorporation of a macrocyclic compound in the polymer framework to afford adsorbent materials with tunable physicochemical properties and unique nanostructure properties. PMID:28347047

Universal mechanism of thermo-mechanical deformation in metallic glasses

DOE PAGES

Dmowski, W.; Tong, Y.; Iwashita, T.; ...

2015-02-11

Here we investigated the atomistic structure of metallic glasses subjected to thermo-mechanical creep deformation using high energy x-ray diffraction and molecular dynamics simulation. The experiments were performed in-situ, at high temperatures as a time dependent deformation in the elastic regime, and ex-situ on samples quenched under stress. We show that all the anisotropic structure functions of the samples undergone thermo-mechanical creep can be scaled into a single curve, regardless of the magnitude of anelastic strain, stress level and the sign of the stress, demonstrating universal behavior and pointing to unique atomistic unit of anelastic deformation. The structural changes due tomore » creep are strongly localized within the second nearest neighbors, involving only a small group of atoms.« less

Molecular analysis of post-harvest withering in grape by AFLP transcriptional profiling

PubMed Central

Zamboni, Anita; Minoia, Leone; Ferrarini, Alberto; Tornielli, Giovanni Battista; Zago, Elisa; Delledonne, Massimo; Pezzotti, Mario

2008-01-01

Post-harvest withering of grape berries is used in the production of dessert and fortified wines to alter must quality characteristics and increase the concentration of simple sugars. The molecular processes that occur during withering are poorly understood, so a detailed transcriptomic analysis of post-harvest grape berries was carried out by AFLP-transcriptional profiling analysis. This will help to elucidate the molecular mechanisms of berry withering and will provide an opportunity to select markers that can be used to follow the drying process and evaluate different drying techniques. AFLP-TP identified 699 withering-specific genes, 167 and 86 of which were unique to off-plant and on-plant withering, respectively. Although similar molecular events were revealed in both withering processes, it was apparent that off-plant withering induced a stronger dehydration stress response resulting in the high level expression of genes involved in stress protection mechanisms, such as dehydrin and osmolite accumulation. Genes involved in hexose metabolism and transport, cell wall composition, and secondary metabolism (particularly the phenolic and terpene compound pathways) were similarly regulated in both processes. This work provides the first comprehensive analysis of the molecular events underpinning post-harvest withering and could help to define markers for different withering processes. PMID:19010774

Molecular analysis of post-harvest withering in grape by AFLP transcriptional profiling.

PubMed

Zamboni, Anita; Minoia, Leone; Ferrarini, Alberto; Tornielli, Giovanni Battista; Zago, Elisa; Delledonne, Massimo; Pezzotti, Mario

2008-01-01

Post-harvest withering of grape berries is used in the production of dessert and fortified wines to alter must quality characteristics and increase the concentration of simple sugars. The molecular processes that occur during withering are poorly understood, so a detailed transcriptomic analysis of post-harvest grape berries was carried out by AFLP-transcriptional profiling analysis. This will help to elucidate the molecular mechanisms of berry withering and will provide an opportunity to select markers that can be used to follow the drying process and evaluate different drying techniques. AFLP-TP identified 699 withering-specific genes, 167 and 86 of which were unique to off-plant and on-plant withering, respectively. Although similar molecular events were revealed in both withering processes, it was apparent that off-plant withering induced a stronger dehydration stress response resulting in the high level expression of genes involved in stress protection mechanisms, such as dehydrin and osmolite accumulation. Genes involved in hexose metabolism and transport, cell wall composition, and secondary metabolism (particularly the phenolic and terpene compound pathways) were similarly regulated in both processes. This work provides the first comprehensive analysis of the molecular events underpinning post-harvest withering and could help to define markers for different withering processes.

Biosynthesis of Polyunsaturated Fatty Acids in Marine Invertebrates: Recent Advances in Molecular Mechanisms

PubMed Central

Monroig, Óscar; Tocher, Douglas R.; Navarro, Juan C.

2013-01-01

Virtually all polyunsaturated fatty acids (PUFA) originate from primary producers but can be modified by bioconversions as they pass up the food chain in a process termed trophic upgrading. Therefore, although the main primary producers of PUFA in the marine environment are microalgae, higher trophic levels have metabolic pathways that can produce novel and unique PUFA. However, little is known about the pathways of PUFA biosynthesis and metabolism in the levels between primary producers and fish that are largely filled by invertebrates. It has become increasingly apparent that, in addition to trophic upgrading, de novo synthesis of PUFA is possible in some lower animals. The unequivocal identification of PUFA biosynthetic pathways in many invertebrates is complicated by the presence of other organisms within them. These organisms include bacteria and algae with PUFA biosynthesis pathways, and range from intestinal flora to symbiotic relationships that can involve PUFA translocation to host organisms. This emphasizes the importance of studying biosynthetic pathways at a molecular level, and the continual expansion of genomic resources and advances in molecular analysis is facilitating this. The present paper highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine invertebrates, particularly focusing on cephalopod molluscs. PMID:24152561

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

NASA Astrophysics Data System (ADS)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Two-dimensional infrared spectroscopy of vibrational polaritons.

PubMed

Xiang, Bo; Ribeiro, Raphael F; Dunkelberger, Adam D; Wang, Jiaxi; Li, Yingmin; Simpkins, Blake S; Owrutsky, Jeffrey C; Yuen-Zhou, Joel; Xiong, Wei

2018-05-08

We report experimental 2D infrared (2D IR) spectra of coherent light-matter excitations--molecular vibrational polaritons. The application of advanced 2D IR spectroscopy to vibrational polaritons challenges and advances our understanding in both fields. First, the 2D IR spectra of polaritons differ drastically from free uncoupled excitations and a new interpretation is needed. Second, 2D IR uniquely resolves excitation of hybrid light-matter polaritons and unexpected dark states in a state-selective manner, revealing otherwise hidden interactions between them. Moreover, 2D IR signals highlight the impact of molecular anharmonicities which are applicable to virtually all molecular systems. A quantum-mechanical model is developed which incorporates both nuclear and electrical anharmonicities and provides the basis for interpreting this class of 2D IR spectra. This work lays the foundation for investigating phenomena of nonlinear photonics and chemistry of molecular vibrational polaritons which cannot be probed with traditional linear spectroscopy.

Protein mechanics: from single molecules to functional biomaterials.

PubMed

Li, Hongbin; Cao, Yi

2010-10-19

Elastomeric proteins act as the essential functional units in a wide variety of biomechanical machinery and serve as the basic building blocks for biological materials that exhibit superb mechanical properties. These proteins provide the desired elasticity, mechanical strength, resilience, and toughness within these materials. Understanding the mechanical properties of elastomeric protein-based biomaterials is a multiscale problem spanning from the atomistic/molecular level to the macroscopic level. Uncovering the design principles of individual elastomeric building blocks is critical both for the scientific understanding of multiscale mechanics of biomaterials and for the rational engineering of novel biomaterials with desirable mechanical properties. The development of single-molecule force spectroscopy techniques has provided methods for characterizing mechanical properties of elastomeric proteins one molecule at a time. Single-molecule atomic force microscopy (AFM) is uniquely suited to this purpose. Molecular dynamic simulations, protein engineering techniques, and single-molecule AFM study have collectively revealed tremendous insights into the molecular design of single elastomeric proteins, which can guide the design and engineering of elastomeric proteins with tailored mechanical properties. Researchers are focusing experimental efforts toward engineering artificial elastomeric proteins with mechanical properties that mimic or even surpass those of natural elastomeric proteins. In this Account, we summarize our recent experimental efforts to engineer novel artificial elastomeric proteins and develop general and rational methodologies to tune the nanomechanical properties of elastomeric proteins at the single-molecule level. We focus on general design principles used for enhancing the mechanical stability of proteins. These principles include the development of metal-chelation-based general methodology, strategies to control the unfolding hierarchy of multidomain elastomeric proteins, and the design of novel elastomeric proteins that exhibit stimuli-responsive mechanical properties. Moving forward, we are now exploring the use of these artificial elastomeric proteins as building blocks of protein-based biomaterials. Ultimately, we would like to rationally tailor mechanical properties of elastomeric protein-based materials by programming the molecular sequence, and thus nanomechanical properties, of elastomeric proteins at the single-molecule level. This step would help bridge the gap between single protein mechanics and material biomechanics, revealing how the mechanical properties of individual elastomeric proteins are translated into the properties of macroscopic materials.

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Photoactuators for Direct Optical-to-Mechanical Energy Conversion: From Nanocomponent Assembly to Macroscopic Deformation.

PubMed

Hu, Ying; Li, Zhe; Lan, Tian; Chen, Wei

2016-12-01

Photoactuators with integrated optical-to-mechanical energy conversion capacity have attracted growing research interest in the last few decades due to their unique features of remote control and their wide applications ranging from bionic robots, biomedical devices, and switches to motors. For the photoactuator design, the energy conversion route and structure assembly are two important parts, which directly affect the performance of the photoactuators. In particular, the architectural designs at the molecular, nano-, micro-, and macro- level, are found to play a significant role in accumulating molecular-scale strain/stress to macroscale strain/stress. Here, recent progress on photoactuators based on photochemical and photothermal effects is summarized, followed by a discussion of the important assembly strategies for the amplification of the photoresponsive components at nanoscale to macroscopic scale motions. The application advancement of current photoactuators is also presented. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanisms of input and output synaptic specificity: finding partners, building synapses, and fine-tuning communication.

PubMed

Rawson, Randi L; Martin, E Anne; Williams, Megan E

2017-08-01

For most neurons to function properly, they need to develop synaptic specificity. This requires finding specific partner neurons, building the correct types of synapses, and fine-tuning these synapses in response to neural activity. Synaptic specificity is common at both a neuron's input and output synapses, whereby unique synapses are built depending on the partnering neuron. Neuroscientists have long appreciated the remarkable specificity of neural circuits but identifying molecular mechanisms mediating synaptic specificity has only recently accelerated. Here, we focus on recent progress in understanding input and output synaptic specificity in the mammalian brain. We review newly identified circuit examples for both and the latest research identifying molecular mediators including Kirrel3, FGFs, and DGLα. Lastly, we expect the pace of research on input and output specificity to continue to accelerate with the advent of new technologies in genomics, microscopy, and proteomics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular, Cellular and Functional Events in Axonal Sprouting after Stroke

PubMed Central

Kathirvelu, Balachander; Schweppe, Catherine A; Nie, Esther H

2016-01-01

Stroke is the leading cause of adult disability. Yet there is a limited degree of recovery in this disease. One of the mechanisms of recovery is the formation of new connections in the brain and spinal cord after stroke: post-stroke axonal sprouting. Studies indicate that post-stroke axonal sprouting occurs in mice, rats, primates and humans. Inducing post-stroke axonal sprouting in specific connections enhances recovery; blocking axonal sprouting impairs recovery. Behavioral activity patterns after stroke modify the axonal sprouting response. A unique regenerative molecular program mediates this aspect of tissue repair in the CNS. The types of connections that are formed after stroke indicate three patterns of axonal sprouting after stroke: Reactive, Reparative and Unbounded Axonal Sprouting. These differ in mechanism, location, relationship to behavioral recovery and, importantly, in their prospect for therapeutic manipulation to enhance tissue repair. PMID:26874223

The ethics of molecular memory modification.

PubMed

Hui, Katrina; Fisher, Carl E

2015-07-01

Novel molecular interventions have recently shown the potential to erase, enhance and alter specific long-term memories. Unique features of this form of memory modification call for a close examination of its possible applications. While there have been discussions of the ethics of memory modification in the literature, molecular memory modification (MMM) can provide special insights. Previously raised ethical concerns regarding memory enhancement, such as safety issues, the 'duty to remember', selfhood and personal identity, require re-evaluation in light of MMM. As a technology that exploits the brain's updating processes, MMM helps correct the common misconception that memory is a static entity by demonstrating how memory is plastic and subject to revision even in the absence of external manipulation. Furthermore, while putatively safer than other speculative technologies because of its high specificity, MMM raises notable safety issues, including potential insidious effects on the agent's emotions and personal identity. Nonetheless, MMM possesses characteristics of a more permissible form of modification, not only because it is theoretically safer, but because its unique mechanism of action requires a heightened level of cooperation from the agent. Discussions of memory modification must consider the specific mechanisms of action, which can alter the weight and relevance of various ethical concerns. MMM also highlights the need for conceptual accuracy regarding the term 'enhancement'; this umbrella term will have to be differentiated as new technologies are applied to a widening array of purposes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Unconventional molecule-resolved current rectification in diamondoid–fullerene hybrids

PubMed Central

Randel, Jason C.; Niestemski, Francis C.; Botello-Mendez, Andrés R.; Mar, Warren; Ndabashimiye, Georges; Melinte, Sorin; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Butova, Ekaterina D.; Fokin, Andrey A.; Schreiner, Peter R.; Charlier, Jean-Christophe; Manoharan, Hari C.

2014-01-01

The unimolecular rectifier is a fundamental building block of molecular electronics. Rectification in single molecules can arise from electron transfer between molecular orbitals displaying asymmetric spatial charge distributions, akin to p–n junction diodes in semiconductors. Here we report a novel all-hydrocarbon molecular rectifier consisting of a diamantane–C60 conjugate. By linking both sp3 (diamondoid) and sp2 (fullerene) carbon allotropes, this hybrid molecule opposingly pairs negative and positive electron affinities. The single-molecule conductances of self-assembled domains on Au(111), probed by low-temperature scanning tunnelling microscopy and spectroscopy, reveal a large rectifying response of the molecular constructs. This specific electronic behaviour is postulated to originate from the electrostatic repulsion of diamantane–C60 molecules due to positively charged terminal hydrogen atoms on the diamondoid interacting with the top electrode (scanning tip) at various bias voltages. Density functional theory computations scrutinize the electronic and vibrational spectroscopic fingerprints of this unique molecular structure and corroborate the unconventional rectification mechanism. PMID:25202942

The Generation of Novel MR Imaging Techniques to Visualize Inflammatory/Degenerative Mechanisms and the Correlation of MR Data with 3D Microscopic Changes

DTIC Science & Technology

2013-09-01

existing MR scanning systems providing the ability to visualize structures that are impossible with current methods . Using techniques to concurrently...and unique system for analysis of affected brain regions and coupled with other imaging techniques and molecular measurements holds significant...scanning systems providing the ability to visualize structures that are impossible with current methods . Using techniques to concurrently stain

New medications for substance use disorders: challenges and opportunities.

PubMed

Volkow, Nora D; Skolnick, Phil

2012-01-01

An increased understanding of the biological mechanisms underlying the process of addiction has led to unique molecular targets and strategies for pharmacotherapies against addiction. However, the successful translation of these discoveries will require: 1) a more active engagement of the pharmaceutical sector, 2) partnership with regulatory agencies to arrive at meaningful outcomes for medication approval and 3) a greater involvement of the healthcare system in the screening and treatment of substance use disorders.

Individualised cancer therapeutics: dream or reality? Therapeutics construction.

PubMed

Shen, Yuqiao; Senzer, Neil; Nemunaitis, John

2005-11-01

The analysis of DNA microarray and proteomic data, and the subsequent integration into functional expression sets, provides a circuit map of the hierarchical cellular networks responsible for sustaining the viability and environmental competitiveness of cancer cells, that is, their robust systematics. These technologies can be used to 'snapshot' the unique patterns of molecular derangements and modified interactions in cancer, and allow for strategic selection of therapeutics that best match the individual profile of the tumour. This review highlights technology that can be used to selectively disrupt critical molecular targets and describes possible vehicles to deliver the synthesised molecular therapeutics to the relevant cellular compartments of the malignant cells. RNA interference (RNAi) involves a group of evolutionarily conserved gene silencing mechanisms in which small sequences of double-stranded RNA or intrinsic antisense RNA trigger mRNA cleavage or translational repression, respectively. Although RNAi molecules can be synthesised to 'silence' virtually any gene, even if upregulated, a mechanism for selective delivery of RNAi effectors to sites of malignant disease remains challenging. The authors will discuss gene-modified conditionally replicating viruses as candidate vehicles for the delivery of RNAi.

Investigations of Takeout proteins' ligand binding and release mechanism using molecular dynamics simulation.

PubMed

Zhang, Huijing; Yu, Hui; Zhao, Xi; Liu, Xiaoguang; Feng, Xianli; Huang, Xuri

2017-05-01

Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.

Advancing neuroscience through epigenetics: molecular mechanisms of learning and memory.

PubMed

Molfese, David L

2011-01-01

Humans share 96% of our 30,000 genes with Chimpanzees. The 1,200 genes that differ appear at first glance insufficient to describe what makes us human and them apes. However, we are now discovering that the mechanisms that regulate how genes are expressed tell a much richer story than our DNA alone. Sections of our DNA are constantly being turned on or off, marked for easy access, or secluded and hidden away, all in response to ongoing cellular activity. In the brain, neurons encode information-in effect memories-at the cellular level. Yet while memories may last a lifetime, neurons are dynamic structures. Every protein in the synapse undergoes some form of turnover, some with half-lives of only hours. How can a memory persist beyond the lifetimes of its constitutive molecular building blocks? Epigenetics-changes in gene expression that do not alter the underlying DNA sequence-may be the answer. In this article, epigenetic mechanisms including DNA methylation and acetylation or methylation of the histone proteins that package DNA are described in the context of animal learning. Through the interaction of these modifications a "histone code" is emerging wherein individual memories leave unique memory traces at the molecular level with distinct time courses. A better understanding of these mechanisms has implications for treatment of memory disorders caused by normal aging or diseases including schizophrenia, Alzheimer's, depression, and drug addiction.

Toughening mechanism in elastomer-modified epoxy resins, part 2

NASA Technical Reports Server (NTRS)

Yee, A. F.; Pearson, R. A.

1984-01-01

The role of matrix ductility on the toughenability and toughening mechanism of elastomer-modified DGEBRA epoxies was investigated. Matrix ductility was varied by using epoxide resins of varying epoxide monomer molecular weights. These epoxide resins were cured using 4,4' diaminodiphenyl sulfone (DDS) and, in some cases, modified with 10% HYCAR(r)CTBN 1300X8. Fracture roughness values for the neat epoxies were found to be almost independent on the monomer molecular weight of the epoxide resin used. However, it was found that the fracture toughness of the elastomer-modified epoxies was very dependent upon the epoxide monomer molecular weight. Tensile dilatometry indicated that the toughening mechanism, when present, is similar to the mechanisms found for the piperidine cured epoxies in Part 1. SEM and OM corroborate this finding. Dynamic mechanical studies were conducted to shed light on the toughenability of the epoxies. The time-dependent small strain behavior of these epoxies were separated into their bulk and shear components. The bulk component is related to brittle fracture, whereas the shear component is related to yielding. It can be shown that the rates of shear and bulk strain energy buildup for a given stress are uniquely determined by the values of Poisson's ratio, nu. It was found that nu increases as the monomer molecular weight of the epoxide resin used increases. This increase in nu can be associated with the low temperature beta relaxation. The effect of increasing cross-link density is to shift the beta relaxation to higher temperatures and to decrease the magnitude of the beta relaxation. Thus, increasing cross-link density decreases nu and increases the tendency towards brittle fracture.

A unique dosing system for the production of OH under high vacuum for the study of environmental heterogeneous reactions.

PubMed

Brown, Matthew A; Johánek, Viktor; Hemminger, John C

2008-02-01

A unique dosing system for the production of hydroxyl radicals under high vacuum for the study of environmental heterogeneous reactions is described. Hydroxyl radicals are produced by the photodissociation of a hydrogen peroxide aqueous gas mixture with 254 nm radiation according to the reaction H2O2+hnu (254 nm)-->OH+OH. Under the conditions of the current design, 0.6% conversion of hydrogen peroxide is expected yielding a hydroxyl number density on the order of 10(10) molecules/cm3. The flux distribution of the dosing system is calculated using a Monte Carlo simulation method and compared with the experimentally determined results. The performance of this unique hydroxyl dosing system is demonstrated for the heterogeneous reaction with a solid surface of potassium iodide. Coupling of the hydroxyl radical dosing system to a quantitative surface analysis system should help provide molecular level insight into detailed reaction mechanisms.

Whipworm kinomes reflect a unique biology and adaptation to the host animal.

PubMed

Stroehlein, Andreas J; Young, Neil D; Korhonen, Pasi K; Chang, Bill C H; Nejsum, Peter; Pozio, Edoardo; La Rosa, Giuseppe; Sternberg, Paul W; Gasser, Robin B

2017-11-01

Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris, using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Molecular Mechanisms behind the Physiological Resistance to Intense Transient Warming in an Iconic Marine Plant

PubMed Central

Marín-Guirao, Lazaro; Entrambasaguas, Laura; Dattolo, Emanuela; Ruiz, Juan M.; Procaccini, Gabriele

2017-01-01

The endemic Mediterranean seagrass Posidonia oceanica is highly threatened by the increased frequency and intensity of heatwaves. Meadows of the species offer a unique opportunity to unravel mechanisms marine plants activate to cope transient warming, since their wide depth distribution impose divergent heat-tolerance. Understanding these mechanisms is imperative for their conservation. Shallow and deep genotypes within the same population were exposed to a simulated heatwave in mesocosms, to analyze their transcriptomic and photo-physiological responses during and after the exposure. Shallow plants, living in a more unstable thermal environment, optimized phenotype variation in response to warming. These plants showed a pre-adaptation of genes in anticipation of stress. Shallow plants also showed a stronger activation of heat-responsive genes and the exclusive activation of genes involved in epigenetic mechanisms and in molecular mechanisms that are behind their higher photosynthetic stability and respiratory acclimation. Deep plants experienced higher heat-induced damage and activated metabolic processes for obtaining extra energy from sugars and amino acids, likely to support the higher protein turnover induced by heat. In this study we identify transcriptomic mechanisms that may facilitate persistence of seagrasses to anomalous warming events and we discovered that P. oceanica plants from above and below the mean depth of the summer thermocline have differential resilience to heat. PMID:28706528

Small interstellar molecules and what they tell us

NASA Astrophysics Data System (ADS)

Neufeld, David A.

2018-06-01

Observations at ultraviolet, visible, infrared and radio wavelengths provide a wealth of information about the molecular inventory of the interstellar medium (ISM). Because of the different chemical pathways responsible for their formation and destruction, different molecules probe specific aspects of the interstellar environment. Carefully interpreted with the use of astrochemical models, they provide unique information of general astrophysical importance, yielding estimates of the cosmic ray density, the molecular fraction, the ultraviolet radiation field, and the dissipation of energy within the turbulent ISM. Laboratory experiments and quantum-mechanical calculations are essential both in providing the spectroscopic data needed to identify interstellar molecules and for elucidating the fundamental physical and chemical processes that must be included in astrochemical models.

Nanomechanics of silk: the fundamentals of a strong, tough and versatile material

NASA Astrophysics Data System (ADS)

Su, Isabelle; Buehler, Markus J.

2016-07-01

Spider silk is a remarkable material that provides a template for upscaling molecular properties to the macroscale. In this article we review fundamental aspects of the mechanisms behind these behaviors, discuss the molecular makeup, chemical designs, and how these integrate in a complex arrangement to form webs, cocoons and other material architectures. Moreover, this review paper explores the unique ability of silk to tolerate various kinds of defects, in a way enabling this material platform to serve as one of the most resilient materials in nature. We conclude the discussion with a summary of key scaling laws, an attempt model and define hierarchical length-scales, and the translation to synthetic materials.

Catalytic processes in the atmospheres of earth and Venus

NASA Technical Reports Server (NTRS)

Demore, W. B.; Yung, Y. L.

1982-01-01

Photochemical processes in planetary atmospheres are strongly influenced by catalytic effects of minor constituents. Catalytic cycles in the atmospheres of Earth and Venus are closely related. For example, chlorine oxides (ClOx) act as catalysts in the two atmospheres. On earth, they serve to convert odd oxygen (atomic oxygen and ozone) to molecular oxygen. On Venus they have a similar effect, but in addition they accelerate the reactions of atomic and molecular oxygen with carbon monoxide. The latter process occurs by a unique combination of ClOx catalysis and sulful dioxide photosensitization. The mechanism provides an explanation for the very low extent of carbon dioxide decomposition by sunlight in the Venus atmosphere.

Nanomechanics of silk: the fundamentals of a strong, tough and versatile material.

PubMed

Su, Isabelle; Buehler, Markus J

2016-07-29

Spider silk is a remarkable material that provides a template for upscaling molecular properties to the macroscale. In this article we review fundamental aspects of the mechanisms behind these behaviors, discuss the molecular makeup, chemical designs, and how these integrate in a complex arrangement to form webs, cocoons and other material architectures. Moreover, this review paper explores the unique ability of silk to tolerate various kinds of defects, in a way enabling this material platform to serve as one of the most resilient materials in nature. We conclude the discussion with a summary of key scaling laws, an attempt model and define hierarchical length-scales, and the translation to synthetic materials.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Transcriptional Mechanisms Underlying Hemoglobin Synthesis

PubMed Central

Katsumura, Koichi R.; DeVilbiss, Andrew W.; Pope, Nathaniel J.; Johnson, Kirby D.; Bresnick, Emery H.

2013-01-01

The physiological switch in expression of the embryonic, fetal, and adult β-like globin genes has garnered enormous attention from investigators interested in transcriptional mechanisms and the molecular basis of hemoglobinopathies. These efforts have led to the discovery of cell type-specific transcription factors, unprecedented mechanisms of transcriptional coregulator function, genome biology principles, unique contributions of nuclear organization to transcription and cell function, and promising therapeutic targets. Given the vast literature accrued on this topic, this article will focus on the master regulator of erythroid cell development and function GATA-1, its associated proteins, and its frontline role in controlling hemoglobin synthesis. GATA-1 is a crucial regulator of genes encoding hemoglobin subunits and heme biosynthetic enzymes. GATA-1-dependent mechanisms constitute an essential regulatory core that nucleates additional mechanisms to achieve the physiological control of hemoglobin synthesis. PMID:23838521

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

NASA Astrophysics Data System (ADS)

Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

2018-04-01

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

PubMed

Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

2018-04-23

Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

Elucidating the Aβ42 Anti-Aggregation Mechanism of Action of Tramiprosate in Alzheimer's Disease: Integrating Molecular Analytical Methods, Pharmacokinetic and Clinical Data.

PubMed

Kocis, Petr; Tolar, Martin; Yu, Jeremy; Sinko, William; Ray, Soumya; Blennow, Kaj; Fillit, Howard; Hey, John A

2017-06-01

Amyloid beta (Aβ) oligomers play a critical role in the pathogenesis of Alzheimer's disease (AD) and represent a promising target for drug development. Tramiprosate is a small-molecule Aβ anti-aggregation agent that was evaluated in phase III clinical trials for AD but did not meet the primary efficacy endpoints; however, a pre-specified subgroup analysis revealed robust, sustained, and clinically meaningful cognitive and functional effects in patients with AD homozygous for the ε4 allele of apolipoprotein E4 (APOE4/4 homozygotes), who carry an increased risk for the disease. Therefore, to build on this important efficacy attribute and to further improve its pharmaceutical properties, we have developed a prodrug of tramiprosate ALZ-801 that is in advanced stages of clinical development. To elucidate how tramiprosate works, we investigated its molecular mechanism of action (MOA) and the translation to observed clinical outcomes. The two main objectives of this research were to (1) elucidate and characterize the MOA of tramiprosate via an integrated application of three independent molecular methodologies and (2) present an integrated translational analysis that links the MOA, conformation of the target, stoichiometry, and pharmacokinetic dose exposure to the observed clinical outcome in APOE4/4 homozygote subjects. We used three molecular analytical methods-ion mobility spectrometry-mass spectrometry (IMS-MS), nuclear magnetic resonance (NMR), and molecular dynamics-to characterize the concentration-related interactions of tramiprosate versus Aβ42 monomers and the resultant conformational alterations affecting aggregation into oligomers. The molecular stoichiometry of the tramiprosate versus Aβ42 interaction was further analyzed in the context of clinical pharmacokinetic dose exposure and central nervous system Aβ42 levels (i.e., pharmacokinetic-pharmacodynamic translation in humans). We observed a multi-ligand interaction of tramiprosate with monomeric Aβ42, which differs from the traditional 1:1 binding. This resulted in the stabilization of Aβ42 monomers and inhibition of oligomer formation and elongation, as demonstrated by IMS-MS and molecular dynamics. Using NMR spectroscopy and molecular dynamics, we also showed that tramiprosate bound to Lys16, Lys28, and Asp23, the key amino acid side chains of Aβ42 that are responsible for both conformational seed formation and neuronal toxicity. The projected molar excess of tramiprosate versus Aβ42 in humans using the dose effective in patients with AD aligned with the molecular stoichiometry of the interaction, providing a clear clinical translation of the MOA. A consistent alignment of these preclinical-to-clinical elements describes a unique example of translational medicine and supports the efficacy seen in symptomatic patients with AD. This unique "enveloping mechanism" of tramiprosate also provides a potential basis for tramiprosate dose selection for patients with homozygous AD at earlier stages of disease. We have identified the molecular mechanism that may account for the observed clinical efficacy of tramiprosate in patients with APOE4/4 homozygous AD. In addition, the integrated application of the molecular methodologies (i.e., IMS-MS, NMR, and thermodynamics analysis) indicates that it is feasible to modulate and control the Aβ42 conformational dynamics landscape by a small molecule, resulting in a favorable Aβ42 conformational change that leads to a clinically relevant amyloid anti-aggregation effect and inhibition of oligomer formation. This novel enveloping MOA of tramiprosate has potential utility in the development of disease-modifying therapies for AD and other neurodegenerative diseases caused by misfolded proteins.

Identification of up-regulated genes from the metal-hyperaccumulator aquatic fern Salvinia minima Baker, in response to lead exposure.

PubMed

Leal-Alvarado, Daniel A; Martínez-Hernández, A; Calderón-Vázquez, C L; Uh-Ramos, D; Fuentes, G; Ramírez-Prado, J H; Sáenz-Carbonell, L; Santamaría, J M

2017-12-01

Lead (Pb) is one of the most serious environmental pollutants. The aquatic fern Salvinia minima Baker is capable to hyper-accumulate Pb in their tissues. However, the molecular mechanisms involved in its Pb accumulation and tolerance capacity are not fully understood. In order to investigate the molecular mechanisms that are activated by S. minima in response to Pb, we constructed a suppression subtractive hybridization library (SSH) in response to an exposure to 40μM of Pb(NO 3 ) 2 for 12h. 365 lead-related differentially expressed sequences tags (ESTs) were isolated and sequenced. Among these ESTs, 143 unique cDNA (97 were registered at the GenBank and 46 ESTs were not registered, because they did not meet the GenBank conditions). Those ESTs were identified and classified into 3 groups according to Blast2GO. In terms of metabolic pathways, they were grouped into 29 KEGG pathways. Among the ESTs, we identified some that might be part of the mechanism that this fern may have to deal with this metal, including abiotic-stress-related transcription factors, some that might be involved in tolerance mechanisms such as ROS scavenging, membrane protection, and those of cell homeostasis recovery. To validate the SSH library, 4 genes were randomly selected from the library and analyzed by qRT-PCR. These 4 genes were transcriptionally up-regulated in response to lead in at least one of the two tested tissues (roots and leaves). The present library is one of the few genomics approaches to study the response to metal stress in an aquatic fern, representing novel molecular information and tools to understand the molecular physiology of its Pb tolerance and hyperaccumulation capacity. Further research is required to elucidate the functions of the lead-induced genes that remain classified as unknown, to perhaps reveal novel molecular mechanisms of Pb tolerance and accumulation capacity in aquatic plants. Copyright © 2017 Elsevier B.V. All rights reserved.

Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review.

PubMed

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-09-01

Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades has yielded remarkable novel insights in understanding the development and progression of certain diseases, such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine. In this paper, we reviewed the utilization of AFM to characterize cell mechanics. First, the principle and method of AFM single-cell mechanical analysis was presented, along with the mechanical responses of cells to representative external stimuli measured by AFM. Next, the unique changes of cell mechanics in two types of physiological processes (stem cell differentiation, cancer metastasis) revealed by AFM were summarized. After that, the molecular mechanisms guiding cell mechanics were analyzed. Finally the challenges and future directions were discussed.

Controlling Hydrogel Mechanics via Bio-Inspired Polymer-Nanoparticle Bond Dynamics.

PubMed

Li, Qiaochu; Barrett, Devin G; Messersmith, Phillip B; Holten-Andersen, Niels

2016-01-26

Interactions between polymer molecules and inorganic nanoparticles can play a dominant role in nanocomposite material mechanics, yet control of such interfacial interaction dynamics remains a significant challenge particularly in water. This study presents insights on how to engineer hydrogel material mechanics via nanoparticle interface-controlled cross-link dynamics. Inspired by the adhesive chemistry in mussel threads, we have incorporated iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network to obtain hydrogels cross-linked via reversible metal-coordination bonds at Fe3O4 NP surfaces. Unique material mechanics result from the supra-molecular cross-link structure dynamics in the gels; in contrast to the previously reported fluid-like dynamics of transient catechol-Fe(3+) cross-links, the catechol-Fe3O4 NP structures provide solid-like yet reversible hydrogel mechanics. The structurally controlled hierarchical mechanics presented here suggest how to develop hydrogels with remote-controlled self-healing dynamics.

Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/β-catenin signaling

PubMed Central

Amen, Melanie; Espinoza, Herbert M.; Cox, Carol; Liang, Xiaowen; Wang, Jianbo; Link, Todd M. E.; Brennan, Richard G.; Martin, James F.; Amendt, Brad A.

2008-01-01

Homeodomain (HD) transcriptional activities are tightly regulated during embryogenesis and require protein interactions for their spatial and temporal activation. The chromatin-associated high mobility group protein (HMG-17) is associated with transcriptionally active chromatin, however its role in regulating gene expression is unclear. This report reveals a unique strategy in which, HMG-17 acts as a molecular switch regulating HD transcriptional activity. The switch utilizes the Wnt/β-catenin signaling pathway and adds to the diverse functions of β-catenin. A high-affinity HMG-17 interaction with the PITX2 HD protein inhibits PITX2 DNA-binding activity. The HMG-17/PITX2 inactive complex is concentrated to specific nuclear regions primed for active transcription. β-Catenin forms a ternary complex with PITX2/HMG-17 to switch it from a repressor to an activator complex. Without β-catenin, HMG-17 can physically remove PITX2 from DNA to inhibit its transcriptional activity. The PITX2/HMG-17 regulatory complex acts independently of promoter targets and is a general mechanism for the control of HD transcriptional activity. HMG-17 is developmentally regulated and its unique role during embryogenesis is revealed by the early embryonic lethality of HMG-17 homozygous mice. This mechanism provides a new role for canonical Wnt/β-catenin signaling in regulating HD transcriptional activity during development using HMG-17 as a molecular switch. PMID:18045789

Glass transition of polymers in bulk, confined geometries, and near interfaces

NASA Astrophysics Data System (ADS)

Napolitano, Simone; Glynos, Emmanouil; Tito, Nicholas B.

2017-03-01

When cooled or pressurized, polymer melts exhibit a tremendous reduction in molecular mobility. If the process is performed at a constant rate, the structural relaxation time of the liquid eventually exceeds the time allowed for equilibration. This brings the system out of equilibrium, and the liquid is operationally defined as a glass—a solid lacking long-range order. Despite almost 100 years of research on the (liquid/)glass transition, it is not yet clear which molecular mechanisms are responsible for the unique slow-down in molecular dynamics. In this review, we first introduce the reader to experimental methodologies, theories, and simulations of glassy polymer dynamics and vitrification. We then analyse the impact of connectivity, structure, and chain environment on molecular motion at the length scale of a few monomers, as well as how macromolecular architecture affects the glass transition of non-linear polymers. We then discuss a revised picture of nanoconfinement, going beyond a simple picture based on interfacial interactions and surface/volume ratio. Analysis of a large body of experimental evidence, results from molecular simulations, and predictions from theory supports, instead, a more complex framework where other parameters are relevant. We focus discussion specifically on local order, free volume, irreversible chain adsorption, the Debye-Waller factor of confined and confining media, chain rigidity, and the absolute value of the vitrification temperature. We end by highlighting the molecular origin of distributions in relaxation times and glass transition temperatures which exceed, by far, the size of a chain. Fast relaxation modes, almost universally present at the free surface between polymer and air, are also remarked upon. These modes relax at rates far larger than those characteristic of glassy dynamics in bulk. We speculate on how these may be a signature of unique relaxation processes occurring in confined or heterogeneous polymeric systems.

A complex mTOR response in habituation paradigms for a social signal in adult songbirds.

PubMed

Ahmadiantehrani, Somayeh; Gores, Elisa O; London, Sarah E

2018-06-01

Nonassociative learning is considered simple because it depends on presentation of a single stimulus, but it likely reflects complex molecular signaling. To advance understanding of the molecular mechanisms of one form of nonassociative learning, habituation, for ethologically relevant signals we examined song recognition learning in adult zebra finches. These colonial songbirds learn the unique song of individuals, which helps establish and maintain mate and other social bonds, and informs appropriate behavioral interactions with specific birds. We leveraged prior work demonstrating behavioral habituation for individual songs, and extended the molecular framework correlated with this behavior by investigating the mechanistic Target of Rapamycin (mTOR) signaling cascade. We hypothesized that mTOR may contribute to habituation because it integrates a variety of upstream signals and enhances associative learning, and it crosstalks with another cascade previously associated with habituation, ERK/ZENK. To begin probing for a possible role for mTOR in song recognition learning, we used a combination of song playback paradigms and bidirectional dysregulation of mTORC1 activation. We found that mTOR demonstrates the molecular signatures of a habituation mechanism, and that its manipulation reveals the complexity of processes that may be invoked during nonassociative learning. These results thus expand the molecular targets for habituation studies and raise new questions about neural processing of complex natural signals. © 2018 Ahmadiantehrani et al.; Published by Cold Spring Harbor Laboratory Press.

Aging and Ambiguous ROS. System Genetics Analysis.

PubMed

Baranov, Vladislav S; Baranova, Elena V

2017-01-01

Famous Free Radical Theory (FRT) of aging, the 50th year anniversary of which is celebrated in 2015 postulates a crucial role of Reactive Oxygen Species (ROS) in aging. Still it is the most robust theory of aging as mitochondria ROS production (mtROSp) correlates well with four principal ''rules" of aging being universal, endogenous, progressive, and deleterious. Vast number of experiments in different species prove mutagenic effect of ROS and their carcinogenic properties. So far, FRT stimulates the search of new pharmaceuticals with antioxidant activity. However, some recent experimental data and clinical findings render doubt to ROS as a principal senescence drivers and come in conflict with original version of FRT. Growth stimulating effects of ROS and their modest antitumor properties support these objections. One should remember that FRT is only one of the numerous theories of aging. Molecular mechanisms of senescence involve all living systems and numerous metabolic pathways which are also variable owing to the unique properties of individual genome and unique epigenetic modulations operating throughout the lifetime thus making aging a unique private matter. Universal theory of aging that incorporates and explains all known and suggested mechanisms of aging, is illusive. However, knowledge of unique peculiarities of individual genome, its feasible editing and efficient epigenetic regulation of metabolic pathways give a chance to postpone aging and extend period of active longevity.

Evaluation of an affinity-amplified immunoassay of graphene oxide using surface plasmon resonance biosensors

NASA Astrophysics Data System (ADS)

Chiu, Nan-Fu; Huang, Teng-Yi; Kuo, Chun-Chuan

2015-05-01

We describe a fundamental study on the plasmonic properties and advanced biosensing mechanisms of functionalized graphene. We discuss a specific design using modified carboxyl groups, which can modulate surface plasmon (SP) coupling and provide an advantage for their binding to the sensing layer with high-performance affinity in an immunological reaction. The functionalized graphene-based surface plasmon resonance (SPR) biosensors have three advantages: high performance, high sensitivity, and excellent molecular kinetic response. In the future, functionalized graphene sheets will make a unique contribution to photonic and SPR diagnosis devices. We wish to highlight the essential characteristics of functionalized graphene-based SPR biosensors to assist researchers in developing and advancing suitable biosensors for unique applications.

Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.

PubMed

Li, Minghui; Goncearenco, Alexander; Panchenko, Anna R

2017-01-01

In this review we describe a protocol to annotate the effects of missense mutations on proteins, their functions, stability, and binding. For this purpose we present a collection of the most comprehensive databases which store different types of sequencing data on missense mutations, we discuss their relationships, possible intersections, and unique features. Next, we suggest an annotation workflow using the state-of-the art methods and highlight their usability, advantages, and limitations for different cases. Finally, we address a particularly difficult problem of deciphering the molecular mechanisms of mutations on proteins and protein complexes to understand the origins and mechanisms of diseases.

Mechanisms of Tooth Eruption and Orthodontic Tooth Movement

PubMed Central

Wise, G.E.; King, G.J.

2008-01-01

Teeth move through alveolar bone, whether through the normal process of tooth eruption or by strains generated by orthodontic appliances. Both eruption and orthodontics accomplish this feat through similar fundamental biological processes, osteoclastogenesis and osteogenesis, but there are differences that make their mechanisms unique. A better appreciation of the molecular and cellular events that regulate osteoclastogenesis and osteogenesis in eruption and orthodontics is not only central to our understanding of how these processes occur, but also is needed for ultimate development of the means to control them. Possible future studies in these areas are also discussed, with particular emphasis on translation of fundamental knowledge to improve dental treatments. PMID:18434571

Management the strength properties of carbon composites

NASA Astrophysics Data System (ADS)

Kolesnikova, A. S.; Mazepa, M. M.

2017-02-01

Perspective materials in adsorption medicine are the composite carbon nanostructures based on carbon nanotubes and graphene because of their unique mechanical properties and because of their ability to attach other types of atoms. The ability to control the pore size in synthesis process is an important feature of this material. The deformation of nanotubes and graphene in the longitudinal direction of the graphene sheet will occur during the filtration of microorganisms by the composite. Investigation the deformation of the composite under tension along the graphene sheet is carried out for the first time in this work by molecular mechanical method based on potential of DFT.

Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis.

PubMed

Hamada, Tsuyoshi; Keum, NaNa; Nishihara, Reiko; Ogino, Shuji

2017-03-01

Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine.

Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis

PubMed Central

Hamada, Tsuyoshi; Keum, NaNa; Nishihara, Reiko; Ogino, Shuji

2016-01-01

Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on “the unique disease principle,” the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine. PMID:27738762

Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield.

PubMed

Bhadra, Pratiti; Pal, Debnath

2017-04-01

Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hormonal interactions during root tropic growth: hydrotropism versus gravitropism.

PubMed

Takahashi, Hideyuki; Miyazawa, Yutaka; Fujii, Nobuharu

2009-03-01

Terrestrial plants have evolved remarkable morphological plasticity that enables them to adapt to their surroundings. One of the most important traits that plants have acquired is the ability to sense environmental cues and use them as a basis for governing their growth orientation. The directional growth of plant organs relative to the direction of environmental stimuli is a tropism. The Cholodny-Went theory proposes that auxin plays a key role in several tropisms. Recent molecular genetic studies have strongly supported this hypothesis for gravitropism. However, the molecular mechanisms of other tropisms are far less clear. Hydrotropism is the response of roots to a moisture gradient. Since its re-discovery in 1985, root hydrotropism has been shown to be common among higher plant species. Additionally, in some species, gravitropism interferes with hydrotropism, suggesting that both shared and divergent mechanisms mediating the two tropisms exist. This hypothesis has been supported by recent studies, which provide an understanding of how roots sense multiple environmental cues and exhibit different tropic responses. In this review, we focus on the overlapping and unique mechanisms of the hormonal regulation underlying gravitropism and hydrotropism in roots.

[Studying of molecular mechanisms of rubella virus attenuation evidence from Russian strain C-77].

PubMed

Dmitriev, G V; Borisova, T K; Faĭzuloev, E B; Zabiiaka, Iu I; Desiatskova, R G; Zverev, V V

2012-01-01

Live attenuated rubella vaccine is used for vaccination. Temperature-sensitive (ts) phenotype was proved for almost all rubella vaccine strains, and the acquisition of the ts phenotype during cold adaptation was strongly correlated with the attenuation of the wild-type viruses. Nevertheless, the molecular mechanisms of the attenuation have been insufficiently understood for rubella virus. Study ofthese mechanisms, identifying genotypic markers of attenuation, which together with the sequence analyses could be used for genetic stability control of vaccine strains, is still of current interest. In this work, we determined nearly complete genome sequences of attenuated (ca) and the wildtype progenitor (wt) of the rubella virus strain C-77 isolated in Russia. Possible genetic determinants of attenuation were detected. Thus, 13 nucleotide differences leading to 6 amino acid substitutions were found. Four amino acid substitutions were found to be almost unique. Special consideration should be given to Tyr1042Cys substitution in the protease domain of C-77 strain, because it most probably plays the crucial role in acquisition of ts-phenotype.

Recent advances in aptasensors based on graphene and graphene-like nanomaterials.

PubMed

Ping, Jianfeng; Zhou, Yubin; Wu, Yuanyuan; Papper, Vladislav; Boujday, Souhir; Marks, Robert S; Steele, Terry W J

2015-02-15

Graphene and graphene-like two-dimensional nanomaterials have aroused tremendous research interest in recent years due to their unique electronic, optical, and mechanical properties associated with their planar structure. Aptamers have exhibited many advantages as molecular recognition elements for sensing devices compared to traditional antibodies. The marriage of two-dimensional nanomaterials and aptamers has emerged many ingenious aptasensing strategies for applications in the fields of clinical diagnosis and food safety. This review highlights current advances in the development and application of two-dimensional nanomaterials-based aptasensors with the focus on two main signal-transducing mechanisms, i.e. electrochemical and optical. A special attention is paid to graphene, a one-atom thick layer of graphite with exceptional properties, representing a fastgrowing field of research. In view of the unique properties of two-dimensional nanostructures and their inherent advantages of synthetic aptamers, we expect that high-performance two-dimensional nanomaterials-based aptasensing devices will find extensive applications in environmental monitoring, biomedical diagnostics, and food safety. Copyright © 2014 Elsevier B.V. All rights reserved.

Discovery and mechanistic study of a class of protein arginine methylation inhibitors.

PubMed

Feng, You; Li, Mingyong; Wang, Binghe; Zheng, Yujun George

2010-08-26

Protein arginine methylation regulates multiple biological processes such as chromatin remodeling and RNA splicing. Malfunction of protein arginine methyltransferases (PRMTs) is correlated with many human diseases. Thus, small molecule inhibitors of protein arginine methylation are of great potential for therapeutic development. Herein, we report a type of compound that blocks PRMT1-mediated arginine methylation at micromolar potency through a unique mechanism. Most of the discovered compounds bear naphthalene and sulfonate groups and are structurally different from typical PRMT substrates, for example, histone H4 and glycine- and arginine-rich sequences. To elucidate the molecular basis of inhibition, we conducted a variety of kinetic and biophysical assays. The combined data reveal that this type of naphthyl-sulfo (NS) molecule directly targets the substrates but not PRMTs for the observed inhibition. We also found that suramin effectively inhibited PRMT1 activity. These findings about novel PRMT inhibitors and their unique inhibition mechanism provide a new way for chemical regulation of protein arginine methylation.

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

PubMed Central

Miao, Yinglong; Walker, Ross C.; Jinek, Martin; McCammon, J. Andrew

2017-01-01

CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature, 527, 110–113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9. PMID:28652374

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations.

