40 results match your criteria: "City College of CUNY[Affiliation]"

Nearly a quarter of the genome encodes for inner membrane proteins of which approximately a third have unassigned or poorly understood function. We had previously demonstrated that the synergy between the functional roles of the inner membrane-spanning YciB and the inner membrane lipoprotein DcrB, is essential in maintaining cell envelope integrity. In cells, the abundant outer membrane lipoprotein, Lpp, mislocalizes to the inner membrane where it forms toxic linkages to peptidoglycan.

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Soil granular dynamics on-a-chip: fluidization inception under scrutiny.

Lab Chip

March 2019

Levich Institute, City College of CUNY, 140th Street and Convent Avenue, New York, NY 10031, USA.

Predicting soil evolution remains a scientific challenge. This process involves poorly understood aspects of disordered granular matter and dense suspension dynamics. This study presents a novel two-dimensional experiment on a small-scale chip structure; this allows the observation of the deformation at the particle scale of a large-grained sediment bed, under conditions where friction dominates over cohesive and thermal forces, and with an imposed fluid flow.

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The bacterial cytoplasmic membrane is a principal site of protein translocation, lipid and peptidoglycan biogenesis, signal transduction, transporters and energy generating components of the respiratory chain. Although 25-30% of bacterial proteomes consist of membrane proteins, a comprehensive understanding of their influence on fundamental cellular processes is incomplete. Here, we show that YciB and DcrB, two small cytoplasmic membrane proteins of previously unknown functions, play an essential synergistic role in maintaining cell envelope integrity of Escherichia coli.

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The Zeeman splitting and degree of circular polarization (DCP) of photoluminescence (PL) from type-II submonolayer ZnTe/ZnSe quantum dots (QDs) have been investigated in magnetic fields up to 18 T. To explain the observed relative intensities and energy positions of the σ and the σ PL, a non-Boltzmann distribution for holes with ultra-long spin-flip time, confined to submonolayer QDs, is proposed. The -factor of electrons, located in the ZnSe barriers, was obtained from fitting the temperature dependence of the DCP, and its value is in excellent agreement with that of bulk ZnSe.

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Rheology of sediment transported by a laminar flow.

Phys Rev E

December 2016

Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

Understanding the dynamics of fluid-driven sediment transport remains challenging, as it occurs at the interface between a granular material and a fluid flow. Boyer, Guazzelli, and Pouliquen [Phys. Rev.

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Polymerization of a ring-like cytoskeletal structure, the Z-ring, at midcell is a highly conserved feature in virtually all bacteria. The Z-ring is composed of short protofilaments of the tubulin homolog FtsZ, randomly arranged and held together through lateral interactions. In vitro, lateral associations between FtsZ protofilaments are stabilized by crowding agents, high concentrations of divalent cations, or in some cases, low pH.

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The bacterial FtsZ-ring is an essential cytokinetic structure under tight spatiotemporal regulation. In Escherichia coli, FtsZ polymerization and assembly into the Z-ring is controlled on multiple levels through interactions with positive and negative regulators. Among these regulatory factors are ZapC, a Z-ring stabilizer, and the conserved protease ClpXP, which has been shown to degrade FtsZ protofilaments in preference to FtsZ monomers.

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In Escherichia coli cell division is driven by the tubulin-like GTPase, FtsZ, which forms the cytokinetic Z-ring. The Z-ring serves as a dynamic platform for the assembly of the multiprotein divisome, which catalyzes membrane cleavage to create equal daughter cells. Several proteins effect FtsZ assembly, thereby providing spatiotemporal control over cell division.

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The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K(+) ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein.

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Computational analysis of residue contributions to coiled-coil topology.

Protein Sci

November 2011

Department of Chemistry, The City College of CUNY, 160 Convent Avenue, New York, New York 10031, USA.

A variety of features are thought to contribute to the oligomeric and topological specificity of coiled coils. In previous work, we examined the determinants of oligomeric state. Here, we examine the energetic basis for the tendency of six coiled-coil peptides to align their α-helices in antiparallel orientation using molecular dynamics simulations with implicit solvation (EEF1.

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Attrition of undergraduates from Biology majors is a long-standing problem. Introductory courses that fail to engage students or spark their curiosity by emphasizing the open-ended and creative nature of biological investigation and discovery could contribute to student detachment from the field. Our hypothesis was that introductory biology books devote relatively few figures to illustration of the design and interpretation of experiments or field studies, thereby de-emphasizing the scientific process.

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Colicins are water-soluble toxins that, upon interaction with membranes, undergo a conformational change, insert, and form pores in them. Pore formation activity is localized in a bundle of 10 α-helices named the pore-forming domain (PFD). There is evidence that colicins attach to the membrane via a hydrophobic hairpin embedded in the core of the PFD.

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Negative staining and cryo-negative staining of macromolecules and viruses for TEM.

Micron

February 2011

Department of Chemistry, and Institute for Macro Molecular Assemblies, The City College of CUNY, 160 Convent Ave, New York, NY, USA.

In this review we cover the technical background to negative staining of biomolecules and viruses, and then expand upon the different possibilities and limitations. Topics range from conventional air-dry negative staining of samples adsorbed to carbon support films, the variant termed the "negative staining-carbon film" technique and negative staining of samples spread across the holes of holey-carbon support films, to a consideration of dynamic/time-dependent negative staining. For each of these approaches examples of attainable data are given.

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Sex steroid hormones are major determinants of bone morphology and quality and are responsible for sexually dimorphic skeletal traits. Hypogonadism results in suboptimal skeletal development and may lead to an increased risk of bone fracture later in life. The etiology of delayed puberty and/or hypothalamic amenorrhea is poorly understood, and experimental animal models addressing this issue are predominantly based upon short-term experimental induction of hormonal suppression via gonadotropin releasing hormone antagonists (GnRH-a).