PubMed

Palermo, Giulia; Miao, Yinglong; Walker, Ross C; Jinek, Martin; McCammon, J Andrew

2017-07-11

CRISPR-Cas9 has become a facile genome editing technology, yet the structural and mechanistic features underlying its function are unclear. Here, we perform extensive molecular simulations in an enhanced sampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes displacements over hundreds of microseconds to milliseconds, to reveal the conformational dynamics of the endonuclease Cas9 during its activation toward catalysis. We disclose the conformational transition of Cas9 from its apo form to the RNA-bound form, suggesting a mechanism for RNA recruitment in which the domain relocations cause the formation of a positively charged cavity for nucleic acid binding. GaMD also reveals the conformation of a catalytically competent Cas9, which is prone for catalysis and whose experimental characterization is still limited. We show that, upon DNA binding, the conformational dynamics of the HNH domain triggers the formation of the active state, explaining how the HNH domain exerts a conformational control domain over DNA cleavage [Sternberg SH et al. (2015) Nature , 527 , 110-113]. These results provide atomic-level information on the molecular mechanism of CRISPR-Cas9 that will inspire future experimental investigations aimed at fully clarifying the biophysics of this unique genome editing machinery and at developing new tools for nucleic acid manipulation based on CRISPR-Cas9.

M4Ag44(p-MBA)30 Molecular Nanoparticles

NASA Astrophysics Data System (ADS)

Conn, Brian E.

In recent years, molecular nanoparticles have attracted much attention due to their unique physical, optical, and electronic properties. The properties of molecular nanoparticles are shown to deviate from their larger bulk counterparts, due to quantum confinement effects and large surface-to-volume ratios. As the size of the nanoparticle shrinks to a cluster of metal atoms (<3 nm in diameter), there is an emergence of a HOMO-LUMO band gap, which is not present in transitional d-block metals. The HOMO-LUMO band gap gives rise to discrete electronic states, leading to new chemical and physical properties. Molecular nanoparticles have had a substantial impact across a diverse range of fields, including catalysis, sensing, photochemistry, optoelectronic, energy conversion, and medicine. Currently many of the synthetic procedures for molecular nanoparticles require low temperatures, long incubation times, multistep purification and hazardous reagents that produce low yields and polydisperse molecular nanoparticles with poor stability. Although silver has very desirable physical properties, good relative abundance and low cost, gold molecular nanoparticles have been widely favored owing to their proved stability and ease of use. Unlike gold, silver is notorious for its susceptibility to oxidation, i.e., tarnishing, which has limited the development of silver-based nanotechnologies. Despite two decades of synthetic efforts, silver molecular nanoparticles that are inert or have long-term stability have remained unrealized. Herein we report a simple synthetic protocol for producing ultrastable M4Ag44(p-MBA)30 nanoparticles as a single-sized molecular product and in exceptionally large quantities. The stability, purity, and yield are substantially better than other metal nanoparticles, including gold, due to several stabilization mechanisms. Also, reported are the structural and mechanical properties of extended crystalline solids of Na4Ag44(p-MBA)30 from large-scale quantum-mechanical simulations based on the atomically-precise X-ray measured structure. Calculations show that cohesion is derived from hydrogen bonds between bundled p-MBA ligands and that the superlattice's mechanical response to hydrostatic compression is characterized by a molecular-solid-like bulk modulus B0 = 16.7 GPa, exhibiting anomalous pressure softening and a compression-induced transition to a soft-solid phase. Such a transition involves ligand flexure, which causes gear-like correlated chiral rotation of the nanoparticles.

Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis

PubMed Central

Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Céline; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.

2011-01-01

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419

Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116

NASA Astrophysics Data System (ADS)

Zhang, Yuan; Palla, Mirkó; Sun, Andrew; Liao, Jung-Chi

2013-09-01

DEAD-box RNA helicases are ATP-dependent proteins implicated in nearly all aspects of RNA metabolism. The yeast DEAD-box helicase Mss116 is unique in its functions of splicing group I and group II introns and activating mRNA translation, but the structural understanding of why it performs these unique functions remains unclear. Here we used sequence analysis and molecular dynamics simulation to identify residues in the flexible linker specific for yeast Mss116, potentially associated with its unique functions. We first identified residues that are 100% conserved in Mss116 of different species of the Saccharomycetaceae family. The amino acids of these conserved residues were then compared with the amino acids of the corresponding residue positions of other RNA helicases to identify residues that have distinct amino acids from other DEAD-box proteins. Four residues in the flexible linker, i.e. N334, E335, P336 and H339, are conserved and Mss116-specific. Molecular dynamics simulation was conducted for the wild-type Mss116 structure and mutant models to examine mutational effects of the linker on the conformational equilibrium. Relatively short MD simulation runs (within 20 ns) were enough for us to observe mutational effects, suggesting serious structural perturbations by these mutations. The mutation of E335 depletes the interactions between E335 and K95 in domain 1. The interactions between N334/P336 and N496/I497 of domain 2 are also abolished by mutation. Our results suggest that tight interactions between the Mss116-specific flexible linker and the two RecA-like domains may be mechanically required to crimp RNA for the unique RNA processes of yeast Mss116.

The Function of Embryonic Stem Cell-expressed RAS (E-RAS), a Unique RAS Family Member, Correlates with Its Additional Motifs and Its Structural Properties.

PubMed

Nakhaei-Rad, Saeideh; Nakhaeizadeh, Hossein; Kordes, Claus; Cirstea, Ion C; Schmick, Malte; Dvorsky, Radovan; Bastiaens, Philippe I H; Häussinger, Dieter; Ahmadian, Mohammad Reza

2015-06-19

E-RAS is a member of the RAS family specifically expressed in embryonic stem cells, gastric tumors, and hepatic stellate cells. Unlike classical RAS isoforms (H-, N-, and K-RAS4B), E-RAS has, in addition to striking and remarkable sequence deviations, an extended 38-amino acid-long unique N-terminal region with still unknown functions. We investigated the molecular mechanism of E-RAS regulation and function with respect to its sequence and structural features. We found that N-terminal extension of E-RAS is important for E-RAS signaling activity. E-RAS protein most remarkably revealed a different mode of effector interaction as compared with H-RAS, which correlates with deviations in the effector-binding site of E-RAS. Of all these residues, tryptophan 79 (arginine 41 in H-RAS), in the interswitch region, modulates the effector selectivity of RAS proteins from H-RAS to E-RAS features. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation.

PubMed

Yang, Feng; Waters, Katrina M; Miller, John H; Gritsenko, Marina A; Zhao, Rui; Du, Xiuxia; Livesay, Eric A; Purvine, Samuel O; Monroe, Matthew E; Wang, Yingchun; Camp, David G; Smith, Richard D; Stenoien, David L

2010-11-30

High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health.

Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

PubMed Central

Yang, Feng; Waters, Katrina M.; Miller, John H.; Gritsenko, Marina A.; Zhao, Rui; Du, Xiuxia; Livesay, Eric A.; Purvine, Samuel O.; Monroe, Matthew E.; Wang, Yingchun; Camp, David G.; Smith, Richard D.; Stenoien, David L.

2010-01-01

Background High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conclusions Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health. PMID:21152398

Length-dependent mechanical properties of gold nanowires

NASA Astrophysics Data System (ADS)

Han, Jing; Fang, Liang; Sun, Jiapeng; Han, Ying; Sun, Kun

2012-12-01

The well-known "size effect" is not only related to the diameter but also to the length of the small volume materials. It is unfortunate that the length effect on the mechanical behavior of nanowires is rarely explored in contrast to the intensive studies of the diameter effect. The present paper pays attention to the length-dependent mechanical properties of <111>-oriented single crystal gold nanowires employing the large-scale molecular dynamics simulation. It is discovered that the ultrashort Au nanowires exhibit a new deformation and failure regime-high elongation and high strength. The constrained dislocation nucleation and transient dislocation slipping are observed as the dominant mechanism for such unique combination of high strength and high elongation. A mechanical model based on image force theory is developed to provide an insight to dislocation nucleation and capture the yield strength and nucleation site of first partial dislocation indicated by simulation results. Increasing the length of the nanowires, the ductile-to-brittle transition is confirmed. And the new explanation is suggested in the predict model of this transition. Inspired by the superior properties, a new approach to strengthen and toughen nanowires-hard/soft/hard sandwich structured nanowires is suggested. A preliminary evidence from the molecular dynamics simulation corroborates the present opinion.

Azadirachtin(A) distinctively modulates subdomain 2 of actin - novel mechanism to induce depolymerization revealed by molecular dynamics study.

PubMed

Pravin Kumar, R; Roopa, L; Sudheer Mohammed, M M; Kulkarni, Naveen

2016-12-01

Azadirachtin(A) (AZA), a potential insecticide from neem, binds to actin and induces depolymerization in Drosophila. AZA binds to the pocket same as that of Latrunculin A (LAT), but LAT inhibits actin polymerization by stiffening the actin structure and affects the ADP-ATP exchange. The mechanism by which AZA induces actin depolymerization is not clearly understood. Therefore, different computational experiments were conducted to delineate the precise mechanism of AZA-induced actin depolymerization. Molecular dynamics studies showed that AZA strongly interacted with subdomain 2 and destabilized the interactions between subdomain 2 of one actin and subdomains 1 and 4 of the adjacent actin, causing the separation of actin subunits. The separation was observed between subdomain 3 of subunit n and subdomain 4 of subunit n + 2. However, the specific triggering point for the separation of the subunits was the destabilization of direct interactions between subdomain 2 of subunit n (Arg39, Val45, Gly46 and Arg62) and subdomain 4 of subunit n + 2 (Asp286, Ile287, Asp288, Ile289, Asp244 and Lys291). These results reveal a unique mechanism of an actin filament modulator that induces depolymerization. This mechanism of AZA can be used to design similar molecules against mammalian actins for cancer therapy.

Mechanosensitive subcellular rheostasis drives emergent single-cell mechanical homeostasis

NASA Astrophysics Data System (ADS)

Weng, Shinuo; Shao, Yue; Chen, Weiqiang; Fu, Jianping

2016-09-01

Mechanical homeostasis--a fundamental process by which cells maintain stable states under environmental perturbations--is regulated by two subcellular mechanotransducers: cytoskeleton tension and integrin-mediated focal adhesions (FAs). Here, we show that single-cell mechanical homeostasis is collectively driven by the distinct, graduated dynamics (rheostasis) of subcellular cytoskeleton tension and FAs. Such rheostasis involves a mechanosensitive pattern wherein ground states of cytoskeleton tension and FA determine their distinct reactive paths through either relaxation or reinforcement. Pharmacological perturbations of the cytoskeleton and molecularly modulated integrin catch-slip bonds biased the rheostasis and induced non-homeostasis of FAs, but not of cytoskeleton tension, suggesting a unique sensitivity of FAs in regulating homeostasis. Theoretical modelling revealed myosin-mediated cytoskeleton contractility and catch-slip-bond-like behaviours in FAs and the cytoskeleton as sufficient and necessary mechanisms for quantitatively recapitulating mechanosensitive rheostasis. Our findings highlight the previously underappreciated physical nature of the mechanical homeostasis of cells.

Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics

NASA Astrophysics Data System (ADS)

Hirokawa, N.; Takemura, R.

Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.

Animal Models of Depression: Molecular Perspectives

PubMed Central

Krishnan, Vaishnav; Nestler, Eric J.

2012-01-01

Much of the current understanding about the pathogenesis of altered mood, impaired concentration and neurovegetative symptoms in major depression has come from animal models. However, because of the unique and complex features of human depression, the generation of valid and insightful depression models has been less straightforward than modeling other disabling diseases like cancer or autoimmune conditions. Today’s popular depression models creatively merge ethologically valid behavioral assays with the latest technological advances in molecular biology and automated video-tracking. This chapter reviews depression assays involving acute stress (e.g., forced swim test), models consisting of prolonged physical or social stress (e.g., social defeat), models of secondary depression, genetic models, and experiments designed to elucidate the mechanisms of antidepressant action. These paradigms are critically evaluated in relation to their ease, validity and replicability, the molecular insights that they have provided, and their capacity to offer the next generation of therapeutics for depression. PMID:21225412

Humic Substances: Determining Potential Molecular Regulatory Processes in Plants

PubMed Central

Shah, Zahid Hussain; Rehman, Hafiz M.; Akhtar, Tasneem; Alsamadany, Hameed; Hamooh, Bahget T.; Mujtaba, Tahir; Daur, Ihsanullah; Al Zahrani, Yahya; Alzahrani, Hind A. S.; Ali, Shawkat; Yang, Seung H.; Chung, Gyuhwa

2018-01-01

Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant’s tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review. PMID:29593751

Mechanistic Understanding of Toxicity from Nanocatalysts

PubMed Central

Jiang, Cuijuan; Jia, Jianbo; Zhai, Shumei

2014-01-01

Nanoparticle-based catalysts, or nanocatalysts, have been applied in various industrial sectors, including refineries, petrochemical plants, the pharmaceutical industry, the chemical industry, food processing, and environmental remediation. As a result, there is an increasing risk of human exposure to nanocatalysts. This review evaluates the toxicity of popular nanocatalysts applied in industrial processes in cell and animal models. The molecular mechanisms associated with such nanotoxicity are emphasized to reveal common toxicity-inducing pathways from various nanocatalysts and the uniqueness of each specific nanocatalyst. PMID:25119861

Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitehead, Lewis; Dobler, Markus R.; Radetich, Branko

2013-11-20

Herein we report the discovery of a family of novel yet simple, amino-acid derived class I HDAC inhibitors that demonstrate isoform selectivity via access to the internal acetate release channel. Isoform selectivity criteria is discussed on the basis of X-ray crystallography and molecular modeling of these novel inhibitors bound to HDAC8, potentially revealing insights into the mechanism of enzymatic function through novel structural features revealed at the atomic level.

A Surface Science Perspective on TiO2 Photocatalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2011-06-15

The field of surface science provides a unique approach to understanding bulk, surface and interfacial phenomena occurring during TiO2 photochemistry and photocatalysis. This review highlights, from a surface science perspective, recent literature providing molecular-level insights into phonon-initiated events on TiO2 surfaces obtained in seven key scientific issues: (1) photon absorption, (2) charge transport and trapping, (3) electron transfer dynamics, (4) the adsorbed state, (5) mechanisms, (6) poisons and promoters, and (7) phase and form.

The Potential Role of Aerobic Exercise to Modulate Cardiotoxicity of Molecularly Targeted Cancer Therapeutics

PubMed Central

Lakoski, Susan; Mackey, John R.; Douglas, Pamela S.; Haykowsky, Mark J.; Jones, Lee W.

2013-01-01

Molecularly targeted therapeutics (MTT) are the future of cancer systemic therapy. They have already moved from palliative therapy for advanced solid malignancies into the setting of curative-intent treatment for early-stage disease. Cardiotoxicity is a frequent and potentially serious adverse complication of some targeted therapies, leading to a broad range of potentially life-threatening complications, therapy discontinuation, and poor quality of life. Low-cost pleiotropic interventions are therefore urgently required to effectively prevent and/or treat MTT-induced cardiotoxicity. Aerobic exercise therapy has the unique capacity to modulate, without toxicity, multiple gene expression pathways in several organ systems, including a plethora of cardiac-specific molecular and cell-signaling pathways implicated in MTT-induced cardiac toxicity. In this review, we examine the molecular signaling of antiangiogenic and HER2-directed therapies that may underpin cardiac toxicity and the hypothesized molecular mechanisms underlying the cardioprotective properties of aerobic exercise. It is hoped that this knowledge can be used to maximize the benefits of small molecule inhibitors, while minimizing cardiac damage in patients with solid malignancies. PMID:23335619

The future of neuropathology in childhood.

PubMed

Rorke, L B

2000-11-01

The current state of knowledge of pediatric neuropathology is based upon a rich historical heritage dating back many centuries and representing the genius of many people, although, relatively speaking, little specific attention was paid to the unique issues relating to infants and children. Aside from descriptions of morphological features of disease (including tumors), advances in understanding basic pathogenetic mechanisms have flowered only in the recent past. Most exciting has been the progress in molecular biology and genetics, which has yielded a phenomenal bank of information in a short time, uncovering details of genes involved in development of the nervous system and specifically associated with various types of tumors. The future of pediatric neuropathology requires partnership with molecular geneticists whose studies hold promise of defining morphology.

Purified monomeric ligand.MD-2 complexes reveal molecular and structural requirements for activation and antagonism of TLR4 by Gram-negative bacterial endotoxins.

PubMed

Gioannini, Theresa L; Teghanemt, Athmane; Zhang, DeSheng; Esparza, Gregory; Yu, Liping; Weiss, Jerrold

2014-08-01

A major focus of work in our laboratory concerns the molecular mechanisms and structural bases of Gram-negative bacterial endotoxin recognition by host (e.g., human) endotoxin-recognition proteins that mediate and/or regulate activation of Toll-like receptor (TLR) 4. Here, we review studies of wild-type and variant monomeric endotoxin.MD-2 complexes first produced and characterized in our laboratories. These purified complexes have provided unique experimental reagents, revealing both quantitative and qualitative determinants of TLR4 activation and antagonism. This review is dedicated to the memory of Dr. Theresa L. Gioannini (1949-2014) who played a central role in many of the studies and discoveries that are reviewed.

Ole e 13 is the unique food allergen in olive: Structure-functional, substrates docking, and molecular allergenicity comparative analysis.

PubMed

Jimenez-Lopez, J C; Robles-Bolivar, P; Lopez-Valverde, F J; Lima-Cabello, E; Kotchoni, S O; Alché, J D

2016-05-01

Thaumatin-like proteins (TLPs) are enzymes with important functions in pathogens defense and in the response to biotic and abiotic stresses. Last identified olive allergen (Ole e 13) is a TLP, which may also importantly contribute to food allergy and cross-allergenicity to pollen allergen proteins. The goals of this study are the characterization of the structural-functionality of Ole e 13 with a focus in its catalytic mechanism, and its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering a) functional-regulatory motifs, b) comparative study of linear sequence, 2-D and 3D structural homology modeling, c) molecular docking with two different β-D-glucans, d) conservational and evolutionary analysis, e) catalytic mechanism modeling, and f) IgE-binding, B- and T-cell epitopes identification and comparison to other allergenic TLPs. Sequence comparison, structure-based features, and phylogenetic analysis identified Ole e 13 as a thaumatin-like protein. 3D structural characterization revealed a conserved overall folding among plants TLPs, with mayor differences in the acidic (catalytic) cleft. Molecular docking analysis using two β-(1,3)-glucans allowed to identify fundamental residues involved in the endo-1,3-β-glucanase activity, and defining E84 as one of the conserved residues of the TLPs responsible of the nucleophilic attack to initiate the enzymatic reaction and D107 as proton donor, thus proposing a catalytic mechanism for Ole e 13. Identification of IgE-binding, B- and T-cell epitopes may help designing strategies to improve diagnosis and immunotherapy to food allergy and cross-allergenic pollen TLPs. Copyright © 2016 Elsevier Inc. All rights reserved.

Power transduction of actin filaments ratcheting in vitro against a load.

PubMed

Démoulin, Damien; Carlier, Marie-France; Bibette, Jérôme; Baudry, Jean

2014-12-16

The actin cytoskeleton has the unique capability of producing pushing forces at the leading edge of motile cells without the implication of molecular motors. This phenomenon has been extensively studied theoretically, and molecular models, including the widely known Brownian ratchet, have been proposed. However, supporting experimental work is lacking, due in part to hardly accessible molecular length scales. We designed an experiment to directly probe the mechanism of force generation in a setup where a population of actin filaments grows against a load applied by magnetic microparticles. The filaments, arranged in stiff bundles by fascin, are constrained to point toward the applied load. In this protrusion-like geometry, we are able to directly measure the velocity of filament elongation and its dependence on force. Using numerical simulations, we provide evidence that our experimental data are consistent with a Brownian ratchet-based model. We further demonstrate the existence of a force regime far below stalling where the mechanical power transduced by the ratcheting filaments to the load is maximal. The actin machinery in migrating cells may tune the number of filaments at the leading edge to work in this force regime.

Janus and Strawberry-like Particles from Azo Molecular Glass and Polydimethylsiloxane Oligomer.

PubMed

Hsu, Chungen; Du, Yi; Wang, Xiaogong

2017-10-10

This study investigated Janus and strawberry-like particles composed of azo molecular glass and polydimethylsiloxane (PDMS) oligomer, focusing on controllable fabrication and formation mechanism of these unique structures and morphologies. Two materials, the azo molecular glass (IA-Chol) and PDMS oligomer (H 2 pdca-PDMS), were prepared for this purpose. The Janus and strawberry-like particles were obtained from the droplets of a dichloromethane (DCM) solution containing both IA-Chol and H 2 pdca-PDMS, dispersed in water and stabilized by poly(vinyl alcohol). Results show that the structured particles are formed through segregation between the two components induced by gradual evaporation of DCM from the droplets, which is controlled by adding ethylene glycol (EG) into the above dispersion. Without the addition of EG, Janus particles are formed through the full segregation of the two components in the droplets. On the other hand, with the existence of EG in the dispersion, strawberry-like particles instead of Janus particles are formed in the phase separation process. The diffusion of EG molecules from the dispersion medium into the droplets causes the PDMS phase deswelling in the interfacial area due to the poor solvent effect. Caused by the surface coagulation, the coalescence of the isolated IA-Chol domains is jammed in the shell region, which results in the formation of the strawberry-like particles. For the particles separated from the dispersion and dried, the PDMS oligomer phase of the Janus particles can adhere and spread on the substrate to form unique "particle-on-pad" morphology due to its low surface energy and swelling ability, while the strawberry-like particles exist as "standstill" objects on the substrates. Upon irradiation with a linearly polarized laser beam at 488 nm, the azo molecular glass parts in the particles are significantly deformed along the light polarization direction, which show unique and distinct morphologies for these two types of the particles.

Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.

PubMed

Koch, Maximilian F; Harteis, Sabrina; Blank, Iris D; Pestel, Galina; Tietze, Lutz F; Ochsenfeld, Christian; Schneider, Sabine; Sieber, Stephan A

2015-11-09

Analogues of the natural product duocarmycin bearing an indole moiety were shown to bind aldehyde dehydrogenase 1A1 (ALDH1A1) in addition to DNA, while derivatives without the indole solely addressed the ALDH1A1 protein. The molecular mechanism of selective ALDH1A1 inhibition by duocarmycin analogues was unraveled through cocrystallization, mutational studies, and molecular dynamics simulations. The structure of the complex shows the compound embedded in a hydrophobic pocket, where it is stabilized by several crucial π-stacking and van der Waals interactions. This binding mode positions the cyclopropyl electrophile for nucleophilic attack by the noncatalytic residue Cys302, thereby resulting in covalent attachment, steric occlusion of the active site, and inhibition of catalysis. The selectivity of duocarmycin analogues for ALDH1A1 is unique, since only minor alterations in the sequence of closely related protein isoforms restrict compound accessibility. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach.

PubMed

Zhen, Cheng; Zhu, Caizhong; Chen, Haoyang; Xiong, Yiru; Tan, Junyuan; Chen, Dong; Li, Jin

2017-02-21

To systematically explore the molecular mechanism for hepatocellular carcinoma (HCC) metastasis and identify regulatory genes with text mining methods. Genes with highest frequencies and significant pathways related to HCC metastasis were listed. A handful of proteins such as EGFR, MDM2, TP53 and APP, were identified as hub nodes in PPI (protein-protein interaction) network. Compared with unique genes for HBV-HCCs, genes particular to HCV-HCCs were less, but may participate in more extensive signaling processes. VEGFA, PI3KCA, MAPK1, MMP9 and other genes may play important roles in multiple phenotypes of metastasis. Genes in abstracts of HCC-metastasis literatures were identified. Word frequency analysis, KEGG pathway and PPI network analysis were performed. Then co-occurrence analysis between genes and metastasis-related phenotypes were carried out. Text mining is effective for revealing potential regulators or pathways, but the purpose of it should be specific, and the combination of various methods will be more useful.

Molecular Dissection of Neuroligin 2 and Slitrk3 Reveals an Essential Framework for GABAergic Synapse Development.

PubMed

Li, Jun; Han, Wenyan; Pelkey, Kenneth A; Duan, Jingjing; Mao, Xia; Wang, Ya-Xian; Craig, Michael T; Dong, Lijin; Petralia, Ronald S; McBain, Chris J; Lu, Wei

2017-11-15

In the brain, many types of interneurons make functionally diverse inhibitory synapses onto principal neurons. Although numerous molecules have been identified to function in inhibitory synapse development, it remains unknown whether there is a unifying mechanism for development of diverse inhibitory synapses. Here we report a general molecular mechanism underlying hippocampal inhibitory synapse development. In developing neurons, the establishment of GABAergic transmission depends on Neuroligin 2 (NL2), a synaptic cell adhesion molecule (CAM). During maturation, inhibitory synapse development requires both NL2 and Slitrk3 (ST3), another CAM. Importantly, NL2 and ST3 interact with nanomolar affinity through their extracellular domains to synergistically promote synapse development. Selective perturbation of the NL2-ST3 interaction impairs inhibitory synapse development with consequent disruptions in hippocampal network activity and increased seizure susceptibility. Our findings reveal how unique postsynaptic CAMs work in concert to control synaptogenesis and establish a general framework for GABAergic synapse development. Published by Elsevier Inc.

Bridging the Gaps: the Promise of Omics Studies in Pediatric Exercise Research

PubMed Central

Radom-Aizik, Shlomit; Cooper, Dan M.

2018-01-01

In this review, we highlight promising new discoveries that may generate useful and clinically relevant insights into the mechanisms that link exercise with growth during critical periods of development. Growth in childhood and adolescence is unique among mammals, and is a dynamic process regulated by an evolution of hormonal and inflammatory mediators, age-dependent progression of gene expression, and environmentally modulated epigenetic mechanisms. Many of these same processes likely affect molecular transducers of physical activity. How the molecular signaling associated with growth is synchronized with signaling associated with exercise is poorly understood. Recent advances in “omics,” namely, genomics and epigenetics, metabolomics, and proteomics, now provide exciting approaches and tools that can be used for the first time to address this gap. A biologic definition of “healthy” exercise that links the metabolic transducers of physical activity with parallel processes that regulate growth will transform health policy and guidelines that promote optimal use of physical activity. PMID:27137166

A glucose-starvation response regulates the diffusion of macromolecules

PubMed Central

Joyner, Ryan P; Tang, Jeffrey H; Helenius, Jonne; Dultz, Elisa; Brune, Christiane; Holt, Liam J; Huet, Sebastien; Müller, Daniel J; Weis, Karsten

2016-01-01

The organization and biophysical properties of the cytosol implicitly govern molecular interactions within cells. However, little is known about mechanisms by which cells regulate cytosolic properties and intracellular diffusion rates. Here, we demonstrate that the intracellular environment of budding yeast undertakes a startling transition upon glucose starvation in which macromolecular mobility is dramatically restricted, reducing the movement of both chromatin in the nucleus and mRNPs in the cytoplasm. This confinement cannot be explained by an ATP decrease or the physiological drop in intracellular pH. Rather, our results suggest that the regulation of diffusional mobility is induced by a reduction in cell volume and subsequent increase in molecular crowding which severely alters the biophysical properties of the intracellular environment. A similar response can be observed in fission yeast and bacteria. This reveals a novel mechanism by which cells globally alter their properties to establish a unique homeostasis during starvation. DOI: http://dx.doi.org/10.7554/eLife.09376.001 PMID:27003290

Modeling and Simulation of Nanoindentation

NASA Astrophysics Data System (ADS)

Huang, Sixie; Zhou, Caizhi

2017-11-01

Nanoindentation is a hardness test method applied to small volumes of material which can provide some unique effects and spark many related research activities. To fully understand the phenomena observed during nanoindentation tests, modeling and simulation methods have been developed to predict the mechanical response of materials during nanoindentation. However, challenges remain with those computational approaches, because of their length scale, predictive capability, and accuracy. This article reviews recent progress and challenges for modeling and simulation of nanoindentation, including an overview of molecular dynamics, the quasicontinuum method, discrete dislocation dynamics, and the crystal plasticity finite element method, and discusses how to integrate multiscale modeling approaches seamlessly with experimental studies to understand the length-scale effects and microstructure evolution during nanoindentation tests, creating a unique opportunity to establish new calibration procedures for the nanoindentation technique.

A Molecular Basis for Bifidobacterial Enrichment in the Infant Gastrointestinal Tract123

PubMed Central

Garrido, Daniel; Barile, Daniela; Mills, David A.

2012-01-01

Bifidobacteria are commonly used as probiotics in dairy foods. Select bifidobacterial species are also early colonizers of the breast-fed infant colon; however, the mechanism for this enrichment is unclear. We previously showed that Bifidobacterium longum subsp. infantis is a prototypical bifidobacterial species that can readily utilize human milk oligosaccharides as the sole carbon source. MS-based glycoprofiling has revealed that numerous B. infantis strains preferentially consume small mass oligosaccharides, abundant in human milks. Genome sequencing revealed that B. infantis possesses a bias toward genes required to use mammalian-derived carbohydrates. Many of these genomic features encode enzymes that are active on milk oligosaccharides including a novel 40-kb region dedicated to oligosaccharide utilization. Biochemical and molecular characterization of the encoded glycosidases and transport proteins has further resolved the mechanism by which B. infantis selectively imports and catabolizes milk oligosaccharides. Expression studies indicate that many of these key functions are only induced during growth on milk oligosaccharides and not expressed during growth on other prebiotics. Analysis of numerous B. infantis isolates has confirmed that these genomic features are common among the B. infantis subspecies and likely constitute a competitive colonization strategy used by these unique bifidobacteria. By detailed characterization of the molecular mechanisms responsible, these studies provide a conceptual framework for bifidobacterial persistence and host interaction in the infant gastrointestinal tract mediated in part through consumption of human milk oligosaccharides. PMID:22585920

Preclinical Magnetic Resonance Imaging and Spectroscopy Studies of Memory, Aging, and Cognitive Decline

PubMed Central

Febo, Marcelo; Foster, Thomas C.

2016-01-01

Neuroimaging provides for non-invasive evaluation of brain structure and activity and has been employed to suggest possible mechanisms for cognitive aging in humans. However, these imaging procedures have limits in terms of defining cellular and molecular mechanisms. In contrast, investigations of cognitive aging in animal models have mostly utilized techniques that have offered insight on synaptic, cellular, genetic, and epigenetic mechanisms affecting memory. Studies employing magnetic resonance imaging and spectroscopy (MRI and MRS, respectively) in animal models have emerged as an integrative set of techniques bridging localized cellular/molecular phenomenon and broader in vivo neural network alterations. MRI methods are remarkably suited to longitudinal tracking of cognitive function over extended periods permitting examination of the trajectory of structural or activity related changes. Combined with molecular and electrophysiological tools to selectively drive activity within specific brain regions, recent studies have begun to unlock the meaning of fMRI signals in terms of the role of neural plasticity and types of neural activity that generate the signals. The techniques provide a unique opportunity to causally determine how memory-relevant synaptic activity is processed and how memories may be distributed or reconsolidated over time. The present review summarizes research employing animal MRI and MRS in the study of brain function, structure, and biochemistry, with a particular focus on age-related cognitive decline. PMID:27468264

Omics approaches to individual variation: modeling networks and the virtual patient.

PubMed

Lehrach, Hans

2016-09-01

Every human is unique. We differ in our genomes, environment, behavior, disease history, and past and current medical treatment-a complex catalog of differences that often leads to variations in the way each of us responds to a particular therapy. We argue here that true personalization of drug therapies will rely on "virtual patient" models based on a detailed characterization of the individual patient by molecular, imaging, and sensor techniques. The models will be based, wherever possible, on the molecular mechanisms of disease processes and drug action but can also expand to hybrid models including statistics/machine learning/artificial intelligence-based elements trained on available data to address therapeutic areas or therapies for which insufficient information on mechanisms is available. Depending on the disease, its mechanisms, and the therapy, virtual patient models can be implemented at a fairly high level of abstraction, with molecular models representing cells, cell types, or organs relevant to the clinical question, interacting not only with each other but also the environment. In the future, "virtual patient/in-silico self" models may not only become a central element of our health care system, reducing otherwise unavoidable mistakes and unnecessary costs, but also act as "guardian angels" accompanying us through life to protect us against dangers and to help us to deal intelligently with our own health and wellness.

Omics approaches to individual variation: modeling networks and the virtual patient

PubMed Central

Lehrach, Hans

2016-01-01

Every human is unique. We differ in our genomes, environment, behavior, disease history, and past and current medical treatment—a complex catalog of differences that often leads to variations in the way each of us responds to a particular therapy. We argue here that true personalization of drug therapies will rely on “virtual patient” models based on a detailed characterization of the individual patient by molecular, imaging, and sensor techniques. The models will be based, wherever possible, on the molecular mechanisms of disease processes and drug action but can also expand to hybrid models including statistics/machine learning/artificial intelligence-based elements trained on available data to address therapeutic areas or therapies for which insufficient information on mechanisms is available. Depending on the disease, its mechanisms, and the therapy, virtual patient models can be implemented at a fairly high level of abstraction, with molecular models representing cells, cell types, or organs relevant to the clinical question, interacting not only with each other but also the environment. In the future, “virtual patient/in-silico self” models may not only become a central element of our health care system, reducing otherwise unavoidable mistakes and unnecessary costs, but also act as “guardian angels” accompanying us through life to protect us against dangers and to help us to deal intelligently with our own health and wellness. PMID:27757060

Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study.

PubMed

Telesco, Shannon E; Radhakrishnan, Ravi

2009-03-18

HER2 (ErbB2/Neu) is a receptor tyrosine kinase belonging to the epidermal growth factor receptor (EGFR)/ErbB family and is overexpressed in 20-30% of human breast cancers. Although several crystal structures of ErbB kinases have been solved, the precise mechanism of HER2 activation remains unknown, and it has been suggested that HER2 is unique in its requirement for phosphorylation of Y877, a key tyrosine residue located in the activation loop. To elucidate mechanistic details of kinase domain regulation, we performed molecular dynamics simulations of a homology-modeled HER2 kinase structure in active and inactive conformations. Principal component analysis of the atomistic fluctuations reveals a tight coupling between the activation loop and catalytic loop that may contribute to alignment of residues required for catalysis in the active kinase. The free energy perturbation method is also employed to predict a role for phosphorylated Y877 in stabilizing the kinase conformations. Finally, simulation results are presented for a HER2/EGFR heterodimer and reveal that the dimeric interface induces a rearrangement of the alphaC helix toward the active conformation. Elucidation of the molecular regulatory mechanisms in HER2 will help establish structure-function relationships in the wild-type kinase, as well as predict mutations with a propensity for constitutive activation in HER2-mediated cancers.

Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials

PubMed Central

2015-01-01

In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers. PMID:26646318

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3.

PubMed

Singh, P; Benjak, A; Carat, S; Kai, M; Busso, P; Avanzi, C; Paniz-Mondolfi, A; Peter, C; Harshman, K; Rougemont, J; Matsuoka, M; Cole, S T

2014-10-01

Genotyping and molecular characterization of drug resistance mechanisms in Mycobacterium leprae enables disease transmission and drug resistance trends to be monitored. In the present study, we performed genome-wide analysis of Airaku-3, a multidrug-resistant strain with an unknown mechanism of resistance to rifampicin. We identified 12 unique non-synonymous single-nucleotide polymorphisms (SNPs) including two in the transporter-encoding ctpC and ctpI genes. In addition, two SNPs were found that improve the resolution of SNP-based genotyping, particularly for Venezuelan and South East Asian strains of M. leprae. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

Molecular mechanisms of floral organ specification by MADS domain proteins.

PubMed

Yan, Wenhao; Chen, Dijun; Kaufmann, Kerstin

2016-02-01

Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on 'simple' recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Poly(ADP-ribosyl)ation is recognized by ECT2 during mitosis.

PubMed

Li, Mo; Bian, Chunjing; Yu, Xiaochun

2014-01-01

Poly(ADP-ribosyl)ation is an unique posttranslational modification and required for spindle assembly and function during mitosis. However, the molecular mechanism of poly(ADP-ribose) (PAR) in mitosis remains elusive. Here, we show the evidence that PAR is recognized by ECT2, a key guanine nucleotide exchange factor in mitosis. The BRCT domain of ECT2 directly binds to PAR both in vitro and in vivo. We further found that α-tubulin is PARylated during mitosis. PARylation of α-tubulin is recognized by ECT2 and recruits ECT2 to mitotic spindle for completing mitosis. Taken together, our study reveals a novel mechanism by which PAR regulates mitosis.

Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations

PubMed Central

Hayashi, Shigehiko

2017-01-01

The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown. Here, we report an atomic structure of the IF form predicted by atomic-level molecular dynamics (MD) simulations of the alternating access transition with a recently developed accelerating technique. We successfully obtained a significantly stable IF structure characterized by newly formed well-packed and -organized inter-domain interactions through the accelerated simulations of unprecedentedly large conformational changes of the alternating access without a prior knowledge of the target protein structure. The simulation also shed light on an atomistic mechanism of the strict transport selectivity of adenosine nucleotides over guanosine and inosine ones. Furthermore, the IF structure was shown to bind ATP and BA, and thus revealed their binding mechanisms. The present study proposes a qualitatively novel view of the alternating access of transporters having the unique three-fold symmetry in atomic details and opens the way for rational drug design targeting the transporter in the dynamic functional cycle. PMID:28727843

A unique dosing system for the production of OH under high vacuum for the study of environmental heterogeneous reactions

NASA Astrophysics Data System (ADS)

Brown, Matthew A.; Johánek, Viktor; Hemminger, John C.

2008-02-01

A unique dosing system for the production of hydroxyl radicals under high vacuum for the study of environmental heterogeneous reactions is described. Hydroxyl radicals are produced by the photodissociation of a hydrogen peroxide aqueous gas mixture with 254nm radiation according to the reaction H2O2+hν (254nm)→OH+OH. Under the conditions of the current design, 0.6% conversion of hydrogen peroxide is expected yielding a hydroxyl number density on the order of 1010molecules/cm3. The flux distribution of the dosing system is calculated using a Monte Carlo simulation method and compared with the experimentally determined results. The performance of this unique hydroxyl dosing system is demonstrated for the heterogeneous reaction with a solid surface of potassium iodide. Coupling of the hydroxyl radical dosing system to a quantitative surface analysis system should help provide molecular level insight into detailed reaction mechanisms.

Tocotrienols: The lesser known form of natural vitamin E

PubMed Central

Patel, Viren; Rink, Cameron; Khanna, Savita; Sen, Chandan K

2014-01-01

A recent and growing body of research has shown that members of this vitamin E family posses unique biologic functions. Tocotrienols have garnered much of this recent attention, and in particular α-tocotrienol has been shown to be the most potent neuroprotective form of vitamin E. Protection exclusively mediated through tocotrienols has been arbitrated to many mechanisms including inhibition of 12-LOX, c-Src, PLA2 and through up-regulation of MRP1. Further, tocotrienols have recently been shown to induce arteriogenesis through induction of TIMP1 and decreased activation of MMP2. However, the unique therapeutic potential of tocotrienols is not limited to neuroprotection. Tocotrienols have been shown to have molecular targets including: apoptotic regulators, cytokines, adhesion molecules, enzymes, kinases, receptors, transcription factors, and growth factors. In spite of this large and unique therapeutic potential, scientific literature on tocotrienols only accounts for approximately 1% of vitamin E research. Given the potential of tocotrienols and relatively scant literature, further investigation is warranted. PMID:22013739

Resonant Soft X-ray Scattering as a Powerful Probe of Buried Polymer Interfaces

NASA Astrophysics Data System (ADS)

Chen, Wei; Jiang, Zhang; Tirrell, Matthew

Elucidation of polymer interfacial structures provides insights into interfacial molecular mechanisms for coating protection, adhesion, lubrication, friction, wettability, biocompatibility, and even charge transport properties. Resonant Soft X-ray Scattering (RSoXS) offers a unique element, site and valence specific probe to study spatial modulations of molecular orbital degrees of freedom on the nanoscopic length scale. This unique sensitivity is achieved by merging small angle x-ray scattering and x-ray absorption spectroscopy into a single experiment, where the scattering provides information about spatial modulations and the spectroscopy provides sensitivity to the molecular anisotropy. Here we applied RSoXS to polystyrene (PS) films at solid-solid interfaces and poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC) brushes at solid-liquid interfaces. It is found that the interfacial width of PS thin film is about one order of magnitude large than those observed by traditional scattering techniques. In addition, although the ion-induced changes of PMPC thickness are not apparent in aqueous solutions, their chain conformations like polyzwitterion distribution and correlation varied, dependent on salt types, ionic strengths and ion valences. Consequently, it is evident that RSoXS is a powerful probe of buried polymer interlaces with both spatial and chemical sensitivities. This work was supported by the U.S. Department of Energy, Office of Science, Program in Basic Energy Sciences, Division of Materials Science and Engineering.

Dynamical Effects in Metal-Organic Frameworks: The Microporous Materials as Shock Absorbers

NASA Astrophysics Data System (ADS)

Banlusan, Kiettipong; Strachan, Alejandro

2017-06-01

Metal-organic frameworks (MOFs) are a class of nano-porous crystalline solids consisting of inorganic units coordinated to organic linkers. The unique molecular structures and outstanding properties with ultra-high porosity and tunable chemical functionality by various choices of metal clusters and organic ligands make this class of materials attractive for many applications. The complex and quite unique responses of these materials to mechanical loading including void collapse make them attractive for applications in energy absorption and storage. We will present using large-scale molecular dynamics simulations to investigate shock propagation in zeolitic imidazolate framework ZIF-8 and MOF-5. We find that for shock strengths above a threshold a two-wave structure develops with a leading elastic precursor followed by a second wave of structural collapse to relax the stress. Structural transition of MOFs in response to shock waves corresponds to the transition between two Hugoniot curves, and results in abrupt change in temperature. The pore-collapse wave propagates at slower velocity than the leading wave and weakens it, resulting in shock attenuation. Increasing piston speed results in faster propagation of pore-collapse wave, but the leading elastic wave remains unchanged below the overdriven regime. We discuss how the molecular structure of the MOFs and shock propagation direction affect the response of the materials and their ability to weaken shocks. Office of Naval Research, MURI 2012 02341 01.

A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid.

PubMed

Alves, Cláudio Nahum; Martí, Sergio; Castillo, Raquel; Andrés, Juan; Moliner, Vicent; Tuñón, Iñaki; Silla, Estanislao

2008-04-01

Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy for wild-type and N155S mutant HIV-1 IN, both complexed with a DKA. This hybrid methodology has the advantage of the inclusion of quantum effects such as ligand polarization upon binding, which can be very important when highly polarizable groups are embedded in anisotropic environments, for example in metal-containing active sites. Furthermore, an energy terms decomposition analysis was performed to determine contributions of individual residues to the enzyme-inhibitor interactions. The results reveal that there is a strong interaction between the Lys-159, Lys-156, and Asn-155 residues and Mg(2+) cation and the DKA inhibitor. Our calculations show that the binding energy is higher in wild-type than in the N155S mutant, in accordance with the experimental results. The role of the mutated residue has thus been checked as maintaining the structure of the ternary complex formed by the protein, the Mg(2+) cation, and the inhibitor. These results might be useful to design compounds with more interesting anti-HIV-1 IN activity on the basis of its three-dimensional structure.

Molecular Aspects of Structure, Gating, and Physiology of pH-Sensitive Background K2P and Kir K+-Transport Channels

PubMed Central

Sepúlveda, Francisco V.; Pablo Cid, L.; Teulon, Jacques; Niemeyer, María Isabel

2015-01-01

K+ channels fulfill roles spanning from the control of excitability to the regulation of transepithelial transport. Here we review two groups of K+ channels, pH-regulated K2P channels and the transport group of Kir channels. After considering advances in the molecular aspects of their gating based on structural and functional studies, we examine their participation in certain chosen physiological and pathophysiological scenarios. Crystal structures of K2P and Kir channels reveal rather unique features with important consequences for the gating mechanisms. Important tasks of these channels are discussed in kidney physiology and disease, K+ homeostasis in the brain by Kir channel-equipped glia, and central functions in the hearing mechanism in the inner ear and in acid secretion by parietal cells in the stomach. K2P channels fulfill a crucial part in central chemoreception probably by virtue of their pH sensitivity and are central to adrenal secretion of aldosterone. Finally, some unorthodox behaviors of the selectivity filters of K2P channels might explain their normal and pathological functions. Although a great deal has been learned about structure, molecular details of gating, and physiological functions of K2P and Kir K+-transport channels, this has been only scratching at the surface. More molecular and animal studies are clearly needed to deepen our knowledge. PMID:25540142

Molecular Genetics of Beauveria bassiana Infection of Insects.

PubMed

Ortiz-Urquiza, A; Keyhani, N O

2016-01-01

Research on the insect pathogenic filamentous fungus, Beauveria bassiana has witnessed significant growth in recent years from mainly physiological studies related to its insect biological control potential, to addressing fundamental questions regarding the underlying molecular mechanisms of fungal development and virulence. This has been in part due to a confluence of robust genetic tools and genomic resources for the fungus, and recognition of expanded ecological interactions with which the fungus engages. Beauveria bassiana is a broad host range insect pathogen that has the ability to form intimate symbiotic relationships with plants. Indeed, there is an increasing realization that the latter may be the predominant environmental interaction in which the fungus participates, and that insect parasitism may be an opportunist lifestyle evolved due to the carbon- and nitrogen-rich resources present in insect bodies. Here, we will review progress on the molecular genetics of B. bassiana, which has largely been directed toward identifying genetic pathways involved in stress response and virulence assumed to have practical applications in improving the insect control potential of the fungus. Important strides have also been made in understanding aspects of B. bassiana development. Finally, although increasingly apparent in a number of studies, there is a need for progressing beyond phenotypic mutant characterization to sufficiently investigate the molecular mechanisms underlying B. bassiana's unique and diverse lifestyles as saprophyte, insect pathogen, and plant mutualist. Copyright © 2016 Elsevier Inc. All rights reserved.

Dissection of Biological Property of Chinese Acupuncture Point Zusanli Based on Long-Term Treatment via Modulating Multiple Metabolic Pathways.

PubMed

Yan, Guangli; Zhang, Aihua; Sun, Hui; Cheng, Weiping; Meng, Xiangcai; Liu, Li; Zhang, Yingzhi; Xie, Ning; Wang, Xijun

2013-01-01

Acupuncture has a history of over 3000 years and is a traditional Chinese medical therapy that uses hair-thin metal needles to puncture the skin at specific points on the body to promote wellbeing, while its molecular mechanism and ideal biological pathways are still not clear. High-throughput metabolomics is the global assessment of endogenous metabolites within a biologic system and can potentially provide a more accurate snap shot of the actual physiological state. We hypothesize that acupuncture-treated human would produce unique characterization of metabolic phenotypes. In this study, UPLC/ESI-HDMS coupled with pattern recognition methods and system analysis were carried out to investigate the mechanism and metabolite biomarkers for acupuncture treatment at "Zusanli" acupoint (ST-36) as a case study. The top 5 canonical pathways including alpha-linolenic acid metabolism, d-glutamine and d-glutamate metabolism, citrate cycle, alanine, aspartate, and glutamate metabolism, and vitamin B6 metabolism pathways were acutely perturbed, and 53 differential metabolites were identified by chemical profiling and may be useful to clarify the physiological basis and mechanism of ST-36. More importantly, network construction has led to the integration of metabolites associated with the multiple perturbation pathways. Urine metabolic profiling might be a promising method to investigate the molecular mechanism of acupuncture.

In-drop capillary spooling of spider capture thread inspires hybrid fibers with mixed solid–liquid mechanical properties

PubMed Central

Elettro, Hervé; Neukirch, Sébastien; Vollrath, Fritz; Antkowiak, Arnaud

2016-01-01

An essential element in the web-trap architecture, the capture silk spun by ecribellate orb spiders consists of glue droplets sitting astride a silk filament. Mechanically this thread presents a mixed solid–liquid behavior unknown to date. Under extension, capture silk behaves as a particularly stretchy solid, owing to its molecular nanosprings, but it totally switches behavior in compression to now become liquid-like: It shrinks with no apparent limit while exerting a constant tension. Here, we unravel the physics underpinning the unique behavior of this ”liquid wire” and demonstrate that its mechanical response originates in the shape-switching of the silk filament induced by buckling within the droplets. Learning from this natural example of geometry and mechanics, we manufactured programmable liquid wires that present previously unidentified pathways for the design of new hybrid solid–liquid materials. PMID:27185930

In-drop capillary spooling of spider capture thread inspires hybrid fibers with mixed solid-liquid mechanical properties.

PubMed

Elettro, Hervé; Neukirch, Sébastien; Vollrath, Fritz; Antkowiak, Arnaud

2016-05-31

An essential element in the web-trap architecture, the capture silk spun by ecribellate orb spiders consists of glue droplets sitting astride a silk filament. Mechanically this thread presents a mixed solid-liquid behavior unknown to date. Under extension, capture silk behaves as a particularly stretchy solid, owing to its molecular nanosprings, but it totally switches behavior in compression to now become liquid-like: It shrinks with no apparent limit while exerting a constant tension. Here, we unravel the physics underpinning the unique behavior of this "liquid wire" and demonstrate that its mechanical response originates in the shape-switching of the silk filament induced by buckling within the droplets. Learning from this natural example of geometry and mechanics, we manufactured programmable liquid wires that present previously unidentified pathways for the design of new hybrid solid-liquid materials.

In-drop capillary spooling of spider capture thread inspires hybrid fibers with mixed solid-liquid mechanical properties

NASA Astrophysics Data System (ADS)

Elettro, Hervé; Neukirch, Sébastien; Vollrath, Fritz; Antkowiak, Arnaud

2016-05-01

An essential element in the web-trap architecture, the capture silk spun by ecribellate orb spiders consists of glue droplets sitting astride a silk filament. Mechanically this thread presents a mixed solid-liquid behavior unknown to date. Under extension, capture silk behaves as a particularly stretchy solid, owing to its molecular nanosprings, but it totally switches behavior in compression to now become liquid-like: It shrinks with no apparent limit while exerting a constant tension. Here, we unravel the physics underpinning the unique behavior of this ”liquid wire” and demonstrate that its mechanical response originates in the shape-switching of the silk filament induced by buckling within the droplets. Learning from this natural example of geometry and mechanics, we manufactured programmable liquid wires that present previously unidentified pathways for the design of new hybrid solid-liquid materials.

Rox, a Rifamycin Resistance Enzyme with an Unprecedented Mechanism of Action.

PubMed

Koteva, Kalinka; Cox, Georgina; Kelso, Jayne K; Surette, Matthew D; Zubyk, Haley L; Ejim, Linda; Stogios, Peter; Savchenko, Alexei; Sørensen, Dan; Wright, Gerard D

2018-04-19

Rifamycin monooxygenases (Rox) are present in a variety of environmental bacteria and are associated with decomposition of the clinically utilized antibiotic rifampin. Here we report the structure and function of a drug-inducible rox gene from Streptomyces venezuelae, which encodes a class A flavoprotein monooxygenase that inactivates a broad range of rifamycin antibiotics. Our findings describe a mechanism of rifamycin inactivation initiated by monooxygenation of the 2-position of the naphthyl group, which subsequently results in ring opening and linearization of the antibiotic. The result is an antibiotic that no longer adopts the basket-like structure essential for binding to the RNA exit tunnel of the target RpoB, thereby providing the molecular logic of resistance. This unique mechanism of enzymatic inactivation underpins the broad spectrum of rifamycin resistance mediated by Rox enzymes and presents a new antibiotic resistance mechanism not yet seen in microbial antibiotic detoxification. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chilling and Drought Stresses in Crop Plants: Implications, Cross Talk, and Potential Management Opportunities

PubMed Central

Hussain, Hafiz A.; Hussain, Saddam; Khaliq, Abdul; Ashraf, Umair; Anjum, Shakeel A.; Men, Shengnan; Wang, Longchang

2018-01-01

Plants face a combination of different abiotic stresses under field conditions which are lethal to plant growth and production. Simultaneous occurrence of chilling and drought stresses in plants due to the drastic and rapid global climate changes, can alter the morphological, physiological and molecular responses. Both these stresses adversely affect the plant growth and yields due to physical damages, physiological and biochemical disruptions, and molecular changes. In general, the co-occurrence of chilling and drought combination is even worse for crop production rather than an individual stress condition. Plants attain various common and different physiological and molecular protective approaches for tolerance under chilling and drought stresses. Nevertheless, plant responses to a combination of chilling and drought stresses are unique from those to individual stress. In the present review, we summarized the recent evidence on plant responses to chilling and drought stresses on shared as well as unique basis and tried to find a common thread potentially underlying these responses. We addressed the possible cross talk between plant responses to these stresses and discussed the potential management strategies for regulating the mechanisms of plant tolerance to drought and/or chilling stresses. To date, various novel approaches have been tested in minimizing the negative effects of combine stresses. Despite of the main improvements there is still a big room for improvement in combination of drought and chilling tolerance. Thus, future researches particularly using biotechnological and molecular approaches should be carried out to develop genetically engineered plants with enhanced tolerance against these stress factors. PMID:29692787

Molecular Origin of Strength and Stiffness in Bamboo Fibrils.

PubMed

Youssefian, Sina; Rahbar, Nima

2015-06-08

Bamboo, a fast-growing grass, has a higher strength-to-weight ratio than steel and concrete. The unique properties of bamboo come from the natural composite structure of fibers that consists mainly of cellulose microfibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have used atomistic simulations to study the mechanical properties of and adhesive interactions between the materials in bamboo fibers. With this aim, we have developed molecular models of lignin, hemicellulose and LCC structures to study the elastic moduli and the adhesion energies between these materials and cellulose microfibril faces. Good agreement was observed between the simulation results and experimental data. It was also shown that the hemicellulose model has stronger mechanical properties than lignin while lignin exhibits greater tendency to adhere to cellulose microfibrils. The study suggests that the abundance of hydrogen bonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose microfibril is responsible for higher adhesion energy between LCC and cellulose microfibrils. We also found out that the amorphous regions of cellulose microfibrils are the weakest interfaces in bamboo fibrils. Hence, they determine the fibril strength.

Molecular Origin of Strength and Stiffness in Bamboo Fibrils

PubMed Central

Youssefian, Sina; Rahbar, Nima

2015-01-01

Bamboo, a fast-growing grass, has a higher strength-to-weight ratio than steel and concrete. The unique properties of bamboo come from the natural composite structure of fibers that consists mainly of cellulose microfibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have used atomistic simulations to study the mechanical properties of and adhesive interactions between the materials in bamboo fibers. With this aim, we have developed molecular models of lignin, hemicellulose and LCC structures to study the elastic moduli and the adhesion energies between these materials and cellulose microfibril faces. Good agreement was observed between the simulation results and experimental data. It was also shown that the hemicellulose model has stronger mechanical properties than lignin while lignin exhibits greater tendency to adhere to cellulose microfibrils. The study suggests that the abundance of hydrogen bonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose microfibril is responsible for higher adhesion energy between LCC and cellulose microfibrils. We also found out that the amorphous regions of cellulose microfibrils are the weakest interfaces in bamboo fibrils. Hence, they determine the fibril strength. PMID:26054045

Molecular Origin of Strength and Stiffness in Bamboo Fibrils

NASA Astrophysics Data System (ADS)

Youssefian, Sina; Rahbar, Nima

2015-06-01

Bamboo, a fast-growing grass, has a higher strength-to-weight ratio than steel and concrete. The unique properties of bamboo come from the natural composite structure of fibers that consists mainly of cellulose microfibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have used atomistic simulations to study the mechanical properties of and adhesive interactions between the materials in bamboo fibers. With this aim, we have developed molecular models of lignin, hemicellulose and LCC structures to study the elastic moduli and the adhesion energies between these materials and cellulose microfibril faces. Good agreement was observed between the simulation results and experimental data. It was also shown that the hemicellulose model has stronger mechanical properties than lignin while lignin exhibits greater tendency to adhere to cellulose microfibrils. The study suggests that the abundance of hydrogen bonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose microfibril is responsible for higher adhesion energy between LCC and cellulose microfibrils. We also found out that the amorphous regions of cellulose microfibrils are the weakest interfaces in bamboo fibrils. Hence, they determine the fibril strength.

Molecular mechanism for adhesion in humid conditions - lessons from spider glue

NASA Astrophysics Data System (ADS)

Amarpuri, Gaurav; Singla, Saranshu; Dhopatkar, Nishad; Blackledge, Todd; Dhinojwal, Ali

Adhesion in humid conditions is a fundamental challenge for both natural and synthetic adhesives. Water lubricates the interface between the adhesive and the substrate resulting in an interfacial failure at high humidity. Yet, glue from most spider species fail cohesively at high humidity, and the spider species from wet habitat show an increase in adhesion with humidity. We use tensile testing, microscopy and surface sensitive spectroscopy techniques to probe the mechanism of spider glue adhesion under high humidity. Humidity responsive structural changes in the glue structure are observed both at the interface and in bulk. However, the humidity responsiveness is lost after washing the water soluble low molecular weight molecules (LMM) from the glue. Many natural systems display a functional response to their environment, but spider glue's humidity responsiveness is a novel adaptation that makes the glue stickiest in each species' preferred habitat. This tuning is achieved by a combination of proteins and hygroscopic LMM that respond to humidity in a unique way. We therefore anticipate that manipulation of polymer-LMM interaction can provide a simple mechanism to design humidity responsive smart adhesives. We acknowledge support from National Science Foundation Grant IOS-1257719.

Theoretic Study on Dispersion Mechanism of Boron Nitride Nanotubes by Polynucleotides

PubMed Central

Liang, Lijun; Hu, Wei; Zhang, Zhisen; Shen, Jia-Wei

2016-01-01

Due to the unique electrical and mechanical properties of boron nitride nanotubes (BNNT), BNNT has been a promising material for many potential applications, especially in biomedical field. Understanding the dispersion of BNNT in aqueous solution by biomolecules is essential for its use in biomedical applications. In this study, BNNT wrapped by polynucleotides in aqueous solution was investigated by molecular dynamics (MD) simulations. Our results demonstrated that the BNNT wrapped by polynucleotides could greatly hinder the aggregation of BNNTs and improve the dispersion of BNNTs in aqueous solution. Dispersion of BNNTs with the assistance of polynucleotides is greatly affected by the wrapping manner of polynucleotides on BNNT, which mainly depends on two factors: the type of polynucleotides and the radius of BNNT. The interaction between polynucleotides and BNNT(9, 9) is larger than that between polynucleotides and BNNT(5, 5), which leads to the fact that dispersion of BNNT(9, 9) is better than that of BNNT(5, 5) with the assistance of polynucleotides in aqueous solution. Our study revealed the molecular-level dispersion mechanism of BNNT with the assistance of polynucleotides in aqueous solution. It shades a light on the understanding of dispersion of single wall nanotubes by biomolecules. PMID:28004832

4-Hydroxyphenylpyruvate Dioxygenase Catalysis

PubMed Central

Raspail, Corinne; Graindorge, Matthieu; Moreau, Yohann; Crouzy, Serge; Lefèbvre, Bertrand; Robin, Adeline Y.; Dumas, Renaud; Matringe, Michel

2011-01-01

4-Hydroxyphenylpyruvate dioxygenase (HPPD) catalyzes the conversion of 4-hydroxyphenylpyruvate (HPP) into homogentisate. HPPD is the molecular target of very effective synthetic herbicides. HPPD inhibitors may also be useful in treating life-threatening tyrosinemia type I and are currently in trials for treatment of Parkinson disease. The reaction mechanism of this key enzyme in both plants and animals has not yet been fully elucidated. In this study, using site-directed mutagenesis supported by quantum mechanical/molecular mechanical theoretical calculations, we investigated the role of catalytic residues potentially interacting with the substrate/intermediates. These results highlight the following: (i) the central role of Gln-272, Gln-286, and Gln-358 in HPP binding and the first nucleophilic attack; (ii) the important movement of the aromatic ring of HPP during the reaction, and (iii) the key role played by Asn-261 and Ser-246 in C1 hydroxylation and the final ortho-rearrangement steps (numbering according to the Arabidopsis HPPD crystal structure 1SQD). Furthermore, this study reveals that the last step of the catalytic reaction, the 1,2 shift of the acetate side chain, which was believed to be unique to the HPPD activity, is also catalyzed by a structurally unrelated enzyme. PMID:21613226

Unraveling the molecular mechanism of photosynthetic toxicity of highly fluorescent silver nanoclusters to Scenedesmus obliquus.

PubMed

Zhang, Li; Goswami, Nirmal; Xie, Jianping; Zhang, Bo; He, Yiliang

2017-11-27

While the discovery of numerous attractive properties of silver at the nanoscale has increased their demand in many sectors including medicine, optics, sensing, painting and cosmetics, it has also raised wide public concerns about their effect on living organisms in aquatic environment. Despite the continuous effort to understand the various aspects of the toxicity of silver nanomaterials, the molecular level understanding on their cytotoxicity mechanism to biological organisms has remained unclear. Herein, we demonstrated the underlying mechanism of the photosynthetic toxicity against green algae namely, Scenedesmus obliquus by using an emerging silver nanomaterial, called silver nanoclusters (defined as r-Ag NCs). By exploiting the unique fluorescence properties of r-Ag NCs along with various other analytical/biological tools, we proposed that the photosynthetic toxicity of r-Ag NCs was largely attributed to the "joint-toxicity" effect of particulate form of r-Ag NCs and its released Ag + , which resulted in the disruption of the electron transport chain of light reaction and affected the content of key enzymes (RuBP carboxylase/ oxygenase) of Calvin cycle of algae cells. We believe that the present study can also be applied to the assessment of the ecological risk derived from other metal nanoparticles.

Polydiacetylene chromism towards toxic chemical detection via molecular size-dependent selectivity

NASA Astrophysics Data System (ADS)

Seo, Donghwan

Polydiacetylene (PDA) is a pi-conjugated polymer that has unique optical properties. PDA changes color from blue to red when subjected to various stimuli such as mechanical stress, heat, photoirradiation, pH change, and binding of specific ligands. The steric effect induced by those stimuli on PDA headgroup has been investigated to understand the mechanism of PDA chromism and to apply those optical properties to the development of various sensors. In this work, pH chromism of PDA was examined in terms of the effects of the molecular size and acidity of acid analytes with the consideration of the molecular design aspect of diacetylene lipids. The pH level is an important parameter, since a low pH will produce a charge on the amine headgroup of PDA, but this does not necessarily result in PDA chromatic transition from 'blue phase' to 'red phase.' The molecular size of the counter anion was identified as another determinant condition to ensure the perturbation of the ene-yne conjugated backbone of PDA, which produces the chromatic transition. In the molecular design of the sensory diacetylene lipids, the alkyl spacer length between the amine as a receptor and the amide linker was found to strongly affect the degree of PDA chromatic transition. The longer alkyl spacer showed the less chromatic transition. The length of alkyl spacer seems to promote the flexibility of the molecule diminishing the extent of the transfer of the steric effect at PDA headgroup to the conjugated backbone. Finally, PDA chromism dependent on the molecular size of acid analytes was applied to develop the colorimetric detection of diethyl phosphate (DEP), a degraded nerve agent simulant. PDA liposome sensors successfully showed selective chromatic transition with fluorescent emission upon binding of DEP compared to other acid analytes. The molecular size and acidity of acid analytes, and alkyl spacer length have proven to be correlated with PDA chromism. These new findings provide further understanding of the mechanism of PDA chromism and the molecular design principle of diacetylene in fundamental studies and in the development of various applications.

A Finite Element Framework for Studying the Mechanical Response of Macromolecules: Application to the Gating of the Mechanosensitive Channel MscL

PubMed Central

Tang, Yuye; Cao, Guoxin; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2006-01-01

The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the membrane. Compared to popular all-atom-based techniques such as targeted or steered molecular-dynamics simulations, the finite element method-based continuum-mechanics framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial scales and long timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:16731564

Molecular parallels between neural and vascular development.

PubMed

Eichmann, Anne; Thomas, Jean-Léon

2013-01-01

The human central nervous system (CNS) features a network of ~400 miles of blood vessels that receives >20% of the body's cardiac output and uses most of its blood glucose. Many human diseases, including stroke, retinopathy, and cancer, are associated with the biology of CNS blood vessels. These vessels originate from extrinsic cell populations, including endothelial cells and pericytes that colonize the CNS and interact with glia and neurons to establish the blood-brain barrier and control cerebrovascular exchanges. Neurovascular interactions also play important roles in adult neurogenic niches, which harbor a unique population of neural stem cells that are intimately associated with blood vessels. We here review the cellular and molecular mechanisms required to establish the CNS vascular network, with a special focus on neurovascular interactions and the functions of vascular endothelial growth factors.

Mudskippers and Their Genetic Adaptations to an Amphibious Lifestyle.

PubMed

You, Xinxin; Sun, Min; Li, Jia; Bian, Chao; Chen, Jieming; Yi, Yunhai; Yu, Hui; Shi, Qiong

2018-02-07

Mudskippers are the largest group of amphibious teleost fish that are uniquely adapted to live on mudflats. During their successful transition from aqueous life to terrestrial living, these fish have evolved morphological and physiological modifications of aerial vision and olfaction, higher ammonia tolerance, aerial respiration, improved immunological defense against terrestrial pathogens, and terrestrial locomotion using protruded pectoral fins. Comparative genomic and transcriptomic data have been accumulated and analyzed for understanding molecular mechanisms of the terrestrial adaptations. Our current review provides a general introduction to mudskippers and recent research advances of their genetic adaptations to the amphibious lifestyle, which will be helpful for understanding the evolutionary transition of vertebrates from water to land. Our insights into the genomes and transcriptomes will also support molecular breeding, functional identification, and natural compound screening.

Novel Molecular Architectures Developed for Improved Solid Polymer Electrolytes for Lithium Polymer Batteries

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Kinder, James D.; Bennett, William R.

2002-01-01

Lithium-based polymer batteries for aerospace applications need the ability to operate in temperatures ranging from -70 to 70 C. Current state-of-the-art solid polymer electrolytes (based on amorphous polyethylene oxide, PEO) have acceptable ionic conductivities (10-4 to 10-3 S/cm) only above 60 C. Higher conductivity can be achieved in the current systems by adding solvent or plasticizers to the solid polymer to improve ion transport. However, this can compromise the dimensional and thermal stability of the electrolyte, as well as compatibility with electrode materials. One of NASA Glenn Research Center's objectives in the PERS program is to develop new electrolytes having unique molecular architectures and/or novel ion transport mechanisms, leading to good ionic conductivity at room temperature and below without solvents or plasticizers.

Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB.

PubMed

Wei, Wei; Sun, Yang; Zhu, Mingli; Liu, Xiangzhi; Sun, Peiqing; Wang, Feng; Gui, Qiu; Meng, Wuyi; Cao, Yi; Zhao, Jing

2015-12-16

The coordination bond between gold and sulfur (Au-S) has been widely studied and utilized in many fields. However, detailed investigations on the basic nature of this bond are still lacking. A gold-specific binding protein, GolB, was recently identified, providing a unique opportunity for the study of the Au-S bond at the molecular level. We probed the mechanical strength of the gold-sulfur bond in GolB using single-molecule force spectroscopy. We measured the rupture force of the Au-S bond to be 165 pN, much lower than Au-S bonds measured on different gold surfaces (∼1000 pN). We further solved the structures of apo-GolB and Au(I)-GolB complex using X-ray crystallography. These structures showed that the average Au-S bond length in GolB is much longer than the reported average value of Au-S bonds. Our results highlight the dramatic influence of the unique biological environment on the stability and strength of metal coordination bonds in proteins.

Loneliness Across Phylogeny and a Call for Comparative Studies and Animal Models

PubMed Central

Cacioppo, John T.; Cacioppo, Stephanie; Cole, Steven W.; Capitanio, John P.; Goossens, Luc; Boomsma, Dorret I.

2016-01-01

Loneliness typically refers to the feelings of distress and dysphoria resulting from a discrepancy between a person’s desired and achieved levels of social relations, and there is now considerable evidence that loneliness is a risk factor for poor psychological and physical health. Loneliness has traditionally been conceptualized as a uniquely human phenomenon. However, over millions of years of evolution, efficient and manifold neural, hormonal, and molecular mechanisms have evolved for promoting companionship and mutual protection/assistance and for organizing adaptive responses when there is a significant discrepancy between the preferred and realized levels of social connection. We review evidence suggesting that loneliness is not a uniquely human phenomenon, but, instead, as a scientific construct, it represents a generally adaptive predisposition that can be found across phylogeny. Central to this argument is the premise that the brain is the key organ of social connections and processes. Comparative studies and animal models, particularly when integrated with human studies, have much to contribute to the understanding of loneliness and its underlying principles, mechanisms, consequences, and potential treatments. PMID:25910390

Fundamentals of pulmonary drug delivery.

PubMed

Groneberg, D A; Witt, C; Wagner, U; Chung, K F; Fischer, A

2003-04-01

Aerosol administration of peptide-based drugs plays an important role in the treatment of pulmonary and systemic diseases and the unique cellular properties of airway epithelium offers a great potential to deliver new compounds. As the relative contributions from the large airways to the alveolar space are important to the local and systemic availability, the sites and mechanism of uptake and transport of different target compounds have to be characterized. Among the different respiratory cells, the ciliated epithelial cells of the larger and smaller airways and the type I and type II pneumocytes are the key players in pulmonary drug transport. With their diverse cellular characteristics, each of these cell types displays a unique uptake possibility. Next to the knowledge of these cellular aspects, the nature of aerosolized drugs, characteristics of delivery systems and the depositional and pulmonary clearance mechanisms display major targets to optimize pulmonary drug delivery. Based on the growing knowledge on pulmonary cell biology and pathophysiology due to modern methods of molecular biology, the future characterization of pulmonary drug transport pathways can lead to new strategies in aerosol drug therapy.

In vitro pathological modelling using patient-specific induced pluripotent stem cells: the case of progeria.

PubMed

Nissan, Xavier; Blondel, Sophie; Peschanski, Marc

2011-12-01

Progeria, also known as HGPS (Hutchinson-Gilford progeria syndrome), is a rare fatal genetic disease characterized by an appearance of accelerated aging in children. This syndrome is typically caused by mutations in codon 608 (C1804T) of the gene encoding lamins A and C, LMNA, leading to the production of a truncated form of the protein called progerin. Owing to their unique potential to self-renew and to differentiate into any cell types of the organism, pluripotent stem cells offer a unique tool to study molecular and cellular mechanisms related to this global and systemic disease. Recent studies have exploited this potential by generating human induced pluripotent stem cells from HGPS patients' fibroblasts displaying several phenotypic defects characteristic of HGPS such as nuclear abnormalities, progerin expression, altered DNA-repair mechanisms and premature senescence. Altogether, these findings provide new insights on the use of pluripotent stem cells for pathological modelling and may open original therapeutic perspectives for diseases that lack pre-clinical in vitro human models, such as HGPS.

The Botulinum Toxin as a Therapeutic Agent: Molecular Structure and Mechanism of Action in Motor and Sensory Systems.

PubMed

Kumar, Raj; Dhaliwal, Harkiran Preet; Kukreja, Roshan Vijay; Singh, Bal Ram

2016-02-01

Botulinum neurotoxin (BoNT) produced by Clostridium botulinum is the most potent molecule known to mankind. Higher potency of BoNT is attributed to several factors, including structural and functional uniqueness, target specificity, and longevity. Although BoNT is an extremely toxic molecule, it is now increasingly used for the treatment of disorders related to muscle hyperactivity and glandular hyperactivity. Weakening of muscles due to peripheral action of BoNT produces a therapeutic effect. Depending on the target tissue, BoNT can block the cholinergic neuromuscular or cholinergic autonomic innervation of exocrine glands and smooth muscles. In recent observations of the analgesic properties of BoNT, the toxin modifies the sensory feedback loop to the central nervous system. Differential effects of BoNT in excitatory and inhibitory neurons provide a unique therapeutic tool. In this review the authors briefly summarize the structure and mechanism of actions of BoNT on motor and sensory neurons to explain its therapeutic effects and future potential. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Neurophotonics: optical methods to study and control the brain

NASA Astrophysics Data System (ADS)

Doronina-Amitonova, L. V.; Fedotov, I. V.; Fedotov, A. B.; Anokhin, K. V.; Zheltikov, A. M.

2015-04-01

Methods of optical physics offer unique opportunities for the investigation of brain and higher nervous activity. The integration of cutting-edge laser technologies and advanced neurobiology opens a new cross-disciplinary area of natural sciences - neurophotonics - focusing on the development of a vast arsenal of tools for functional brain diagnostics, stimulation of individual neurons and neural networks, and the molecular engineering of brain cells aimed at the diagnosis and therapy of neurodegenerative and psychic diseases. Optical fibers help to confront the most challenging problems in brain research, including the analysis of molecular-cellular mechanisms of the formation of memory and behavior. New generation optical fibers provide new solutions for the development of fundamentally new, unique tools for neurophotonics and laser neuroengineering - fiber-optic neuroendoscopes and neurointerfaces. These instruments broaden research horizons when investigating the most complex brain functions, enabling a long-term multiplex detection of fluorescent protein markers, as well as photostimulation of neuronal activity in deep brain areas in living, freely moving animals with an unprecedented spatial resolution and minimal invasiveness. This emerging technology opens new horizons for understanding learning and long-term memory through experiments with living, freely moving mammals. Here, we present a brief review of this rapidly growing field of research.

Rotaxane and catenane host structures for sensing charged guest species.

PubMed

Langton, Matthew J; Beer, Paul D

2014-07-15

CONSPECTUS: The promise of mechanically interlocked architectures, such as rotaxanes and catenanes, as prototypical molecular switches and shuttles for nanotechnological applications, has stimulated an ever increasing interest in their synthesis and function. The elaborate host cavities of interlocked structures, however, can also offer a novel approach toward molecular recognition: this Account describes the use of rotaxane and catenane host systems for binding charged guest species, and for providing sensing capability through an integrated optical or electrochemical reporter group. Particular attention is drawn to the exploitation of the unusual dynamic properties of interlocked molecules, such as guest-induced shuttling or conformational switching, as a sophisticated means of achieving a selective and functional sensor response. We initially survey interlocked host systems capable of sensing cationic guests, before focusing on our accomplishments in synthesizing rotaxanes and catenanes designed for the more challenging task of selective anion sensing. In our group, we have developed the use of discrete anionic templation to prepare mechanically interlocked structures for anion recognition applications. Removal of the anion template reveals an interlocked host system, possessing a unique three-dimensional geometrically restrained binding cavity formed between the interlocked components, which exhibits impressive selectivity toward complementary anionic guest species. By incorporating reporter groups within such systems, we have developed both electrochemical and optical anion sensors which can achieve highly selective sensing of anionic guests. Transition metals, lanthanides, and organic fluorophores integrated within the mechanically bonded structural framework of the receptor are perturbed by the binding of the guest, with a concomitant change in the emission profile. We have also exploited the unique dynamics of interlocked hosts by demonstrating that an anion-induced conformational change can be used as a means of signal transduction. Electrochemical sensing has been realized by integration of the redox-active ferrocene functionality within a range of rotaxane and catenanes; binding of an anion perturbs the metallocene, leading to a cathodic shift in the ferrocene/ferrocenium redox couple. In order to obtain practical sensors for target charged guest species, confinement of receptors at a surface is necessary in order to develop robust, reuseable devices. Surface confinement also offers advantages over solution based receptors, including amplification of signal, enhanced guest binding thermodynamics and the negation of solubility problems. We have fabricated anion-templated rotaxanes and catenanes on gold electrode surfaces and demonstrated that the resulting mechanically bonded self-assembled monolayers are electrochemically responsive to the binding of anions, a crucial first step toward the advancement of sophisticated, highly selective, anion sensory devices. Rotaxane and catenane host molecules may be engineered to offer a superior level of molecular recognition, and the incorporation of optical or electrochemical reporter groups within these interlocked frameworks can allow for guest sensing. Advances in synthetic templation strategies has facilitated the synthesis of interlocked architectures and widened their interest as prototype molecular machines. However, their unique host-guest properties are only now beginning to be exploited as a sophisticated approach to chemical sensing. The development of functional host-guest sensory systems such as these is of great interest to the interdisciplinary field of supramolecular chemistry.

Switching modes in corticogenesis: mechanisms of neuronal subtype transitions and integration in the cerebral cortex

PubMed Central

Toma, Kenichi; Hanashima, Carina

2015-01-01

Information processing in the cerebral cortex requires the activation of diverse neurons across layers and columns, which are established through the coordinated production of distinct neuronal subtypes and their placement along the three-dimensional axis. Over recent years, our knowledge of the regulatory mechanisms of the specification and integration of neuronal subtypes in the cerebral cortex has progressed rapidly. In this review, we address how the unique cytoarchitecture of the neocortex is established from a limited number of progenitors featuring neuronal identity transitions during development. We further illuminate the molecular mechanisms of the subtype-specific integration of these neurons into the cerebral cortex along the radial and tangential axis, and we discuss these key features to exemplify how neocortical circuit formation accomplishes economical connectivity while maintaining plasticity and evolvability to adapt to environmental changes. PMID:26321900

Structural insights into simocyclinone as an antibiotic, effector ligand and substrate

PubMed Central

Buttner, Mark J; Schäfer, Martin; Lawson, David M

2017-01-01

Abstract Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins. PMID:29126195

Structural insights into simocyclinone as an antibiotic, effector ligand and substrate.

PubMed

Buttner, Mark J; Schäfer, Martin; Lawson, David M; Maxwell, Anthony

2018-01-01

Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins. © FEMS 2017.

Calcium Signaling Is Required for Erythroid Enucleation

PubMed Central

Russell, Sarah M.; Humbert, Patrick O.

2016-01-01

Although erythroid enucleation, the property of erythroblasts to expel their nucleus, has been known for 7ore than a century, surprisingly little is known regarding the molecular mechanisms governing this unique developmental process. Here we show that similar to cytokinesis, nuclear extrusion requires intracellular calcium signaling and signal transduction through the calmodulin (CaM) pathway. However, in contrast to cytokinesis we found that orthochromatic erythroblasts require uptake of extracellular calcium to enucleate. Together these functional studies highlight a critical role for calcium signaling in the regulation of erythroid enucleation. PMID:26731108

Ultrathin nanoporous membranes for insulator-based dielectrophoresis

NASA Astrophysics Data System (ADS)

Mukaibo, Hitomi; Wang, Tonghui; Perez-Gonzalez, Victor H.; Getpreecharsawas, Jirachai; Wurzer, Jack; Lapizco-Encinas, Blanca H.; McGrath, James L.

2018-06-01

Insulator-based dielectrophoresis (iDEP) is a simple, scalable mechanism that can be used for directly manipulating particle trajectories in pore-based filtration and separation processes. However, iDEP manipulation of nanoparticles presents unique challenges as the dielectrophoretic force ({F}{{D}{{E}}{{P}}}) exerted on the nanoparticles can easily be overshadowed by opposing kinetic forces. In this study, a molecularly thin, SiN-based nanoporous membrane (NPN) is explored as a breakthrough technology that enhances {F}{{D}{{E}}{{P}}}. By numerically assessing the gradient of the electric field square ({{\

Universal optimal working cycles of molecular motors.

PubMed

Efremov, Artem; Wang, Zhisong

2011-04-07

Molecular motors capable of directional track-walking or rotation are abundant in living cells, and inspire the emerging field of artificial nanomotors. Some biomotors can convert 90% of free energy from chemical fuels into usable mechanical work, and the same motors still maintain a speed sufficient for cellular functions. This study exposed a new regime of universal optimization that amounts to a thermodynamically best working regime for molecular motors but is unfamiliar in macroscopic engines. For the ideal case of zero energy dissipation, the universally optimized working cycle for molecular motors is infinitely slow like Carnot cycle for heat engines. But when a small amount of energy dissipation reduces energy efficiency linearly from 100%, the speed is recovered exponentially due to Boltzmann's law. Experimental data on a major biomotor (kinesin) suggest that the regime of universal optimization has been largely approached in living cells, underpinning the extreme efficiency-speed trade-off in biomotors. The universal optimization and its practical approachability are unique thermodynamic advantages of molecular systems over macroscopic engines in facilitating motor functions. The findings have important implications for the natural evolution of biomotors as well as the development of artificial counterparts.

Solvent fluctuations and nuclear quantum effects modulate the molecular hyperpolarizability of water

NASA Astrophysics Data System (ADS)

Liang, Chungwen; Tocci, Gabriele; Wilkins, David M.; Grisafi, Andrea; Roke, Sylvie; Ceriotti, Michele

2017-07-01

Second-harmonic scattering (SHS) experiments provide a unique approach to probe noncentrosymmetric environments in aqueous media, from bulk solutions to interfaces, living cells, and tissue. A central assumption made in analyzing SHS experiments is that each molecule scatters light according to a constant molecular hyperpolarizability tensor β(2 ). Here, we investigate the dependence of the molecular hyperpolarizability of water on its environment and internal geometric distortions, in order to test the hypothesis of constant β(2 ). We use quantum chemistry calculations of the hyperpolarizability of a molecule embedded in point-charge environments obtained from simulations of bulk water. We demonstrate that both the heterogeneity of the solvent configurations and the quantum mechanical fluctuations of the molecular geometry introduce large variations in the nonlinear optical response of water. This finding has the potential to change the way SHS experiments are interpreted: In particular, isotopic differences between H2O and D2O could explain recent SHS observations. Finally, we show that a machine-learning framework can predict accurately the fluctuations of the molecular hyperpolarizability. This model accounts for the microscopic inhomogeneity of the solvent and represents a step towards quantitative modeling of SHS experiments.

Understanding the Synthesis and Properties of Molecular Silver Nanoparticles

NASA Astrophysics Data System (ADS)

Ashenfelter, Brian A.

Molecular nanoparticles have emerged as an interesting class of materials whose atomically precise structures and discrete properties set them apart from their larger counterparts. Molecular silver nanoparticles are of particular interest because they provide a host of advantages as optical materials for possible use in sensing and imaging applications. However, relatively little is known about molecular silver nanoparticles including the details of their formation and their optical and mechanical properties. Size control remains a longstanding challenge in the production of glutathionate (SG) protected silver nanoparticles. Singular Ag:SG nanoparticle products have been difficult to obtain directly, but size focusing of larger distributions through attrition has been found to lead to useful isolation of particular species. Here, we present a methodology for controlling the size of Ag:SG molecular nanoparticles that leverages the stability of the most robust species. These results were then used to develop a facile approach for achieving two of the most stable species in the Ag:SG system. Molecular metal nanoparticles are known to be much more fluorescent than larger plasmonic nanoparticles, however the nature and origin of this fluorescence are not fully understood. Fluorescence can originate from either the quantum states within the metal core or mixed ligand states at the inorganic-organic interface. We have presented compelling evidence that fluorescence from molecular silver glutathionate nanoparticles has its origin in interfacial electronic states. Fluorescence spectra were found to be independent of size, with very similar wavelength and bandwidth, although the quantum yield was not. Excitation spectra indicated that the strongest fluorescence had its origin in that part of the spectrum that is dominated by ligand-related states. Further, excitations to strictly core states and to higher lying d-band states had little to no contribution to the fluorescence. Time-resolved spectroscopic measurements show that Ag32(SG)19 and Ag15(SG)11 have a common emissive state, with the same emission wavelength and dynamic, which can be assigned to the metal-ligand state. As hybrid materials whose properties meet at the confluence of hard and soft matter, the structures of molecular silver nanoparticles also have interesting mechanical properties. High-pressure powder x-ray diffraction has been used to investigate the mechanical response to compression by a superlattice of Na4Ag44(p-MBA)30 molecular nanoparticles. Two unique pressure-induced phase transformations have been identified. The bulk modulus and axial compressibility of the material has also been determined. These measurements were also compared to a quantum mechanical simulation of the material under compression.

Chemodiversity of dissolved organic matter in the Amazon Basin

NASA Astrophysics Data System (ADS)

Gonsior, Michael; Valle, Juliana; Schmitt-Kopplin, Philippe; Hertkorn, Norbert; Bastviken, David; Luek, Jenna; Harir, Mourad; Bastos, Wanderley; Enrich-Prast, Alex

2016-07-01

Regions in the Amazon Basin have been associated with specific biogeochemical processes, but a detailed chemical classification of the abundant and ubiquitous dissolved organic matter (DOM), beyond specific indicator compounds and bulk measurements, has not yet been established. We sampled water from different locations in the Negro, Madeira/Jamari and Tapajós River areas to characterize the molecular DOM composition and distribution. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with excitation emission matrix (EEM) fluorescence spectroscopy and parallel factor analysis (PARAFAC) revealed a large proportion of ubiquitous DOM but also unique area-specific molecular signatures. Unique to the DOM of the Rio Negro area was the large abundance of high molecular weight, diverse hydrogen-deficient and highly oxidized molecular ions deviating from known lignin or tannin compositions, indicating substantial oxidative processing of these ultimately plant-derived polyphenols indicative of these black waters. In contrast, unique signatures in the Madeira/Jamari area were defined by presumably labile sulfur- and nitrogen-containing molecules in this white water river system. Waters from the Tapajós main stem did not show any substantial unique molecular signatures relative to those present in the Rio Madeira and Rio Negro, which implied a lower organic molecular complexity in this clear water tributary, even after mixing with the main stem of the Amazon River. Beside ubiquitous DOM at average H / C and O / C elemental ratios, a distinct and significant unique DOM pool prevailed in the black, white and clear water areas that were also highly correlated with EEM-PARAFAC components and define the frameworks for primary production and other aspects of aquatic life.

Lymph Nodes and Cancer Metastasis: New Perspectives on the Role of Intranodal Lymphatic Sinuses.

PubMed

Ji, Rui-Cheng

2016-12-28

The lymphatic system is essential for transporting interstitial fluid, soluble antigen, and immune cells from peripheral tissues to lymph nodes (LNs). Functional integrity of LNs is dependent on intact lymphatics and effective lymph drainage. Molecular mechanisms that facilitate interactions between tumor cells and lymphatic endothelial cells (LECs) during tumor progression still remain to be identified. The cellular and molecular structures of LNs are optimized to trigger a rapid and efficient immune response, and to participate in the process of tumor metastasis by stimulating lymphangiogenesis and establishing a premetastatic niche in LNs. Several molecules, e.g., S1P, CCR7-CCL19/CCL21, CXCL12/CXCR4, IL-7, IFN-γ, TGF-β, and integrin α4β1 play an important role in controlling the activity of LN stromal cells including LECs, fibroblastic reticular cells (FRCs) and follicular dendritic cells (DCs). The functional stromal cells are critical for reconstruction and remodeling of the LN that creates a unique microenvironment of tumor cells and LECs for cancer metastasis. LN metastasis is a major determinant for the prognosis of most human cancers and clinical management. Ongoing work to elucidate the function and molecular regulation of LN lymphatic sinuses will provide insight into cancer development mechanisms and improve therapeutic approaches for human malignancy.

Mechanisms of Candida biofilm drug resistance

PubMed Central

Taff, Heather T; Mitchell, Kaitlin F; Edward, Jessica A; Andes, David R

2013-01-01

Candida commonly adheres to implanted medical devices, growing as a resilient biofilm capable of withstanding extraordinarily high antifungal concentrations. As currently available antifungals have minimal activity against biofilms, new drugs to treat these recalcitrant infections are urgently needed. Recent investigations have begun to shed light on the mechanisms behind the profound resistance associated with the biofilm mode of growth. This resistance appears to be multifactorial, involving both mechanisms similar to conventional, planktonic antifungal resistance, such as increased efflux pump activity, as well as mechanisms specific to the biofilm lifestyle. A unique biofilm property is the production of an extracellular matrix. Two components of this material, β-glucan and extracellular DNA, promote biofilm resistance to multiple antifungals. Biofilm formation also engages several stress response pathways that impair the activity of azole drugs. Resistance within a biofilm is often heterogeneous, with the development of a subpopulation of resistant persister cells. In this article we review the molecular mechanisms underlying Candida biofilm antifungal resistance and their relative contributions during various growth phases. PMID:24059922

Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support.

PubMed

Wang, Jack T H

2017-08-15

Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The crosstalk between hematopoietic stem cells and their niches.

PubMed

Durand, Charles; Charbord, Pierre; Jaffredo, Thierry

2018-07-01

Hematopoietic stem cells (HSCs) reside in specific microenvironments also called niches that regulate HSC functions. Understanding the molecular and cellular mechanisms involved in the crosstalk between HSCs and niche cells is a major issue in stem cell biology and regenerative medicine. The purpose of this review is to discuss recent advances in this field with particular emphasis on the transcriptional landscape of HSC niche cells and the roles of extracellular vesicles (EVs) in the dialog between HSCs and their microenvironments. The development of high-throughput technologies combined with computational methods has considerably improved our knowledge on the molecular identity of HSC niche cells. Accumulating evidence strongly suggest that the dialog between HSCs and their niches is bidirectional and that EVs play an important role in this process. These advances bring a unique conceptual and methodological framework for understanding the molecular complexity of the HSC niche and identifying novel HSC regulators. They are also promising for exploring the reciprocal influence of HSCs on niche cells and delivering specific molecules to HSCs in regenerative medicine.

Suppressing molecular vibrations in organic semiconductors by inducing strain

PubMed Central

Kubo, Takayoshi; Häusermann, Roger; Tsurumi, Junto; Soeda, Junshi; Okada, Yugo; Yamashita, Yu; Akamatsu, Norihisa; Shishido, Atsushi; Mitsui, Chikahiko; Okamoto, Toshihiro; Yanagisawa, Susumu; Matsui, Hiroyuki; Takeya, Jun

2016-01-01

Organic molecular semiconductors are solution processable, enabling the growth of large-area single-crystal semiconductors. Improving the performance of organic semiconductor devices by increasing the charge mobility is an ongoing quest, which calls for novel molecular and material design, and improved processing conditions. Here we show a method to increase the charge mobility in organic single-crystal field-effect transistors, by taking advantage of the inherent softness of organic semiconductors. We compress the crystal lattice uniaxially by bending the flexible devices, leading to an improved charge transport. The mobility increases from 9.7 to 16.5 cm2 V−1 s−1 by 70% under 3% strain. In-depth analysis indicates that compressing the crystal structure directly restricts the vibration of the molecules, thus suppresses dynamic disorder, a unique mechanism in organic semiconductors. Since strain can be easily induced during the fabrication process, we expect our method to be exploited to build high-performance organic devices. PMID:27040501

Suppressing molecular vibrations in organic semiconductors by inducing strain.

PubMed

Kubo, Takayoshi; Häusermann, Roger; Tsurumi, Junto; Soeda, Junshi; Okada, Yugo; Yamashita, Yu; Akamatsu, Norihisa; Shishido, Atsushi; Mitsui, Chikahiko; Okamoto, Toshihiro; Yanagisawa, Susumu; Matsui, Hiroyuki; Takeya, Jun

2016-04-04

Organic molecular semiconductors are solution processable, enabling the growth of large-area single-crystal semiconductors. Improving the performance of organic semiconductor devices by increasing the charge mobility is an ongoing quest, which calls for novel molecular and material design, and improved processing conditions. Here we show a method to increase the charge mobility in organic single-crystal field-effect transistors, by taking advantage of the inherent softness of organic semiconductors. We compress the crystal lattice uniaxially by bending the flexible devices, leading to an improved charge transport. The mobility increases from 9.7 to 16.5 cm(2) V(-1) s(-1) by 70% under 3% strain. In-depth analysis indicates that compressing the crystal structure directly restricts the vibration of the molecules, thus suppresses dynamic disorder, a unique mechanism in organic semiconductors. Since strain can be easily induced during the fabrication process, we expect our method to be exploited to build high-performance organic devices.

Protective and destructive immunity in the periodontium: Part 1--innate and humoral immunity and the periodontium.

PubMed

Teng, Y-T A

2006-03-01

Based on the results of recent research in the field, the present paper will discuss the protective and destructive aspects of the innate vs. adaptive (humoral and cell-mediated) immunity associated with the bacterial virulent factors or antigenic determinants during periodontal pathogenesis. Attention will be focused on: (i) the Toll-like receptors (TLR), the innate immune repertoire for recognizing the unique molecular patterns of microbial components that trigger innate and adaptive immunity for effective host defenses, in some general non-oral vs. periodontal microbial infections; (ii) T-cell-mediated immunity, Th-cytokines, and osteoclastogenesis in periodontal disease progression; and (iii) some molecular techniques developed and used to identify critical microbial virulence factors or antigens associated with host immunity (using Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis as the model species). Therefore, further understanding of the molecular interactions and mechanisms associated with the host's innate and adaptive immune responses will facilitate the development of new and innovative therapeutics for future periodontal treatments.

Genetically Encoded Chemical Probes In Cells Reveal the Binding Path of Urocortin-I to CRF Class B GPCR

PubMed Central

Coin, Irene; Katritch, Vsevolod; Sun, Tingting; Xiang, Zheng; Siu, Fai Yiu; Beyermann, Michael; Stevens, Raymond C.; Wang, Lei

2014-01-01

SUMMARY Molecular determinants regulating the activation of class B G-protein coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photo-chemical and new click-chemical probes into the receptor, 44 inter-molecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation. The experimental strategy provides unique information on full-length post-translationally modified GPCRs in the native membrane of the live cell, complementing in vitro biophysical reductionist approaches. PMID:24290358

Wearable and flexible electronics for continuous molecular monitoring.

PubMed

Yang, Yiran; Gao, Wei

2018-04-03

Wearable biosensors have received tremendous attention over the past decade owing to their great potential in predictive analytics and treatment toward personalized medicine. Flexible electronics could serve as an ideal platform for personalized wearable devices because of their unique properties such as light weight, low cost, high flexibility and great conformability. Unlike most reported flexible sensors that mainly track physical activities and vital signs, the new generation of wearable and flexible chemical sensors enables real-time, continuous and fast detection of accessible biomarkers from the human body, and allows for the collection of large-scale information about the individual's dynamic health status at the molecular level. In this article, we review and highlight recent advances in wearable and flexible sensors toward continuous and non-invasive molecular analysis in sweat, tears, saliva, interstitial fluid, blood, wound exudate as well as exhaled breath. The flexible platforms, sensing mechanisms, and device and system configurations employed for continuous monitoring are summarized. We also discuss the key challenges and opportunities of the wearable and flexible chemical sensors that lie ahead.

Structure and Function of the Hair Cell Ribbon Synapse

PubMed Central

Nouvian, R.; Beutner, D.; Parsons, T.D.

2006-01-01

Faithful information transfer at the hair cell afferent synapse requires synaptic transmission to be both reliable and temporally precise. The release of neurotransmitter must exhibit both rapid on and off kinetics to accurately follow acoustic stimuli with a periodicity of 1 ms or less. To ensure such remarkable temporal fidelity, the cochlear hair cell afferent synapse undoubtedly relies on unique cellular and molecular specializations. While the electron microscopy hallmark of the hair cell afferent synapse — the electron-dense synaptic ribbon or synaptic body — has been recognized for decades, dissection of the synapse’s molecular make-up has only just begun. Recent cell physiology studies have added important insights into the synaptic mechanisms underlying fidelity and reliability of sound coding. The presence of the synaptic ribbon links afferent synapses of cochlear and vestibular hair cells to photoreceptors and bipolar neurons of the retina. This review focuses on major advances in understanding the hair cell afferent synapse molecular anatomy and function that have been achieved during the past years. PMID:16773499

Computational Insights into the Molecular Mechanism of the High Immunomodulatory Activity of LZ-8 Protein Isolated from the Lingzhi or Reishi Medicinal Mushroom Ganoderma lucidum (Agaricomycetes).