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The coiled coil is one of the simplest and best-studied protein structural motifs, consisting of two to five helices wound around each other. Empirical rules have been established on the tendency of different core sequences to form a certain oligomeric state but the physical forces behind this specificity are unclear. In this work, we model four sequences onto the structures of dimeric, trimeric, tetrameric, and pentameric coiled coils.

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The effect of water displacement on binding thermodynamics: concanavalin A.

J Phys Chem B

January 2005

Department of Chemistry, City College of CUNY, New York, New York 10031, USA.

Interactions at the binding interface of biomolecular complexes are often mediated by ordered water molecules. In this work, we considered two concanavalin A-carbohydrate complexes. In the first, a water molecule is buried at the binding interface.

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Triplet correlation in sheared suspensions of Brownian particles.

J Chem Phys

May 2006

Benjamin Levich Institute for Physico-Chemical Hydrodynamics and Department of Chemical Engineering, City College of CUNY, New York, New York 10031, USA.

Triplet microstructure of sheared concentrated suspensions of Brownian monodisperse spherical particles is studied by sampling realizations of a three-dimensional unit cell subject to periodic boundary conditions obtained in accelerated Stokesian dynamics simulations. Triplets are regarded as a bridge between particle pairs and many-particle clusters thought responsible for shear thickening. Triplet-correlation data for weakly sheared near-equilibrium systems display an excluded volume effect of accumulated correlation for equilateral contacting triplets.

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Interfacial slip in sheared polymer blends.

Phys Rev E Stat Nonlin Soft Matter Phys

October 2005

The Levich Institute, City College of CUNY, New York, New York 10031, USA.

We have developed a dynamic self-consistent field theory, without any adjustable parameters, for unentangled polymer blends under shear. Our model accounts for the interaction between polymers, and enables one to compute the evolution of the local rheology, microstructure, and the conformations of the polymer chains under shear self-consistently. We use this model to study the interfacial dynamics in sheared polymer blends and make a quantitative comparison between this model and molecular dynamics simulations.

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The naked mole-rat: a new long-living model for human aging research.

J Gerontol A Biol Sci Med Sci

November 2005

Department of Biology, City College of CUNY, Convent Ave. at 138th St., New York, NY 10031, USA.

Tremendous variation in maximum life span among species overshadows modest increases in longevity resulting from experimental manipulation. Few aging studies focus on long-lived mammals even though these species may expose mechanisms involved in resisting aging. Naked mole-rats (NMRs approximately 35 grams) are the longest-living (>28.

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Full pockets, empty lives: a psychoanalytic exploration of the contemporary culture of greed.

Am J Psychoanal

June 2003

Doctoral Program in Clinical Psychology, City College of CUNY, New York, NY 10031, USA.

This paper offers a psychoanalytic exploration of the dynamics of greed in individual lives and ways that those dynamics both reflect and influence the surrounding culture. The paper discusses the contradictions associated with the consumerist pursuit of wealth and goods, and finds evidence for the failure of such pursuit to provide the satisfaction that is anticipated. It also examines the implications for psychoanalytic theorizing on the ways in which ongoing social forces and institutions contribute to shaping the psyche.

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Single-electron oxidation of the carcinogenic hydrocarbon benzo[a]pyrene (BaP) is thought to result in a radical cation intermediate and this species has been proposed to cause alkylation at the nitrogens of the purine nucleobases. Although several different nucleoside adducts have been isolated as arising from this mode of metabolic activation, there are no selective, total syntheses of the stable exocyclic amino group adducts formed by the single-electron oxidation of any hydrocarbon with the purine 2'-deoxynucleosides to date. In this paper we disclose the synthesis of the model adducts N(6)-(1-pyrenyl)-2'-deoxyadenosine and N(2)-(1-pyrenyl)-2'-deoxyguanosine as well as the first synthesis of the carcinogen-linked nucleoside derivatives N(6)-(6-benzo[a]pyrenyl)-2'-deoxyadenosine and N(2)-(6-benzo[a]pyrenyl)-2'-deoxyguanosine via a palladium-mediated C-N bond formation.

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Thermodynamic contributions of the ordered water molecule in HIV-1 protease.

J Am Chem Soc

June 2003

Department of Chemistry, City College of CUNY, Convent Avenue and 138th Street, New York, NY 10031, USA.

Binding between biomolecules is usually accompanied by the formation of direct interactions with displacement of water from the binding sites. In some cases, however, the interactions are mediated by ordered water molecules, whose effect on binding affinity and the other thermodynamic functions is unclear. In this work, we compute the contribution of one such water molecule, the strongly bound water molecule at the binding site of HIV-1 protease, to the thermodynamic properties using statistical mechanical formulas for the energy and entropy.

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Pd-catalyzed coupling of the axially constrained, less reactive benzo[a]pyrene bay-region amino benzoates, derived from the tetrahydro and diol epoxides, with C-6 and C-2 halopurine deoxynucleosides offers an efficient approach to the synthesis of the corresponding nucleoside-epoxide adducts. Also reported are the first examples involving the coupling of a 6-chloropurine deoxynucleoside with these amines, a reaction that is difficult by direct halide displacement. Certain mechanistic aspects of this metal-catalyzed C-N bond formation are also discussed.

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Cellular senescence is a terminal growth phase characteristic of normal human diploid fibroblasts. Altered gene expression during cellular senescence is numerous compared to that of younger proliferative cells in culture. We have previously reported that the levels and activities of hnRNP A1 and A2 RNA binding proteins are decreased in senescent human fibroblasts.

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