PubMed

Bao, Da-Peng; Bai, Rui; Gao, Ying-Nv; Wu, Ying-Ying; Wang, Ying

2018-01-01

Ling zhi-8 (LZ-8) is the first fungal immunomodulatory protein (FIP) isolated from the lingzhi or reishi medicinal mushroom, Ganoderma lucidum. LZ-8 effectively induces interleukin 2 expression and secretion by forming a stable homodimer, and it is regarded as a good candidate to become a new therapeutic agent and/or functional food supplement. However, the molecular mechanism by which LZ-8 dimerization influences the regulation of interleukin 2 is not clear. In this study we performed structure-based multiple alignment of LZ-8 and an FIP from Volvariella volvacea, compared the electrostatic potential of their protein surfaces, and developed a model summarizing the unique electrostatic interaction in LZ-8 dimerization. In addition, further electrostatic potential and virtual amino acid mutation analyses suggested that L10, W12, and D45 are the key amino acid residues responsible for the protein's high immunomodulatory activity. These findings may provide useful insights into the design and construction of a new FIP mutant for use in treating and preventing autoimmune diseases.

Triazole nucleoside derivatives bearing aryl functionalities on the nucleobases show antiviral and anticancer activity.

PubMed

Xia, Yi; Qu, Fanqi; Peng, Ling

2010-08-01

Synthetic nucleoside mimics are important candidates in the searing for antiviral and anticancer drugs. Ribavirin, the first antiviral nucleoside drug, is unique in its antiviral activity with mutilple modes of action, which are mainly due to its special triazole heterocycle as nucleobase. Additionally, introducing aromatic functionalities to the nucleobase is able to confer novel mechanisms of action for nucleoside mimics. With the aim to combine the special characteristics of unnatural triazole heterocycles with those of the appended aromatic groups on the nucleobases, novel 1,2,4-triazole nucleoside analogs bearing aromatic moieties were designed and developed. The present short review summarizes the molecular design, chemical synthesis and biological activity of these triazole nucleoside analogs. Indeed, the discovery of antiviral and anticancer activities shown by these triazole nucleosides as well as the new mechanism underlying the biological activity by one of the anticancer leads has validated the rationale for molecular design and impacted us to further explore the concept with the aim of developing structurally novel nucleoside drug candidates with new modes of action.

Induction of polyploidization in leukemic cell lines and primary bone marrow by Src kinase inhibitor SU6656

PubMed Central

Lannutti, Brian J.; Blake, Noel; Gandhi, Manish J.; Reems, Jo Anna; Drachman, Jonathan G.

2005-01-01

Megakaryocytes (MKs) undergo successive rounds of endomitosis during differentiation, resulting in polyploidy (typically, 16-64N). Previous studies have demonstrated that this occurs through an interruption of normal cell cycle progression during anaphase. However, the molecular mechanism(s) controlling this unique process is undefined. In the present report, we examine the effect of an Src kinase inhibitor, SU6656, on thrombopoietin (TPO)-induced growth and differentiation. Remarkably, when SU6656 (2.5 μM) was added to a megakaryocytic cell line, UT-7/TPO, the cells ceased cell division but continued to accumulate DNA by endomitosis. During this interval, CD41 and CD61 expression on the cell surface increased. Similar effects on polyploidization and MK differentiation were seen with expanded primary MKs, bone marrow from 2 patients with myelodysplastic syndrome, and other cell lines with MK potential. Our data suggest that SU6656 might be useful as a differentiation-inducing agent for MKs and is an important tool for understanding the molecular basis of MK endomitosis. PMID:15677565

Emerging drug treatments for solid tumours.

PubMed

Schellens, J H; Pronk, L C; Verweij, J

1996-01-01

A number of novel anticancer agents have emerged during the past few decades, which show high activity in preclinical tumour models and promising activity in early trials in patients with solid tumours. Most of the agents have novel and unique mechanisms of action, and show activity against a variety of malignancies, including tumours which are notoriously resistant to systemic treatment. Recently, our understanding of the molecular basis of cancer has increased considerably. This is reflected in the development of agents that are directed at well defined molecular targets, such as the mitotic tubulin/microtubuli system (taxoids), nuclear enzymes (topoisomerase I inhibitors) and cell signal transduction pathways (protein kinase C inhibitors). In addition, significant advances have been made in our understanding of mechanisms of toxicity, especially of cisplatin. This has resulted in the development of agents modulating cisplatin toxicity, among which amifostine (WR-2721) is one of the most promising. The outlined emerging drug therapies with novel anticancer agents and treatment modalities will, it is hoped, result in increased response rates of advanced tumours, longer disease-free and total survival and better palliative care.

Personalized skincare: from molecular basis to clinical and commercial applications.

PubMed

Markiewicz, Ewa; Idowu, Olusola Clement

2018-01-01

Individual responses of human skin to the environmental stress are determined by differences in the anatomy and physiology that are closely linked to the genetic characteristics such as pigmentation. Ethnic skin phenotypes can be distinguished based on defined genotypic traits, structural organization and compartmentalized sensitivity to distinct extrinsic aging factors. These differences are not only responsible for the variation in skin performance after exposure to damaging conditions, but can also affect the mechanisms of drug absorption, sensitization and other longer term effects. The unique characteristics of the individual skin function and, particularly, of the ethnic skin type are currently considered to shape the future of clinical and pharmacologic interventions as a basis for personalized skincare. Individual approaches to skincare render a novel and actively growing area with a range of biomedical and commercial applications within cosmetics industry. In this review, we summarize the aspects of the molecular and clinical manifestations of the environmental stress on human skin and proposed protective mechanisms that are linked to ethnic differences and pathophysiology of extrinsic skin aging. We subsequently discuss the possible applications and translation of this knowledge into personalized skincare.

Personalized skincare: from molecular basis to clinical and commercial applications

PubMed Central

Markiewicz, Ewa; Idowu, Olusola Clement

2018-01-01

Individual responses of human skin to the environmental stress are determined by differences in the anatomy and physiology that are closely linked to the genetic characteristics such as pigmentation. Ethnic skin phenotypes can be distinguished based on defined genotypic traits, structural organization and compartmentalized sensitivity to distinct extrinsic aging factors. These differences are not only responsible for the variation in skin performance after exposure to damaging conditions, but can also affect the mechanisms of drug absorption, sensitization and other longer term effects. The unique characteristics of the individual skin function and, particularly, of the ethnic skin type are currently considered to shape the future of clinical and pharmacologic interventions as a basis for personalized skincare. Individual approaches to skincare render a novel and actively growing area with a range of biomedical and commercial applications within cosmetics industry. In this review, we summarize the aspects of the molecular and clinical manifestations of the environmental stress on human skin and proposed protective mechanisms that are linked to ethnic differences and pathophysiology of extrinsic skin aging. We subsequently discuss the possible applications and translation of this knowledge into personalized skincare. PMID:29692619

DNA methylation in memory formation: Emerging insights

PubMed Central

Heyward, Frankie D.; Sweatt, J. David

2016-01-01

The establishment of synaptic plasticity and long-term memory requires lasting cellular and molecular modifications that, as a whole, must endure despite the rapid turnover of their constituent parts. Such a molecular feat must be mediated by a stable, self-perpetuating, cellular information storage mechanism. DNA methylation, being the archetypal cellular information storage mechanism, has been heavily implicated as being necessary for stable activity-dependent transcriptional alterations within the central nervous system (CNS). This review details the foundational discoveries from both gene-targeted, as well as whole-genome sequencing, studies that have successfully brought DNA methylation to our attention as a chief regulator of activity- and experience-dependent transcriptional alterations within the CNS. We present a hypothetical framework with which the disparate experimental findings dealing with distinct manipulations of the DNA methylation, and their effect on memory, might be resolved while taking into account the unique impact activity-dependent alterations in DNA methylation potentially have on both memory promoting and memory-suppressing gene expression. And last, we discuss potential avenues for future inquiry into the role of DNA methylation during remote memory formation. PMID:25832671

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Feng; Waters, Katrina M.; Miller, John H.

2010-11-30

Background: High doses of ionizing radiation result in biological damage, however the precise relationships between long term health effects, including cancer, and low dose exposures remain poorly understood and are currently extrapolated using high dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose dependent responses to radiation. Principle Findings: We have identified 6845 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts one hour post-exposure. Dual statistical analyses based on spectral counts and peakmore » intensities identified 287 phosphopeptides (from 231 proteins) and 244 phosphopeptides (from 182 proteins) that varied significantly following exposure to 2 and 50 cGy respectively. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatics analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role of MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conlcusions: Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provides a basis for the systems level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low dose radiation exposure on human health.« less

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.

PubMed

Venko, Katja; Roy Choudhury, A; Novič, Marjana

2017-01-01

The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix-helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.

Programmed proteome response for drought avoidance/tolerance in the root of a C(3) xerophyte (wild watermelon) under water deficits.

PubMed

Yoshimura, Kazuya; Masuda, Akiko; Kuwano, Masayoshi; Yokota, Akiho; Akashi, Kinya

2008-02-01

Water availability is a critical determinant for the growth and ecological distribution of terrestrial plants. Although some xerophytes are unique regarding their highly developed root architecture and the successful adaptation to arid environments, virtually nothing is known about the molecular mechanisms underlying this adaptation. Here, we report physiological and molecular responses of wild watermelon (Citrullus lanatus sp.), which exhibits extraordinarily high drought resistance. At the early stage of drought stress, root development of wild watermelon was significantly enhanced compared with that of the irrigated plants, indicating the activation of a drought avoidance mechanism for absorbing water from deep soil layers. Consistent with this observation, comparative proteome analysis revealed that many proteins induced in the early stage of drought stress are involved in root morphogenesis and carbon/nitrogen metabolism, which may contribute to the drought avoidance via the enhancement of root growth. On the other hand, lignin synthesis-related proteins and molecular chaperones, which may function in the enhancement of physical desiccation tolerance and maintenance of protein integrity, respectively, were induced mostly at the later stage of drought stress. Our findings suggest that this xerophyte switches survival strategies from drought avoidance to drought tolerance during the progression of drought stress, by regulating its root proteome in a temporally programmed manner. This study provides new insights into the complex molecular networks within plant roots involved in the adaptation to adverse environments.

Molecular inimitability amongst tumors: implications for precision cancer medicine in the age of personalized oncology.

PubMed

Patel, Sandip P; Schwaederle, Maria; Daniels, Gregory A; Fanta, Paul T; Schwab, Richard B; Shimabukuro, Kelly A; Kesari, Santosh; Piccioni, David E; Bazhenova, Lyudmila A; Helsten, Teresa L; Lippman, Scott M; Parker, Barbara A; Kurzrock, Razelle

2015-10-20

Tumor sequencing has revolutionized oncology, allowing for detailed interrogation of the molecular underpinnings of cancer at an individual level. With this additional insight, it is increasingly apparent that not only do tumors vary within a sample (tumor heterogeneity), but also that each patient's individual tumor is a constellation of unique molecular aberrations that will require an equally unique personalized therapeutic regimen. We report here the results of 439 patients who underwent Clinical Laboratory Improvement Amendment (CLIA)-certified next generation sequencing (NGS) across histologies. Among these patients, 98.4% had a unique molecular profile, and aside from three primary brain tumor patients with a single genetic lesion (IDH1 R132H), no two patients within a given histology were molecularly identical. Additionally, two sets of patients had identical profiles consisting of two mutations in common and no other anomalies. However, these profiles did not segregate by histology (lung adenocarcinoma-appendiceal cancer (KRAS G12D and GNAS R201C), and lung adenocarcinoma-liposarcoma (CDK4 and MDM2 amplification pairs)). These findings suggest that most advanced tumors are molecular singletons within and between histologies, and that tumors that differ in histology may still nonetheless exhibit identical molecular portraits, albeit rarely.

Molecular Parallels between Neural and Vascular Development

PubMed Central

Eichmann, Anne; Thomas, Jean-Léon

2013-01-01

The human central nervous system (CNS) features a network of ∼400 miles of blood vessels that receives >20% of the body’s cardiac output and uses most of its blood glucose. Many human diseases, including stroke, retinopathy, and cancer, are associated with the biology of CNS blood vessels. These vessels originate from extrinsic cell populations, including endothelial cells and pericytes that colonize the CNS and interact with glia and neurons to establish the blood–brain barrier and control cerebrovascular exchanges. Neurovascular interactions also play important roles in adult neurogenic niches, which harbor a unique population of neural stem cells that are intimately associated with blood vessels. We here review the cellular and molecular mechanisms required to establish the CNS vascular network, with a special focus on neurovascular interactions and the functions of vascular endothelial growth factors. PMID:23024177

Pomegranate extracts and cancer prevention: molecular and cellular activities.

PubMed

Syed, Deeba N; Chamcheu, Jean-Christopher; Adhami, Vaqar M; Mukhtar, Hasan

2013-10-01

There is increased appreciation by the scientific community that dietary phytochemicals can be potential weapons in the fight against cancer. Emerging data has provided new insights into the molecular and cellular framework needed to establish novel mechanism-based strategies for cancer prevention by selective bioactive food components. The unique chemical composition of the pomegranate fruit, rich in antioxidant tannins and flavonoids has drawn the attention of many investigators. Polyphenol rich fractions derived from the pomegranate fruit have been studied for their potential chemopreventive and/or cancer therapeutic effects in several animal models. Although data from in vitro and in vivo studies look convincing, well designed clinical trials in humans are needed to ascertain whether pomegranate can become part of our armamentarium against cancer. This review summarizes the available literature on the effects of pomegranate against various cancers.

Effects of growth rate on structural property and adatom migration behaviors for growth of GaInNAs/GaAs (001) by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Jingling; Gao, Peng; Zhang, Shuguang; Wen, Lei; Gao, Fangliang; Li, Guoqiang

2018-03-01

We have investigated the structural properties and the growth mode of GaInNAs films prepared at different growth rates (Rg) by molecular beam epitaxy. The crystalline structure is studied by high resolution X-ray diffraction, and the evolution of GaInNAs film surface morphologies is studied by atomic force microscopy. It is found that both the crystallinity and the surface roughness are improved by increasing Rg, and the change in the growth mode is attributed to the adatom migration behaviors particularly for In atoms, which is verified by elemental analysis. In addition, we have presented some theoretical calculation results related to the N adsorption energy to show the unique N migration behavior, which is instructive to interpret the growth mechanism of GaInNAs films.

Pomegranate Extracts and Cancer Prevention: Molecular and Cellular Activities

PubMed Central

Syed, Deeba N.; Chamcheu, Jean-Christopher; Adhami, Vaqar M.; Mukhtar, Hasan

2014-01-01

There is increased appreciation by the scientific community that dietary phytochemicals can be potential weapons in the fight against cancer. Emerging data has provided new insights into the molecular and cellular framework needed to establish novel mechanism-based strategies for cancer prevention by selective bioactive food components. The unique chemical composition of the pomegranate fruit, rich in antioxidant tannins and flavonoids has drawn the attention of many investigators. Polyphenol rich fractions derived from the pomegranate fruit have been studied for their potential chemopreventive and/or cancer therapeutic effects in several animal models. Although data from in vitro and in vivo studies look convincing, well designed clinical trials in humans are needed to ascertain whether pomegranate can become part of our armamentarium against cancer. This review summarizes the available literature on the effects of pomegranate against various cancers. PMID:23094914

Poly(ether ester) Ionomers as Water-Soluble Polymers for Material Extrusion Additive Manufacturing Processes.

PubMed

Pekkanen, Allison M; Zawaski, Callie; Stevenson, André T; Dickerman, Ross; Whittington, Abby R; Williams, Christopher B; Long, Timothy E

2017-04-12

Water-soluble polymers as sacrificial supports for additive manufacturing (AM) facilitate complex features in printed objects. Few water-soluble polymers beyond poly(vinyl alcohol) enable material extrusion AM. In this work, charged poly(ether ester)s with tailored rheological and mechanical properties serve as novel materials for extrusion-based AM at low temperatures. Melt transesterification of poly(ethylene glycol) (PEG, 8k) and dimethyl 5-sulfoisophthalate afforded poly(ether ester)s of sufficient molecular weight to impart mechanical integrity. Quantitative ion exchange provided a library of poly(ether ester)s with varying counterions, including both monovalent and divalent cations. Dynamic mechanical and tensile analysis revealed an insignificant difference in mechanical properties for these polymers below the melting temperature, suggesting an insignificant change in final part properties. Rheological analysis, however, revealed the advantageous effect of divalent countercations (Ca 2+ , Mg 2+ , and Zn 2+ ) in the melt state and exhibited an increase in viscosity of two orders of magnitude. Furthermore, time-temperature superposition identified an elevation in modulus, melt viscosity, and flow activation energy, suggesting intramolecular interactions between polymer chains and a higher apparent molecular weight. In particular, extrusion of poly(PEG 8k -co-CaSIP) revealed vast opportunities for extrusion AM of well-defined parts. The unique melt rheological properties highlighted these poly(ether ester) ionomers as ideal candidates for low-temperature material extrusion additive manufacturing of water-soluble parts.

Acclimation of microorganisms to harsh soil crust conditions: Experimental and genomic approaches

NASA Astrophysics Data System (ADS)

Raanan, Hagai; Kaplan, Aaron

2015-04-01

Biological soil crusts (BSC) are formed by the adhesion of sand particles to cyanobacterial exo- polysaccharides and play an important role in stabilizing sandy desert. Its destruction promotes desertification. These organisms cope with extreme temperatures, excess light and frequent hydration/dehydration cycles; the mechanisms involved are largely unknown. With the genome of newly sequenced Leptolyngbya, isolated from Nizzana BSC, we conduct comparative genomics of three desiccation tolerant cyanobacteria. This yield 46 unique genes, some of them similar to genes involve in sporulation of the gram positive bacteria Bacillus. In order to understand the molecular mechanisms taking place during desiccation we built an environmental chamber capable of simulating dynamic changes of environmental conditions in the crust. This chamber allows us to perform repetitive and accurate desiccation/rehydration experiments and follow cyanobacterial physiological and molecular response to such environmental changes. When we compared fast desiccation (less than 5 min) of isolated cyanobacteria to simulation of natural desiccation, we observed a 60% lower fluorescence recovery rate. The extent of damage from desiccation depended on the stress conditions during the dry period. These results suggest that cyanobacteria activated protection mechanisms in response to desiccation stress but which were not activated in 5 min desiccation tests. Gene expression patterns during desiccation are being analyzed in order to provide a better understanding of desiccation stress protection mechanisms.

Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.

PubMed

Tian, Xiaoxu; Chen, Lei; Wang, Jiangxin; Qiao, Jianjun; Zhang, Weiwen

2013-01-14

Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress. Copyright © 2012 Elsevier B.V. All rights reserved.

Conferring Virulence: Structure and Function of the chimeric A2B5 Typhoid Toxin

PubMed Central

Song, Jeongmin; Gao, Xiang; Galán, Jorge E.

2013-01-01

Salmonella Typhi differs from most other salmonellae in that it causes a life-threatening systemic infection known as typhoid fever1. The molecular bases for its unique clinical presentation are unknown2. Here we found that in an animal model, the systemic administration of typhoid toxin, a unique virulence factor of S. Typhi, reproduces many of the acute symptoms of typhoid fever. We identified specific carbohydrate moieties on specific surface glycoproteins that serve as receptors for typhoid toxin, which explains its broad cell target specificity. We present the atomic structure of typhoid toxin, which shows an unprecedented A2B5 organization with two covalently-linked A subunits non-covalently-associated to a pentameric B subunit. The structure provides insight into the toxin’s receptor-binding specificity and delivery mechanisms and reveals how the activities of two powerful toxins have been coopted into a single, unique toxin that can induce many of the symptoms characteristic of typhoid fever. These findings may lead to the development of potentially life-saving therapeutics against typhoid fever. PMID:23842500

Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction.

PubMed

Dimasi, Nazzareno

2007-01-01

The Grb2-like adaptor protein GADS is essential for tyrosine kinase-dependent signaling in T lymphocytes. Following T cell receptor ligation, GADS interacts through its C-terminal SH3 domain with the adaptors SLP-76 and LAT, to form a multiprotein signaling complex that is crucial for T cell activation. To understand the structural basis for the selective recognition of GADS by SLP-76, herein is reported the crystal structure at 1.54 Angstrom of the C-terminal SH3 domain of GADS bound to the SLP-76 motif 233-PSIDRSTKP-241, which represents the minimal binding site. In addition to the unique structural features adopted by the bound SLP-76 peptide, the complex structure reveals a unique SH3-SH3 interaction. This homophilic interaction, which is observed in presence of the SLP-76 peptide and is present in solution, extends our understanding of the molecular mechanisms that could be employed by modular proteins to increase their signaling transduction specificity.

Elucidating the Activation Mechanism of the Insulin-Family Proteins with Molecular Dynamics Simulations.

PubMed

Papaioannou, Anastasios; Kuyucak, Serdar; Kuncic, Zdenka

2016-01-01

The insulin-family proteins bind to their own receptors, but insulin-like growth factor II (IGF-II) can also bind to the A isoform of the insulin receptor (IR-A), activating unique and alternative signaling pathways from those of insulin. Although extensive studies of insulin have revealed that its activation is associated with the opening of the B chain-C terminal (BC-CT), the activation mechanism of the insulin-like growth factors (IGFs) still remains unknown. Here, we present the first comprehensive study of the insulin-family proteins comparing their activation process and mechanism using molecular dynamics simulations to reveal new insights into their specificity to the insulin receptor. We have found that all the proteins appear to exhibit similar stochastic dynamics in their conformational change to an active state. For the IGFs, our simulations show that activation involves two opening locations: the opening of the BC-CT section away from the core, similar to insulin; and the additional opening of the BC-CT section away from the C domain. Furthermore, we have found that these two openings occur simultaneously in IGF-I, but not in IGF-II, where they can occur independently. This suggests that the BC-CT section and the C domain behave as a unified domain in IGF-I, but as two independent domains in IGF-II during the activation process, implying that the IGFs undergo different activation mechanisms for receptor binding. The probabilities of the active and inactive states of the proteins suggest that IGF-II is hyperactive compared to IGF-I. The hinge residue and the hydrophobic interactions in the core are found to play a critical role in the stability and activity of IGFs. Overall, our simulations have elucidated the crucial differences and similarities in the activation mechanisms of the insulin-family proteins, providing new insights into the molecular mechanisms responsible for the observed differences between IGF-I and IGF-II in receptor binding.

Effect of Changing the Joint Kinematics of Knees With a Ruptured Anterior Cruciate Ligament on the Molecular Biological Responses and Spontaneous Healing in a Rat Model.

PubMed

Kokubun, Takanori; Kanemura, Naohiko; Murata, Kenji; Moriyama, Hideki; Morita, Sadao; Jinno, Tetsuya; Ihara, Hidetoshi; Takayanagi, Kiyomi

2016-11-01

The poor healing capacity of a completely ruptured anterior cruciate ligament (ACL) has been attributed to an insufficient vascular supply, cellular metabolism, and deficient premature scaffold formation because of the unique intra-articular environment. However, previous studies have focused on intra-articular factors without considering extra-articular factors, including the biomechanical aspects of ACL-deficient knees. Changing the joint kinematics of an ACL-ruptured knee will improve cellular biological responses and lead to spontaneous healing through the mechanotransduction mechanism. Controlled laboratory study. A total of 66 skeletally mature Wistar rats were randomly assigned to a sham-operated group (SO), ACL-transection group (ACL-T), controlled abnormal movement group (CAM), and an intact group (IN). The ACL was completely transected at the midportion in the ACL-T and CAM groups, and the CAM group underwent extra-articular braking to control for abnormal tibial translation. The SO group underwent skin and joint capsule incisions and tibial drilling, without ACL transection and extra-articular braking. The animals were allowed full cage activity until sacrifice at 1, 2, 4, 6, and 8 weeks postoperatively for histological, molecular biological, and biomechanical assessment. All injured ACLs in the ACL-T group were not healed, but those in the CAM group healed spontaneously, showing a typical ligament healing response. Regarding the molecular biological response, there was an upregulation of anabolic factors (ie, transforming growth factor-β) and downregulation of catabolic factors (ie, matrix metalloproteinase). Examination of the mechanical properties at 8 weeks after injury showed that >50% of the strength of the intact ACL had returned. Our results suggest that changing the joint kinematics of knees with a ruptured ACL alters the molecular biological responses and leads to spontaneous healing. These data support our hypothesis that the mechanotransduction mechanism mediates molecular responses and determines whether the ACL will heal. Elucidating the relationship between the mechanotransduction mechanism and healing responses in knees with completely ruptured ACLs may result in the development of novel nonsurgical treatment that enables the ACL to spontaneously heal in patients who are not suitable for reconstruction. © 2016 The Author(s).

Arsenic, asbestos and radon: emerging players in lung tumorigenesis

PubMed Central

2012-01-01

The cause of lung cancer is generally attributed to tobacco smoking. However lung cancer in never smokers accounts for 10 to 25% of all lung cancer cases. Arsenic, asbestos and radon are three prominent non-tobacco carcinogens strongly associated with lung cancer. Exposure to these agents can lead to genetic and epigenetic alterations in tumor genomes, impacting genes and pathways involved in lung cancer development. Moreover, these agents not only exhibit unique mechanisms in causing genomic alterations, but also exert deleterious effects through common mechanisms, such as oxidative stress, commonly associated with carcinogenesis. This article provides a comprehensive review of arsenic, asbestos, and radon induced molecular mechanisms responsible for the generation of genetic and epigenetic alterations in lung cancer. A better understanding of the mode of action of these carcinogens will facilitate the prevention and management of lung cancer related to such environmental hazards. PMID:23173984

Understanding the mechanism of catalytic fast pyrolysis by unveiling reactive intermediates in heterogeneous catalysis

NASA Astrophysics Data System (ADS)

Hemberger, Patrick; Custodis, Victoria B. F.; Bodi, Andras; Gerber, Thomas; van Bokhoven, Jeroen A.

2017-06-01

Catalytic fast pyrolysis is a promising way to convert lignin into fine chemicals and fuels, but current approaches lack selectivity and yield unsatisfactory conversion. Understanding the pyrolysis reaction mechanism at the molecular level may help to make this sustainable process more economic. Reactive intermediates are responsible for product branching and hold the key to unveiling these mechanisms, but are notoriously difficult to detect isomer-selectively. Here, we investigate the catalytic pyrolysis of guaiacol, a lignin model compound, using photoelectron photoion coincidence spectroscopy with synchrotron radiation, which allows for isomer-selective detection of reactive intermediates. In combination with ambient pressure pyrolysis, we identify fulvenone as the central reactive intermediate, generated by catalytic demethylation to catechol and subsequent dehydration. The fulvenone ketene is responsible for the phenol formation. This technique may open unique opportunities for isomer-resolved probing in catalysis, and holds the potential for achieving a mechanistic understanding of complex, real-life catalytic processes.

Emergence of an apical epithelial cell surface in vivo

PubMed Central

Sedzinski, Jakub; Hannezo, Edouard; Tu, Fan; Biro, Maté; Wallingford, John B.

2016-01-01

Epithelial sheets are crucial components of all metazoan animals, enclosing organs and protecting the animal from its environment. Epithelial homeostasis poses unique challenges, as addition of new cells and loss of old cells must be achieved without disrupting the fluid-tight barrier and apicobasal polarity of the epithelium. Several studies have identified cell biological mechanisms underlying extrusion of cells from epithelia, but far less is known of the converse mechanism by which new cells are added. Here, we combine molecular, pharmacological and laser-dissection experiments with theoretical modelling to characterize forces driving emergence of an apical surface as single nascent cells are added to a vertebrate epithelium in vivo. We find that this process involves the interplay between cell-autonomous actin-generated pushing forces in the emerging cell and mechanical properties of neighboring cells. Our findings define the forces driving this cell behavior, contributing to a more comprehensive understanding of epithelial homeostasis. PMID:26766441

DNA Protection Protein, a Novel Mechanism of Radiation Tolerance: Lessons from Tardigrades

PubMed Central

Hashimoto, Takuma; Kunieda, Takekazu

2017-01-01

Genomic DNA stores all genetic information and is indispensable for maintenance of normal cellular activity and propagation. Radiation causes severe DNA lesions, including double-strand breaks, and leads to genome instability and even lethality. Regardless of the toxicity of radiation, some organisms exhibit extraordinary tolerance against radiation. These organisms are supposed to possess special mechanisms to mitigate radiation-induced DNA damages. Extensive study using radiotolerant bacteria suggested that effective protection of proteins and enhanced DNA repair system play important roles in tolerability against high-dose radiation. Recent studies using an extremotolerant animal, the tardigrade, provides new evidence that a tardigrade-unique DNA-associating protein, termed Dsup, suppresses the occurrence of DNA breaks by radiation in human-cultured cells. In this review, we provide a brief summary of the current knowledge on extremely radiotolerant animals, and present novel insights from the tardigrade research, which expand our understanding on molecular mechanism of exceptional radio-tolerability. PMID:28617314

Recent advances in the study of age-related hearing loss - A Mini-Review

PubMed Central

Kidd, Ambrose R; Bao, Jianxin

2013-01-01

Hearing loss is a common age-associated affliction that can result from the loss of hair cells and spiral ganglion neurons (SGNs) in the cochlea. Although hair cells and SGNs are typically lost in the same cochlea, recent analysis suggests that they can occur independently, via unique mechanisms. Research has identified both environmental and genetic factors that contribute to degeneration of cochlear cells. Additionally, molecular analysis has identified multiple cell signaling mechanisms that likely contribute to pathological changes that result in hearing deficiencies. These analyses should serve as useful primers for future work, including genomic and proteomic analysis, to elucidate the mechanisms driving cell loss in the aging cochlea. Significant progress in this field has occurred in the past decade. As our understanding of aging-induced cochlear changes continues to improve, our ability to offer medical intervention will surely benefit the growing elderly population. PMID:22710288

Transcriptome analysis of hexaploid hulless oat in response to salinity stress

PubMed Central

Wu, Bin; Hu, Yani; Huo, Pengjie; Zhang, Qian; Chen, Xin; Zhang, Zongwen

2017-01-01

Background Oat is a cereal crop of global importance used for food, feed, and forage. Understanding salinity stress tolerance mechanisms in plants is an important step towards generating crop varieties that can cope with environmental stresses. To date, little is known about the salt tolerance of oat at the molecular level. To better understand the molecular mechanisms underlying salt tolerance in oat, we investigated the transcriptomes of control and salt-treated oat using RNA-Seq. Results Using Illumina HiSeq 4000 platform, we generated 72,291,032 and 356,891,432 reads from non-stressed control and salt-stressed oat, respectively. Assembly of 64 Gb raw sequence data yielded 128,414 putative unique transcripts with an average length of 1,189 bp. Analysis of the assembled unigenes from the salt stressed and control libraries indicated that about 65,000 unigenes were differentially expressed at different stages. Functional annotation showed that ABC transporters, plant hormone signal transduction, plant-pathogen interactions, starch and sucrose metabolism, arginine and proline metabolism, and other secondary metabolite pathways were enriched under salt stress. Based on the RPKM values of assembled unigenes, 24 differentially expressed genes under salt stress were selected for quantitative RT-PCR validation, which successfully confirmed the results of RNA-Seq. Furthermore, we identified 18,039 simple sequence repeats, which may help further elucidate salt tolerance mechanisms in oat. Conclusions Our global survey of transcriptome profiles of oat plants in response to salt stress provides useful insights into the molecular mechanisms underlying salt tolerance in this crop. These findings also represent a rich resource for further analysis of salt tolerance and for breeding oat with improved salt tolerance through the use of salt-related genes. PMID:28192458

Multiscale Investigation of the Depth-Dependent Mechanical Anisotropy of the Human Corneal Stroma

PubMed Central

Labate, Cristina; Lombardo, Marco; De Santo, Maria P.; Dias, Janice; Ziebarth, Noel M.; Lombardo, Giuseppe

2015-01-01

Purpose. To investigate the depth-dependent mechanical anisotropy of the human corneal stroma at the tissue (stroma) and molecular (collagen) level by using atomic force microscopy (AFM). Methods. Eleven human donor corneas were dissected at different stromal depths by using a microkeratome. Mechanical measurements were performed in 15% dextran on the surface of the exposed stroma of each sample by using a custom-built AFM in force spectroscopy mode using both microspherical (38-μm diameter) and nanoconical (10-nm radius of curvature) indenters at 2-μm/s and 15-μm/s indentation rates. Young's modulus was determined by fitting force curve data using the Hertz and Hertz-Sneddon models for a spherical and a conical indenter, respectively. The depth-dependent anisotropy of stromal elasticity was correlated with images of the corneal stroma acquired by two-photon microscopy. Results. The force curves were obtained at stromal depths ranging from 59 to 218 μm. At the tissue level, Young's modulus (ES) showed a steep decrease at approximately 140-μm stromal depth (from 0.8 MPa to 0.3 MPa; P = 0.03) and then was stable in the posterior stroma. At the molecular level, Young's modulus (EC) was significantly greater than at the tissue level; EC decreased nonlinearly with increasing stromal depth from 3.9 to 2.6 MPa (P = 0.04). The variation of microstructure through the thickness correlated highly with a nonconstant profile of the mechanical properties in the stroma. Conclusions. The corneal stroma exhibits unique anisotropic elastic behavior at the tissue and molecular levels. This knowledge may benefit modeling of corneal behavior and help in the development of biomimetic materials. PMID:26098472

Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

PubMed Central

Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

2013-01-01

Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

Milk Glycans and Their Interaction with the Infant-Gut Microbiota

PubMed Central

Kirmiz, Nina; Robinson, Randall C.; Shah, Ishita M.; Barile, Daniela; Mills, David A.

2018-01-01

Human milk is a unique and complex fluid that provides infant nutrition and delivers an array of bioactive molecules that serve various functions. Glycans, abundant in milk, can be found as free oligosaccharides or as glycoconjugates. Milk glycans are increasingly linked to beneficial outcomes in neonates through protection from pathogens and modulation of the immune system. Indeed, these glycans influence the development of the infant and the infant-gut microbiota. Bifidobacterium species commonly are enriched in breastfed infants and are among a limited group of bacteria that readily consume human milk oligosaccharides (HMOs) and milk glycoconjugates. Given the importance of bifidobacteria in infant health, numerous studies have examined the molecular mechanisms they employ to consume HMOs and milk glycans, thus providing insight into this unique enrichment and shedding light on a range of translational opportunities to benefit at-risk infants. PMID:29580136

Game theory and neural basis of social decision making

PubMed Central

Lee, Daeyeol

2008-01-01

Decision making in a social group displays two unique features. First, humans and other animals routinely alter their behaviors in response to changes in their physical and social environment. As a result, the outcomes of decisions that depend on the behaviors of multiple decision makers are difficult to predict, and this requires highly adaptive decision-making strategies. Second, decision makers may have other-regarding preferences and therefore choose their actions to improve or reduce the well-beings of others. Recently, many neurobiological studies have exploited game theory to probe the neural basis of decision making, and found that these unique features of social decision making might be reflected in the functions of brain areas involved in reward evaluation and reinforcement learning. Molecular genetic studies have also begun to identify genetic mechanisms for personal traits related to reinforcement learning and complex social decision making, further illuminating the biological basis of social behavior. PMID:18368047

Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)

PubMed Central

Jayaswall, Kuldip; Mahajan, Pallavi; Singh, Gagandeep; Parmar, Rajni; Seth, Romit; Raina, Aparnashree; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Shankar, Ravi; Sharma, Ram Kumar

2016-01-01

To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans, transcriptome of BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day disease cycle. Approximately 69 million high quality reads were assembled de novo, yielding 37,790 unique transcripts with more than 55% being functionally annotated. Differentially expressed, 149 defense related transcripts/genes, namely defense related enzymes, resistance genes, multidrug resistant transporters, transcription factors, retrotransposons, metacaspases and chaperons were observed in RG, suggesting their role in defending against BB. Being present in the major hub, putative master regulators among these candidates were identified from predetermined protein-protein interaction network of Arabidopsis thaliana. Further, confirmation of abundant expression of well-known RPM1, RPS2 and RPP13 in quantitative Real Time PCR indicates salicylic acid and jasmonic acid, possibly induce synthesis of antimicrobial compounds, required to overcome the virulence of E. vexans. Compendiously, the current study provides a comprehensive gene expression and insights into the molecular mechanism of tea defense against BB to serve as a resource for unravelling the possible regulatory mechanism of immunity against various biotic stresses in tea and other crops. PMID:27465480

Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)

NASA Astrophysics Data System (ADS)

Jayaswall, Kuldip; Mahajan, Pallavi; Singh, Gagandeep; Parmar, Rajni; Seth, Romit; Raina, Aparnashree; Swarnkar, Mohit Kumar; Singh, Anil Kumar; Shankar, Ravi; Sharma, Ram Kumar

2016-07-01

To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans, transcriptome of BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day disease cycle. Approximately 69 million high quality reads were assembled de novo, yielding 37,790 unique transcripts with more than 55% being functionally annotated. Differentially expressed, 149 defense related transcripts/genes, namely defense related enzymes, resistance genes, multidrug resistant transporters, transcription factors, retrotransposons, metacaspases and chaperons were observed in RG, suggesting their role in defending against BB. Being present in the major hub, putative master regulators among these candidates were identified from predetermined protein-protein interaction network of Arabidopsis thaliana. Further, confirmation of abundant expression of well-known RPM1, RPS2 and RPP13 in quantitative Real Time PCR indicates salicylic acid and jasmonic acid, possibly induce synthesis of antimicrobial compounds, required to overcome the virulence of E. vexans. Compendiously, the current study provides a comprehensive gene expression and insights into the molecular mechanism of tea defense against BB to serve as a resource for unravelling the possible regulatory mechanism of immunity against various biotic stresses in tea and other crops.

Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

PubMed

Bressuire-Isoard, Christelle; Broussolle, Véronique; Carlin, Frédéric

2018-05-17

Bacterial spores are resistant to physical and chemical insults, which make them a major concern for public health and for industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection, and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination, and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.

Graphene and its elemental analogue: A molecular dynamics view of fracture phenomenon

NASA Astrophysics Data System (ADS)

Rakib, Tawfiqur; Mojumder, Satyajit; Das, Sourav; Saha, Sourav; Motalab, Mohammad

2017-06-01

Graphene and some graphene like two dimensional materials; hexagonal boron nitride (hBN) and silicene have unique mechanical properties which severely limit the suitability of conventional theories used for common brittle and ductile materials to predict the fracture response of these materials. This study revealed the fracture response of graphene, hBN and silicene nanosheets under different tiny crack lengths by molecular dynamics (MD) simulations using LAMMPS. The useful strength of these two dimensional materials are determined by their fracture toughness. Our study shows a comparative analysis of mechanical properties among the elemental analogues of graphene and suggested that hBN can be a good substitute for graphene in terms of mechanical properties. We have also found that the pre-cracked sheets fail in brittle manner and their failure is governed by the strength of the atomic bonds at the crack tip. The MD prediction of fracture toughness shows significant difference with the fracture toughness determined by Griffth's theory of brittle failure which restricts the applicability of Griffith's criterion for these materials in case of nano-cracks. Moreover, the strengths measured in armchair and zigzag directions of nanosheets of these materials implied that the bonds in armchair direction have the stronger capability to resist crack propagation compared to zigzag direction.

Fibrin mechanical properties and their structural origins.

PubMed

Litvinov, Rustem I; Weisel, John W

2017-07-01

Fibrin is a protein polymer that is essential for hemostasis and thrombosis, wound healing, and several other biological functions and pathological conditions that involve extracellular matrix. In addition to molecular and cellular interactions, fibrin mechanics has been recently shown to underlie clot behavior in the highly dynamic intra- and extravascular environments. Fibrin has both elastic and viscous properties. Perhaps the most remarkable rheological feature of the fibrin network is an extremely high elasticity and stability despite very low protein content. Another important mechanical property that is common to many filamentous protein polymers but not other polymers is stiffening occurring in response to shear, tension, or compression. New data has begun to provide a structural basis for the unique mechanical behavior of fibrin that originates from its complex multi-scale hierarchical structure. The mechanical behavior of the whole fibrin gel is governed largely by the properties of single fibers and their ensembles, including changes in fiber orientation, stretching, bending, and buckling. The properties of individual fibrin fibers are determined by the number and packing arrangements of double-stranded half-staggered protofibrils, which still remain poorly understood. It has also been proposed that forced unfolding of sub-molecular structures, including elongation of flexible and relatively unstructured portions of fibrin molecules, can contribute to fibrin deformations. In spite of a great increase in our knowledge of the structural mechanics of fibrin, much about the mechanisms of fibrin's biological functions remains unknown. Fibrin deformability is not only an essential part of the biomechanics of hemostasis and thrombosis, but also a rapidly developing field of bioengineering that uses fibrin as a versatile biomaterial with exceptional and tunable biochemical and mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Novel mechanisms power bacterial gliding motility.

PubMed

Nan, Beiyan; Zusman, David R

2016-07-01

For many bacteria, motility is essential for survival, growth, virulence, biofilm formation and intra/interspecies interactions. Since natural environments differ, bacteria have evolved remarkable motility systems to adapt, including swimming in aqueous media, and swarming, twitching and gliding on solid and semi-solid surfaces. Although tremendous advances have been achieved in understanding swimming and swarming motilities powered by flagella, and twitching motility powered by Type IV pili, little is known about gliding motility. Bacterial gliders are a heterogeneous group containing diverse bacteria that utilize surface motilities that do not depend on traditional flagella or pili, but are powered by mechanisms that are less well understood. Recently, advances in our understanding of the molecular machineries for several gliding bacteria revealed the roles of modified ion channels, secretion systems and unique machinery for surface movements. These novel mechanisms provide rich source materials for studying the function and evolution of complex microbial nanomachines. In this review, we summarize recent findings made on the gliding mechanisms of the myxobacteria, flavobacteria and mycoplasmas. © 2016 John Wiley & Sons Ltd.

The SRAP based molecular diversity related to antifungal and antioxidant bioactive constituents for biocontrol potentials of Trichoderma against Sclerotium rolfsii Scc.

PubMed

Hirpara, Darshna G; Gajera, H P; Bhimani, R D; Golakiya, B A

2016-08-01

The study was performed to examine 11 isolates of Trichoderma for their bio-control potentials against Sclerotium rolfsii Sacc. causing stem rot in groundnut. The antagonists Trichoderma were subjected to sequence related amplified polymorphism (SRAP) based molecular diversity analysis and compared with their hardness to S. rolfsii with respect to secretary antifungal and antioxidant profile. T. virens NBAII Tvs 12 evident highest (87.91 %) growth inhibition of test pathogen followed by T. koningii MTCC 796 (67.03 %) at 7 days after inoculation (DAI). Microscopic study confirmed biocontrol mechanism as mycoparasitism for Tvs 12 and antibiosis for MTCC 796. The growth inhibition of test pathogen was significantly negatively correlated with sclerotia formation and lipid peroxidation during antagonism due to release of secretary bioactive antioxidants by antagonists to terminate oxidative burst generated by S. rolfsii and causing inhibition of sclerotium formation. The GC-MS profile identified antifungal and antioxidant constituents hexadecane, 1,2-benzenedicarboxylic acid, mono (2-ethylhexyl) ester, 1-hexadecanesulfonyl chloride, and octadecane in potent antagonists Tvs 12; and nonacosane and octadecane in MTCC 796 along with two novel compounds 1-pentadecene and 1-heneicosyl formate for biocontrol activity. Molecular diversity of Trichoderma isolates associated with antagonistic activity was assessed by SRAP markers. The 115 primer combinations generate total 1328 amplified products of which, 1095 are shared polymorphic and 199 are unique polymorphic. The 15 SRAP combinations produced 18 bands to diagnose best antagonist Tvs 12 and 13 SRAP combinations generated 19 unique bands for identification of MTCC 796. The mycoparasitic antagonist Tvs 12 would be the best antagonist and released unique antifungal and antioxidant constituents to combat pathogen infection. The SRAP based genetic diversity indicates Tvs12 strain clustered with T. viride NBAII Tv23 and shared only 52 % similarity with other isolates of Trichoderma. The SRAP similarities explained substantial diversity (19-68 %) across Trichoderma isolates.

Perioperative circulating tumor cell detection: Current perspectives

PubMed Central

Kaifi, Jussuf T.; Li, Guangfu; Clawson, Gary; Kimchi, Eric T.; Staveley-O'Carroll, Kevin F.

2016-01-01

ABSTRACT Primary cancer resections and in selected cases surgical metastasectomies significantly improve survival, however many patients develop recurrences. Circulating tumor cells (CTCs) function as an independent marker that could be used in the prognostication of different cancers. Sampling of blood and bone marrow compartments during cancer resections is a unique opportunity to increase individual tumor cell capture efficiency. This review will address the diagnostic and therapeutic potentials of perioperative tumor isolation and highlight the focus of future studies on characterization of single disseminated cancer cells to identify targets for molecular therapy and immune escape mechanisms. PMID:27045201

Local ice melting by an antifreeze protein.

PubMed

Calvaresi, Matteo; Höfinger, Siegfried; Zerbetto, Francesco

2012-07-09

Antifreeze proteins, AFP, impede freezing of bodily fluids and damaging of cellular tissues by low temperatures. Adsorption-inhibition mechanisms have been developed to explain their functioning. Using in silico Molecular Dynamics, we show that type I AFP can also induce melting of the local ice surface. Simulations of antifreeze-positive and antifreeze-negative mutants show a clear correlation between melting induction and antifreeze activity. The presence of local melting adds a function to type I AFPs that is unique to these proteins. It may also explain some apparently conflicting experimental results where binding to ice appears both quasipermanent and reversible.

SNARE-mediated membrane fusion in autophagy

PubMed Central

Wang, Yongyao; Li, Linsen; Hou, Chen; Lai, Ying; Long, Jiangang; Liu, Jiankang; Zhong, Qing; Diao, Jiajie

2016-01-01

Autophagy, a conserved self-eating process for the bulk degradation of cytoplasmic materials, involves double-membrane autophagosomes formed when an isolation membrane emerges and their direct fusion with lysosomes for degradation. For the early biogenesis of autophagosomes and their later degradation in lysosomes, membrane fusion is necessary, although different sets of genes and autophagy-related proteins involved in distinct fusion steps have been reported. To clarify the molecular mechanism of membrane fusion in autophagy, to not only expand current knowledge of autophagy, but also benefit human health, this review discusses key findings that elucidate the unique membrane dynamics of autophagy. PMID:27422330

Primary Cilia and Dendritic Spines: Different but Similar Signaling Compartments

PubMed Central

Nechipurenko, Inna V.; Doroquez, David B.; Sengupta, Piali

2013-01-01

Primary non-motile cilia and dendritic spines are cellular compartments that are specialized to sense and transduce environmental cues and presynaptic signals, respectively. Despite their unique cellular roles, both compartments exhibit remarkable parallels in the general principles, as well as molecular mechanisms, by which their protein composition, membrane domain architecture, cellular interactions, and structural and functional plasticity are regulated. We compare and contrast the pathways required for the generation and function of cilia and dendritic spines, and suggest that insights from the study of one may inform investigations into the other of these critically important signaling structures. PMID:24048681

Recent Advances in Understanding the Control of Secretory Proteins by the Unfolded Protein Response in Plants

PubMed Central

Hayashi, Shimpei; Wakasa, Yuhya; Takaiwa, Fumio

2013-01-01

The membrane transport system is built on the proper functioning of the endoplasmic reticulum (ER). The accumulation of unfolded proteins in the ER lumen (ER stress) disrupts ER homeostasis and disturbs the transport system. In response to ER stress, eukaryotic cells activate intracellular signaling (named the unfolded protein response, UPR), which contributes to the quality control of secretory proteins. On the other hand, the deleterious effects of UPR on plant health and growth characteristics have frequently been overlooked, due to limited information on this mechanism. However, recent studies have shed light on the molecular mechanism of plant UPR, and a number of its unique characteristics have been elucidated. This study briefly reviews the progress of understanding what is happening in plants under ER stress conditions. PMID:23629671

Signaling Mechanism of Poly(ADP-Ribose) Polymerase-1 (PARP-1) in Inflammatory Diseases

PubMed Central

Ba, Xueqing; Garg, Nisha Jain

2011-01-01

Poly(ADP-ribosyl)ation, attaching the ADP-ribose polymer chain to the receptor protein, is a unique posttranslational modification. Poly(ADP-ribose) polymerase-1 (PARP-1) is a well-characterized member of the PARP family. In this review, we provide a general update on molecular structure and structure-based activity of this enzyme. However, we mainly focus on the roles of PARP-1 in inflammatory diseases. Specifically, we discuss the signaling pathway context that PARP-1 is involved in to regulate the pathogenesis of inflammation. PARP-1 facilitates diverse inflammatory responses by promoting inflammation-relevant gene expression, such as cytokines, oxidation-reduction–related enzymes, and adhesion molecules. Excessive activation of PARP-1 induces mitochondria-associated cell death in injured tissues and constitutes another mechanism for exacerbating inflammation. PMID:21356345

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

PubMed Central

Ferreira, Thais H. S.; Tsunada, Max S.; Bassi, Denis; Araújo, Pedro; Mattiello, Lucia; Guidelli, Giovanna V.; Righetto, Germanna L.; Gonçalves, Vanessa R.; Lakshmanan, Prakash; Menossi, Marcelo

2017-01-01

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments. PMID:28690620

High-frequency microrheology reveals cytoskeleton dynamics in living cells

NASA Astrophysics Data System (ADS)

Rigato, Annafrancesca; Miyagi, Atsushi; Scheuring, Simon; Rico, Felix

2017-08-01

Living cells are viscoelastic materials, dominated by an elastic response on timescales longer than a millisecond. On shorter timescales, the dynamics of individual cytoskeleton filaments are expected to emerge, but active microrheology measurements on cells accessing this regime are scarce. Here, we develop high-frequency microrheology experiments to probe the viscoelastic response of living cells from 1 Hz to 100 kHz. We report the viscoelasticity of different cell types under cytoskeletal drug treatments. On previously inaccessible short timescales, cells exhibit rich viscoelastic responses that depend on the state of the cytoskeleton. Benign and malignant cancer cells revealed remarkably different scaling laws at high frequencies, providing a unique mechanical fingerprint. Microrheology over a wide dynamic range--up to the frequency characterizing the molecular components--provides a mechanistic understanding of cell mechanics.

Life in hot acid: Pathway analyses in extremely thermoacidophilic archaea

PubMed Central

Auernik, Kathryne S.; Cooper, Charlotte R.; Kelly, Robert M.

2013-01-01

SUMMARY The extremely thermoacidophilic archaea are a particularly intriguing group of microorganisms that must simultaneously cope with biologically extreme pHs (≤ 4) and temperatures (Topt ≥ 60°C) in their natural environments. Their expandi ng biotechnological significance relates to their role in biomining of base and precious metals and their unique mechanisms of survival in hot acid, at both the cellular and biomolecular levels. Recent developments, such as advances in understanding of heavy metal tolerance mechanisms, implementation of a genetic system, and discovery of a new carbon fixation pathway, have been facilitated by availability of genome sequence data and molecular genetic systems. As a result, new insights into the metabolic pathways and physiological features that define extreme thermoacidophily have been obtained, in some cases suggesting prospects for biotechnological opportunities. PMID:18760359

Nitrogenase Reduction of Carbon-Containing Compounds

PubMed Central

Seefeldt, Lance C.; Yang, Zhi-Yong; Duval, Simon; Dean, Dennis R.

2013-01-01

Nitrogenase is an enzyme found in many bacteria and archaea that catalyzes biological dinitrogen fixation, the reduction of N2 to NH3, accounting for the major input of fixed nitrogen into the biogeochemical N cycle. In addition to reducing N2 and protons, nitrogenase can reduce a number of small, non-physiological substrates. Among these alternative substrates are included a wide array of carbon containing compounds. These compounds have provided unique insights into aspects of the nitrogenase mechanism. Recently, it was shown that carbon monoxide (CO) and carbon dioxide (CO2) can also be reduced by nitrogenase to yield hydrocarbons, opening new insights into the mechanism of small molecule activation and reduction by this complex enzyme as well as providing clues for the design of novel molecular catalysts. PMID:23597875

Live Imaging of the Lung

PubMed Central

Looney, Mark R.; Bhattacharya, Jahar

2015-01-01

Live lung imaging has spanned the discovery of capillaries in the frog lung by Malpighi to the current use of single and multiphoton imaging of intravital and isolated perfused lung preparations incorporating fluorescent molecular probes and transgenic reporter mice. Along the way, much has been learned about the unique microcirculation of the lung, including immune cell migration and the mechanisms by which cells at the alveolar-capillary interface communicate with each other. In this review, we highlight live lung imaging techniques as applied to the role of mitochondria in lung immunity, mechanisms of signal transduction in lung compartments, studies on the composition of alveolar wall liquid, and neutrophil and platelet trafficking in the lung under homeostatic and inflammatory conditions. New applications of live lung imaging and the limitations of current techniques are discussed. PMID:24245941

Unique pattern of dietary adaptation in the dentition of Carnivora: its advantage and developmental origin

PubMed Central

Saito, Kazuyuki; Kishida, Takushi; Takahashi, Katsu; Bessho, Kazuhisa

2016-01-01

Carnivora is a successful taxon in terms of dietary diversity. We investigated the dietary adaptations of carnivoran dentition and the developmental background of their dental diversity, which may have contributed to the success of the lineage. A developmental model was tested and extended to explain the unique variability and exceptional phenotypes observed in carnivoran dentition. Carnivorous mammalian orders exhibited two distinct patterns of dietary adaptation in molars and only Carnivora evolved novel variability, exhibiting a high correlation between relative molar size and the shape of the first molar. Studies of Bmp7-hetero-deficient mice, which may exhibit lower Bmp7 expression, suggested that Bmp7 has pleiotropic effects on these two dental traits. Its effects are consistent with the pattern of dietary adaptation observed in Carnivora, but not that observed in other carnivorous mammals. A molecular evolutionary analysis revealed that Bmp7 sequence evolved by natural selection during ursid evolution, suggesting that it plays an evolutionary role in the variation of carnivoran dentition. Using mouse experiments and a molecular evolutionary analysis, we extrapolated the causal mechanism of the hitherto enigmatic ursid dentition (larger M2 than M1 and M3). Our results demonstrate how carnivorans acquired novel dental variability that benefits their dietary divergence.

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution.

PubMed

Greiner, Stephan; Wang, Xi; Rauwolf, Uwe; Silber, Martina V; Mayer, Klaus; Meurer, Jörg; Haberer, Georg; Herrmann, Reinhold G

2008-04-01

The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome-genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I-III in one clade, while plastome IV appears to be closest to the common ancestor.

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution†

PubMed Central

Greiner, Stephan; Wang, Xi; Rauwolf, Uwe; Silber, Martina V.; Mayer, Klaus; Meurer, Jörg; Haberer, Georg; Herrmann, Reinhold G.

2008-01-01

The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome–genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I–III in one clade, while plastome IV appears to be closest to the common ancestor. PMID:18299283

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

Antimicrobial applications of nanotechnology: methods and literature.

PubMed

Seil, Justin T; Webster, Thomas J

2012-01-01

The need for novel antibiotics comes from the relatively high incidence of bacterial infection and the growing resistance of bacteria to conventional antibiotics. Consequently, new methods for reducing bacteria activity (and associated infections) are badly needed. Nanotechnology, the use of materials with dimensions on the atomic or molecular scale, has become increasingly utilized for medical applications and is of great interest as an approach to killing or reducing the activity of numerous microorganisms. While some natural antibacterial materials, such as zinc and silver, possess greater antibacterial properties as particle size is reduced into the nanometer regime (due to the increased surface to volume ratio of a given mass of particles), the physical structure of a nanoparticle itself and the way in which it interacts with and penetrates into bacteria appears to also provide unique bactericidal mechanisms. A variety of techniques to evaluate bacteria viability, each with unique advantages and disadvantages, has been established and must be understood in order to determine the effectiveness of nanoparticles (diameter ≤ 100 nm) as antimicrobial agents. In addition to addressing those techniques, a review of select literature and a summary of bacteriostatic and bactericidal mechanisms are covered in this manuscript.

Elucidation of molecular kinetic schemes from macroscopic traces using system identification

PubMed Central

González-Maeso, Javier; Sealfon, Stuart C.; Galocha-Iragüen, Belén; Brezina, Vladimir

2017-01-01

Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully applied to accurately derive molecular kinetic schemes from experimental macroscopic traces, and we anticipate that it may be useful in the study of a wide variety of biological systems. PMID:28192423

Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates

PubMed Central

Xue, Liang; Wang, Wen-Horng; Iliuk, Anton; Hu, Lianghai; Galan, Jacob A.; Yu, Shuai; Hans, Michael; Geahlen, Robert L.; Tao, W. Andy

2012-01-01

Our understanding of the molecular control of many disease pathologies requires the identification of direct substrates targeted by specific protein kinases. Here we describe an integrated proteomic strategy, termed kinase assay linked with phosphoproteomics, which combines a sensitive kinase reaction with endogenous kinase-dependent phosphoproteomics to identify direct substrates of protein kinases. The unique in vitro kinase reaction is carried out in a highly efficient manner using a pool of peptides derived directly from cellular kinase substrates and then dephosphorylated as substrate candidates. The resulting newly phosphorylated peptides are then isolated and identified by mass spectrometry. A further comparison of these in vitro phosphorylated peptides with phosphopeptides derived from endogenous proteins isolated from cells in which the kinase is either active or inhibited reveals new candidate protein substrates. The kinase assay linked with phosphoproteomics strategy was applied to identify unique substrates of spleen tyrosine kinase (Syk), a protein-tyrosine kinase with duel properties of an oncogene and a tumor suppressor in distinctive cell types. We identified 64 and 23 direct substrates of Syk specific to B cells and breast cancer cells, respectively. Both known and unique substrates, including multiple centrosomal substrates for Syk, were identified, supporting a unique mechanism that Syk negatively affects cell division through its centrosomal kinase activity. PMID:22451900

Translational analysis of mouse and human placental protein and mRNA reveals distinct molecular pathologies in human preeclampsia.

PubMed

Cox, Brian; Sharma, Parveen; Evangelou, Andreas I; Whiteley, Kathie; Ignatchenko, Vladimir; Ignatchenko, Alex; Baczyk, Dora; Czikk, Marie; Kingdom, John; Rossant, Janet; Gramolini, Anthony O; Adamson, S Lee; Kislinger, Thomas

2011-12-01

Preeclampsia (PE) adversely impacts ~5% of pregnancies. Despite extensive research, no consistent biomarkers or cures have emerged, suggesting that different molecular mechanisms may cause clinically similar disease. To address this, we undertook a proteomics study with three main goals: (1) to identify a panel of cell surface markers that distinguish the trophoblast and endothelial cells of the placenta in the mouse; (2) to translate this marker set to human via the Human Protein Atlas database; and (3) to utilize the validated human trophoblast markers to identify subgroups of human preeclampsia. To achieve these goals, plasma membrane proteins at the blood tissue interfaces were extracted from placentas using intravascular silica-bead perfusion, and then identified using shotgun proteomics. We identified 1181 plasma membrane proteins, of which 171 were enriched at the maternal blood-trophoblast interface and 192 at the fetal endothelial interface with a 70% conservation of expression in humans. Three distinct molecular subgroups of human preeclampsia were identified in existing human microarray data by using expression patterns of trophoblast-enriched proteins. Analysis of all misexpressed genes revealed divergent dysfunctions including angiogenesis (subgroup 1), MAPK signaling (subgroup 2), and hormone biosynthesis and metabolism (subgroup 3). Subgroup 2 lacked expected changes in known preeclampsia markers (sFLT1, sENG) and uniquely overexpressed GNA12. In an independent set of 40 banked placental specimens, GNA12 was overexpressed during preeclampsia when co-incident with chronic hypertension. In the current study we used a novel translational analysis to integrate mouse and human trophoblast protein expression with human microarray data. This strategy identified distinct molecular pathologies in human preeclampsia. We conclude that clinically similar preeclampsia patients exhibit divergent placental gene expression profiles thus implicating divergent molecular mechanisms in the origins of this disease.

Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors.

PubMed

Selvaraj, Chandrabose; Omer, Ankur; Singh, Poonam; Singh, Sanjeev Kumar

2015-01-01

Retroviruses HIV-1 and HTLV-1 are chiefly considered to be the most dangerous pathogens in Homo sapiens. These two viruses have structurally unique protease (PR) enzymes, which are having common function of its replication mechanism. Though HIV PR drugs failed to inhibit HTLV-1 infections, they emphatically emphasise the need for designing new lead compounds against HTLV-1 PR. Therefore, we tried to understand the binding level interactions through the charge environment present in both ligand and protein active sites. The domino effect illustrates that libraries of purvalanol-A are attuned to fill allosteric binding site of HTLV-1 PR through molecular recognition and shows proper binding of ligand pharmacophoric features in receptor contours. Our screening evaluates seven compounds from purvalanol-A libraries, and these compounds' pharmacophore searches for an appropriate place in the binding site and it places well according to respective receptor contour surfaces. Thus our result provides a platform for the progress of more effective compounds, which are better in free energy calculation, molecular docking, ADME and molecular dynamics studies. Finally, this research provided novel chemical scaffolds for HTLV-1 drug discovery.

Bioactive Nutrients and Nutrigenomics in Age-Related Diseases.

PubMed

Rescigno, Tania; Micolucci, Luigina; Tecce, Mario F; Capasso, Anna

2017-01-08

The increased life expectancy and the expansion of the elderly population are stimulating research into aging. Aging may be viewed as a multifactorial process that results from the interaction of genetic and environmental factors, which include lifestyle. Human molecular processes are influenced by physiological pathways as well as exogenous factors, which include the diet. Dietary components have substantive effects on metabolic health; for instance, bioactive molecules capable of selectively modulating specific metabolic pathways affect the development/progression of cardiovascular and neoplastic disease. As bioactive nutrients are increasingly identified, their clinical and molecular chemopreventive effects are being characterized and systematic analyses encompassing the "omics" technologies (transcriptomics, proteomics and metabolomics) are being conducted to explore their action. The evolving field of molecular pathological epidemiology has unique strength to investigate the effects of dietary and lifestyle exposure on clinical outcomes. The mounting body of knowledge regarding diet-related health status and disease risk is expected to lead in the near future to the development of improved diagnostic procedures and therapeutic strategies targeting processes relevant to nutrition. The state of the art of aging and nutrigenomics research and the molecular mechanisms underlying the beneficial effects of bioactive nutrients on the main aging-related disorders are reviewed herein.

Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

NASA Astrophysics Data System (ADS)

Gazit, Ehud

2013-03-01

The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

Chromosomal aberrations in soft tissue tumors. Relevance to diagnosis, classification, and molecular mechanisms.

PubMed Central

Sreekantaiah, C.; Ladanyi, M.; Rodriguez, E.; Chaganti, R. S.

1994-01-01

In recent years, significant progress has been made in identifying characteristic chromosomal rearrangements associated with several solid tumor types, notably sarcomas, a relatively rare subset of human cancer. Most sarcomas analyzed have been found to be characterized by recurrent chromosome translocations that are specific to histological types. We have reviewed published reports of chromosomal aberrations in benign and malignant soft tissue tumors and found an incidence of specific translocations in these neoplasms that ranged from 20% to 93% within histological tumor types. Identification of recurrent chromosomal abnormalities in benign tumors has resulted in a reappraisal of the general concept that benign tumors have a normal (diploid) chromosome constitution. The variety of recurrent changes present in the different tumor types attests to the cytogenetic diversity inherent in these tumors. The chromosomal rearrangements in each of the tumor types were unique and did not correspond to cancer-associated aberrations known from other solid or hematopoietic malignancies. Cytogenetics thus provides an essential adjunct to diagnostic surgical pathology in the case of malignant soft tissue tumors, which often present substantial diagnostic challenges. In addition, it represents another approach to determine the histogenetic origin of some tumors and identifies sites of gene deregulation for molecular analysis. Indeed, recent molecular analyses of several sarcoma-associated translocations have identified novel genes and novel mechanisms of their dysregulation. PMID:8203453

A de novo transcriptome and valid reference genes for quantitative real-time PCR in Colaphellus bowringi.

PubMed

Tan, Qian-Qian; Zhu, Li; Li, Yi; Liu, Wen; Ma, Wei-Hua; Lei, Chao-Liang; Wang, Xiao-Ping

2015-01-01

The cabbage beetle Colaphellus bowringi Baly is a serious insect pest of crucifers and undergoes reproductive diapause in soil. An understanding of the molecular mechanisms of diapause regulation, insecticide resistance, and other physiological processes is helpful for developing new management strategies for this beetle. However, the lack of genomic information and valid reference genes limits knowledge on the molecular bases of these physiological processes in this species. Using Illumina sequencing, we obtained more than 57 million sequence reads derived from C. bowringi, which were assembled into 39,390 unique sequences. A Clusters of Orthologous Groups classification was obtained for 9,048 of these sequences, covering 25 categories, and 16,951 were assigned to 255 Kyoto Encyclopedia of Genes and Genomes pathways. Eleven candidate reference gene sequences from the transcriptome were then identified through reverse transcriptase polymerase chain reaction. Among these candidate genes, EF1α, ACT1, and RPL19 proved to be the most stable reference genes for different reverse transcriptase quantitative polymerase chain reaction experiments in C. bowringi. Conversely, aTUB and GAPDH were the least stable reference genes. The abundant putative C. bowringi transcript sequences reported enrich the genomic resources of this beetle. Importantly, the larger number of gene sequences and valid reference genes provide a valuable platform for future gene expression studies, especially with regard to exploring the molecular mechanisms of different physiological processes in this species.

Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations.

PubMed

Sprenger, K G; Prakash, Arushi; Drobny, Gary; Pfaendtner, Jim

2018-01-23

Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.

Molecular clamp mechanism of substrate binding by hydrophobic coiled-coil residues of the archaeal chaperone prefoldin

PubMed Central

Lundin, Victor F.; Stirling, Peter C.; Gomez-Reino, Juan; Mwenifumbo, Jill C.; Obst, Jennifer M.; Valpuesta, José M.; Leroux, Michel R.

2004-01-01

Prefoldin (PFD) is a jellyfish-shaped molecular chaperone that has been proposed to play a general role in de novo protein folding in archaea and is known to assist the biogenesis of actins, tubulins, and potentially other proteins in eukaryotes. Using point mutants, chimeras, and intradomain swap variants, we show that the six coiledcoil tentacles of archaeal PFD act in concert to bind and stabilize nonnative proteins near the opening of the cavity they form. Importantly, the interaction between chaperone and substrate depends on the mostly buried interhelical hydrophobic residues of the coiled coils. We also show by electron microscopy that the tentacles can undergo an en bloc movement to accommodate an unfolded substrate. Our data reveal how archael PFD uses its unique architecture and intrinsic coiled-coil properties to interact with nonnative polypeptides. PMID:15070724

High performance carbon fibers from very high molecular weight polyacrylonitrile precursors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, E. Ashley; Weisenberger, Matthew C.; Abdallah, Mohamed G.

In this study, carbon fibers are unique reinforcing agents for lightweight composite materials due to their outstanding mechanical properties and low density. Current technologies are capable of producing carbon fibers with 90-95% of the modulus of perfect graphite (~1025 GPa). However, these same carbon fibers possess less than 10% of the theoretical carbon fiber strength, estimated to be about 100 GPa.[1] Indeed, attempts to increase carbon fiber rigidity results in lower breaking strength. To develop advanced carbon fibers with both very high strength and modulus demands a new manufacturing methodology. Here, we report a method of manufacturing high strength, verymore » high modulus carbon fibers from a very high molecular weight (VHMW) polyacrylonitrile (PAN) precursor without the use of nanomaterial additives such as nucleating or structure-templating agents, as have been used by others.[2,3]« less

Recent molecular insights into rickettsial pathogenesis and immunity

PubMed Central

Sahni, Sanjeev K; Narra, Hema P; Sahni, Abha; Walker, David H

2013-01-01

Human infections with arthropod-borne Rickettsia species remain a major global health issue, causing significant morbidity and mortality. Epidemic typhus due to Rickettsia prowazekii has an established reputation as the ‘scourge of armies’, and as a major determinant of significant ‘historical turning points’. No suitable vaccines for human use are currently available to prevent rickettsial diseases. The unique lifestyle features of rickettsiae include obligate intracellular parasitism, intracytoplasmic niche within the host cell, predilection for infection of microvascular endothelium in mammalian hosts, association with arthropods and the tendency for genomic reduction. The fundamental research in the field of Rickettsiology has witnessed significant recent progress in the areas of pathogen adhesion/invasion and host immune responses, as well as the genomics, proteomics, metabolomics, phylogenetics, motility and molecular manipulation of important rickettsial pathogens. The focus of this review article is to capture a snapshot of the latest developments pertaining to the mechanisms of rickettsial pathogenesis and immunity. PMID:24059918

Signaling, Regulation, and Specificity of the Type II p21-activated Kinases.

PubMed

Ha, Byung Hak; Morse, Elizabeth M; Turk, Benjamin E; Boggon, Titus J

2015-05-22

The p21-activated kinases (PAKs) are a family of six serine/threonine kinases that act as key effectors of RHO family GTPases in mammalian cells. PAKs are subdivided into two groups: type I PAKs (PAK1, PAK2, and PAK3) and type II PAKs (PAK4, PAK5, and PAK6). Although these groups are involved in common signaling pathways, recent work indicates that the two groups have distinct modes of regulation and have both unique and common substrates. Here, we review recent insights into the molecular level details that govern regulation of type II PAK signaling. We also consider mechanisms by which signal transduction is regulated at the level of substrate specificity. Finally, we discuss the implications of these studies for clinical targeting of these kinases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural basis for the antifolding activity of a molecular chaperone

NASA Astrophysics Data System (ADS)

Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

2016-09-01

Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

PubMed Central

Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

2016-01-01

Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

Diabetes reversal by inhibition of the low molecular weight tyrosine phosphatase

PubMed Central

Stanford, Stephanie M; Aleshin, Alexander E; Zhang, Vida; Ardecky, Robert J; Hedrick, Michael P; Zou, Jiwen; Ganji, Santhi R.; Bliss, Matthew R; Yamamoto, Fusayo; Bobkov, Andrey A.; Kiselar, Janna; Liu, Yingge; Cadwell, Gregory W; Khare, Shilpi; Yu, Jinghua; Barquilla, Antonio; Chung, Thomas DY; Mustelin, Tomas; Schenk, Simon; Bankston, Laurie A; Liddington, Robert C; Pinkerton, Anthony B; Bottini, Nunzio

2017-01-01

Obesity-associated insulin resistance plays a central role in type 2 diabetes. As such, tyrosine phosphatases that dephosphorylate the insulin receptor (IR) are potential therapeutic targets. The low molecular weight protein tyrosine phosphatase (LMPTP) is a proposed IR phosphatase, yet its role in insulin signaling in vivo has not been defined. Here we show that global and liver-specific LMPTP deletion protects mice from high-fat diet-induced diabetes without affecting body weight. To examine the role of the catalytic activity of LMPTP, we developed a small-molecule inhibitor with a novel uncompetitive mechanism, a unique binding site at the opening of the catalytic pocket, and exquisite selectivity over other phosphatases. This inhibitor is orally bioavailable, increases liver IR phosphorylation in vivo, and reverses high-fat diet induced diabetes. Our findings suggest that LMPTP is a key promoter of insulin resistance and that LMPTP inhibitors would be beneficial for treating type 2 diabetes. PMID:28346406

Cardiac Embryology and Molecular Mechanisms of Congenital Heart Disease: A Primer for Anesthesiologists.

PubMed

Kloesel, Benjamin; DiNardo, James A; Body, Simon C

2016-09-01

Congenital heart disease is diagnosed in 0.4% to 5% of live births and presents unique challenges to the pediatric anesthesiologist. Furthermore, advances in surgical management have led to improved survival of those patients, and many adult anesthesiologists now frequently take care of adolescents and adults who have previously undergone surgery to correct or palliate congenital heart lesions. Knowledge of abnormal heart development on the molecular and genetic level extends and improves the anesthesiologist's understanding of congenital heart disease. In this article, we aim to review current knowledge pertaining to genetic alterations and their cellular effects that are involved in the formation of congenital heart defects. Given that congenital heart disease can currently only occasionally be traced to a single genetic mutation, we highlight some of the difficulties that researchers face when trying to identify specific steps in the pathogenetic development of heart lesions.

Nonlinear Developmental trajectory of fear learning and memory

PubMed Central

King, Elizabeth C.; Pattwell, Siobhan S.; Sun, Alice; Glatt, Charles E.; Lee, Francis S.

2013-01-01

The transition into and out of adolescence represents a unique developmental period during which neuronal circuits are particularly susceptible to modification by experience. Adolescence is associated with an increased incidence of anxiety disorders in humans,1–3 and an estimated 75% of adults with fear-related disorders met diagnostic criteria as children and adolescents.4,5 Conserved neural circuitry between rodents and humans has facilitated neurodevelopmental studies of behavioral and molecular processes associated with fear learning and memory, which lie at the heart of many anxiety disorders. Here, we review the non-linear developmental aspects of fear learning and memory during a transition period into and out of adolescence and provide a discussion of the molecular mechanisms that may underlie these alterations in behavior. We provide a model that may help to inform novel treatment strategies for children and adolescents with fear-related disorders. PMID:24176014

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice.

PubMed

Marco, Maria L; de Vries, Maaike C; Wels, Michiel; Molenaar, Douwe; Mangell, Peter; Ahrne, Siv; de Vos, Willem M; Vaughan, Elaine E; Kleerebezem, Michiel

2010-11-01

Probiotic bacteria provide unique opportunities to study the global responses and molecular mechanisms underlying the effects of gut-associated microorganisms in the human digestive tract. In this study, we show by comparative transcriptome analysis using DNA microarrays that the established probiotic Lactobacillus plantarum 299v specifically adapts its metabolic capacity in the human intestine for carbohydrate acquisition and expression of exopolysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a commensal microorganism in the human gut. A core L. plantarum transcriptome expressed in the mammalian intestine was also determined through comparisons of L. plantarum 299v activities in humans to those found for L. plantarum WCFS1 in germ-free mice. These results identify the niche-specific adaptations of a dietary microorganism to the intestinal ecosystem and provide novel targets for molecular analysis of microbial-host interactions which affect human health.

The spatial response of nonlinear strain propagation in response to actively driven microspheres through entangled actin networks

NASA Astrophysics Data System (ADS)

Falzone, Tobias; Blair, Savanna; Robertson-Anderson, Rae

2015-03-01

The semiflexible biopolymer actin, a ubiquitous component of nearly all biological organisms, plays an important role in many mechanically-driven processes such as muscle contraction, cancer invasion and cell motility. As such, entangled actin networks, which possess unique and complex viscoelastic properties, have been the subject of much theoretical and experimental work. However, due to this viscoelastic complexity, much is still unknown regarding the correlation of the applied stress on actin networks to the induced filament strain at the molecular and micro scale. Here, we use simultaneous optical trapping and fluorescence microscopy to characterize the link between applied microscopic forces and strain propagation as a function of strain rate and concentration. Specifically, we track fiduciary markers on entangled actin filaments before, during and after actively driving embedded microspheres through the network. These measurements provide much needed insight into the molecular-level dynamics connecting stress and strain in semiflexible polymer networks.

High performance carbon fibers from very high molecular weight polyacrylonitrile precursors

DOE PAGES

Morris, E. Ashley; Weisenberger, Matthew C.; Abdallah, Mohamed G.; ...

2016-02-02

In this study, carbon fibers are unique reinforcing agents for lightweight composite materials due to their outstanding mechanical properties and low density. Current technologies are capable of producing carbon fibers with 90-95% of the modulus of perfect graphite (~1025 GPa). However, these same carbon fibers possess less than 10% of the theoretical carbon fiber strength, estimated to be about 100 GPa.[1] Indeed, attempts to increase carbon fiber rigidity results in lower breaking strength. To develop advanced carbon fibers with both very high strength and modulus demands a new manufacturing methodology. Here, we report a method of manufacturing high strength, verymore » high modulus carbon fibers from a very high molecular weight (VHMW) polyacrylonitrile (PAN) precursor without the use of nanomaterial additives such as nucleating or structure-templating agents, as have been used by others.[2,3]« less

Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly.

PubMed

Alberstein, Robert; Suzuki, Yuta; Paesani, Francesco; Tezcan, F Akif

2018-04-30

De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.

Molecular basis of ancestral vertebrate electroreception

PubMed Central

Bellono, Nicholas W.; Leitch, Duncan B.; Julius, David

2017-01-01

Elasmobranch fishes, including sharks, rays, and skates, use specialized electrosensory organs called Ampullae of Lorenzini to detect extremely small changes in environmental electric fields. Electrosensory cells within these ampullae are able to discriminate and respond to minute changes in environmental voltage gradients through an as-yet unknown mechanism. Here we show that the voltage-gated calcium channel CaV1.3 and big conductance calcium-activated potassium (BK) channel are preferentially expressed by electrosensory cells in little skate (Leucoraja erinacea) and functionally couple to mediate electrosensory cell membrane voltage oscillations, which are important in the detection of specific, weak electrical signals. Both channels exhibit unique properties compared with their mammalian orthologues to support electrosensory functions: structural adaptations in CaV1.3 mediate a low voltage threshold for activation, while alterations in BK support specifically tuned voltage oscillations. These findings reveal a molecular basis of electroreception and demonstrate how discrete evolutionary changes in ion channel structure facilitate sensory adaptation. PMID:28264196

Molecular biology of testicular germ cell tumors.

PubMed

Gonzalez-Exposito, R; Merino, M; Aguayo, C

2016-06-01

Testicular germ cell tumors (TGCTs) are the most common solid tumors in young adult men. They constitute a unique pathology because of their embryonic and germ origin and their special behavior. Genetic predisposition, environmental factors involved in their development and genetic aberrations have been under study in many works throughout the last years trying to explain the susceptibility and the transformation mechanism of TGCTs. Despite the high rate of cure in this type of tumors because its particular sensitivity to cisplatin, there are tumors resistant to chemotherapy for which it is needed to find new therapies. In the present work, it has been carried out a literature review on the most important molecular aspects involved in the onset and development of such tumors, as well as a review of the major developments regarding prognostic factors, new prognostic biomarkers and the possibility of new targeted therapies.

Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.

PubMed

Stanford, Stephanie M; Aleshin, Alexander E; Zhang, Vida; Ardecky, Robert J; Hedrick, Michael P; Zou, Jiwen; Ganji, Santhi R; Bliss, Matthew R; Yamamoto, Fusayo; Bobkov, Andrey A; Kiselar, Janna; Liu, Yingge; Cadwell, Gregory W; Khare, Shilpi; Yu, Jinghua; Barquilla, Antonio; Chung, Thomas D Y; Mustelin, Tomas; Schenk, Simon; Bankston, Laurie A; Liddington, Robert C; Pinkerton, Anthony B; Bottini, Nunzio

2017-06-01

Obesity-associated insulin resistance plays a central role in type 2 diabetes. As such, tyrosine phosphatases that dephosphorylate the insulin receptor (IR) are potential therapeutic targets. The low-molecular-weight protein tyrosine phosphatase (LMPTP) is a proposed IR phosphatase, yet its role in insulin signaling in vivo has not been defined. Here we show that global and liver-specific LMPTP deletion protects mice from high-fat diet-induced diabetes without affecting body weight. To examine the role of the catalytic activity of LMPTP, we developed a small-molecule inhibitor with a novel uncompetitive mechanism, a unique binding site at the opening of the catalytic pocket, and an exquisite selectivity over other phosphatases. This inhibitor is orally bioavailable, and it increases liver IR phosphorylation in vivo and reverses high-fat diet-induced diabetes. Our findings suggest that LMPTP is a key promoter of insulin resistance and that LMPTP inhibitors would be beneficial for treating type 2 diabetes.

Tissue-like Neural Probes for Understanding and Modulating the Brain.

PubMed

Hong, Guosong; Viveros, Robert D; Zwang, Theodore J; Yang, Xiao; Lieber, Charles M

2018-03-19

Electrophysiology tools have contributed substantially to understanding brain function, yet the capabilities of conventional electrophysiology probes have remained limited in key ways because of large structural and mechanical mismatches with respect to neural tissue. In this Perspective, we discuss how the general goal of probe design in biochemistry, that the probe or label have a minimal impact on the properties and function of the system being studied, can be realized by minimizing structural, mechanical, and topological differences between neural probes and brain tissue, thus leading to a new paradigm of tissue-like mesh electronics. The unique properties and capabilities of the tissue-like mesh electronics as well as future opportunities are summarized. First, we discuss the design of an ultraflexible and open mesh structure of electronics that is tissue-like and can be delivered in the brain via minimally invasive syringe injection like molecular and macromolecular pharmaceuticals. Second, we describe the unprecedented tissue healing without chronic immune response that leads to seamless three-dimensional integration with a natural distribution of neurons and other key cells through these tissue-like probes. These unique characteristics lead to unmatched stable long-term, multiplexed mapping and modulation of neural circuits at the single-neuron level on a year time scale. Last, we offer insights on several exciting future directions for the tissue-like electronics paradigm that capitalize on their unique properties to explore biochemical interactions and signaling in a "natural" brain environment.

Molecular environmental geochemistry

NASA Astrophysics Data System (ADS)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at mineral surfaces and mineral-water interfaces. A review of recent studies employing molecular characterizations of soils, sediments, and biological samples from contaminated sites exemplifies the utility and benefits, as well as the challenge, of applying molecular probes to complicated natural materials. New techniques, technological advances, and the crossover of methods from other disciplines such as biochemistry and materials science promise better examination of environmental chemical processes in real time and at higher resolution, and will further the integration of molecular information into field-scale chemical and hydrologic models.

Two-dimensional materials for novel liquid separation membranes.

PubMed

Ying, Yulong; Yang, Yefeng; Ying, Wen; Peng, Xinsheng

2016-08-19

Demand for a perfect molecular-level separation membrane with ultrafast permeation and a robust mechanical property for any kind of species to be blocked in water purification and desalination is urgent. In recent years, due to their intrinsic characteristics, such as a unique mono-atom thick structure, outstanding mechanical strength and excellent flexibility, as well as facile and large-scale production, graphene and its large family of two-dimensional (2D) materials are regarded as ideal membrane materials for ultrafast molecular separation. A perfect separation membrane should be as thin as possible to maximize its flux, mechanically robust and without failure even if under high loading pressure, and have a narrow nanochannel size distribution to guarantee its selectivity. The latest breakthrough in 2D material-based membranes will be reviewed both in theories and experiments, including their current state-of-the-art fabrication, structure design, simulation and applications. Special attention will be focused on the designs and strategies employed to control microstructures to enhance permeation and selectivity for liquid separation. In addition, critical views on the separation mechanism within two-dimensional material-based membranes will be provided based on a discussion of the effects of intrinsic defects during growth, predefined nanopores and nanochannels during subsequent fabrication processes, the interlayer spacing of stacking 2D material flakes and the surface charge or functional groups. Furthermore, we will summarize the significant progress of these 2D material-based membranes for liquid separation in nanofiltration/ultrafiltration and pervaporation. Lastly, we will recall issues requiring attention, and discuss existing questionable conclusions in some articles and emerging challenges. This review will serve as a valuable platform to provide a compact source of relevant and timely information about the development of 2D material-based membranes as well as fully explain up-to-date mechanisms and models of water transport and molecular separation behavior, which will arouse great interest among researchers entering or already working in the field of 2D material-based membranes.

Two-dimensional materials for novel liquid separation membranes

NASA Astrophysics Data System (ADS)

Ying, Yulong; Yang, Yefeng; Ying, Wen; Peng, Xinsheng

2016-08-01

Demand for a perfect molecular-level separation membrane with ultrafast permeation and a robust mechanical property for any kind of species to be blocked in water purification and desalination is urgent. In recent years, due to their intrinsic characteristics, such as a unique mono-atom thick structure, outstanding mechanical strength and excellent flexibility, as well as facile and large-scale production, graphene and its large family of two-dimensional (2D) materials are regarded as ideal membrane materials for ultrafast molecular separation. A perfect separation membrane should be as thin as possible to maximize its flux, mechanically robust and without failure even if under high loading pressure, and have a narrow nanochannel size distribution to guarantee its selectivity. The latest breakthrough in 2D material-based membranes will be reviewed both in theories and experiments, including their current state-of-the-art fabrication, structure design, simulation and applications. Special attention will be focused on the designs and strategies employed to control microstructures to enhance permeation and selectivity for liquid separation. In addition, critical views on the separation mechanism within two-dimensional material-based membranes will be provided based on a discussion of the effects of intrinsic defects during growth, predefined nanopores and nanochannels during subsequent fabrication processes, the interlayer spacing of stacking 2D material flakes and the surface charge or functional groups. Furthermore, we will summarize the significant progress of these 2D material-based membranes for liquid separation in nanofiltration/ultrafiltration and pervaporation. Lastly, we will recall issues requiring attention, and discuss existing questionable conclusions in some articles and emerging challenges. This review will serve as a valuable platform to provide a compact source of relevant and timely information about the development of 2D material-based membranes as well as fully explain up-to-date mechanisms and models of water transport and molecular separation behavior, which will arouse great interest among researchers entering or already working in the field of 2D material-based membranes.

Modelling approaches for evaluating multiscale tendon mechanics

PubMed Central

Fang, Fei; Lake, Spencer P.

2016-01-01

Tendon exhibits anisotropic, inhomogeneous and viscoelastic mechanical properties that are determined by its complicated hierarchical structure and varying amounts/organization of different tissue constituents. Although extensive research has been conducted to use modelling approaches to interpret tendon structure–function relationships in combination with experimental data, many issues remain unclear (i.e. the role of minor components such as decorin, aggrecan and elastin), and the integration of mechanical analysis across different length scales has not been well applied to explore stress or strain transfer from macro- to microscale. This review outlines mathematical and computational models that have been used to understand tendon mechanics at different scales of the hierarchical organization. Model representations at the molecular, fibril and tissue levels are discussed, including formulations that follow phenomenological and microstructural approaches (which include evaluations of crimp, helical structure and the interaction between collagen fibrils and proteoglycans). Multiscale modelling approaches incorporating tendon features are suggested to be an advantageous methodology to understand further the physiological mechanical response of tendon and corresponding adaptation of properties owing to unique in vivo loading environments. PMID:26855747

Biological response on a titanium implant-grade surface functionalized with modular peptides☆

PubMed Central

Yazici, H.; Fong, H.; Wilson, B.; Oren, E.E.; Amos, F.A.; Zhang, H.; Evans, J.S.; Snead, M.L.; Sarikaya, M.; Tamerler, C.

2015-01-01

Titanium (Ti) and its alloys are among the most successful implantable materials for dental and orthopedic applications. The combination of excellent mechanical and corrosion resistance properties makes them highly desirable as endosseous implants that can withstand a demanding biomechanical environment. Yet, the success of the implant depends on its osteointegration, which is modulated by the biological reactions occurring at the interface of the implant. A recent development for improving biological responses on the Ti-implant surface has been the realization that bifunctional peptides can impart material binding specificity not only because of their molecular recognition of the inorganic material surface, but also through their self-assembly and ease of biological conjugation properties. To assess peptide-based functionalization on bioactivity, the present authors generated a set of peptides for implant-grade Ti, using cell surface display methods. Out of 60 unique peptides selected by this method, two of the strongest titanium binding peptides, TiBP1 and TiBP2, were further characterized for molecular structure and adsorption properties. These two peptides demonstrated unique, but similar molecular conformations different from that of a weak binder peptide, TiBP60. Adsorption measurements on a Ti surface revealed that their disassociation constants were 15-fold less than TiBP60. Their flexible and modular use in biological surface functionalization were demonstrated by conjugating them with an integrin recognizing peptide motif, RGDS. The functionalization of the Ti surface by the selected peptides significantly enhanced the bioactivity of osteoblast and fibroblast cells on implant-grade materials. PMID:23159566

Gene Signature in Sessile Serrated Polyps Identifies Colon Cancer Subtype

PubMed Central

Kanth, Priyanka; Bronner, Mary P.; Boucher, Kenneth M.; Burt, Randall W.; Neklason, Deborah W.; Hagedorn, Curt H.; Delker, Don A.

2016-01-01

Sessile serrated colon adenoma/polyps (SSA/Ps) are found during routine screening colonoscopy and may account for 20–30% of colon cancers. However, differentiating SSA/Ps from hyperplastic polyps (HP) with little risk of cancer is challenging and complementary molecular markers are needed. Additionally, the molecular mechanisms of colon cancer development from SSA/Ps are poorly understood. RNA sequencing was performed on 21 SSA/Ps, 10 HPs, 10 adenomas, 21 uninvolved colon and 20 control colon specimens. Differential expression and leave-one-out cross validation methods were used to define a unique gene signature of SSA/Ps. Our SSA/P gene signature was evaluated in colon cancer RNA-Seq data from The Cancer Genome Atlas (TCGA) to identify a subtype of colon cancers that may develop from SSA/Ps. A total of 1422 differentially expressed genes were found in SSA/Ps relative to controls. Serrated polyposis syndrome (n=12) and sporadic SSA/Ps (n=9) exhibited almost complete (96%) gene overlap. A 51-gene panel in SSA/P showed similar expression in a subset of TCGA colon cancers with high microsatellite instability (MSI-H). A smaller seven-gene panel showed high sensitivity and specificity in identifying BRAF mutant, CpG island methylator phenotype high (CIMP-H) and MLH1 silenced colon cancers. We describe a unique gene signature in SSA/Ps that identifies a subset of colon cancers likely to develop through the serrated pathway. These gene panels may be utilized for improved differentiation of SSA/Ps from HPs and provide insights into novel molecular pathways altered in colon cancer arising from the serrated pathway. PMID:27026680

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell.

PubMed

Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2016-03-01

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Unraveling Fungal Radiation Resistance Regulatory Networks through the Genome-Wide Transcriptome and Genetic Analyses of Cryptococcus neoformans

PubMed Central

Jung, Kwang-Woo; Yang, Dong-Hoon; Kim, Min-Kyu; Seo, Ho Seong

2016-01-01

ABSTRACT The basidiomycetous fungus Cryptococcus neoformans has been known to be highly radiation resistant and has been found in fatal radioactive environments such as the damaged nuclear reactor at Chernobyl. To elucidate the mechanisms underlying the radiation resistance phenotype of C. neoformans, we identified genes affected by gamma radiation through genome-wide transcriptome analysis and characterized their functions. We found that genes involved in DNA damage repair systems were upregulated in response to gamma radiation. Particularly, deletion of recombinase RAD51 and two DNA-dependent ATPase genes, RAD54 and RDH54, increased cellular susceptibility to both gamma radiation and DNA-damaging agents. A variety of oxidative stress response genes were also upregulated. Among them, sulfiredoxin contributed to gamma radiation resistance in a peroxiredoxin/thioredoxin-independent manner. Furthermore, we found that genes involved in molecular chaperone expression, ubiquitination systems, and autophagy were induced, whereas genes involved in the biosynthesis of proteins and fatty acids/sterols were downregulated. Most importantly, we discovered a number of novel C. neoformans genes, the expression of which was modulated by gamma radiation exposure, and their deletion rendered cells susceptible to gamma radiation exposure, as well as DNA damage insults. Among these genes, we found that a unique transcription factor containing the basic leucine zipper domain, named Bdr1, served as a regulator of the gamma radiation resistance of C. neoformans by controlling expression of DNA repair genes, and its expression was regulated by the evolutionarily conserved DNA damage response protein kinase Rad53. Taken together, the current transcriptome and functional analyses contribute to the understanding of the unique molecular mechanism of the radiation-resistant fungus C. neoformans. PMID:27899501

Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes.

PubMed

Tsai, Chi-Lin; Tainer, John A

2018-01-01

[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes. © 2018 Elsevier Inc. All rights reserved.

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants1[W][OA

PubMed Central

O’Rourke, Jamie A.; Yang, S. Samuel; Miller, Susan S.; Bucciarelli, Bruna; Liu, Junqi; Rydeen, Ariel; Bozsoki, Zoltan; Uhde-Stone, Claudia; Tu, Zheng Jin; Allan, Deborah; Gronwald, John W.; Vance, Carroll P.

2013-01-01

Phosphorus, in its orthophosphate form (Pi), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to Pi deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in Pi-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to Pi deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to Pi deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the Pi status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in Pi deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to Pi deficiency. PMID:23197803

An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants.

PubMed

O'Rourke, Jamie A; Yang, S Samuel; Miller, Susan S; Bucciarelli, Bruna; Liu, Junqi; Rydeen, Ariel; Bozsoki, Zoltan; Uhde-Stone, Claudia; Tu, Zheng Jin; Allan, Deborah; Gronwald, John W; Vance, Carroll P

2013-02-01

Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.

Unique Aspects of the Structure and Dynamics of Elementary Iβ Cellulose Microfibrils Revealed by Computational Simulations1[OPEN

PubMed Central

Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.; Wagner, John; Gidley, Michael J.; Bacic, Antony

2015-01-01

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. PMID:25786828

Hydrogenation-assisted graphene origami and its application in programmable molecular mass uptake, storage, and release.

PubMed

Zhu, Shuze; Li, Teng

2014-03-25

The malleable nature of atomically thin graphene makes it a potential candidate material for nanoscale origami, a promising bottom-up nanomanufacturing approach to fabricating nanobuilding blocks of desirable shapes. The success of graphene origami hinges upon precise and facile control of graphene morphology, which still remains as a significant challenge. Inspired by recent progresses on functionalization and patterning of graphene, we demonstrate hydrogenation-assisted graphene origami (HAGO), a feasible and robust approach to enabling the formation of unconventional carbon nanostructures, through systematic molecular dynamics simulations. A unique and desirable feature of HAGO-enabled nanostructures is the programmable tunability of their morphology via an external electric field. In particular, we demonstrate reversible opening and closing of a HAGO-enabled graphene nanocage, a mechanism that is crucial to achieve molecular mass uptake, storage, and release. HAGO holds promise to enable an array of carbon nanostructures of desirable functionalities by design. As an example, we demonstrate HAGO-enabled high-density hydrogen storage with a weighted percentage exceeding the ultimate goal of US Department of Energy.

Protocorms and Protocorm-Like Bodies Are Molecularly Distinct from Zygotic Embryonic Tissues in Phalaenopsis aphrodite1[OPEN

PubMed Central

Chen, Jhun-Chen; Wei, Miao-Ju

2016-01-01

The distinct reproductive program of orchids provides a unique evolutionary model with pollination-triggered ovule development and megasporogenesis, a modified embryogenesis program resulting in seeds with immature embryos, and mycorrhiza-induced seed germination. However, the molecular mechanisms that have evolved to establish these unparalleled developmental programs are largely unclear. Here, we conducted comparative studies of genome-wide gene expression of various reproductive tissues and captured the molecular events associated with distinct reproductive programs in Phalaenopsis aphrodite. Importantly, our data provide evidence to demonstrate that protocorm-like body (PLB) regeneration (the clonal regeneration practice used in the orchid industry) does not follow the embryogenesis program. Instead, we propose that SHOOT MERISTEMLESS, a class I KNOTTED-LIKE HOMEOBOX gene, is likely to play a role in PLB regeneration. Our studies challenge the current understanding of the embryonic identity of PLBs. Taken together, the data obtained establish a fundamental framework for orchid reproductive development and provide a valuable new resource to enable the prediction of gene regulatory networks that is required for specialized developmental programs of orchid species. PMID:27338813

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

PubMed

Egorov, Evgeny S; Merzlyak, Ekaterina M; Shelenkov, Andrew A; Britanova, Olga V; Sharonov, George V; Staroverov, Dmitriy B; Bolotin, Dmitriy A; Davydov, Alexey N; Barsova, Ekaterina; Lebedev, Yuriy B; Shugay, Mikhail; Chudakov, Dmitriy M

2015-06-15

Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications. Copyright © 2015 by The American Association of Immunologists, Inc.

Production & Characterization of a Unique Dextran from an Indigenous Leuconostoc mesenteroides CMG713

PubMed Central

Sarwat, Farwa; Qader, Shah Ali Ul; Aman, Afsheen; Ahmed, Nuzhat

2008-01-01

On the basis of high enzyme activity a newly isolated strain of L. mesenteroides CMG713 was selected for dextran production. For maximum yield of dextran, effects of various parameters such as pH, temperature, sucrose concentration and incubation period were studied. L. mesenteroides CMG713 produced maximum dextran after 20 hours of incubation at 30ºC with 15% sucrose at pH 7.0. The molecular mass distribution of dextran produced by this strain showed that its molecular mass was about 2.0 million Da. Dextran analysis by 13C-NMR spectrometry showed no signals corresponding to any other linkages except α-(1→6) glycosidic linkage in the main chain, which has not been reported before. Physico-chemical properties of this unique dextran were also studied. These optimised conditions could be used for the commercial production of this unique high molecular weight dextran, which have significant industrial perspectives. PMID:18953402

Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations.

PubMed

Itoyama, Shuhei; Doitomi, Kazuki; Kamachi, Takashi; Shiota, Yoshihito; Yoshizawa, Kazunari

2016-03-21

Enzymatic methane hydroxylation is proposed to efficiently occur at the dinuclear copper site of particulate methane monooxygenase (pMMO), which is an integral membrane metalloenzyme in methanotrophic bacteria. The resting state and a possible peroxo state of the dicopper active site of pMMO are discussed by using combined quantum mechanics and molecular mechanics calculations on the basis of reported X-ray crystal structures of the resting state of pMMO by Rosenzweig and co-workers. The dicopper site has a unique structure, in which one copper is coordinated by two histidine imidazoles and another is chelated by a histidine imidazole and primary amine of an N-terminal histidine. The resting state of the dicopper site is assignable to the mixed-valent Cu(I)Cu(II) state from a computed Cu-Cu distance of 2.62 Å from calculations at the B3LYP-D/TZVP level of theory. A μ-η(2):η(2)-peroxo-Cu(II)2 structure similar to those of hemocyanin and tyrosinase is reasonably obtained by using the resting state structure and dioxygen. Computed Cu-Cu and O-O distances are 3.63 and 1.46 Å, respectively, in the open-shell singlet state. Structural features of the dicopper peroxo species of pMMO are compared with those of hemocyanin and tyrosinase and synthetic dicopper model compounds. Optical features of the μ-η(2):η(2)-peroxo-Cu(II)2 state are calculated and analyzed with TD-DFT calculations.

Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations.

PubMed

Vanegas, Juan M; Torres-Sánchez, Alejandro; Arroyo, Marino

2014-02-11

Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions. However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations (e.g. nonconstant normal stress profiles along an isotropic bilayer in equilibrium) is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations.

Experimental and modeling study on charge storage/transfer mechanism of graphene-based supercapacitors

NASA Astrophysics Data System (ADS)

Ban, Shuai; Jing, Xie; Zhou, Hongjun; Zhang, Lei; Zhang, Jiujun

2014-12-01

A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g-1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g-1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.

Mudskippers and Their Genetic Adaptations to an Amphibious Lifestyle

PubMed Central

You, Xinxin; Sun, Min; Li, Jia; Bian, Chao; Chen, Jieming; Yu, Hui; Shi, Qiong

2018-01-01

Simple Summary Mudskippers are an interesting group of goggle-eyed amphibious fish that can live both in water and on land. They are a useful model for obtaining insights into the genetic mechanisms underlying the terrestrial adaptations of amphibious fish. This review summarizes the morphological and physiological modifications of representative mudskippers, and focuses on the recent advancement of genomic studies on their genetic adaptations to the amphibious lifestyle. Abstract Mudskippers are the largest group of amphibious teleost fish that are uniquely adapted to live on mudflats. During their successful transition from aqueous life to terrestrial living, these fish have evolved morphological and physiological modifications of aerial vision and olfaction, higher ammonia tolerance, aerial respiration, improved immunological defense against terrestrial pathogens, and terrestrial locomotion using protruded pectoral fins. Comparative genomic and transcriptomic data have been accumulated and analyzed for understanding molecular mechanisms of the terrestrial adaptations. Our current review provides a general introduction to mudskippers and recent research advances of their genetic adaptations to the amphibious lifestyle, which will be helpful for understanding the evolutionary transition of vertebrates from water to land. Our insights into the genomes and transcriptomes will also support molecular breeding, functional identification, and natural compound screening. PMID:29414871

Functional and structural analysis of Pichia pastoris-expressed Aspergillus niger 1,4-β-endoglucanase.

PubMed

Yan, Junjie; Liu, Weidong; Li, Yujie; Lai, Hui-Lin; Zheng, Yingying; Huang, Jian-Wen; Chen, Chun-Chi; Chen, Yun; Jin, Jian; Li, Huazhong; Guo, Rey-Ting

2016-06-17

Eukaryotic 1,4-β-endoglucanases (EC 3.2.1.4) have shown great potentials in many commercial applications because they effectively catalyze hydrolysis of cellulose, the main component of the plant cell wall. Here we expressed a glycoside hydrolase family (GH) 5 1,4-β-endoglucanase from Aspergillus niger (AnCel5A) in Pichia pastoris, which exhibits outstanding pH and heat stability. In order to further investigate the molecular mechanism of AnCel5A, apo-form and cellotetraose (CTT) complex enzyme crystal structures were solved to high resolution. AnCel5A folds into a typical (β/α)8-TIM barrel architecture, resembling other GH5 members. In the substrate binding cavity, CTT is found to bind to -4 - -1 subsites, and several polyethylene glycol molecules are found in positive subsites. In addition, several unique N-glycosylation motifs that may contribute to protein higher stability were observed from crystal structures. These results are of great importance for understanding the molecular mechanism of AnCel5A, and also provide guidance for further applications of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

Proteomics in Heart Failure: Top-down or Bottom-up?

PubMed Central

Gregorich, Zachery R.; Chang, Ying-Hua; Ge, Ying

2014-01-01

Summary The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics—each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and the analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research. PMID:24619480

High yield bacterial expression, purification and characterisation of bioactive Human Tousled-like Kinase 1B involved in cancer.

PubMed

Bhoir, Siddhant; Shaik, Althaf; Thiruvenkatam, Vijay; Kirubakaran, Sivapriya

2018-03-19

Human Tousled-like kinases (TLKs) are highly conserved serine/threonine protein kinases responsible for cell proliferation, DNA repair, and genome surveillance. Their possible involvement in cancer via efficient DNA repair mechanisms have made them clinically relevant molecular targets for anticancer therapy. Innovative approaches in chemical biology have played a key role in validating the importance of kinases as molecular targets. However, the detailed understanding of the protein structure and the mechanisms of protein-drug interaction through biochemical and biophysical techniques demands a method for the production of an active protein of exceptional stability and purity on a large scale. We have designed a bacterial expression system to express and purify biologically active, wild-type Human Tousled-like Kinase 1B (hTLK1B) by co-expression with the protein phosphatase from bacteriophage λ. We have obtained remarkably high amounts of the soluble and homogeneously dephosphorylated form of biologically active hTLK1B with our unique, custom-built vector design strategy. The recombinant hTLK1B can be used for the structural studies and may further facilitate the development of new TLK inhibitors for anti-cancer therapy using a structure-based drug design approach.

Unique nonstructural proteins of Pneumonia Virus of Mice (PVM) promote degradation of interferon (IFN) pathway components and IFN-stimulated gene proteins.

PubMed

Dhar, Jayeeta; Barik, Sailen

2016-12-01

Pneumonia Virus of Mice (PVM) is the only virus that shares the Pneumovirus genus of the Paramyxoviridae family with Respiratory Syncytial Virus (RSV). A deadly mouse pathogen, PVM has the potential to serve as a robust animal model of RSV infection, since human RSV does not fully replicate the human pathology in mice. Like RSV, PVM also encodes two nonstructural proteins that have been implicated to suppress the IFN pathway, but surprisingly, they exhibit no sequence similarity with their RSV equivalents. The molecular mechanism of PVM NS function, therefore, remains unknown. Here, we show that recombinant PVM NS proteins degrade the mouse counterparts of the IFN pathway components. Proteasomal degradation appears to be mediated by ubiquitination promoted by PVM NS proteins. Interestingly, NS proteins of PVM lowered the levels of several ISG (IFN-stimulated gene) proteins as well. These results provide a molecular foundation for the mechanisms by which PVM efficiently subverts the IFN response of the murine cell. They also reveal that in spite of their high sequence dissimilarity, the two pneumoviral NS proteins are functionally and mechanistically similar.

The ins and outs of lncRNA structure: How, why and what comes next?

PubMed

Blythe, Amanda J; Fox, Archa H; Bond, Charles S

2016-01-01

The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

Dystrophic Cardiomyopathy: Complex Pathobiological Processes to Generate Clinical Phenotype

PubMed Central

Tsuda, Takeshi; Fitzgerald, Kristi K.

2017-01-01

Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), and X-linked dilated cardiomyopathy (XL-DCM) consist of a unique clinical entity, the dystrophinopathies, which are due to variable mutations in the dystrophin gene. Dilated cardiomyopathy (DCM) is a common complication of dystrophinopathies, but the onset, progression, and severity of heart disease differ among these subgroups. Extensive molecular genetic studies have been conducted to assess genotype-phenotype correlation in DMD, BMD, and XL-DCM to understand the underlying mechanisms of these diseases, but the results are not always conclusive, suggesting the involvement of complex multi-layers of pathological processes that generate the final clinical phenotype. Dystrophin protein is a part of dystrophin-glycoprotein complex (DGC) that is localized in skeletal muscles, myocardium, smooth muscles, and neuronal tissues. Diversity of cardiac phenotype in dystrophinopathies suggests multiple layers of pathogenetic mechanisms in forming dystrophic cardiomyopathy. In this review article, we review the complex molecular interactions involving the pathogenesis of dystrophic cardiomyopathy, including primary gene mutations and loss of structural integrity, secondary cellular responses, and certain epigenetic and other factors that modulate gene expressions. Involvement of epigenetic gene regulation appears to lead to specific cardiac phenotypes in dystrophic hearts. PMID:29367543

Functional Architecture of the Retina: Development and Disease

PubMed Central

Hoon, Mrinalini; Okawa, Haruhisa; Santina, Luca Della; Wong, Rachel O.L.

2014-01-01

Structure and function are highly correlated in the vertebrate retina, a sensory tissue that is organized into cell layers with microcircuits working in parallel and together to encode visual information. All vertebrate retinas share a fundamental plan, comprising five major neuronal cell classes with cell body distributions and connectivity arranged in stereotypic patterns. Conserved features in retinal design have enabled detailed analysis and comparisons of structure, connectivity and function across species. Each species, however, can adopt structural and/or functional retinal specializations, implementing variations to the basic design in order to satisfy unique requirements in visual function. Recent advances in molecular tools, imaging and electrophysiological approaches have greatly facilitated identification of the cellular and molecular mechanisms that establish the fundamental organization of the retina and the specializations of its microcircuits during development. Here, we review advances in our understanding of how these mechanisms act to shape structure and function at the single cell level, to coordinate the assembly of cell populations, and to define their specific circuitry. We also highlight how structure is rearranged and function is disrupted in disease, and discuss current approaches to re-establish the intricate functional architecture of the retina. PMID:24984227

Functional architecture of the retina: development and disease.

PubMed

Hoon, Mrinalini; Okawa, Haruhisa; Della Santina, Luca; Wong, Rachel O L

2014-09-01

Structure and function are highly correlated in the vertebrate retina, a sensory tissue that is organized into cell layers with microcircuits working in parallel and together to encode visual information. All vertebrate retinas share a fundamental plan, comprising five major neuronal cell classes with cell body distributions and connectivity arranged in stereotypic patterns. Conserved features in retinal design have enabled detailed analysis and comparisons of structure, connectivity and function across species. Each species, however, can adopt structural and/or functional retinal specializations, implementing variations to the basic design in order to satisfy unique requirements in visual function. Recent advances in molecular tools, imaging and electrophysiological approaches have greatly facilitated identification of the cellular and molecular mechanisms that establish the fundamental organization of the retina and the specializations of its microcircuits during development. Here, we review advances in our understanding of how these mechanisms act to shape structure and function at the single cell level, to coordinate the assembly of cell populations, and to define their specific circuitry. We also highlight how structure is rearranged and function is disrupted in disease, and discuss current approaches to re-establish the intricate functional architecture of the retina. Copyright © 2014 Elsevier Ltd. All rights reserved.

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.

PubMed

Huh, Yang Hoon; Cohen, Justin; Sherley, James L

2013-10-15

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs "know" the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency.

Arabidopsis thaliana—Myzus persicae interaction: shaping the understanding of plant defense against phloem-feeding aphids

PubMed Central

Louis, Joe; Shah, Jyoti

2013-01-01

The phloem provides a unique niche for several organisms. Aphids are a large group of Hemipteran insects that utilize stylets present in their mouthparts to pierce sieve elements and drink large volumes of phloem sap. In addition, many aphids also vector viral diseases. Myzus persicae, commonly known as the green peach aphid (GPA), is an important pest of a large variety of plants that includes Arabidopsis thaliana. This review summarizes recent studies that have exploited the compatible interaction between Arabidopsis and GPA to understand the molecular and physiological mechanisms utilized by plants to control aphid infestation, as well as genes and mechanisms that contribute to susceptibility. In addition, recent efforts to identify aphid-delivered elicitors of plant defenses and novel aphid salivary components that facilitate infestation are also discussed. PMID:23847627

Expansion of TALE homeobox genes and the evolution of spiralian development.

PubMed

Morino, Yoshiaki; Hashimoto, Naoki; Wada, Hiroshi

2017-12-01

Spiralians, including molluscs, annelids and platyhelminths, share a unique development process that includes the typical geometry of early cleavage and early segregation of cell fate in blastomeres along the animal-vegetal axis. However, the molecular mechanisms underlying this early cell fate segregation are largely unknown. Here, we report spiralian-specific expansion of the three-amino-acid loop extension (TALE) class of homeobox genes. During early development, some of these TALE genes are expressed in staggered domains along the animal-vegetal axis in the limpet Nipponacmea fuscoviridis and the polychaete Spirobranchus kraussii. Inhibition or overexpression of these genes alters the developmental fate of blastomeres, as predicted by the gene expression patterns. These results suggest that the expansion of novel TALE genes plays a critical role in the establishment of a novel cell fate segregation mechanism in spiralians.

Biominerals- hierarchical nanocomposites: the example of bone

PubMed Central

Beniash, Elia

2010-01-01

Many organisms incorporate inorganic solids in their tissues to enhance their functional, primarily mechanical, properties. These mineralized tissues, also called biominerals, are unique organo-mineral nanocomposites, organized at several hierarchical levels, from nano- to macroscale. Unlike man made composite materials, which often are simple physical blends of their components, the organic and inorganic phases in biominerals interface at the molecular level. Although these tissues are made of relatively weak components at ambient conditions, their hierarchical structural organization and intimate interactions between different elements lead to superior mechanical properties. Understanding basic principles of formation, structure and functional properties of these tissues might lead to novel bioinspired strategies for material design and better treatments for diseases of the mineralized tissues. This review focuses on general principles of structural organization, formation and functional properties of biominerals on the example the bone tissues. PMID:20827739

On the molecular basis of the receptor mosaic hypothesis of the engram.

PubMed

Agnati, Luigi F; Ferré, Sergi; Leo, Giuseppina; Lluis, Carme; Canela, Enric I; Franco, Rafael; Fuxe, Kjell

2004-08-01

1. This paper revisits the so-called "receptor mosaic hypothesis" for memory trace formation in the light of recent findings in "functional (or interaction) proteomics." The receptor mosaic hypothesis maintains that receptors may form molecular aggregates at the plasma membrane level representing part of the computational molecular networks. 2. Specific interactions between receptors occur as a consequence of the pattern of transmitter release from the source neurons, which release the chemical code impinging on the receptor mosaics of the target neuron. Thus, the decoding of the chemical message depends on the receptors forming the receptor mosaics and on the type of interactions among receptors and other proteins in the molecular network with novel long-term mosaics formed by their stabilization via adapter proteins formed in target neurons through the incoming neurotransmitter code. The internalized receptor heteromeric complexes or parts of them may act as transcription factors for the formation of such adapter proteins. 3. Receptor mosaics are formed both at the pre- and postsynaptic level of the plasma membranes and this phenomenon can play a role in the Hebbian behavior of some synaptic contacts. The appropriate "matching" of the pre- with the postsynaptic receptor mosaic can be thought of as the "clamping of the synapse to the external teaching signal." According to our hypothesis the behavior of the molecular networks at plasma membrane level to which the receptor mosaics belong can be set in a "frozen" conformation (i.e. in a frozen functional state) and this may represent a mechanism to maintain constant the input to a neuron. 4. Thus, we are suggesting that molecular networks at plasma membrane level may display multiple "attractors" each of which stores the memory of a specific neurotransmitter code due to a unique firing pattern. Hence, this mechanism may play a role in learning processes where the input to a neuron is likely to remain constant for a while.

Blood miRNomes and transcriptomes reveal novel longevity mechanisms in the long-lived bat, Myotis myotis.

PubMed

Huang, Zixia; Jebb, David; Teeling, Emma C

2016-11-10

Chiroptera, the bats, are the only order of mammals capable of true self-powered flight. Bats exhibit a number of other exceptional traits such as echolocation, viral tolerance and, perhaps most puzzlingly, extreme longevity given their body size. Little is known about the molecular mechanisms driving their extended longevity particularly at the levels of gene expression and post-transcriptional regulation. To elucidate the molecular mechanisms that may underlie their unusual longevity, we have deep sequenced 246.5 million small RNA reads from whole blood of the long-lived greater mouse-eared bats, Myotis myotis, and conducted a series of genome-wide comparative analyses between bat and non-bat mammals (human, pig and cow) in both blood miRNomes and transcriptomes, for the first time. We identified 539 miRNA gene candidates from bats, of which 468 unique mature miRNA were obtained. More than half of these miRNA (65.1 %) were regarded as bat-specific, regulating genes involved in the immune, ageing and tumorigenesis pathways. We have also developed a stringent pipeline for genome-wide miRNome comparisons across species, and identified 37 orthologous miRNA groups shared with bat, human, pig and cow, 6 of which were differentially expressed. For bats, 3 out of 4 up-regulated miRNA (miR-101-3p, miR-16-5p, miR-143-3p) likely function as tumor suppressors against various kinds of cancers, while one down-regulated miRNA (miR-221-5p) acts as a tumorigenesis promoter in human breast and pancreatic cancers. Additionally, a genome-wide comparison of mRNA transcriptomes across species also revealed specific gene expression patterns in bats. 127 up-regulated genes were enriched mainly in mitotic cell cycle and DNA repair mechanisms, while 364 down-regulated genes were involved primarily in mitochondrial activity. Our comprehensive and integrative analyses revealed bat-specific and differentially expressed miRNA and mRNA that function in key longevity pathways, producing a distinct bat gene expression pattern. For the first time, we show that bats may possess unique regulatory mechanisms for resisting tumorigenesis, repairing cellular damage and preventing oxidative stresses, all of which likely contribute to the extraordinary lifespan of Myotis myotis.

Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures

PubMed Central

Park, Paul J.; Fuchs, Robert; Wei, Lai; Jorgensen, Brian G.; Redelman, Doug; Ward, Sean M.; Sanders, Kenton M.

2017-01-01

Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC), which serve as slow-wave electrical pacemakers for gastrointestinal (GI) smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome) based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies. PMID:28426719

YopJ Family Effectors Promote Bacterial Infection through a Unique Acetyltransferase Activity

PubMed Central

2016-01-01

SUMMARY Gram-negative bacterial pathogens rely on the type III secretion system to inject virulence proteins into host cells. These type III secreted “effector” proteins directly manipulate cellular processes to cause disease. Although the effector repertoires in different bacterial species are highly variable, the Yersinia outer protein J (YopJ) effector family is unique in that its members are produced by diverse animal and plant pathogens as well as a nonpathogenic microsymbiont. All YopJ family effectors share a conserved catalytic triad that is identical to that of the C55 family of cysteine proteases. However, an accumulating body of evidence demonstrates that many YopJ effectors modify their target proteins in hosts by acetylating specific serine, threonine, and/or lysine residues. This unique acetyltransferase activity allows the YopJ family effectors to affect the function and/or stability of their targets, thereby dampening innate immunity. Here, we summarize the current understanding of this prevalent and evolutionarily conserved type III effector family by describing their enzymatic activities and virulence functions in animals and plants. In particular, the molecular mechanisms by which representative YopJ family effectors subvert host immunity through posttranslational modification of their target proteins are discussed. PMID:27784797

Effect of in vitro enzymatic degradation on 3D printed poly(ε-caprolactone) scaffolds: morphological, chemical and mechanical properties.

PubMed

Ferreira, Joana; Gloria, Antonio; Cometa, Stefania; Coelho, Jorge F J; Domingos, Marco

2017-07-27

In recent years, the tissue engineering (TE) field has significantly benefited from advanced techniques such as additive manufacturing (AM), for the design of customized 3D scaffolds with the aim of guided tissue repair. Among the wide range of materials available to biomanufacture 3D scaffolds, poly(ε-caprolactone) (PCL) clearly arises as the synthetic polymer with the greatest potential, due to its unique properties - namely, biocompatibility, biodegradability, thermal and chemical stability and processability. This study aimed for the first time to investigate the effect of pore geometry on the in vitro enzymatic chain cleavage mechanism of PCL scaffolds manufactured by the AM extrusion process. Methods: Morphological properties of 3D printed PCL scaffolds before and after degradation were evaluated using Scanning Electron Microscopy (SEM) and micro-computed tomography (μ-CT). Differential Scanning Calorimetry (DSC) was employed to determine possible variations in the crystallinity of the scaffolds during the degradation period. The molecular weight was assessed using Size Exclusion Chromatography (SEC) while the mechanical properties were investigated under static compression conditions. Morphological results suggested a uniform reduction of filament diameter, while increasing the scaffolds' porosity. DSC analysis revealed and increment in the crystallinity degree while the molecular weight, evaluated through SEC, remained almost constant during the incubation period (25 days). Mechanical analysis highlighted a decrease in the compressive modulus and maximum stress over time, probably related to the significant weight loss of the scaffolds. All of these results suggest that PCL scaffolds undergo enzymatic degradation through a surface erosion mechanism, which leads to significant variations in mechanical, physical and chemical properties, but which has little influence on pore geometry.

The multifaceted biology of plasmacytoid dendritic cells

PubMed Central

Swiecki, Melissa; Colonna, Marco

2015-01-01

Plasmacytoid dendritic cells (pDCs) are a unique dendritic cell subset that specializes in the production of type I interferons (IFNs). pDCs promote antiviral immune responses and have been implicated in the pathogenesis of autoimmune diseases characterized by a type I IFN signature. However, pDCs can also induce tolerogenic immune responses. Here, we review recent progress from the field of pDC biology, focusing on: the molecular mechanisms that regulate pDC development and functions; the pathways involved in their sensing of pathogens and endogenous nucleic acids; the function of pDCs at mucosal sites; and their roles in infections, autoimmunity and cancer. PMID:26160613

Why Do SGLT2 Inhibitors Inhibit Only 30–50% of Renal Glucose Reabsorption in Humans?

PubMed Central

Liu, Jiwen (Jim); Lee, TaeWeon; DeFronzo, Ralph A.

2012-01-01

Sodium glucose cotransporter 2 (SGLT2) inhibition is a novel and promising treatment for diabetes under late-stage clinical development. It generally is accepted that SGLT2 mediates 90% of renal glucose reabsorption. However, SGLT2 inhibitors in clinical development inhibit only 30–50% of the filtered glucose load. Why are they unable to inhibit 90% of glucose reabsorption in humans? We will try to provide an explanation to this puzzle in this perspective analysis of the unique pharmacokinetic and pharmacodynamic profiles of SGLT2 inhibitors in clinical trials and examine possible mechanisms and molecular properties that may be responsible. PMID:22923645

Why Do SGLT2 inhibitors inhibit only 30-50% of renal glucose reabsorption in humans?

PubMed

Liu, Jiwen Jim; Lee, TaeWeon; DeFronzo, Ralph A

2012-09-01

Sodium glucose cotransporter 2 (SGLT2) inhibition is a novel and promising treatment for diabetes under late-stage clinical development. It generally is accepted that SGLT2 mediates 90% of renal glucose reabsorption. However, SGLT2 inhibitors in clinical development inhibit only 30-50% of the filtered glucose load. Why are they unable to inhibit 90% of glucose reabsorption in humans? We will try to provide an explanation to this puzzle in this perspective analysis of the unique pharmacokinetic and pharmacodynamic profiles of SGLT2 inhibitors in clinical trials and examine possible mechanisms and molecular properties that may be responsible.

Animal models of serotonergic psychedelics.

PubMed

Hanks, James B; González-Maeso, Javier

2013-01-16

The serotonin 5-HT(2A) receptor is the major target of psychedelic drugs such as lysergic acid diethylamide (LSD), mescaline, and psilocybin. Serotonergic psychedelics induce profound effects on cognition, emotion, and sensory processing that often seem uniquely human. This raises questions about the validity of animal models of psychedelic drug action. Nonetheless, recent findings suggest behavioral abnormalities elicited by psychedelics in rodents that predict such effects in humans. Here we review the behavioral effects induced by psychedelic drugs in rodent models, discuss the translational potential of these findings, and define areas where further research is needed to better understand the molecular mechanisms and neuronal circuits underlying their neuropsychological effects.

Animal Models of Serotonergic Psychedelics

PubMed Central

2012-01-01

The serotonin 5-HT2A receptor is the major target of psychedelic drugs such as lysergic acid diethylamide (LSD), mescaline, and psilocybin. Serotonergic psychedelics induce profound effects on cognition, emotion, and sensory processing that often seem uniquely human. This raises questions about the validity of animal models of psychedelic drug action. Nonetheless, recent findings suggest behavioral abnormalities elicited by psychedelics in rodents that predict such effects in humans. Here we review the behavioral effects induced by psychedelic drugs in rodent models, discuss the translational potential of these findings, and define areas where further research is needed to better understand the molecular mechanisms and neuronal circuits underlying their neuropsychological effects. PMID:23336043

SNARE-mediated membrane fusion in autophagy.

PubMed

Wang, Yongyao; Li, Linsen; Hou, Chen; Lai, Ying; Long, Jiangang; Liu, Jiankang; Zhong, Qing; Diao, Jiajie

2016-12-01

Autophagy, a conserved self-eating process for the bulk degradation of cytoplasmic materials, involves double-membrane autophagosomes formed when an isolation membrane emerges and their direct fusion with lysosomes for degradation. For the early biogenesis of autophagosomes and their later degradation in lysosomes, membrane fusion is necessary, although different sets of genes and autophagy-related proteins involved in distinct fusion steps have been reported. To clarify the molecular mechanism of membrane fusion in autophagy, to not only expand current knowledge of autophagy, but also benefit human health, this review discusses key findings that elucidate the unique membrane dynamics of autophagy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Zipper model for the melting of thin films

NASA Astrophysics Data System (ADS)

Abdullah, Mikrajuddin; Khairunnisa, Shafira; Akbar, Fathan

2016-01-01

We propose an alternative model to Lindemann’s criterion for melting that explains the melting of thin films on the basis of a molecular zipper-like mechanism. Using this model, a unique criterion for melting is obtained. We compared the results of the proposed model with experimental data of melting points and heat of fusion for many materials and obtained interesting results. The interesting thing reported here is how complex physics problems can sometimes be modeled with simple objects around us that seemed to have no correlation. This kind of approach is sometimes very important in physics education and should always be taught to undergraduate or graduate students.

The effect of sulfated polysaccharides on the crystallization of calcite superstructures

NASA Astrophysics Data System (ADS)

Fried, Ruth; Mastai, Yitzhak

2012-01-01

Calcite with unique morphology and uniform size has been successfully synthesized in the presence of classes of polysaccharides based on carrageenans. In the crystallization of calcite, the choice of different carrageenans, (iota, lambda and kappa), as additives concedes systematic study of the influence of different chemical structures and particularly molecular charge on the formation of CaCO 3 crystals. The uniform calcite superstructures are formed by assemblies and aggregation of calcite crystals. The mechanism for the formation of calcite superstructures was studied by a variety of techniques, SEM, TEM, XRD, time-resolved conductivity and light scattering measurements, focusing on the early stages of crystals' nucleation and aggregation.

Molecular mechanisms underlying the exceptional adaptations of batoid fins.

PubMed

Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R; Shubin, Neil H

2015-12-29

Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)-Fibroblast growth factor (Fgf)-Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies.

A Novel Approach to Primary Cell Culture for Octopus vulgaris Neurons

PubMed Central

Maselli, Valeria; Xu, Fenglian; Syed, Naweed I.; Polese, Gianluca; Di Cosmo, Anna

2018-01-01

Octopus vulgaris is a unique model system for studying complex behaviors in animals. It has a large and centralized nervous system made up of lobes that are involved in controlling various sophisticated behaviors. As such, it may be considered as a model organism for untangling the neuronal mechanisms underlying behaviors—including learning and memory. However, despite considerable efforts, Octopus lags behind its other counterparts vis-à-vis its utility in deciphering the cellular, molecular and synaptic mechanisms underlying various behaviors. This study represents a novel approach designed to establish a neuronal cell culture protocol that makes this species amenable to further exploitation as a model system. Here we developed a protocol that enables dissociation of neurons from two specific Octopus' brain regions, the vertical-superior frontal system and the optic lobes, which are involved in memory, learning, sensory integration and adult neurogenesis. In particular, cells dissociated with enzyme papain and cultured on Poly-D-Lysine-coated dishes with L15-medium and fetal bovine serum yielded high neuronal survival, axon growth, and re-growth after injury. This model was also explored to define optimal culture conditions and to demonstrate the regenerative capabilities of adult Octopus neurons after axotomy. This study thus further underscores the importance of Octopus neurons as a model system for deciphering fundamental molecular and cellular mechanism of complex brain function and underlying behaviors. PMID:29666582

In vitro three-dimensional cancer metastasis modeling: Past, present, and future

NASA Astrophysics Data System (ADS)

Wei-jing, Han; Wei, Yuan; Jiang-rui, Zhu; Qihui, Fan; Junle, Qu; Li-yu, Liu

2016-01-01

Metastasis is the leading cause of most cancer deaths, as opposed to dysregulated cell growth of the primary tumor. Molecular mechanisms of metastasis have been studied for decades and the findings have evolved our understanding of the progression of malignancy. However, most of the molecular mechanisms fail to address the causes of cancer and its evolutionary origin, demonstrating an inability to find a solution for complete cure of cancer. After being a neglected area of tumor biology for quite some time, recently several studies have focused on the impact of the tumor microenvironment on cancer growth. The importance of the tumor microenvironment is gradually gaining attention, particularly from the perspective of biophysics. In vitro three-dimensional (3-D) metastatic models are an indispensable platform for investigating the tumor microenvironment, as they mimic the in vivo tumor tissue. In 3-D metastatic in vitro models, static factors such as the mechanical properties, biochemical factors, as well as dynamic factors such as cell-cell, cell-ECM interactions, and fluid shear stress can be studied quantitatively. With increasing focus on basic cancer research and drug development, the in vitro 3-D models offer unique advantages in fundamental and clinical biomedical studies. Project supported by the National Basic Research Program of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345), and the Beijing Natural Science Foundation, China (Grant No. 7154221).

Passive mechanical properties of rat abdominal wall muscles suggest an important role of the extracellular connective tissue matrix.

PubMed

Brown, Stephen H M; Carr, John Austin; Ward, Samuel R; Lieber, Richard L

2012-08-01

Abdominal wall muscles have a unique morphology suggesting a complex role in generating and transferring force to the spinal column. Studying passive mechanical properties of these muscles may provide insights into their ability to transfer force among structures. Biopsies from rectus abdominis (RA), external oblique (EO), internal oblique (IO), and transverse abdominis (TrA) were harvested from male Sprague-Dawley rats, and single muscle fibers and fiber bundles (4-8 fibers ensheathed in their connective tissue matrix) were isolated and mechanically stretched in a passive state. Slack sarcomere lengths were measured and elastic moduli were calculated from stress-strain data. Titin molecular mass was also measured from single muscle fibers. No significant differences were found among the four abdominal wall muscles in terms of slack sarcomere length or elastic modulus. Interestingly, across all four muscles, slack sarcomere lengths were quite long in individual muscle fibers (>2.4 µm), and demonstrated a significantly longer slack length in comparison to fiber bundles (p < 0.0001). Also, the extracellular connective tissue matrix provided a stiffening effect and enhanced the resistance to lengthening at long muscle lengths. Titin molecular mass was significantly less in TrA compared to each of the other three muscles (p < 0.0009), but this difference did not correspond to hypothesized differences in stiffness. Copyright © 2012 Orthopaedic Research Society.

Molecular mechanisms underlying the exceptional adaptations of batoid fins

PubMed Central

Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R.; Shubin, Neil H.

2015-01-01

Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)–Fibroblast growth factor (Fgf)–Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies. PMID:26644578

Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga1[OPEN

PubMed Central

Winge, Per; El Assimi, Aimen; Jouhet, Juliette; Vadstein, Olav

2017-01-01

Molecular mechanisms of phosphorus (P) limitation are of great interest for understanding algal production in aquatic ecosystems. Previous studies point to P limitation-induced changes in lipid composition. As, in microalgae, the molecular mechanisms of this specific P stress adaptation remain unresolved, we reveal a detailed phospholipid-recycling scheme in Nannochloropsis oceanica and describe important P acquisition genes based on highly corresponding transcriptome and lipidome data. Initial responses to P limitation showed increased expression of genes involved in P uptake and an expansion of the P substrate spectrum based on purple acid phosphatases. Increase in P trafficking displayed a rearrangement between compartments by supplying P to the chloroplast and carbon to the cytosol for lipid synthesis. We propose a novel phospholipid-recycling scheme for algae that leads to the rapid reduction of phospholipids and synthesis of the P-free lipid classes. P mobilization through membrane lipid degradation is mediated mainly by two glycerophosphoryldiester phosphodiesterases and three patatin-like phospholipases A on the transcriptome level. To compensate for low phospholipids in exponential growth, N. oceanica synthesized sulfoquinovosyldiacylglycerol and diacylglyceroltrimethylhomoserine. In this study, it was shown that an N. oceanica strain has a unique repertoire of genes that facilitate P acquisition and the degradation of phospholipids compared with other stramenopiles. The novel phospholipid-recycling scheme opens new avenues for metabolic engineering of lipid composition in algae. PMID:29051196

Primordial dwarfism: overview of clinical and genetic aspects.

PubMed

Khetarpal, Preeti; Das, Satrupa; Panigrahi, Inusha; Munshi, Anjana

2016-02-01

Primordial dwarfism is a group of genetic disorders which include Seckel Syndrome, Silver-Russell Syndrome, Microcephalic Osteodysplastic Primordial Dwarfism types I/III, II and Meier-Gorlin Syndrome. This genetic disorder group is characterized by intra-uterine growth retardation and post-natal growth abnormalities which occur as a result of disorganized molecular and genomic changes in embryonic stage and, thus, it represents a unique area to study growth and developmental abnormalities. Lot of research has been carried out on different aspects; however, a consolidated review that discusses an overall spectrum of this disorder is not accessible. Recent research in this area points toward important molecular and cellular mechanisms in human body that regulate the complexity of growth process. Studies have emerged that have clearly associated with a number of abnormal chromosomal, genetic and epigenetic alterations that can predispose an embryo to develop PD-associated developmental defects. Finding and associating such fundamental changes to its subtypes will help in re-examination of alleged functions at both cellular and developmental levels and thus reveal the intrinsic mechanism that leads to a balanced growth. Although such findings have unraveled a subtle understanding of growth process, we further require active research in terms of identification of reliable biomarkers for different subtypes as an immediate requirement for clinical utilization. It is hoped that further study will advance the understanding of basic mechanisms regulating growth relevant to human health. Therefore, this review has been written with an aim to present an overview of chromosomal, molecular and epigenetic modifications reported to be associated with different subtypes of this heterogenous disorder. Further, latest findings with respect to clinical and molecular genetics research have been summarized to aid the medical fraternity in their clinical utility, for diagnosing disorders where there are overlapping physical attributes and simultaneously inform about the latest developments in PD biology.

Molecular evolution of the clustered MMIC-3 multigene family of Gossypium species

USDA-ARS?s Scientific Manuscript database

Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 supergene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate supergenes in allopolyploids. Here we report molecular evolutionary rates...

A new mechanism for selective adsorption of rubber on carbon black surface caused by nano-confinement in SBR/NBR solution

NASA Astrophysics Data System (ADS)

Kawazoe, Masayuki

A novel mechanism of selective adsorption of rubber molecules onto carbon black surface in a binary immiscible rubber blend solution has been proposed in this dissertation. The phenomenon leads to uneven distribution of carbon black to the specific polymer in the blend and the obtained electrically conductive composite showed drastic reduction of percolation threshold concentration (PTC). The mechanism and the feature of conductive network formation have much potential concerning both fundamental understanding and industrial application to improve conductive polymer composites. In chapter I, carbon black filled conductive polymer composites are briefly reviewed. Then, in chapter II, a mechanism of rubber molecular confinement into carbon black aggregate structure is introduced to explain the selective adsorption of a specific rubber onto carbon black surface in an immiscible rubber solution blend (styrene butadiene rubber (SBR) and acrylonitrile butadiene rubber (NBR) with toluene or chloroform). Next, in chapters III and IV, polymers with various radius of gyration (Rg) and carbon blacks with various aggregate structure are examined to verify the selective adsorption mechanism. Finally, in chapter V, the novel mechanism was applied to create unique meso-/micro-unit conductive network in carbon black dispersed SBR/NBR composites.

Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating

PubMed Central

Cusick, Kathleen D.; Lin, Baochuan; Malanoski, Anthony P.; Strycharz-Glaven, Sarah M.; Cockrell-Zugell, Allison; Fitzgerald, Lisa A.; Cramer, Jeffrey A.; Barlow, Daniel E.; Boyd, Thomas J.

2016-01-01

ABSTRACT The effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth of Thermus scotoductus SA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response of T. scotoductus SA-01 to dielectric heating during growth. IMPORTANCE The residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating using Thermus scotoductus SA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation. PMID:27520819

The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation.

PubMed

Machado, Luciana E S F; Shen, Tun-Li; Page, Rebecca; Peti, Wolfgang

2017-05-26

The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H 2 O 2 , which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H 2 O 2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

pH-responsive, gluconeogenic renal epithelial LLC-PK1-FBPase+cells: a versatile in vitro model to study renal proximal tubule metabolism and function

PubMed Central

Curthoys, Norman P.

2014-01-01

Ammoniagenesis and gluconeogenesis are prominent metabolic features of the renal proximal convoluted tubule that contribute to maintenance of systemic acid-base homeostasis. Molecular analysis of the mechanisms that mediate the coordinate regulation of the two pathways required development of a cell line that recapitulates these features in vitro. By adapting porcine renal epithelial LLC-PK1 cells to essentially glucose-free medium, a gluconeogenic subline, termed LLC-PK1-FBPase+ cells, was isolated. LLC-PK1-FBPase+ cells grow in the absence of hexoses and pentoses and exhibit enhanced oxidative metabolism and increased levels of phosphate-dependent glutaminase. The cells also express significant levels of the key gluconeogenic enzymes, fructose-1,6-bisphosphatase (FBPase) and phosphoenolpyruvate carboxykinase (PEPCK). Thus the altered phenotype of LLC-PK1-FBPase+ cells is pleiotropic. Most importantly, when transferred to medium that mimics a pronounced metabolic acidosis (9 mM HCO3−, pH 6.9), the LLC-PK1-FBPase+ cells exhibit a gradual increase in NH4+ ion production, accompanied by increases in glutaminase and cytosolic PEPCK mRNA levels and proteins. Therefore, the LLC-PK1-FBPase+ cells retained in culture many of the metabolic pathways and pH-responsive adaptations characteristic of renal proximal tubules. The molecular mechanisms that mediate enhanced expression of the glutaminase and PEPCK in LLC-PK1-FBPase+ cells have been extensively reviewed. The present review describes novel properties of this unique cell line and summarizes the molecular mechanisms that have been defined more recently using LLC-PK1-FBPase+ cells to model the renal proximal tubule. It also identifies future studies that could be performed using these cells. PMID:24808535

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms

PubMed Central

Chavda, Kalyan D.; Chen, Liang; Fouts, Derrick E.; Sutton, Granger; Brinkac, Lauren; Jenkins, Stephen G.; Bonomo, Robert A.

2016-01-01

ABSTRACT Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed blaKPC-2, 40 had blaKPC-3, 2 had blaKPC-4, and 2 had blaNDM-1. Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups—18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes. Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of blaKPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the blaKPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique blaKPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus. PMID:27965456

(Per)chlorate in Biology on Earth and Beyond.

PubMed

Youngblut, Matthew D; Wang, Ouwei; Barnum, Tyler P; Coates, John D

2016-09-08

Respiration of perchlorate and chlorate [collectively, (per)chlorate] was only recognized in the last 20 years, yet substantial advances have been made in our understanding of the underlying metabolisms. Although it was once considered solely anthropogenic, pervasive natural sources, both terrestrial and extraterrestrial, indicate an ancient (per)chlorate presence across our solar system. These discoveries stimulated interest in (per)chlorate microbiology, and the application of advanced approaches highlights exciting new facets. Forward and reverse genetics revealed new information regarding underlying molecular biology and associated regulatory mechanisms. Structural and functional analysis characterized core enzymes and identified novel reaction sequences. Comparative genomics elucidated evolutionary aspects, and stress analysis identified novel response mechanisms to reactive chlorine species. Finally, systems biology identified unique metabolic versatility and novel mechanisms of (per)chlorate respiration, including symbiosis and a hybrid enzymatic-abiotic metabolism. While many published studies focus on (per)chlorate and their basic metabolism, this review highlights seminal advances made over the last decade and identifies new directions and potential novel applications.

Ketamine: 50 Years of Modulating the Mind

PubMed Central

Li, Linda; Vlisides, Phillip E.

2016-01-01

Ketamine was introduced into clinical practice in the 1960s and continues to be both clinically useful and scientifically fascinating. With considerably diverse molecular targets and neurophysiological properties, ketamine’s effects on the central nervous system remain incompletely understood. Investigators have leveraged the unique characteristics of ketamine to explore the invariant, fundamental mechanisms of anesthetic action. Emerging evidence indicates that ketamine-mediated anesthesia may occur via disruption of corticocortical information transfer in a frontal-to-parietal (“top down”) distribution. This proposed mechanism of general anesthesia has since been demonstrated with anesthetics in other pharmacological classes as well. Ketamine remains invaluable to the fields of anesthesiology and critical care medicine, in large part due to its ability to maintain cardiorespiratory stability while providing effective sedation and analgesia. Furthermore, there may be an emerging role for ketamine in treatment of refractory depression and Post-Traumatic Stress Disorder. In this article, we review the history of ketamine, its pharmacology, putative mechanisms of action and current clinical applications. PMID:27965560

Understanding the mechanism of catalytic fast pyrolysis by unveiling reactive intermediates in heterogeneous catalysis

PubMed Central

Hemberger, Patrick; Custodis, Victoria B. F.; Bodi, Andras; Gerber, Thomas; van Bokhoven, Jeroen A.

2017-01-01

Catalytic fast pyrolysis is a promising way to convert lignin into fine chemicals and fuels, but current approaches lack selectivity and yield unsatisfactory conversion. Understanding the pyrolysis reaction mechanism at the molecular level may help to make this sustainable process more economic. Reactive intermediates are responsible for product branching and hold the key to unveiling these mechanisms, but are notoriously difficult to detect isomer-selectively. Here, we investigate the catalytic pyrolysis of guaiacol, a lignin model compound, using photoelectron photoion coincidence spectroscopy with synchrotron radiation, which allows for isomer-selective detection of reactive intermediates. In combination with ambient pressure pyrolysis, we identify fulvenone as the central reactive intermediate, generated by catalytic demethylation to catechol and subsequent dehydration. The fulvenone ketene is responsible for the phenol formation. This technique may open unique opportunities for isomer-resolved probing in catalysis, and holds the potential for achieving a mechanistic understanding of complex, real-life catalytic processes. PMID:28660882

Designing molecular structure to achieve ductile fracture behavior in a stiff and strong 2D polymer, "graphylene".

PubMed

Sandoz-Rosado, E; Beaudet, T D; Balu, R; Wetzel, E D

2016-06-07

As the simplest two-dimensional (2D) polymer, graphene has immensely high intrinsic strength and elastic stiffness but has limited toughness due to brittle fracture. We use atomistic simulations to explore a new class of graphene/polyethylene hybrid 2D polymer, "graphylene", that exhibits ductile fracture mechanisms and has a higher fracture toughness and flaw tolerance than graphene. A specific configuration of this 2D polymer hybrid, denoted "GrE-2" for the two-carbon-long ethylene chains connecting benzene rings in the inherent framework, is prioritized for study. MD simulations of crack propagation show that the energy release rate to propagate a crack in GrE-2 is twice that of graphene. We also demonstrate that GrE-2 exhibits delocalized failure and other energy-dissipating fracture mechanisms such as crack branching and bridging. These results demonstrate that 2D polymers can be uniquely tailored to achieve a balance of fracture toughness with mechanical stiffness and strength.

Why Do Silver Trimers Intercalated in DNA Exhibit Unique Nonlinear Properties That Are Promising for Applications?

PubMed

Bonačić-Koutecký, Vlasta; Perić, Martina; Sanader, Željka

2018-05-17

Our investigation of one-photon absorption (OPA) and nonlinear optical (NLO) properties such as two-photon absorption (TPA) of silver trimer intercalated in DNA based on TDDFT approach allowed us to propose a mechanism responsible for large TPA cross sections of such NLO-phores. We present a concept that illustrates the key role of quantum cluster as well as of nucleotide bases from the immediate neighborhood. For this purpose, different surroundings consisting of guanine-cytosine and adenine-thymine such as (GCGC) and (ATAT) have been investigated that are exhibiting substantially different values of TPA cross sections. This has been confirmed by extending the immediate surroundings as well as using the two-layer quantum mechanics/molecular mechanics (QM/MM) approach. We focus on the cationic closed-shell system and illustrate that the neutral open-shell system shifts OPA spectra into the NIR regime, which is suitable for applications. Thus, in this contribution, we propose novel NLO-phores inducing large TPA cross sections, opening the route for multiphoton imaging.

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stingele, Julian; Bellelli, Roberto; Alte, Ferdinand

Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled bymore » several sophisticated regulatory mechanisms. Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage. Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome.« less

Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN

DOE PAGES

Stingele, Julian; Bellelli, Roberto; Alte, Ferdinand; ...

2016-10-27

Covalent DNA-protein crosslinks (DPCs) are toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription. Little was known about DPC-specific repair mechanisms until the recent identification of a DPC-processing protease in yeast. The existence of a DPC protease in higher eukaryotes is inferred from data in Xenopus laevis egg extracts, but its identity remains elusive. Here we identify the metalloprotease SPRTN as the DPC protease acting in metazoans. Loss of SPRTN results in failure to repair DPCs and hypersensitivity to DPC-inducing agents. SPRTN accomplishes DPC processing through a unique DNA-induced protease activity, which is controlled bymore » several sophisticated regulatory mechanisms. Cellular, biochemical, and structural studies define a DNA switch triggering its protease activity, a ubiquitin switch controlling SPRTN chromatin accessibility, and regulatory autocatalytic cleavage. Our data also provide a molecular explanation on how SPRTN deficiency causes the premature aging and cancer predisposition disorder Ruijs-Aalfs syndrome.« less

Reversible mechanical protection: building a 3D “suit” around a T-shaped benzimidazole axle† †Electronic supplementary information (ESI) available: Synthetic details and full characterisation of all new compounds. CCDC 1533271 and 1533272. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc00790f Click here for additional data file. Click here for additional data file.

PubMed Central

Baggi, Giorgio; Vukotic, V. Nicholas

2017-01-01

The T-shaped benzimidazolium/crown ether recognition motif was used to prepare suit[1]anes. These novel mechanically interlocked molecules (MIMs) were fully characterized by 1H and 13C NMR spectroscopy, single-crystal X-ray diffraction, UV-vis absorption and fluorescence spectroscopy. By conversion to a suit[1]ane, a simple benzimidazole was shown to be protected from deprotonation by strong base. Moreover, it was demonstrated that this unique three-dimensional encapsulation can be made reversible, thus introducing the concept of “reversible mechanical protection”; a protecting methodology that may have potential applications in synthetic organic chemistry and the design of molecular machinery. PMID:28626559

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea

PubMed Central

2013-01-01

Background The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life cycle of many basidiomycete fungi. Understanding the molecular mechanisms underlying this process has long been a goal of research on basidiomycetes. Large scale assessment of the expressed transcriptomes of these developmental stages will facilitate the generation of a more comprehensive picture of the mushroom fruiting process. In this study, we coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. Results We evaluated the expression of >3,000 genes in the two respective growth stages and discovered that almost one-third of these genes were preferentially expressed in either stage. This identified a significant turnover of the transcriptome during the course of fruiting body development. Additionally, we annotated more than 79,000 transcription start sites (TSSs) based on the transcriptomes of the mycelium and stage 1 primoridum stages. Patterns of enrichment based on gene annotations from the GO and KEGG databases indicated that various structural and functional protein families were uniquely employed in either stage and that during primordial growth, cellular metabolism is highly up-regulated. Various signaling pathways such as the cAMP-PKA, MAPK and TOR pathways were also identified as up-regulated, consistent with the model that sensing of nutrient levels and the environment are important in this developmental transition. More than 100 up-regulated genes were also found to be unique to mushroom forming basidiomycetes, highlighting the novelty of fruiting body development in the fungal kingdom. Conclusions We implicated a wealth of new candidate genes important to early stages of mushroom fruiting development, though their precise molecular functions and biological roles are not yet fully known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea. PMID:23514374

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

PubMed Central

Koumakis, Lefteris; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Vassou, Despoina; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-01-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers’ exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes. PMID:27832067

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

NASA Astrophysics Data System (ADS)

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-04-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices.We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00459g

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.

PubMed

Koumakis, Lefteris; Kanterakis, Alexandros; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Tsiknakis, Manolis; Vassou, Despoina; Kafetzopoulos, Dimitris; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-11-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.

Novel Anthra[1,2-c][1,2,5]Thiadiazole-6,11-Diones as Promising Anticancer Lead Compounds: Biological Evaluation, Characterization & Molecular Targets Determination.

PubMed

Ali, Ahmed Atef Ahmed; Lee, Yu-Ru; Chen, Tsung-Chih; Chen, Chun-Liang; Lee, Chia-Chung; Shiau, Chia-Yang; Chiang, Chiao-Hsi; Huang, Hsu-Shan

2016-01-01

The novel compounds NSC745885 and NSC757963 developed at our laboratory were tested against a panel of 60 cancer cell lines at the National Cancer Institute, USA, and a panel of 39 cancer cell lines at the Japanese Foundation of Cancer Research. Both compounds demonstrated selective unique multi-log differential patterns of activity, with GI50 values in the sub-micro molar range against cancer cells rather than normal cardiac cells. NSC757963 showed high selectivity towards the leukemia subpanel. Activities of both compounds strongly correlated to expression of NFKB1 and CSNK2B genes, implying that they may inhibit the NF-κB pathway. Immunocytochemical microscopy of OVCAR-3 cells showed clear cytosolic accumulation of the NF-κB p65 subunit following treatment. Western blotting showed dose dependent inhibition of the nuclear expression of the NF-κB p65 subunit with subsequent accumulation in the cytosol following treatment. Docking experiments showed binding of both compounds to the NF-κB activator IKKβ subunit preventing its translocation to the nucleus. Collectively, these results confirm the ability of our compounds to inhibit the constitutively active NF-κB pathway of OVCAR-3 cells. Furthermore, COMPARE analysis indicated that the activity of NSC757963 is similar to the antituberculosis agent rifamycin SV, this was confirmed by testing the antimycobacterial activity of NSC757963 against Mycobacterium tuberculosis, results revealed potent activity suitable for use in clinical practice. Molecular properties and Lipinski's parameters predicted acceptable bioavailability properties with no indication of mutagenicity, tumorigenicity, irritability and reproductive effects. Oral absorption experiments using the human Caco-2 model showed high intestinal absorption of NSC745885 by passive transport mechanism with no intestinal efflux or active transport mechanisms. The unique molecular characterization as well as the illustrated anticancer spectra of activity and bioavailability properties warrant further development of our compounds and present a foundation brick in the pre-clinical investigations to implement such compounds in clinical practice.

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

PubMed

Cook, Michael A; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-02-06

Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Regional control of Drosophila gut stem cell proliferation: EGF establishes GSSC proliferative set point & controls emergence from quiescence.

PubMed

Strand, Marie; Micchelli, Craig A

2013-01-01

Adult stem cells vary widely in their rates of proliferation. Some stem cells are constitutively active, while others divide only in response to injury. The mechanism controlling this differential proliferative set point is not well understood. The anterior-posterior (A/P) axis of the adult Drosophila midgut has a segmental organization, displaying physiological compartmentalization and region-specific epithelia. These distinct midgut regions are maintained by defined stem cell populations with unique division schedules, providing an excellent experimental model with which to investigate this question. Here, we focus on the quiescent gastric stem cells (GSSCs) of the acidic copper cell region (CCR), which exhibit the greatest period of latency between divisions of all characterized gut stem cells, to define the molecular basis of differential stem cell activity. Our molecular genetic analysis demonstrates that the mitogenic EGF signaling pathway is a limiting factor controlling GSSC proliferation. We find that under baseline conditions, when GSSCs are largely quiescent, the lowest levels of EGF ligands in the midgut are found in the CCR. However, acute epithelial injury by enteric pathogens leads to an increase in EGF ligand expression in the CCR and rapid expansion of the GSSC lineage. Thus, the unique proliferative set points for gut stem cells residing in physiologically distinct compartments are governed by regional control of niche signals along the A/P axis.

COPA mutations impair ER-Golgi transport causing hereditary autoimmune-mediated lung disease and arthritis

PubMed Central

Watkin, Levi B.; Jessen, Birthe; Wiszniewski, Wojciech; Vece, Timothy; Jan, Max; Sha, Youbao; Thamsen, Maike; Santos-Cortez, Regie L. P.; Lee, Kwanghyuk; Gambin, Tomasz; Forbes, Lisa; Law, Christopher S.; Stray-Petersen, Asbjørg; Cheng, Mickie H.; Mace, Emily M.; Anderson, Mark S.; Liu, Dongfang; Tang, Ling Fung; Nicholas, Sarah K.; Nahmod, Karen; Makedonas, George; Canter, Debra; Kwok, Pui-Yan; Hicks, John; Jones, Kirk D.; Penney, Samantha; Jhangiani, Shalini N.; Rosenblum, Michael D.; Dell, Sharon D.; Waterfield, Michael R.; Papa, Feroz R.; Muzny, Donna M.; Zaitlen, Noah; Leal, Suzanne M.; Gonzaga-Jauregui, Claudia; Boerwinkle, Eric; Eissa, N. Tony; Gibbs, Richard A.; Lupski, James R.; Orange, Jordan S.; Shum, Anthony K.

2015-01-01

Advances in genomics have allowed unbiased genetic studies of human disease with unexpected insights into the molecular mechanisms of cellular immunity and autoimmunity1. We performed whole exome sequencing (WES) and targeted sequencing in patients with an apparent Mendelian syndrome of autoimmune disease characterized by high-titer autoantibodies, inflammatory arthritis and interstitial lung disease (ILD). In five families, we identified four unique deleterious variants in the Coatomer subunit alpha (COPA) gene all located within the same functional domain. We hypothesized that mutant COPA leads to a defect in intracellular transport mediated by coat protein complex I (COPI)2–4. We show that COPA variants impair binding of proteins targeted for retrograde Golgi to ER transport and demonstrate that expression of mutant COPA leads to ER stress and the upregulation of Th17 priming cytokines. Consistent with this pattern of cytokine expression, patients demonstrated a significant skewing of CD4+ T cells toward a T helper 17 (Th17) phenotype, an effector T cell population implicated in autoimmunity5,6. Our findings uncover an unexpected molecular link between a vesicular transport protein and a syndrome of autoimmunity manifested by lung and joint disease. These findings provide a unique opportunity to understand how alterations in cellular homeostasis caused by a defect in the intracellular trafficking pathway leads to the generation of human autoimmune disease. PMID:25894502

In vivo molecular and genomic imaging: new challenges for imaging physics.

PubMed

Cherry, Simon R

2004-02-07

The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.

TOPICAL REVIEW: In vivo molecular and genomic imaging: new challenges for imaging physics

NASA Astrophysics Data System (ADS)

Cherry, Simon R.

2004-02-01

The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Computational Evaluation of Mg–Salen Compounds as Subsurface Fluid Tracers: Molecular Dynamics Simulations in Toluene–Water Mixtures and Clay Mineral Nanopores

DOE PAGES

Greathouse, Jeffery A.; Boyle, Timothy J.; Kemp, Richard A.

2018-04-11

Molecular tracers that can be selectively placed underground and uniquely identified at the surface using simple on-site spectroscopic methods would significantly enhance subsurface fluid monitoring capabilities. To ensure their widespread utility, the solubility of these tracers must be easily tuned to oil- or water-wet conditions as well as reducing or eliminating their propensity to adsorb onto subsurface rock and/or mineral phases. In this work, molecular dynamics simulations were used to investigate the relative solubilities and mineral surface adsorption properties of three candidate tracer compounds comprising Mg–salen derivatives of varying degrees of hydrophilic character. Simulations in water–toluene liquid mixtures indicate thatmore » the partitioning of each Mg–salen compound relative to the interface is strongly influenced by the degree of hydrophobicity of the compound. Simulations of these complexes in fluid-filled mineral nanopores containing neutral (kaolinite) and negatively charged (montmorillonite) mineral surfaces reveal that adsorption tendencies depend upon a variety of parameters, including tracer chemical properties, mineral surface type, and solvent type (water or toluene). Simulation snapshots and averaged density profiles reveal insight into the solvation and adsorption mechanisms that control the partitioning of these complexes in mixed liquid phases and nanopore environments. As a result, this work demonstrates the utility of molecular simulation in the design and screening of molecular tracers for use in subsurface applications.« less

Decision Processes During Development of Molecular Biomarkers for Gonadal Phenotypic Sex

EPA Science Inventory

Molecular biomarkers for determination of gonadal phenotypic sex in the Japanese medaka (Oryzias latipes), will serve as a case study. The medaka has unique features that aid in the development of appropriate molecular biomarkers of gonad phenotype, a) genetic sex can be determin...

Amyloidogenesis of Natively Unfolded Proteins

PubMed Central

Uversky, Vladimir N.

2009-01-01

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis. PMID:18537543

Environmental bacteria produce abundant and diverse antibiofilm compounds.

PubMed

Farmer, J T; Shimkevitch, A V; Reilly, P S; Mlynek, K D; Jensen, K S; Callahan, M T; Bushaw-Newton, K L; Kaplan, J B

2014-12-01

The aim of this study was to isolate novel antibiofilm compounds produced by environmental bacteria. Cell-free extracts were prepared from lawns of bacteria cultured on agar. A total of 126 bacteria isolated from soil, cave and river habitats were employed. Extracts were tested for their ability to inhibit Staphylococcus aureus biofilm in a 96-well microtitre plate assay. A total of 55/126 extracts (44%) significantly inhibited Staph. aureus biofilm. Seven extracts were selected for further analysis. The antibiofilm activities in all seven extracts exhibited unique patterns of molecular mass, chemical polarity, heat stability and spectrum of activity against Staph. aureus, Staphylococcus epidermidis and Pseudomonas fluorescens, suggesting that these seven antibiofilm activities were mediated by unique chemical compounds with different mechanisms of action. Environmental bacteria produce abundant and diverse antibiofilm compounds. Screening cell-free extracts is a useful method for identifying secreted compounds that regulate biofilm formation. Such compounds may represent a novel source of antibiofilm agents for technological development. © 2014 The Society for Applied Microbiology.

The caveolin-cavin system plays a conserved and critical role in mechanoprotection of skeletal muscle.

PubMed

Lo, Harriet P; Nixon, Susan J; Hall, Thomas E; Cowling, Belinda S; Ferguson, Charles; Morgan, Garry P; Schieber, Nicole L; Fernandez-Rojo, Manuel A; Bastiani, Michele; Floetenmeyer, Matthias; Martel, Nick; Laporte, Jocelyn; Pilch, Paul F; Parton, Robert G

2015-08-31

Dysfunction of caveolae is involved in human muscle disease, although the underlying molecular mechanisms remain unclear. In this paper, we have functionally characterized mouse and zebrafish models of caveolae-associated muscle disease. Using electron tomography, we quantitatively defined the unique three-dimensional membrane architecture of the mature muscle surface. Caveolae occupied around 50% of the sarcolemmal area predominantly assembled into multilobed rosettes. These rosettes were preferentially disassembled in response to increased membrane tension. Caveola-deficient cavin-1(-/-) muscle fibers showed a striking loss of sarcolemmal organization, aberrant T-tubule structures, and increased sensitivity to membrane tension, which was rescued by muscle-specific Cavin-1 reexpression. In vivo imaging of live zebrafish embryos revealed that loss of muscle-specific Cavin-1 or expression of a dystrophy-associated Caveolin-3 mutant both led to sarcolemmal damage but only in response to vigorous muscle activity. Our findings define a conserved and critical role in mechanoprotection for the unique membrane architecture generated by the caveolin-cavin system. © 2015 Lo et al.

The caveolin–cavin system plays a conserved and critical role in mechanoprotection of skeletal muscle

PubMed Central

Lo, Harriet P.; Nixon, Susan J.; Hall, Thomas E.; Cowling, Belinda S.; Ferguson, Charles; Morgan, Garry P.; Schieber, Nicole L.; Fernandez-Rojo, Manuel A.; Bastiani, Michele; Floetenmeyer, Matthias; Martel, Nick; Laporte, Jocelyn; Pilch, Paul F.

2015-01-01

Dysfunction of caveolae is involved in human muscle disease, although the underlying molecular mechanisms remain unclear. In this paper, we have functionally characterized mouse and zebrafish models of caveolae-associated muscle disease. Using electron tomography, we quantitatively defined the unique three-dimensional membrane architecture of the mature muscle surface. Caveolae occupied around 50% of the sarcolemmal area predominantly assembled into multilobed rosettes. These rosettes were preferentially disassembled in response to increased membrane tension. Caveola-deficient cavin-1−/− muscle fibers showed a striking loss of sarcolemmal organization, aberrant T-tubule structures, and increased sensitivity to membrane tension, which was rescued by muscle-specific Cavin-1 reexpression. In vivo imaging of live zebrafish embryos revealed that loss of muscle-specific Cavin-1 or expression of a dystrophy-associated Caveolin-3 mutant both led to sarcolemmal damage but only in response to vigorous muscle activity. Our findings define a conserved and critical role in mechanoprotection for the unique membrane architecture generated by the caveolin–cavin system. PMID:26323694

Identification of a unique Ca2+-binding site in rat acid-sensing ion channel 3.

PubMed

Zuo, Zhicheng; Smith, Rachel N; Chen, Zhenglan; Agharkar, Amruta S; Snell, Heather D; Huang, Renqi; Liu, Jin; Gonzales, Eric B

2018-05-25

Acid-sensing ion channels (ASICs) evolved to sense changes in extracellular acidity with the divalent cation calcium (Ca 2+ ) as an allosteric modulator and channel blocker. The channel-blocking activity is most apparent in ASIC3, as removing Ca 2+ results in channel opening, with the site's location remaining unresolved. Here we show that a ring of rat ASIC3 (rASIC3) glutamates (Glu435), located above the channel gate, modulates proton sensitivity and contributes to the formation of the elusive Ca 2+ block site. Mutation of this residue to glycine, the equivalent residue in chicken ASIC1, diminished the rASIC3 Ca 2+ block effect. Atomistic molecular dynamic simulations corroborate the involvement of this acidic residue in forming a high-affinity Ca 2+ site atop the channel pore. Furthermore, the reported observations provide clarity for past controversies regarding ASIC channel gating. Our findings enhance understanding of ASIC gating mechanisms and provide structural and energetic insights into this unique calcium-binding site.

Unique low-molecular-weight lignin with high purity extracted from wood by deep eutectic solvents (DES): a source of lignin for valorization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alvarez-Vasco, Carlos; Ma, Ruoshui; Quintero, Melissa

This paper reports a new method of applying Deep Eutectic Solvents (DES) for extracting lignin from woody biomass with high yield and high purity. DES mixtures prepared from Choline Chloride (ChCl) and four hydrogen-bond donors–acetic acid, lactic acid, levulinic acid and glycerol–were evaluated for treatment of hardwood (poplar) and softwood (D. fir). It was found that these DES treatments can selectively extract a significant amount of lignin from wood with high yields: 78% from poplar and 58% from D. fir. The extracted lignin has high purity (95%) with unique structural properties. We discover that DES can selectively cleave ether linkagesmore » in wood lignin and facilitate lignin removal from wood. The mechanism of DES cleavage of ether bonds between phenylpropane units was investigated. The results from this study demonstrate that DES is a promising solvent for wood delignification and the production of a new source of lignin with promising potential applications.« less

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao, Xiao; Yang, Hanjing; Arutiunian, Vagan

The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species aftermore » RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.« less

Bioinformatics Analysis Reveals Distinct Molecular Characteristics of Hepatitis B-Related Hepatocellular Carcinomas from Very Early to Advanced Barcelona Clinic Liver Cancer Stages.

PubMed

Kong, Fan-Yun; Wei, Xiao; Zhou, Kai; Hu, Wei; Kou, Yan-Bo; You, Hong-Juan; Liu, Xiao-Mei; Zheng, Kui-Yang; Tang, Ren-Xian

2016-01-01

Hepatocellular carcinoma (HCC)is the fifth most common malignancy associated with high mortality. One of the risk factors for HCC is chronic hepatitis B virus (HBV) infection. The treatment strategy for the disease is dependent on the stage of HCC, and the Barcelona clinic liver cancer (BCLC) staging system is used in most HCC cases. However, the molecular characteristics of HBV-related HCC in different BCLC stages are still unknown. Using GSE14520 microarray data from HBV-related HCC cases with BCLC stages from 0 (very early stage) to C (advanced stage) in the gene expression omnibus (GEO) database, differentially expressed genes (DEGs), including common DEGs and unique DEGs in different BCLC stages, were identified. These DEGs were located on different chromosomes. The molecular functions and biology pathways of DEGs were identified by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and the interactome networks of DEGs were constructed using the NetVenn online tool. The results revealed that both common DEGs and stage-specific DEGs were associated with various molecular functions and were involved in special biological pathways. In addition, several hub genes were found in the interactome networks of DEGs. The identified DEGs and hub genes promote our understanding of the molecular mechanisms underlying the development of HBV-related HCC through the different BCLC stages, and might be used as staging biomarkers or molecular targets for the treatment of HCC with HBV infection.

Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets

PubMed Central

Bourne, Christina R.; Wakeham, Nancy; Bunce, Richard A.; Berlin, K. Darrell; Barrow, William W.

2013-01-01

Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major set-back. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an anti-folate. The second and third compounds’ MOA were not clearly identified, likely due to unique MOA not represented within the commercial database. The availability of the database generated in this report for S. aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but distinction of unique or broadly acting MOA at this time is less clear. PMID:22434711

Structure-property-glass transition relationships in non-isocyanate polyurethanes investigated by dynamic nanoindentation

NASA Astrophysics Data System (ADS)

Weyand, Stephan; Blattmann, Hannes; Schimpf, Vitalij; Mülhaupt, Rolf; Schwaiger, Ruth

2016-07-01

Newly developed green-chemistry approaches towards the synthesis of non-isocyanate polyurethane (NIPU) systems represent a promising alternative to polyurethanes (PU) eliminating the need for harmful ingredients. A series of NIPU systems were studied using different nanoindentation techniques in order to understand the influence of molecular parameters on the mechanical behavior. Nanoindentation revealed a unique characteristic feature of those materials, i.e. stiffening with increasing deformation. It is argued that the origin of this observed stiffening is a consequence of the thermodynamic state of the polymer network, the molecular characteristics of the chemical building blocks and resulting anisotropic elastic response of the network structure. Flat-punch nanoindentation was applied in order to characterize the constitutive viscoelastic nature of the materials. The complex modulus shows distinct changes as a function of the NIPU network topology illustrating the influence of the chemical building blocks. The reproducibility of the data indicates that the materials are homogeneous over the volumes sampled by nanoindentation. Our study demonstrates that nanoindentation is very well-suited to investigate the molecular characteristics of NIPU materials that cannot be quantified in conventional experiments. Moreover, the technique provides insight into the functional significance of complex molecular architectures thereby supporting the development of NIPU materials with tailored properties.

Using Solid-state NMR to Monitor the Molecular Consequences of Cryptococcus neoformans Melanization with Different Catecholamine Precursors

PubMed Central

Chatterjee, Subhasish; Prados-Rosales, Rafael; Frases, Susana; Itin, Boris; Casadevall, Arturo; Stark, Ruth E.

2012-01-01

Melanins are a class of natural pigments associated with a wide range of biological functions, including microbial virulence, energy transduction, and protection against solar radiation. Because of their insolubility and structural heterogeneity, solid-state nuclear magnetic resonance (NMR) spectroscopy provides an unprecedented means to define the molecular architecture of these enigmatic pigments. The requirement of obligatory catecholamines for melanization of the pathogenic fungus Cryptococcus neoformans also offers unique opportunities for investigating melanin development. In the current study, pigments produced with L-dopa, methyl-L-dopa, epinephrine, and norepinephrine precursors are compared structurally using 13C and 1H magic-angle spinning (MAS) NMR. Striking structural differences were observed for both aromatic and aliphatic molecular constituents of the mature fungal pigment assemblies, thus making it possible to redefine the molecular prerequisites for formation of the aromatic domains of insoluble indole-based biopolymers, to rationalize their distinctive physical characteristics, and to delineate the role of cellular constituents in assembly of the melanized macromolecules with polysaccharides and fatty acyl chain-containing moieties. By achieving an augmented understanding of the mechanisms of C. neoformans melanin biosynthesis and cellular assembly, such studies can guide future drug discovery efforts related to melanin-associated virulence, resistance to tumor therapy, and production of melanin mimetics under cell-free conditions. PMID:22765382

A novel multi-tiered experimental approach unfolding the mechanisms behind cyclodextrin-vitamin inclusion complexes for enhanced vitamin solubility and stability.

PubMed

Braithwaite, Miles C; Kumar, Pradeep; Choonara, Yahya E; du Toit, Lisa C; Tomar, Lomas K; Tyagi, Charu; Pillay, Viness

2017-10-30

This study was conducted to provide a mechanistic account for understanding the synthesis, characterization and solubility phenomena of vitamin complexes with cyclodextrins (CD) for enhanced solubility and stability employing experimental and in silico molecular modeling strategies. New geometric, molecular and energetic analyses were pursued to explicate experimentally derived cholecalciferol complexes. Various CD molecules (α-, β-, γ-, and hydroxypropyl β-) were complexed with three vitamins: cholecalciferol, ascorbic acid and α-tocopherol. The Inclusion Efficiency (IE%) was computed for each CD-vitamin complex. The highest IE% achieved for a cholecalciferol complex was for 'βCDD 3 -8', after utilizing a unique CD:cholecalciferol molar synthesis ratio of 2.5:1, never before reported as successful. 2HPβCD-cholecalciferol, γCD-cholecalciferol and α-tocopherol inclusion complexes (IC's) reached maximal IE% with a CD:vitamin molar ratio of 5:1. The results demonstrate that IE%, thermal stability, concentration, carrier solubility, molecular mechanics and intended release profile are key factors to consider when synthesizing vitamin-CD complexes. Phase-solubility data provided insights into the design of formulations with IC's that may provide analogous oral vitamin release profiles even when hydrophobic and hydrophilic vitamins are co-incorporated. Static lattice atomistic simulations were able to validate experimentally derived cholecalciferol IE phenomena and are invaluable parameters when approaching formulation strategies using CD's for improved solubility and efficacy of vitamins. Copyright © 2017 Elsevier B.V. All rights reserved.

CAMD studies of coal structure and coal liquefaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faulon, J.L.; Carlson, G.A.

The macromolecular structure of coal is essential to understand the mechanisms occurring during coal liquefaction. Many attempts to model coal structure can be found in the literature. More specifically for high volatile bituminous coal, the subject of interest the most commonly quoted models are the models of Given, Wiser, Solomon, and Shinn. In past work, the authors`s have used computer-aided molecular design (CAMD) to develop three-dimensional representations for the above coal models. The three-dimensional structures were energy minimized using molecular mechanics and molecular dynamics. True density and micopore volume were evaluated for each model. With the exception of Given`s model,more » the computed density values were found to be in agreement with the corresponding experimental results. The above coal models were constructed by a trial and error technique consisting of a manual fitting of the-analytical data. It is obvious that for each model the amount of data is small compared to the actual complexity of coal, and for all of the models more than one structure can be built. Hence, the process by which one structure is chosen instead of another is not clear. In fact, all the authors agree that the structure they derived was only intended to represent an {open_quotes}average{close_quotes} coal model rather than a unique correct structure. The purpose of this program is further develop CAMD techniques to increase the understanding of coal structure and its relationship to coal liquefaction.« less

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism

PubMed Central

Shah, Faheem Afzal; Wang, Qiaojian; Wang, Zhaocheng; Wu, Lifang

2018-01-01

Pecan is an economically important nut crop tree due to its unique texture and flavor properties. The pecan seed is rich of unsaturated fatty acid and protein. However, little is known about the molecular mechanisms of the biosynthesis of fatty acids in the developing seeds. In this study, transcriptome sequencing of the developing seeds was performed using Illumina sequencing technology. Pecan seed embryos at different developmental stages were collected and sequenced. The transcriptomes of pecan seeds at two key developing stages (PA, the initial stage and PS, the fast oil accumulation stage) were also compared. A total of 82,155 unigenes, with an average length of 1,198 bp from seven independent libraries were generated. After functional annotations, we detected approximately 55,854 CDS, among which, 2,807 were Transcription Factor (TF) coding unigenes. Further, there were 13,325 unigenes that showed a 2-fold or greater expression difference between the two groups of libraries (two developmental stages). After transcriptome analysis, we identified abundant unigenes that could be involved in fatty acid biosynthesis, degradation and some other aspects of seed development in pecan. This study presents a comprehensive dataset of transcriptomic changes during the seed development of pecan. It provides insights in understanding the molecular mechanisms responsible for fatty acid biosynthesis in the seed development. The identification of functional genes will also be useful for the molecular breeding work of pecan. PMID:29694395

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism.

PubMed

Xu, Zheng; Ni, Jun; Shah, Faheem Afzal; Wang, Qiaojian; Wang, Zhaocheng; Wu, Lifang; Fu, Songling

2018-01-01

Pecan is an economically important nut crop tree due to its unique texture and flavor properties. The pecan seed is rich of unsaturated fatty acid and protein. However, little is known about the molecular mechanisms of the biosynthesis of fatty acids in the developing seeds. In this study, transcriptome sequencing of the developing seeds was performed using Illumina sequencing technology. Pecan seed embryos at different developmental stages were collected and sequenced. The transcriptomes of pecan seeds at two key developing stages (PA, the initial stage and PS, the fast oil accumulation stage) were also compared. A total of 82,155 unigenes, with an average length of 1,198 bp from seven independent libraries were generated. After functional annotations, we detected approximately 55,854 CDS, among which, 2,807 were Transcription Factor (TF) coding unigenes. Further, there were 13,325 unigenes that showed a 2-fold or greater expression difference between the two groups of libraries (two developmental stages). After transcriptome analysis, we identified abundant unigenes that could be involved in fatty acid biosynthesis, degradation and some other aspects of seed development in pecan. This study presents a comprehensive dataset of transcriptomic changes during the seed development of pecan. It provides insights in understanding the molecular mechanisms responsible for fatty acid biosynthesis in the seed development. The identification of functional genes will also be useful for the molecular breeding work of pecan.

Molecular Mechanisms That Underlie the Dynamic Adaptation of Innate Monocyte Memory to Varying Stimulant Strength of TLR Ligands.

PubMed

Yuan, Ruoxi; Geng, Shuo; Li, Liwu

2016-01-01

In adaptation to rising stimulant strength, innate monocytes can be dynamically programed to preferentially express either pro- or anti-inflammatory mediators. Such dynamic innate adaptation or programing may bear profound relevance in host health and disease. However, molecular mechanisms that govern innate adaptation to varying strength of stimulants are not well understood. Using lipopolysaccharide (LPS), the model stimulant of toll-like-receptor 4 (TLR4), we reported that the expressions of pro-inflammatory mediators are preferentially sustained in monocytes adapted by lower doses of LPS, and suppressed/tolerized in monocytes adapted by higher doses of LPS. Mechanistically, monocytes adapted by super-low dose LPS exhibited higher levels of transcription factor, interferon regulatory factor 5 (IRF5), and reduced levels of transcriptional modulator B lymphocyte-induced maturation protein-1 (Blimp-1). Intriguingly, the inflammatory monocyte adaptation by super-low dose LPS is dependent upon TRAM/TRIF but not MyD88. Similar to LPS, we also observed biphasic inflammatory adaptation and tolerance in monocytes challenged with varying dosages of TLR7 agonist. In sharp contrast, rising doses of TLR3 agonist preferentially caused inflammatory adaptation without inducing tolerance. At the molecular level, the differential regulation of IRF5 and Blimp-1 coincides with unique monocyte adaptation dynamics by TLR4/7 and TLR3 agonists. Our study provides novel clue toward the understanding of monocyte adaptation and memory toward distinct TLR ligands.

Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime.

PubMed

Hung, Ivan; Wu, Gang; Gan, Zhehong

NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17 O NMR of solid NaNO 3 in which the NO 3 - ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO 3 acquired in the temperature range of 173-413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO 3 - ion jumps span eight orders of magnitude (10 2 -10 10 s -1 ) covering both transitions of the dynamic 17 O line shape. Copyright © 2016 Elsevier Inc. All rights reserved.

Magnetic-graphitic-nanocapsule templated diacetylene assembly and photopolymerization for sensing and multicoded anti-counterfeiting

NASA Astrophysics Data System (ADS)

Nie, Xiang-Kun; Xu, Yi-Ting; Song, Zhi-Ling; Ding, Ding; Gao, Feng; Liang, Hao; Chen, Long; Bian, Xia; Chen, Zhuo; Tan, Weihong

2014-10-01

Molecular self-assembly, a process to design molecular entities to aggregate into desired structures, represents a promising bottom-up route towards precise construction of functional systems. Here we report a multifunctional, self-assembled system based on magnetic-graphitic-nanocapsule (MGN) templated diacetylene assembly and photopolymerization. The as-prepared assembly system maintains the unique color and fluorescence change properties of the polydiacetylene (PDA) polymers, while also pursues the superior Raman, NIR, magnetic and superconducting properties from the MGN template. Based on both fluorescence and magnetic resonance imaging (MRI) T2 relaxivity, the MGN@PDA system could efficiently monitor the pH variations which could be used as a pH sensor. The MGN@PDA system further demonstrates potential as unique ink for anti-counterfeiting applications. Reversible color change, strong and unique Raman scattering and fluorescence emission, sensitive NIR thermal response, and distinctive magnetic properties afford this assembly system with multicoded anti-counterfeiting capabilities.Molecular self-assembly, a process to design molecular entities to aggregate into desired structures, represents a promising bottom-up route towards precise construction of functional systems. Here we report a multifunctional, self-assembled system based on magnetic-graphitic-nanocapsule (MGN) templated diacetylene assembly and photopolymerization. The as-prepared assembly system maintains the unique color and fluorescence change properties of the polydiacetylene (PDA) polymers, while also pursues the superior Raman, NIR, magnetic and superconducting properties from the MGN template. Based on both fluorescence and magnetic resonance imaging (MRI) T2 relaxivity, the MGN@PDA system could efficiently monitor the pH variations which could be used as a pH sensor. The MGN@PDA system further demonstrates potential as unique ink for anti-counterfeiting applications. Reversible color change, strong and unique Raman scattering and fluorescence emission, sensitive NIR thermal response, and distinctive magnetic properties afford this assembly system with multicoded anti-counterfeiting capabilities. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03837a

Salt-Stress Response Mechanisms Using de Novo Transcriptome Sequencing of Salt-Tolerant and Sensitive Corchorus spp. Genotypes

PubMed Central

Yang, Zemao; Lu, Ruike; Dai, Zhigang; Yan, An; Tang, Qing; Cheng, Chaohua; Xu, Ying; Yang, Wenting; Su, Jianguang

2017-01-01

High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes in leaf and root tissues under salt stress and control conditions. In total, 68,961 unigenes were identified. Additionally, 11,100 unigenes (including 385 transcription factors (TFs)) exhibited significant differential expression in salt-tolerant or salt-sensitive genotypes. Numerous common and unique differentially expressed unigenes (DEGs) between the two genotypes were discovered. Fewer DEGs were observed in salt-tolerant jute genotypes whether in root or leaf tissues. These DEGs were involved in various pathways, such as ABA signaling, amino acid metabolism, etc. Among the enriched pathways, plant hormone signal transduction (ko04075) and cysteine/methionine metabolism (ko00270) were the most notable. Eight common DEGs across both tissues and genotypes with similar expression profiles were part of the PYL-ABA-PP2C (pyrabactin resistant-like/regulatory components of ABA receptors-abscisic acid-protein phosphatase 2C). The methionine metabolism pathway was only enriched in salt-tolerant jute root tissue. Twenty-three DEGs were involved in methionine metabolism. Overall, numerous common and unique salt-stress response DEGs and pathways between salt-tolerant and salt-sensitive jute have been discovered, which will provide valuable information regarding salt-stress response mechanisms and help improve salt-resistance molecular breeding in jute. PMID:28927022

Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

USDA-ARS?s Scientific Manuscript database

Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of t...

Molecular time-course and the metabolic basis of entry into dauer in Caenorhabditis elegans.

PubMed

Jeong, Pan-Young; Kwon, Min-Seok; Joo, Hyoe-Jin; Paik, Young-Ki

2009-01-01

When Caenorhabditis elegans senses dauer pheromone (daumone), signaling inadequate growth conditions, it enters the dauer state, which is capable of long-term survival. However, the molecular pathway of dauer entry in C. elegans has remained elusive. To systematically monitor changes in gene expression in dauer paths, we used a DNA microarray containing 22,625 gene probes corresponding to 22,150 unique genes from C. elegans. We employed two different paths: direct exposure to daumone (Path 1) and normal growth media plus liquid culture (Path 2). Our data reveal that entry into dauer is accomplished through the multi-step process, which appears to be compartmentalized in time and according to metabolic flux. That is, a time-course of dauer entry in Path 1 shows that dauer larvae formation begins at post-embryonic stage S4 (48 h) and is complete at S6 (72 h). Our results also suggest the presence of a unique adaptive metabolic control mechanism that requires both stage-specific expression of specific genes and tight regulation of different modes of fuel metabolite utilization to sustain the energy balance in the context of prolonged survival under adverse growth conditions. It is apparent that worms entering dauer stage may rely heavily on carbohydrate-based energy reserves, whereas dauer larvae utilize fat or glyoxylate cycle-based energy sources. We created a comprehensive web-based dauer metabolic database for C. elegans (www.DauerDB.org) that makes it possible to search any gene and compare its relative expression at a specific stage, or evaluate overall patterns of gene expression in both paths. This database can be accessed by the research community and could be widely applicable to other related nematodes as a molecular atlas.

Comparative 2D-DIGE analysis of salinity responsive microsomal proteins from leaves of salt-sensitive Arabidopsis thaliana and salt-tolerant Thellungiella salsuginea.

PubMed

Vera-Estrella, Rosario; Barkla, Bronwyn J; Pantoja, Omar

2014-12-05

Halophytes have evolved unique molecular strategies to overcome high soil salinity but we still know very little about the main mechanisms that these plants use to complete their lifecycle under salinity stress. One useful approach to further our understanding in this area is to directly compare the response to salinity of two closely related species which show diverse levels of salt tolerance. Here we present a comparative proteomic study using DIGE of leaf microsomal proteins to identify salt-responsive membrane associated proteins in Arabidopsis thaliana (a glycophyte) and Thellungiella salsuginea (a halophyte). While a small number of distinct protein abundance changes were observed upon salt stress in both species, the most notable differences were observed between species and specifically, in untreated plants with a total of 36 proteins displaying significant abundance changes. Gene ontology (GO) term enrichment analysis showed that the majority of these proteins were distributed into two functional categories; transport (31%) and carbohydrate metabolism (17%). Results identify several novel salt responsive proteins in this system and support the theory that T. salsuginea shows a high degree of salt-tolerance because molecular mechanisms are primed to deal with the stress. This intrinsic ability to anticipate salinity stress distinguishes it from the glycophyte A. thaliana. There is significant interest in understanding the molecular mechanisms that plants use to tolerate salinity as soil salinization is becoming an increasing concern for agriculture with high soil Na(+) levels leading to reduced yields and economic loss. Much of our knowledge on the molecular mechanisms employed by plants to combat salinity stress has come from work on salt-sensitive plants, but studies on naturally occurring highly salt-resistant plants, halophytes, and direct comparisons between closely related glycophytes and halophytes, could help to further our understanding of salinity tolerance mechanisms. In this study, employing two closely related species which differ markedly in their salt-tolerance, we carried out a quantitative proteomic approach using 2D-DIGE to identify salt-responsive proteins and compare and contrast the differences between the two plant species. Our work complements a previous study using iTRAQ technology (34) and highlights the benefits of using alternative technologies and approaches to gain a broader representation of the salt-responsive proteome in these species. Copyright © 2014 Elsevier B.V. All rights reserved.

Dolastatin 15, a mollusk linear peptide, and Celecoxib, a selective cyclooxygenase-2 inhibitor, prevent preneoplastic colonic lesions and induce apoptosis through inhibition of the regulatory transcription factor NF-κB and an inflammatory protein, iNOS.

PubMed

Piplani, Honit; Vaish, Vivek; Sanyal, Sankar Nath

2012-11-01

The marine ecosystem is a unique and enormously rich source of natural products with potential chemopreventive applications in cancer. In the present study, we explored the chemopreventive role and the molecular mechanism of Dolastatin, a linear peptide from an Indian Ocean mollusk, and Celecoxib, a well-established cyclooxygenase-2 (COX-2) inhibitor in an individual as well as in a combination regimen in 1,2-dimethylhydrazine dihydrochloride (DMH)-induced colon carcinogenesis in a rat model. After a 6-week treatment with DMH, morphological analysis revealed a marked occurrence of preneoplastic features in the colonic mucosa, whereas histologically well-characterized dysplasia and hyperplasia were observed in DMH-treated animals. Simultaneous administration of Celecoxib and Dolastatin reduced these features significantly. DMH treatment affected the number of apoptotic cells in colonic enterocytes, which reverted to the normal level with the use of Celecoxib and Dolastatin. Inflammation remains the dominant molecular mechanism in the development of multiple plaque lesions, the carcinogenic lesions in a DMH-induced process that may be mediated by COX-2. Western blot and immunofluorescence analysis revealed a higher expression of COX-2 and nuclear factor-κB, the transcription factors responsible for proinflammatory proteins such as TNFα, and also the inducible nitric oxide synthase in the DMH group, which was further recovered significantly with the use of Celecoxib and Dolastatin. In-silico molecular docking analysis of Dolastatin as a ligand with various regulatory proteins suggests that although the peptide failed to dock to COX-2, it successfully did so with inducible nitric oxide synthase, thereby indicating the potential of this inflammatory protein as a molecular anticancer target in colon carcinogenesis.

Unique aspects of the structure and dynamics of elementary Iβ cellulose microfibrils revealed by computational simulations.

PubMed

Oehme, Daniel P; Downton, Matthew T; Doblin, Monika S; Wagner, John; Gidley, Michael J; Bacic, Antony

2015-05-01

The question of how many chains an elementary cellulose microfibril contains is critical to understanding the molecular mechanism(s) of cellulose biosynthesis and regulation. Given the hexagonal nature of the cellulose synthase rosette, it is assumed that the number of chains must be a multiple of six. We present molecular dynamics simulations on three different models of Iβ cellulose microfibrils, 18, 24, and 36 chains, to investigate their structure and dynamics in a hydrated environment. The 36-chain model stays in a conformational space that is very similar to the initial crystalline phase, while the 18- and 24-chain models sample a conformational space different from the crystalline structure yet similar to conformations observed in recent high-temperature molecular dynamics simulations. Major differences in the conformations sampled between the different models result from changes to the tilt of chains in different layers, specifically a second stage of tilt, increased rotation about the O2-C2 dihedral, and a greater sampling of non-TG exocyclic conformations, particularly the GG conformation in center layers and GT conformation in solvent-exposed exocyclic groups. With a reinterpretation of nuclear magnetic resonance data, specifically for contributions made to the C6 peak, data from the simulations suggest that the 18- and 24-chain structures are more viable models for an elementary cellulose microfibril, which also correlates with recent scattering and diffraction experimental data. These data inform biochemical and molecular studies that must explain how a six-particle cellulose synthase complex rosette synthesizes microfibrils likely comprised of either 18 or 24 chains. © 2015 American Society of Plant Biologists. All Rights Reserved.

Viscoelastic properties of model segments of collagen molecules.

PubMed

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

2012-03-01

Collagen is the prime construction material in vertebrate biology, determining the mechanical behavior of connective tissues such as tendon, bone and skin. Despite extensive efforts in the investigation of the origin of collagen unique mechanical properties, a deep understanding of the relationship between molecular structure and mechanical properties remains elusive, hindered by the complex hierarchical structure of collagen-based tissues. In particular, although extensive studies of viscoelastic properties have been pursued at the macroscopic (fiber/tissue) level, fewer investigations have been performed at the smaller scales, including in particular collagen molecules and fibrils. These scales are, however, important for a complete understanding of the role of collagen as an important constituent in the extracellular matrix. Here, using an atomistic modeling approach, we perform in silico creep tests of a collagen-like peptide, monitoring the strain-time response for different values of applied external load. The results show that individual collagen molecules exhibit a nonlinear viscoelastic behavior, with a Young's modulus increasing from 6 to 16GPa (for strains up to 20%), a viscosity of 3.84.±0.38Pa·s, and a relaxation time in the range of 0.24-0.64ns. The single molecule viscosity, for the first time reported here, is several orders of magnitude lower than the viscosity found for larger-scale single collagen fibrils, suggesting that the viscous behavior of collagen fibrils and fibers involves additional mechanisms, such as molecular sliding between collagen molecules within the fibril or the effect of relaxation of larger volumes of solvent. Based on our molecular modeling results we propose a simple structural model that describes collagen tissue as a hierarchical structure, providing a bottom-up description of elastic and viscous properties form the properties of the tissue basic building blocks. Copyright © 2011 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Molecular Innovation in Ciliates with Complex Genome Rearrangements

NASA Astrophysics Data System (ADS)

Neme, R.; Landweber, L. F.

2017-07-01

We study molecular innovation in several ciliate species with unique massive genome rearrangements to understand how a radically distinct genome architecture can shape the process of acquiring new functions, genes and structures.

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

PubMed

Bae, Brian; Chen, James; Davis, Elizabeth; Leon, Katherine; Darst, Seth A; Campbell, Elizabeth A

2015-09-08

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

Mating and male pheromone kill Caenorhabditis males through distinct mechanisms.

PubMed

Shi, Cheng; Runnels, Alexi M; Murphy, Coleen T

2017-03-14

Differences in longevity between sexes is a mysterious yet general phenomenon across great evolutionary distances. To test the roles of responses to environmental cues and sexual behaviors in longevity regulation, we examined Caenorhabditis male lifespan under solitary, grouped, and mated conditions. We find that neurons and the germline are required for male pheromone-dependent male death. Hermaphrodites with a masculinized nervous system secrete male pheromone and are susceptible to male pheromone killing. Male pheromone-mediated killing is unique to androdioecious Caenorhabditis , and may reduce the number of males in hermaphroditic populations; neither males nor females of gonochoristic species are susceptible to male pheromone killing. By contrast, mating-induced death, which is characterized by germline-dependent shrinking, glycogen loss, and ectopic vitellogenin expression, utilizes distinct molecular pathways and is shared between the sexes and across species. The study of sex- and species-specific regulation of aging reveals deeply conserved mechanisms of longevity and population structure regulation.

RecA: Regulation and Mechanism of a Molecular Search Engine.

PubMed

Bell, Jason C; Kowalczykowski, Stephen C

2016-06-01

Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

NASA Astrophysics Data System (ADS)

Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

2014-04-01

Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

Presentation of lipid antigens to T cells.

PubMed

Mori, Lucia; De Libero, Gennaro

2008-04-15

T cells specific for lipid antigens participate in regulation of the immune response during infections, tumor immunosurveillance, allergy and autoimmune diseases. T cells recognize lipid antigens as complexes formed with CD1 antigen-presenting molecules, thus resembling recognition of MHC-peptide complexes. The biophysical properties of lipids impose unique mechanisms for their delivery, internalization into antigen-presenting cells, membrane trafficking, processing, and loading of CD1 molecules. Each of these steps is controlled at molecular and celular levels and determines lipid immunogenicity. Lipid antigens may derive from microbes and from the cellular metabolism, thus allowing the immune system to survey a large repertoire of immunogenic molecules. Recognition of lipid antigens facilitates the detection of infectious agents and the initiation of responses involved in immunoregulation and autoimmunity. This review focuses on the presentation mechanisms and specific recognition of self and bacterial lipid antigens and discusses the important open issues.

The Die Is Cast: Precision Electrophilic Modifications Contribute to Cellular Decision Making

PubMed Central

2016-01-01

This perspective sets out to critically evaluate the scope of reactive electrophilic small molecules as unique chemical signal carriers in biological information transfer cascades. We consider these electrophilic cues as a new volatile cellular currency and compare them to canonical signaling circulation such as phosphate in terms of chemical properties, biological specificity, sufficiency, and necessity. The fact that nonenzymatic redox sensing properties are found in proteins undertaking varied cellular tasks suggests that electrophile signaling is a moonlighting phenomenon manifested within a privileged set of sensor proteins. The latest interrogations into these on-target electrophilic responses set forth a new horizon in the molecular mechanism of redox signal propagation wherein direct low-occupancy electrophilic modifications on a single sensor target are biologically sufficient to drive functional redox responses with precision timing. We detail how the various mechanisms through which redox signals function could contribute to their interesting phenotypic responses, including hormesis. PMID:27617777

The Die Is Cast: Precision Electrophilic Modifications Contribute to Cellular Decision Making.

PubMed

Long, Marcus J C; Aye, Yimon

2016-10-02

This perspective sets out to critically evaluate the scope of reactive electrophilic small molecules as unique chemical signal carriers in biological information transfer cascades. We consider these electrophilic cues as a new volatile cellular currency and compare them to canonical signaling circulation such as phosphate in terms of chemical properties, biological specificity, sufficiency, and necessity. The fact that nonenzymatic redox sensing properties are found in proteins undertaking varied cellular tasks suggests that electrophile signaling is a moonlighting phenomenon manifested within a privileged set of sensor proteins. The latest interrogations into these on-target electrophilic responses set forth a new horizon in the molecular mechanism of redox signal propagation wherein direct low-occupancy electrophilic modifications on a single sensor target are biologically sufficient to drive functional redox responses with precision timing. We detail how the various mechanisms through which redox signals function could contribute to their interesting phenotypic responses, including hormesis.

Initial Atomic Motion Immediately Following Femtosecond-Laser Excitation in Phase-Change Materials.

PubMed

Matsubara, E; Okada, S; Ichitsubo, T; Kawaguchi, T; Hirata, A; Guan, P F; Tokuda, K; Tanimura, K; Matsunaga, T; Chen, M W; Yamada, N

2016-09-23

Despite the fact that phase-change materials are widely used for data storage, no consensus exists on the unique mechanism of their ultrafast phase change and its accompanied large and rapid optical change. By using the pump-probe observation method combining a femtosecond optical laser and an x-ray free-electron laser, we substantiate experimentally that, in both GeTe and Ge_{2}Sb_{2}Te_{5} crystals, rattling motion of mainly Ge atoms takes place with keeping the off-center position just after femtosecond-optical-laser irradiation, which eventually leads to a higher symmetry or disordered state. This very initial rattling motion in the undistorted lattice can be related to instantaneous optical change due to the loss of resonant bonding that characterizes GeTe-based phase change materials. Based on the amorphous structure derived by first-principles molecular dynamics simulation, we infer a plausible ultrafast amorphization mechanism via nonmelting.

Expanded complexity of unstable repeat diseases

PubMed Central

Polak, Urszula; McIvor, Elizabeth; Dent, Sharon Y.R.; Wells, Robert D.; Napierala, Marek

2015-01-01

Unstable Repeat Diseases (URDs) share a common mutational phenomenon of changes in the copy number of short, tandemly repeated DNA sequences. More than 20 human neurological diseases are caused by instability, predominantly expansion, of microsatellite sequences. Changes in the repeat size initiate a cascade of pathological processes, frequently characteristic of a unique disease or a small subgroup of the URDs. Understanding of both the mechanism of repeat instability and molecular consequences of the repeat expansions is critical to developing successful therapies for these diseases. Recent technological breakthroughs in whole genome, transcriptome and proteome analyses will almost certainly lead to new discoveries regarding the mechanisms of repeat instability, the pathogenesis of URDs, and will facilitate development of novel therapeutic approaches. The aim of this review is to give a general overview of unstable repeats diseases, highlight the complexities of these diseases, and feature the emerging discoveries in the field. PMID:23233240

Kinesins and Myosins: Molecular Motors that Coordinate Cellular Functions in Plants.

PubMed

Nebenführ, Andreas; Dixit, Ram

2018-04-29

Kinesins and myosins are motor proteins that can move actively along microtubules and actin filaments, respectively. Plants have evolved a unique set of motors that function as regulators and organizers of the cytoskeleton and as drivers of long-distance transport of various cellular components. Recent progress has established the full complement of motors encoded in plant genomes and has revealed valuable insights into the cellular functions of many kinesin and myosin isoforms. Interestingly, several of the motors were found to functionally connect the two cytoskeletal systems and thereby to coordinate their activities. In this review, we discuss the available genetic, cell biological, and biochemical data for each of the plant kinesin and myosin families from the context of their subcellular mechanism of action as well as their physiological function in the whole plant. We particularly emphasize work that illustrates mechanisms by which kinesins and myosins coordinate the activities of the cytoskeletal system.

Sex differences in prenatal epigenetic programming of stress pathways.

PubMed

Bale, Tracy L

2011-07-01

Maternal stress experience is associated with neurodevelopmental disorders including schizophrenia and autism. Recent studies have examined mechanisms by which changes in the maternal milieu may be transmitted to the developing embryo and potentially translated into programming of the epigenome. Animal models of prenatal stress have identified important sex- and temporal-specific effects on offspring stress responsivity. As dysregulation of stress pathways is a common feature in most neuropsychiatric diseases, molecular and epigenetic analyses at the maternal-embryo interface, especially in the placenta, may provide unique insight into identifying much-needed predictive biomarkers. In addition, as most neurodevelopmental disorders present with a sex bias, examination of sex differences in the inheritance of phenotypic outcomes may pinpoint gene targets and specific windows of vulnerability in neurodevelopment, which have been disrupted. This review discusses the association and possible contributing mechanisms of prenatal stress in programming offspring stress pathway dysregulation and the importance of sex.

Reusable glucose sensing using carbon nanotube-based self-assembly

NASA Astrophysics Data System (ADS)

Bhattacharyya, Tamoghna; Samaddar, Sarbani; Dasgupta, Anjan Kr.

2013-09-01

Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes.Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr02609d

A Network Pharmacology Approach to Understanding the Mechanisms of Action of Traditional Medicine: Bushenhuoxue Formula for Treatment of Chronic Kidney Disease

PubMed Central

Zheng, Xiao-yong; Cao, Dong-sheng; Ye, Fa-qing; Xiang, Zheng

2014-01-01

Traditional Chinese medicine (TCM) has unique therapeutic effects for complex chronic diseases. However, for the lack of an effective systematic approach, the research progress on the effective substances and pharmacological mechanism of action has been very slow. In this paper, by incorporating network biology, bioinformatics and chemoinformatics methods, an integrated approach was proposed to systematically investigate and explain the pharmacological mechanism of action and effective substances of TCM. This approach includes the following main steps: First, based on the known drug targets, network biology was used to screen out putative drug targets; Second, the molecular docking method was used to calculate whether the molecules from TCM and drug targets related to chronic kidney diseases (CKD) interact or not; Third, according to the result of molecular docking, natural product-target network, main component-target network and compound-target network were constructed; Finally, through analysis of network characteristics and literature mining, potential effective multi-components and their synergistic mechanism were putatively identified and uncovered. Bu-shen-Huo-xue formula (BSHX) which was frequently used for treating CKD, was used as the case to demonstrate reliability of our proposed approach. The results show that BSHX has the therapeutic effect by using multi-channel network regulation, such as regulating the coagulation and fibrinolytic balance, and the expression of inflammatory factors, inhibiting abnormal ECM accumulation. Tanshinone IIA, rhein, curcumin, calycosin and quercetin may be potential effective ingredients of BSHX. This research shows that the integration approach can be an effective means for discovering active substances and revealing their pharmacological mechanisms of TCM. PMID:24598793

Molecular Mechanism of Flocculation Self-Recognition in Yeast and Its Role in Mating and Survival

PubMed Central

Goossens, Katty V. Y.; Ielasi, Francesco S.; Nookaew, Intawat; Stals, Ingeborg; Alonso-Sarduy, Livan; Daenen, Luk; Van Mulders, Sebastiaan E.; Stassen, Catherine; van Eijsden, Rudy G. E.; Siewers, Verena; Delvaux, Freddy R.; Kasas, Sandor; Nielsen, Jens; Devreese, Bart

2015-01-01

ABSTRACT We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. PMID:25873380

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells

PubMed Central

Huh, Yang Hoon; Cohen, Justin; Sherley, James L.

2013-01-01

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs “know” the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency. PMID:24082118

Mechanisms and evolution of plant resistance to aphids.

PubMed

Züst, Tobias; Agrawal, Anurag A

2016-01-06

Aphids are important herbivores of both wild and cultivated plants. Plants rely on unique mechanisms of recognition, signalling and defence to cope with the specialized mode of phloem feeding by aphids. Aspects of the molecular mechanisms underlying aphid-plant interactions are beginning to be understood. Recent advances include the identification of aphid salivary proteins involved in host plant manipulation, and plant receptors involved in aphid recognition. However, a complete picture of aphid-plant interactions requires consideration of the ecological outcome of these mechanisms in nature, and the evolutionary processes that shaped them. Here we identify general patterns of resistance, with a special focus on recognition, phytohormonal signalling, secondary metabolites and induction of plant resistance. We discuss how host specialization can enable aphids to co-opt both the phytohormonal responses and defensive compounds of plants for their own benefit at a local scale. In response, systemically induced resistance in plants is common and often involves targeted responses to specific aphid species or even genotypes. As co-evolutionary adaptation between plants and aphids is ongoing, the stealthy nature of aphid feeding makes both the mechanisms and outcomes of these interactions highly distinct from those of other herbivore-plant interactions.

A Simple, Inexpensive Molecular Weight Measurement for Water-Soluble Polymers Using Microemulsions.

ERIC Educational Resources Information Center

Mathias, Lon J.; Moore, D. Roger

1985-01-01

Describes an experiment involving use of a microemulsion and its characteristic thermal phase change to determine molecular weights of polyoxyethylene samples. The experiment provides students with background information on polymers and organized media and with experience in evaluating polymer molecular weight by using a unique property of a…

Role of magnetic and diamagnetic interactions in molecular optics and scattering

NASA Astrophysics Data System (ADS)

Forbes, Kayn A.

2018-05-01

This paper aims to explicitly clarify the role and interpretation of diamagnetic interactions between molecules and light in quantum electrodynamics. In contrast to their electric and magnetic counterparts, the diamagnetic couplings between light and matter have received relatively little interest in the field of molecular optics. This intriguing disregard of an interaction term is puzzling. The diamagnetic couplings possess unique physical properties that warrant their inclusion in any multiphoton process, and the lack of gauge invariance for paramagnetic and diamagnetic susceptibilities necessitates their inclusion. Their role and importance within nonrelativistic molecular quantum electrodynamics in the Coulomb gauge is illuminated, and it is highlighted how for any multiphoton process their inclusion should be implicit. As an indicative example of the theory presented, the diamagnetic contributions to both forward and nonforward Rayleigh scattering are derived and put into context alongside the electric and magnetic molecular responses. The work represents clarification of diamagnetic couplings in molecular quantum electrodynamics, which subsequently should proffer the study of diamagnetic interactions in molecular optics due to their unique physical attributes and necessary inclusion in multiphoton processes.

LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis.

PubMed

Thomas, James R; Gedeon, Patrick C; Grant, Barry J; Madura, Jeffry D

2012-07-03

Monoamine transporters (MATs) function by coupling ion gradients to the transport of dopamine, norepinephrine, or serotonin. Despite their importance in regulating neurotransmission, the exact conformational mechanism by which MATs function remains elusive. To this end, we have performed seven 250 ns accelerated molecular dynamics simulations of the leucine transporter, a model for neurotransmitter MATs. By varying the presence of binding-pocket leucine substrate and sodium ions, we have sampled plausible conformational states representative of the substrate transport cycle. The resulting trajectories were analyzed using principal component analysis of transmembrane helices 1b and 6a. This analysis revealed seven unique structures: two of the obtained conformations are similar to the currently published crystallographic structures, one conformation is similar to a proposed open inward structure, and four conformations represent novel structures of potential importance to the transport cycle. Further analysis reveals that the presence of binding-pocket sodium ions is necessary to stabilize the locked-occluded and open-inward conformations. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Drug Discovery in Fish, Flies, and Worms

PubMed Central

Strange, Kevin

2016-01-01

Abstract Nonmammalian model organisms such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the zebrafish Danio rerio provide numerous experimental advantages for drug discovery including genetic and molecular tractability, amenability to high-throughput screening methods and reduced experimental costs and increased experimental throughput compared to traditional mammalian models. An interdisciplinary approach that strategically combines the study of nonmammalian and mammalian animal models with diverse experimental tools has and will continue to provide deep molecular and genetic understanding of human disease and will significantly enhance the discovery and application of new therapies to treat those diseases. This review will provide an overview of C. elegans, Drosophila, and zebrafish biology and husbandry and will discuss how these models are being used for phenotype-based drug screening and for identification of drug targets and mechanisms of action. The review will also describe how these and other nonmammalian model organisms are uniquely suited for the discovery of drug-based regenerative medicine therapies. PMID:28053067

Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

PubMed Central

Flowers, G. Parker; Timberlake, Andrew T.; Mclean, Kaitlin C.; Monaghan, James R.; Crews, Craig M.

2014-01-01

Among tetrapods, only urodele salamanders, such as the axolotl Ambystoma mexicanum, can completely regenerate limbs as adults. The mystery of why salamanders, but not other animals, possess this ability has for generations captivated scientists seeking to induce this phenomenon in other vertebrates. Although many recent advances in molecular biology have allowed limb regeneration and tissue repair in the axolotl to be investigated in increasing detail, the molecular toolkit for the study of this process has been limited. Here, we report that the CRISPR-Cas9 RNA-guided nuclease system can efficiently create mutations at targeted sites within the axolotl genome. We identify individual animals treated with RNA-guided nucleases that have mutation frequencies close to 100% at targeted sites. We employ this technique to completely functionally ablate EGFP expression in transgenic animals and recapitulate developmental phenotypes produced by loss of the conserved gene brachyury. Thus, this advance allows a reverse genetic approach in the axolotl and will undoubtedly provide invaluable insight into the mechanisms of salamanders' unique regenerative ability. PMID:24764077

Atomic force microscopy-based characterization and design of biointerfaces

NASA Astrophysics Data System (ADS)

Alsteens, David; Gaub, Hermann E.; Newton, Richard; Pfreundschuh, Moritz; Gerber, Christoph; Müller, Daniel J.

2017-03-01

Atomic force microscopy (AFM)-based methods have matured into a powerful nanoscopic platform, enabling the characterization of a wide range of biological and synthetic biointerfaces ranging from tissues, cells, membranes, proteins, nucleic acids and functional materials. Although the unprecedented signal-to-noise ratio of AFM enables the imaging of biological interfaces from the cellular to the molecular scale, AFM-based force spectroscopy allows their mechanical, chemical, conductive or electrostatic, and biological properties to be probed. The combination of AFM-based imaging and spectroscopy structurally maps these properties and allows their 3D manipulation with molecular precision. In this Review, we survey basic and advanced AFM-related approaches and evaluate their unique advantages and limitations in imaging, sensing, parameterizing and designing biointerfaces. It is anticipated that in the next decade these AFM-related techniques will have a profound influence on the way researchers view, characterize and construct biointerfaces, thereby helping to solve and address fundamental challenges that cannot be addressed with other techniques.

Molecular control of steady-state dendritic cell maturation and immune homeostasis.

PubMed

Hammer, Gianna Elena; Ma, Averil

2013-01-01

Dendritic cells (DCs) are specialized sentinels responsible for coordinating adaptive immunity. This function is dependent upon coupled sensitivity to environmental signs of inflammation and infection to cellular maturation-the programmed alteration of DC phenotype and function to enhance immune cell activation. Although DCs are thus well equipped to respond to pathogens, maturation triggers are not unique to infection. Given that immune cells are exquisitely sensitive to the biological functions of DCs, we now appreciate that multiple layers of suppression are required to restrict the environmental sensitivity, cellular maturation, and even life span of DCs to prevent aberrant immune activation during the steady state. At the same time, steady-state DCs are not quiescent but rather perform key functions that support homeostasis of numerous cell types. Here we review these functions and molecular mechanisms of suppression that control steady-state DC maturation. Corruption of these steady-state operatives has diverse immunological consequences and pinpoints DCs as potent drivers of autoimmune and inflammatory disease.

Gene expression profiling--Opening the black box of plant ecosystem responses to global change

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leakey, A.D.B.; Ainsworth, E.A.; Bernard, S.M.

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in modelmore » and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.« less

Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

NASA Astrophysics Data System (ADS)

Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

2016-10-01

STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

Mass spectrometry-based metabolomics: applications to biomarker and metabolic pathway research.

PubMed

Zhang, Aihua; Sun, Hui; Yan, Guangli; Wang, Ping; Wang, Xijun

2016-01-01

Mass spectrometry-based metabolomics has become increasingly popular in molecular medicine. High-definition mass spectrometry (MS), coupled with pattern recognition methods, have been carried out to obtain comprehensive metabolite profiling and metabolic pathway of large biological datasets. This sets the scene for a new and powerful diagnostic approach. Analysis of the key metabolites in body fluids has become an important part of improving disease diagnosis. With technological advances in analytical techniques, the ability to measure low-molecular-weight metabolites in bio-samples provides a powerful platform for identifying metabolites that are uniquely correlated with a specific human disease. MS-based metabolomics can lead to enhanced understanding of disease mechanisms and to new diagnostic markers and has a strong potential to contribute to improving early diagnosis of diseases. This review will highlight the importance and benefit with certain characteristic examples of MS-metabolomics for identifying metabolic pathways and metabolites that accurately screen for potential diagnostic biomarkers of diseases. Copyright © 2015 John Wiley & Sons, Ltd.

Atomistic simulation of hydrophobin HFBII conformation in aqueous and fluorous media and at the water/vacuum interface.

PubMed

Raffaini, Giuseppina; Milani, Roberto; Ganazzoli, Fabio; Resnati, Giuseppe; Metrangolo, Pierangelo

2016-01-01

Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. Copyright © 2015 Elsevier Inc. All rights reserved.

The Presynaptic Component of the Serotonergic System is Required for Clozapine's Efficacy

PubMed Central

Yadav, Prem N; Abbas, Atheir I; Farrell, Martilias S; Setola, Vincent; Sciaky, Noah; Huang, Xi-Ping; Kroeze, Wesley K; Crawford, LaTasha K; Piel, David A; Keiser, Michael J; Irwin, John J; Shoichet, Brian K; Deneris, Evan S; Gingrich, Jay; Beck, Sheryl G; Roth, Bryan L

2011-01-01

Clozapine, by virtue of its absence of extrapyramidal side effects and greater efficacy, revolutionized the treatment of schizophrenia, although the mechanisms underlying this exceptional activity remain controversial. Combining an unbiased cheminformatics and physical screening approach, we evaluated clozapine's activity at >2350 distinct molecular targets. Clozapine, and the closely related atypical antipsychotic drug olanzapine, interacted potently with a unique spectrum of molecular targets. This distinct pattern, which was not shared with the typical antipsychotic drug haloperidol, suggested that the serotonergic neuronal system was a key determinant of clozapine's actions. To test this hypothesis, we used pet1−/− mice, which are deficient in serotonergic presynaptic markers. We discovered that the antipsychotic-like properties of the atypical antipsychotic drugs clozapine and olanzapine were abolished in a pharmacological model that mimics NMDA-receptor hypofunction in pet1−/− mice, whereas haloperidol's efficacy was unaffected. These results show that clozapine's ability to normalize NMDA-receptor hypofunction, which is characteristic of schizophrenia, depends on an intact presynaptic serotonergic neuronal system. PMID:21048700

Nematode-Trapping Fungi.

PubMed

Jiang, Xiangzhi; Xiang, Meichun; Liu, Xingzhong

2017-01-01

Nematode-trapping fungi are a unique and intriguing group of carnivorous microorganisms that can trap and digest nematodes by means of specialized trapping structures. They can develop diverse trapping devices, such as adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and nonconstricting rings. Nematode-trapping fungi have been found in all regions of the world, from the tropics to Antarctica, from terrestrial to aquatic ecosystems. They play an important ecological role in regulating nematode dynamics in soil. Molecular phylogenetic studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Nematode-trapping fungi serve as an excellent model system for understanding fungal evolution and interaction between fungi and nematodes. With the development of molecular techniques and genome sequencing, their evolutionary origins and divergence, and the mechanisms underlying fungus-nematode interactions have been well studied. In recent decades, an increasing concern about the environmental hazards of using chemical nematicides has led to the application of these biological control agents as a rapidly developing component of crop protection.

Molecular architecture of the Spire-actin nucleus and its implication for actin filament assembly.

PubMed

Sitar, Tomasz; Gallinger, Julia; Ducka, Anna M; Ikonen, Teemu P; Wohlhoefler, Michael; Schmoller, Kurt M; Bausch, Andreas R; Joel, Peteranne; Trybus, Kathleen M; Noegel, Angelika A; Schleicher, Michael; Huber, Robert; Holak, Tad A

2011-12-06

The Spire protein is a multifunctional regulator of actin assembly. We studied the structures and properties of Spire-actin complexes by X-ray scattering, X-ray crystallography, total internal reflection fluorescence microscopy, and actin polymerization assays. We show that Spire-actin complexes in solution assume a unique, longitudinal-like shape, in which Wiskott-Aldrich syndrome protein homology 2 domains (WH2), in an extended configuration, line up actins along the long axis of the core of the Spire-actin particle. In the complex, the kinase noncatalytic C-lobe domain is positioned at the side of the first N-terminal Spire-actin module. In addition, we find that preformed, isolated Spire-actin complexes are very efficient nucleators of polymerization and afterward dissociate from the growing filament. However, under certain conditions, all Spire constructs--even a single WH2 repeat--sequester actin and disrupt existing filaments. This molecular and structural mechanism of actin polymerization by Spire should apply to other actin-binding proteins that contain WH2 domains in tandem.

Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

PubMed

Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

2016-09-05

The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Intestinal barrier dysfunction in cirrhosis: Current concepts in pathophysiology and clinical implications

PubMed Central

Tsiaoussis, Georgios I; Assimakopoulos, Stelios F; Tsamandas, Athanassios C; Triantos, Christos K; Thomopoulos, Konstantinos C

2015-01-01

The intestinal lumen is a host place for a wide range of microbiota and sets a unique interplay between local immune system, inflammatory cells and intestinal epithelium, forming a physical barrier against microbial invaders and toxins. Bacterial translocation is the migration of viable or nonviable microorganisms or their pathogen-associated molecular patterns, such as lipopolysaccharide, from the gut lumen to the mesenteric lymph nodes, systemic circulation and other normally sterile extraintestinal sites. A series of studies have shown that translocation of bacteria and their products across the intestinal barrier is a commonplace in patients with liver disease. The deterioration of intestinal barrier integrity and the consulting increased intestinal permeability in cirrhotic patients play a pivotal pathophysiological role in the development of severe complications as high rate of infections, spontaneous bacterial peritonitis, hepatic encephalopathy, hepatorenal syndrome, variceal bleeding, progression of liver injury and hepatocellular carcinoma. Nevertheless, the exact cellular and molecular mechanisms implicated in the phenomenon of microbial translocation in liver cirrhosis have not been fully elucidated yet. PMID:26301048

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations.

PubMed

Lee, Mal-Soon; Peter McGrail, B; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

2015-10-12

The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.

Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

PubMed Central

2018-01-01

To understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes. PMID:29671739

Relationships Between Dissolved Organic Matter Composition and Photochemistry in Lakes of Diverse Trophic Status.

PubMed

Maizel, Andrew C; Li, Jing; Remucal, Christina K

2017-09-05

The North Temperate Lakes Long-Term Ecological Research site includes seven lakes in northern Wisconsin that vary in hydrology, trophic status, and landscape position. We examine the molecular composition of dissolved organic matter (DOM) within these lakes using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) and quantify DOM photochemical activity using probe compounds. Correlations between the relative intensity of individual molecular formulas and reactive species production demonstrate the influence of DOM composition on photochemistry. For example, highly aromatic, tannin-like formulas correlate positively with triplet formation rates, but negatively with triplet quantum yields, as waters enriched in highly aromatic formulas exhibit much higher rates of light absorption, but only slightly higher rates of triplet production. While commonly utilized optical properties also correlate with DOM composition, the ability of FT-ICR MS to characterize DOM subpopulations provides unique insight into the mechanisms through which DOM source and environmental processing determine composition and photochemical activity.

Bosutinib, dasatinib, imatinib, nilotinib, and ponatinib differentially affect the vascular molecular pathways and functionality of human endothelial cells.

PubMed

Gover-Proaktor, Ayala; Granot, Galit; Pasmanik-Chor, Metsada; Pasvolsky, Oren; Shapira, Saar; Raz, Oshrat; Raanani, Pia; Leader, Avi

2018-05-09

The tyrosine kinase inhibitors (TKIs), nilotinib, ponatinib, and dasatinib (but not bosutinib or imatinib), are associated with vascular adverse events (VAEs) in chronic myeloid leukemia (CML). Though the mechanism is inadequately understood, an effect on vascular cells has been suggested. We investigated the effect of imatinib, nilotinib, dasatinib, bosutinib, and ponatinib on tube formation, cell viability, and gene expression of human vascular endothelial cells (HUVECs). We found a distinct genetic profile in HUVECs treated with dasatinib, ponatinib, and nilotinib compared to bosutinib and imatinib, who resembled untreated samples. However, unique gene expression and molecular pathway alterations were detected between dasatinib, ponatinib, and nilotinib. Angiogenesis/blood vessel-related pathways and HUVEC function (tube formation/viability) were adversely affected by dasatinib, ponatinib, and nilotinib but not by imatinib or bosutinib. These results correspond to the differences in VAE profiles of these TKIs, support a direct effect on vascular cells, and provide direction for future research.

Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

PubMed Central

Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

2016-01-01

STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development. PMID:27752093

Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians.

PubMed

Newmark, Phillip A; Reddien, Peter W; Cebrià, Francesc; Sánchez Alvarado, Alejandro

2003-09-30

Freshwater planarian flatworms are capable of regenerating complete organisms from tiny fragments of their bodies; the basis for this regenerative prowess is an experimentally accessible stem cell population that is present in the adult planarian. The study of these organisms, classic experimental models for investigating metazoan regeneration, has been revitalized by the application of modern molecular biological approaches. The identification of thousands of unique planarian ESTs, coupled with large-scale whole-mount in situ hybridization screens, and the ability to inhibit planarian gene expression through double-stranded RNA-mediated genetic interference, provide a wealth of tools for studying the molecular mechanisms that regulate tissue regeneration and stem cell biology in these organisms. Here we show that, as in Caenorhabditis elegans, ingestion of bacterially expressed double-stranded RNA can inhibit gene expression in planarians. This inhibition persists throughout the process of regeneration, allowing phenotypes with disrupted regenerative patterning to be identified. These results pave the way for large-scale screens for genes involved in regenerative processes.

Plastic Transition to Switch Nonlinear Optical Properties Showing the Record High Contrast in a Single-Component Molecular Crystal.

PubMed

Sun, Zhihua; Chen, Tianliang; Liu, Xitao; Hong, Maochun; Luo, Junhua

2015-12-23

To switch bulk nonlinear optical (NLO) effects represents an exciting new branch of NLO material science, whereas it remains a great challenge to achieve high contrast for "on/off" of quadratic NLO effects in crystalline materials. Here, we report the supereminent NLO-switching behaviors of a single-component plastic crystal, 2-(hydroxymethyl)-2-nitro-1,3-propanediol (1), which shows a record high contrast of at least ∼150, exceeding all the known crystalline switches. Such a breakthrough is clearly elucidated from the slowing down of highly isotropic molecular motions during plastic-to-rigid transition. The deep understanding of its intrinsic plasticity and superior NLO property allows the construction of a feasible switching mechanism. As a unique class of substances with short-range disorder embedded in long-range ordered crystalline lattice, plastic crystals enable response to external stimuli and fulfill specific photoelectric functions, which open a newly conceptual avenue for the designing of new functional materials.

Personalized Medicine Approach for an Exceptional Response to Multiple-recurrent and Metastatic HER2-positive Oropharyngeal Squamous Cell Carcinoma.

PubMed

Seim, Nolan B; Kang, Stephen Y; Bhandari, Milan; Jones, Riley G; Teknos, Theodoros N

2017-04-01

Advanced stage squamous cell carcinoma of the head and neck carries an overall poor prognosis, and survivorship gains have remained relatively stagnant compared to other malignancies due to its complex tumor biology and lack of proven effective targeting agents. We present a case of an exceptional responder to molecular-targeted therapy for metastatic oropharyngeal squamous cell carcinoma using a chemotherapeutic agent FDA approved for breast cancer and targeting the HER2/Neu receptor in order to discuss the larger clinical implications. The National Cancer Institute (NCI) has recently instituted the Exceptional Responders Initiative in order to identify such patients with unexpected outcomes in order to expedite the development of additional targeted therapies. This case illustrates the opportunity for cure using targeted oncogene identification in a scenario of recurrent squamous cell carcinoma with lung metastasis typically considered fatal. Molecular tumor analysis is an infrequently utilized tool in head and neck squamous cell carcinoma; however, as understanding of biologic mechanisms improves, additional molecular targets will become available and expand treatment opportunities such as HER2/Neu targeting. The Exceptional Responders Initiative is a unique strategy with potential to expedite progress.

Molecular Gas Feeding the Circumnuclear Disk of the Galactic Center

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsieh, Pei-Ying; Koch, Patrick M.; Ho, Paul T. P.

The interaction between a supermassive black hole (SMBH) and the surrounding material is of primary importance in modern astrophysics. The detection of the molecular 2 pc circumnuclear disk (CND) immediately around the Milky Way SMBH, SgrA*, provides a unique opportunity to study SMBH accretion at subparsec scales. Our new wide-field CS( J = 2 − 1) map toward the Galactic center (GC) reveals multiple dense molecular streamers that originated from the ambient clouds 20 pc further out, and that are connected to the central 2 pc of the CND. These dense gas streamers appear to carry gas directly toward themore » nuclear region and might be captured by the central potential. Our phase-plot analysis indicates that these streamers show a signature of rotation and inward radial motion with progressively higher velocities as the gas approaches the CND and finally ends up corotating with the CND. Our results might suggest a possible mechanism of gas feeding the CND from 20 pc around 2 pc in the GC. In this paper, we discuss the morphology and the kinematics of these streamers. As the nearest observable Galactic nucleus, this feeding process may have implications for understanding the processes in extragalactic nuclei.« less

Stroma-associated master regulators of molecular subtypes predict patient prognosis in ovarian cancer.

PubMed

Zhang, Shengzhe; Jing, Ying; Zhang, Meiying; Zhang, Zhenfeng; Ma, Pengfei; Peng, Huixin; Shi, Kaixuan; Gao, Wei-Qiang; Zhuang, Guanglei

2015-11-04

High-grade serous ovarian carcinoma (HGS-OvCa) has the lowest survival rate among all gynecologic cancers and is hallmarked by a high degree of heterogeneity. The Cancer Genome Atlas network has described a gene expression-based molecular classification of HGS-OvCa into Differentiated, Mesenchymal, Immunoreactive and Proliferative subtypes. However, the biological underpinnings and regulatory mechanisms underlying the distinct molecular subtypes are largely unknown. Here we showed that tumor-infiltrating stromal cells significantly contributed to the assignments of Mesenchymal and Immunoreactive clusters. Using reverse engineering and an unbiased interrogation of subtype regulatory networks, we identified the transcriptional modules containing master regulators that drive gene expression of Mesenchymal and Immunoreactive HGS-OvCa. Mesenchymal master regulators were associated with poor prognosis, while Immunoreactive master regulators positively correlated with overall survival. Meta-analysis of 749 HGS-OvCa expression profiles confirmed that master regulators as a prognostic signature were able to predict patient outcome. Our data unraveled master regulatory programs of HGS-OvCa subtypes with prognostic and potentially therapeutic relevance, and suggested that the unique transcriptional and clinical characteristics of ovarian Mesenchymal and Immunoreactive subtypes could be, at least partially, ascribed to tumor microenvironment.

Modeling Molecular and Cellular Aspects of Human Disease using the Nematode Caenorhabditis elegans

PubMed Central

Silverman, Gary A.; Luke, Cliff J.; Bhatia, Sangeeta R.; Long, Olivia S.; Vetica, Anne C.; Perlmutter, David H.; Pak, Stephen C.

2009-01-01

As an experimental system, Caenorhabditis elegans, offers a unique opportunity to interrogate in vivo the genetic and molecular functions of human disease-related genes. For example, C. elegans has provided crucial insights into fundamental biological processes such as cell death and cell fate determinations, as well as pathological processes such as neurodegeneration and microbial susceptibility. The C. elegans model has several distinct advantages including a completely sequenced genome that shares extensive homology with that of mammals, ease of cultivation and storage, a relatively short lifespan and techniques for generating null and transgenic animals. However, the ability to conduct unbiased forward and reverse genetic screens in C. elegans remains one of the most powerful experimental paradigms for discovering the biochemical pathways underlying human disease phenotypes. The identification of these pathways leads to a better understanding of the molecular interactions that perturb cellular physiology, and forms the foundation for designing mechanism-based therapies. To this end, the ability to process large numbers of isogenic animals through automated work stations suggests that C. elegans, manifesting different aspects of human disease phenotypes, will become the platform of choice for in vivo drug discovery and target validation using high-throughput/content screening technologies. PMID:18852689

Molecular Gas Feeding the Circumnuclear Disk of the Galactic Center

NASA Astrophysics Data System (ADS)

Hsieh, Pei-Ying; Koch, Patrick M.; Ho, Paul T. P.; Kim, Woong-Tae; Tang, Ya-Wen; Wang, Hsiang-Hsu; Yen, Hsi-Wei; Hwang, Chorng-Yuan

2017-09-01

The interaction between a supermassive black hole (SMBH) and the surrounding material is of primary importance in modern astrophysics. The detection of the molecular 2 pc circumnuclear disk (CND) immediately around the Milky Way SMBH, SgrA*, provides a unique opportunity to study SMBH accretion at subparsec scales. Our new wide-field CS(J = 2 - 1) map toward the Galactic center (GC) reveals multiple dense molecular streamers that originated from the ambient clouds 20 pc further out, and that are connected to the central 2 pc of the CND. These dense gas streamers appear to carry gas directly toward the nuclear region and might be captured by the central potential. Our phase-plot analysis indicates that these streamers show a signature of rotation and inward radial motion with progressively higher velocities as the gas approaches the CND and finally ends up corotating with the CND. Our results might suggest a possible mechanism of gas feeding the CND from 20 pc around 2 pc in the GC. In this paper, we discuss the morphology and the kinematics of these streamers. As the nearest observable Galactic nucleus, this feeding process may have implications for understanding the processes in extragalactic nuclei.

Formation of Benzene in the Interstellar Medium

NASA Technical Reports Server (NTRS)

Jones, Brant M.; Zhang, Fangtong; Kaiser, Ralf I.; Jamal, Adeel; Mebel, Alexander M.; Cordiner, Martin A.; Charnley, Steven B.; Crim, F. Fleming (Editor)

2010-01-01

Polycyclic aromatic hydrocarbons and related species have been suggested to play a key role in the astrochemical evolution of the interstellar medium, but the formation mechanism of even their simplest building block-the aromatic benzene molecule-has remained elusive for decades. Here we demonstrate in crossed molecular beam experiments combined with electronic structure and statistical calculations that benzene (C6H6) can be synthesized via the barrierless, exoergic reaction of the ethynyl radical and 1,3- butadiene, C2H + H2CCHCHCH2 --> C6H6, + H, under single collision conditions. This reaction portrays the simplest representative of a reaction class in which aromatic molecules with a benzene core can be formed from acyclic precursors via barrierless reactions of ethynyl radicals with substituted 1,3-butadlene molecules. Unique gas-grain astrochemical models imply that this low-temperature route controls the synthesis of the very first aromatic ring from acyclic precursors in cold molecular clouds, such as in the Taurus Molecular Cloud. Rapid, subsequent barrierless reactions of benzene with ethynyl radicals can lead to naphthalene-like structures thus effectively propagating the ethynyl-radical mediated formation of aromatic molecules in the interstellar medium.

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

PubMed Central

Skjaerven, Lars; Grant, Barry; Muga, Arturo; Teigen, Knut; McCammon, J. Andrew; Reuter, Nathalie; Martinez, Aurora

2011-01-01

GroEL is an ATP dependent molecular chaperone that promotes the folding of a large number of substrate proteins in E. coli. Large-scale conformational transitions occurring during the reaction cycle have been characterized from extensive crystallographic studies. However, the link between the observed conformations and the mechanisms involved in the allosteric response to ATP and the nucleotide-driven reaction cycle are not completely established. Here we describe extensive (in total long) unbiased molecular dynamics (MD) simulations that probe the response of GroEL subunits to ATP binding. We observe nucleotide dependent conformational transitions, and show with multiple 100 ns long simulations that the ligand-induced shift in the conformational populations are intrinsically coded in the structure-dynamics relationship of the protein subunit. Thus, these simulations reveal a stabilization of the equatorial domain upon nucleotide binding and a concomitant “opening” of the subunit, which reaches a conformation close to that observed in the crystal structure of the subunits within the ADP-bound oligomer. Moreover, we identify changes in a set of unique intrasubunit interactions potentially important for the conformational transition. PMID:21423709

Formation of benzene in the interstellar medium

PubMed Central

Jones, Brant M.; Zhang, Fangtong; Kaiser, Ralf I.; Jamal, Adeel; Mebel, Alexander M.; Cordiner, Martin A.; Charnley, Steven B.

2011-01-01

Polycyclic aromatic hydrocarbons and related species have been suggested to play a key role in the astrochemical evolution of the interstellar medium, but the formation mechanism of even their simplest building block—the aromatic benzene molecule—has remained elusive for decades. Here we demonstrate in crossed molecular beam experiments combined with electronic structure and statistical calculations that benzene (C6H6) can be synthesized via the barrierless, exoergic reaction of the ethynyl radical and 1,3-butadiene, C2H + H2CCHCHCH2 → C6H6 + H, under single collision conditions. This reaction portrays the simplest representative of a reaction class in which aromatic molecules with a benzene core can be formed from acyclic precursors via barrierless reactions of ethynyl radicals with substituted 1,3-butadiene molecules. Unique gas-grain astrochemical models imply that this low-temperature route controls the synthesis of the very first aromatic ring from acyclic precursors in cold molecular clouds, such as in the Taurus Molecular Cloud. Rapid, subsequent barrierless reactions of benzene with ethynyl radicals can lead to naphthalene-like structures thus effectively propagating the ethynyl-radical mediated formation of aromatic molecules in the interstellar medium. PMID:21187430

Molecular sensing using monolayer floating gate, fully depleted SOI MOSFET acting as an exponential transducer.

PubMed

Takulapalli, Bharath R

2010-02-23

Field-effect transistor-based chemical sensors fall into two broad categories based on the principle of signal transduction-chemiresistor or Schottky-type devices and MOSFET or inversion-type devices. In this paper, we report a new inversion-type device concept-fully depleted exponentially coupled (FDEC) sensor, using molecular monolayer floating gate fully depleted silicon on insulator (SOI) MOSFET. Molecular binding at the chemical-sensitive surface lowers the threshold voltage of the device inversion channel due to a unique capacitive charge-coupling mechanism involving interface defect states, causing an exponential increase in the inversion channel current. This response of the device is in opposite direction when compared to typical MOSFET-type sensors, wherein inversion current decreases in a conventional n-channel sensor device upon addition of negative charge to the chemical-sensitive device surface. The new sensor architecture enables ultrahigh sensitivity along with extraordinary selectivity. We propose the new sensor concept with the aid of analytical equations and present results from our experiments in liquid phase and gas phase to demonstrate the new principle of signal transduction. We present data from numerical simulations to further support our theory.

Proteomic analysis of hydrogen photoproduction in sulfur-deprived Chlamydomonas cells.

PubMed

Chen, Mei; Zhao, Le; Sun, Yong-Le; Cui, Su-Xia; Zhang, Li-Fang; Yang, Bin; Wang, Jie; Kuang, Ting-Yun; Huang, Fang

2010-08-06

The green alga Chlamydomonas reinhardtii is a model organism to study H(2) metabolism in photosynthetic eukaryotes. To understand the molecular mechanism of H(2) metabolism, we used 2-DE coupled with MALDI-TOF and MALDI-TOF/TOF-MS to investigate proteomic changes of Chlamydomonas cells that undergo sulfur-depleted H(2) photoproduction process. In this report, we obtained 2-D PAGE soluble protein profiles of Chlamydomonas at three time points representing different phases leading to H(2) production. We found over 105 Coomassie-stained protein spots, corresponding to 82 unique gene products, changed in abundance throughout the process. Major changes included photosynthetic machinery, protein biosynthetic apparatus, molecular chaperones, and 20S proteasomal components. A number of proteins related to sulfate, nitrogen and acetate assimilation, and antioxidative reactions were also changed significantly. Other proteins showing alteration during the sulfur-depleted H(2) photoproduction process were proteins involved in cell wall and flagella metabolisms. In addition, among these differentially expressed proteins, 11 were found to be predicted proteins without functional annotation in the Chlamydomonas genome database. The results of this proteomic analysis provide new insight into molecular basis of H(2) photoproduction in Chlamydomonas under sulfur depletion.

Bottlebrush elastomers: a promising molecular engineering route to tunable, prestrain-free dielectric elastomers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Vatankhah-Varnosfaderani, Mohammad; Daniel, William F. M.; Zhushma, Alexandr P.; Li, Qiaoxi; Morgan, Benjamin J.; Matyjaszewski, Krzysztof; Armstrong, Daniel P.; Dobrynin, Andrey V.; Sheyko, Sergei S.; Spontak, Richard J.

2017-04-01

Electroactive polymers (EAPs) refer to a broad range of relatively soft materials that change size and/or shape upon application of an electrical stimulus. Of these, dielectric elastomers (DEs) generated from either chemically- or physically-crosslinked polymer networks afford the highest levels of electroactuation strain, thereby making this class of EAPs the leading technology for artificial-muscle applications. While mechanically prestraining elastic networks remarkably enhances DEs electroactuation, external prestrain protocols severely limit both actuator performance and device implementation due to gradual DE stress relaxation and the presence of a cumbersome load frame. These drawbacks have persisted with surprisingly minimal advances in the actuation of single-component elastomers since the dawn of the "pre-strain era" introduced by Pelrine et al. (Science, 2000). In this work, we present a bottom-up, molecular-based strategy for the design of prestrain-free (freestanding) DEs derived from covalently-crosslinked bottlebrush polymers. This architecture, wherein design factors such as crosslink density, graft density and graft length can all be independently controlled, yields inherently strained polymer networks that can be readily adapted to a variety of chemistries. To validate the use of these molecularly-tunable materials as DEs, we have synthesized a series of bottlebrush silicone elastomers in as-cast shapes. Examination of these materials reveals that they undergo giant electroactuation strains (>300%) at relatively low fields (<10 V/m), thereby outperforming all commercial DEs to date and opening new opportunities in responsive soft-material technologies (e.g., robotics). The molecular design approach to controlling (electro)mechanical developed here is independent of chemistry and permits access to an unprecedented range of actuation properties from elastomeric materials with traditionally modest electroactuation performance (e.g., polydimethylsiloxane, PDMS). Experimental results obtained here compare favorably with theoretical predictions and demonstrate that the unique behavior of these materials is a direct consequence of the molecular architecture.

New Insights into the Organization, Recombination, Expression and Functional Mechanism of Low Molecular Weight Glutenin Subunit Genes in Bread Wheat

PubMed Central

Fan, Huajie; Sun, Jiazhu; Zhang, Zhongjuan; Qin, Huanju; Li, Bin; Hao, Shanting; Li, Zhensheng; Wang, Daowen; Zhang, Aimin; Ling, Hong-Qing

2010-01-01

The bread-making quality of wheat is strongly influenced by multiple low molecular weight glutenin subunit (LMW-GS) proteins expressed in the seeds. However, the organization, recombination and expression of LMW-GS genes and their functional mechanism in bread-making are not well understood. Here we report a systematic molecular analysis of LMW-GS genes located at the orthologous Glu-3 loci (Glu-A3, B3 and D3) of bread wheat using complementary approaches (genome wide characterization of gene members, expression profiling, proteomic analysis). Fourteen unique LMW-GS genes were identified for Xiaoyan 54 (with superior bread-making quality). Molecular mapping and recombination analyses revealed that the three Glu-3 loci of Xiaoyan 54 harbored dissimilar numbers of LMW-GS genes and covered different genetic distances. The number of expressed LMW-GS in the seeds was higher in Xiaoyan 54 than in Jing 411 (with relatively poor bread-making quality). This correlated with the finding of higher numbers of active LMW-GS genes at the A3 and D3 loci in Xiaoyan 54. Association analysis using recombinant inbred lines suggested that positive interactions, conferred by genetic combinations of the Glu-3 locus alleles with more numerous active LMW-GS genes, were generally important for the recombinant progenies to attain high Zeleny sedimentation value (ZSV), an important indicator of bread-making quality. A higher number of active LMW-GS genes tended to lead to a more elevated ZSV, although this tendency was influenced by genetic background. This work provides substantial new insights into the genomic organization and expression of LMW-GS genes, and molecular genetic evidence suggesting that these genes contribute quantitatively to bread-making quality in hexaploid wheat. Our analysis also indicates that selection for high numbers of active LMW-GS genes can be used for improvement of bread-making quality in wheat breeding. PMID:20975830

Analysis of the skin transcriptome in two oujiang color varieties of common carp.

PubMed

Wang, Chenghui; Wachholtz, Michael; Wang, Jun; Liao, Xiaolin; Lu, Guoqing

2014-01-01

Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding. In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW. The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.

Quantitative proteomics analysis highlights the role of redox hemostasis and energy metabolism in human embryonic stem cell differentiation to neural cells.

PubMed

Fathi, Ali; Hatami, Maryam; Vakilian, Haghighat; Han, Chia-Li; Chen, Yu-Ju; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

2014-04-14

Neural differentiation of human embryonic stem cells (hESCs) is a unique opportunity for in vitro analyses of neurogenesis in humans. Extrinsic cues through neural plate formation are well described in the hESCs although intracellular mechanisms underlying neural development are largely unknown. Proteome analysis of hESC differentiation to neural cells will help to further define molecular mechanisms involved in neurogenesis in humans. Using a two-dimensional differential gel electrophoresis (2D-DIGE) system, we analyzed the proteome of hESC differentiation to neurons at three stages, early neural differentiation, neural ectoderm and mature neurons. Out of 137 differentially accumulated protein spots, 118 spots were identified using MALDI-TOF/TOF and LC MS/MS. We observed that proteins involved in redox hemostasis, vitamin and energy metabolism and ubiquitin dependent proteolysis were more abundant in differentiated cells, whereas the abundance of proteins associated with RNA processing and protein folding was higher in hESCs. Higher abundance of proteins involved in maintaining cellular redox state suggests the importance of redox hemostasis in neural differentiation. Furthermore, our results support the concept of a coupling mechanism between neuronal activity and glucose utilization. The protein network analysis showed that the majority of the interacting proteins were associated with the cell cycle and cellular proliferation. These results enhanced our understanding of the molecular dynamics that underlie neural commitment and differentiation. In highlighting the role of redox and unique metabolic properties of neuronal cells, the present findings add insight to our understanding of hESC differentiation to neurons. The abundance of fourteen proteins involved in maintaining cellular redox state, including 10 members of peroxiredoxin (Prdx) family, mainly increased during differentiation, thus highlighting a link of neural differentiation to redox. Our results revealed markedly higher expression of genes encoding enzymes involved in the glycolysis and amino acid synthesis during differentiation. Protein network analysis predicted a number of critical mediators in hESC differentiation. These proteins included TP53, CTNNB1, SMARCA4, TNF, TERT, E2F1, MYC, RB1, and AR. Copyright © 2014 Elsevier B.V. All rights reserved.

Production of a novel neuromelanin at the sevoflurane-water interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, Ryan D.; Fibuch, Eugene E.; Elisabeth Heal, M.

2007-11-09

Postoperative cognitive dysfunction (POCD) occurs in the elderly following surgery that requires inhaled anesthetics. The molecular mechanism associated with this process is unknown. This study examined the possible role of serotonin, a neurotransmitter involved in cognition. We observed that sevoflurane, a common inhaled anesthetic, formed a separate phase in water similar to that of chloroform. Additionally, sevoflurane sequestered acrolein, which is a lipid peroxidation product associated with aging and is elevated in the elderly brain. The enhanced partitioning of acrolein increased the focal concentration and hence reactivity to serotonin which preferentially occurred at the sevoflurane-water interface. The resulting product exhibitedmore » unique properties similar to catecholamine-derived neuromelanin.« less