bluuebunny/crossref_metadata_2025 huggingface dataset:
Prácticas de fronterización, pluralización y diferencia
Authors: Briones Claudia , Del Cairo Carlos
Published: September 2015

En este artículo exploramos prácticas de fronterización, entendidas como las diversas maneras enque colectivos sociales marcan un adentro y un afuera, en correlato con la diferenciación nosotros/otros. Buscamos identificar cómo operan esas prácticas en la dialéctica Estado-minorías étnicas,central en la configuración histórica de las sociedades latinoamericanas. Aunque como constructossociales esas fronteras emerjan como divisorias nítidas, las abordamos como membranas porosasy selectivamente cambiantes, abiertas a reconexiones. Para sugerir algunos desplazamientosanalíticos relevantes y necesarios que la época actual propicia, organizamos el texto en cuatro pasosimbricados pero distinguibles. Abordamos primero las dis/continuidades en la conceptualización dela frontera en el pensamiento social. Enunciamos luego cómo las fronteras políticas gravitan sobreprácticas de fronterización resultantes de políticas de marcación de diferencias y de reconocimiento.Examinamos después lo que entendemos como una pluralización de las fronteras espaciales,categoriales y sociales. Abordamos, por último, los desafíos sociales y disciplinares que apareja elreconocimiento de fronteras epistémicas.
Una reflexión sobre la violencia y la construcción de paz desde el teatro y el arte
Authors: Tovar Patricia
Published: September 2015

Este artículo es una invitación a pensar en el arte y el legado de la violencia y la injusticia en la historia de la humanidad y en los esfuerzos trabajados desde diferentes proyectos artísticos en la resolución de conflictos y en la promoción de la paz en el mundo. Se presentan y analizan algunas de esas experiencias y se examina cómo han sido aplicadas por diferentes disciplinas para resolver o avanzar sobre algunos de los problemas que aquejan a la sociedad. Es también importante pensar en el uso del arte, del teatro y de la creatividad como estrategia metodológica y como un ejercicio de investigación participativa que permita la investigación transformativa en el campo de la violencia y el trabajo en grupo desde las comunidades afectadas.
Sobre malentendidos interétnicos
Authors: Rita Ramos Alcida
Published: September 2015

Examino el fenómeno conocido por términos como méconaissance, cross purposes, malentendidos productivos, compatibilidades equivocadas, etc. que se refieren a las consecuencias sociopolíticas de la comunicación imperfecta en el contexto de las relaciones interétnicas entre pueblos indígenas y la sociedad englobante. Dentro de una gama variada, elijo tres conceptos por el contraste evidente entre las interpretaciones indígenas y las nacionales: democracia, poder y nepotismo. Estos conceptos y sus prácticas respectivas ejemplifican una nueva fase del indigenismo que, tanto en Brasil como más allá, podríamos llamar no más fricción interétnica sino fricción epistémica.
¿Existe una filosofía de la ingeniería?
Authors: Jaramillo Patiño Diego Fernando
Published: September 2015

En tanto que la ciencia y la tecnología han sido objetos legítimos de reflexión filosófica, este no es el caso de la ingeniería. Hoy día, la filosofía de la ciencia y la de la tecnología son disciplinas profesionales perfectamente establecidas. Este trabajo pretende mostrar que la Filosofía de la Ingeniería es un campo en construcción que cumple las condiciones para ser una disciplina filosófica profesional: comunidad académica, agenda de investigación y órganos de difusión. Para ello, realizamos una exploración bibliográfica descriptiva que nos permita identificar los momentos que constituyen la disciplina, ubicándolos en una línea de tiempo entre 1998 y 2014, a partir del “giro empírico” en la filosofía de la tecnología, como evento fundacional de la filosofía de la ingeniería, a través de la serie de eventos que, como consecuencia del “giro empírico”, componen propiamente la disciplina en el tiempo.
Lo que no podemos hacernos el uno al otro. Sobre el perdón y la vulnerabilidad moral
Authors: Fricke Christel
Published: September 2015

Típicamente, el perdón se convierte en un problema cuando un ofensor ha dañado a una víctima. Cuando se comprometen en un proceso de dar y conceder perdón, al ofensor y a su víctima les interesan las relaciones sociales que previamente existieron entre ellos. Partiendo del trasfondo de estas relaciones surge la pregunta de si para la víctima perdonar es un deber y si el ofensor tiene el derecho de ser perdonado. Sugiero distinguir entre relaciones personales y morales entre personas: las morales vinculan a todo agente racional a la comunidad de todos los agentes morales, mientras que las primeras son de carácter personal. En este sentido, distingo entre perdón personal y moral. Y discuto que el ofensor tiene derecho a ser moralmente perdonado, o por la misma víctima o por otro miembro de la comunidad de agentes morales; pero la víctima no tiene un deber de perdonar personalmente al ofensor.
Effect of substrate composition on atomic layer deposition using self-assembled monolayers as blocking layers
Authors: Zhang Wenyu , Engstrom James R.
Published: September 2015

The authors have examined the effect of two molecules that form self-assembled monolayers (SAMs) on the subsequent growth of TaNx by atomic layer deposition (ALD) on two substrate surfaces, SiO2 and Cu. The SAMs that the authors have investigated include two vapor phase deposited, fluorinated alkyl silanes: Cl3Si(CH2)2(CF2)5CF3 (FOTS) and (C2H5O)3Si(CH2)2(CF2)7CF3 (HDFTEOS). Both the SAMs themselves and the TaNx thin films, grown using Ta[N(CH3)2]5 and NH3, were analyzed ex situ using contact angle, spectroscopic ellipsometry, x-ray photoelectron spectroscopy (XPS), and low energy ion-scattering spectroscopy (LEISS). First, the authors find that both SAMs on SiO2 are nominally stable at Ts ∼ 300 °C, the substrate temperature used for ALD, while on Cu, the authors find that HDFTEOS thermally desorbs, while FOTS is retained on the surface. The latter result reflects the difference in the head groups of these two molecules. The authors find that both SAMs strongly attenuate the ALD growth of TaNx on SiO2, by about a factor of 10, while on Cu, the SAMs have no effect on ALD growth. Results from LEISS and XPS are decisive in determining the nature of the mechanism of growth of TaNx on all surfaces. Growth on SiO2 is 2D and approximately layer-by-layer, while on the surfaces terminated by the SAMs, it nucleates at defect sites, is islanded, and is 3D. In the latter case, our results support growth of the TaNx thin film over the SAM, with a considerable delay in formation of a continuous thin film. Growth on Cu, with or without the SAMs, is also 3D and islanded, and there is also a delay in the formation of a continuous thin film as compared to growth on SiO2. These results highlight the power of coupling measurements from both LEISS and XPS in examinations of ultrathin films formed by ALD.
Role of low-energy ion irradiation in the formation of an aluminum germanate layer on a germanium substrate by radical-enhanced atomic layer deposition
Authors: Fukuda Yukio , Yamada Daichi , Yokohira Tomoya , Yanachi Kosei , Yamamoto Chiaya , Yoo Byeonghak , Yamanaka Junji , Sato Tetsuya , Takamatsu Toshiyuki , Okamoto Hiroshi
Published: September 2015

Radical-enhanced atomic layer deposition uses oxygen radicals generated by a remote microwave-induced plasma as an oxidant to change the surface reactions of the alternately supplied trimethylaluminum precursor and oxygen radicals on a Ge substrate, which leads to the spontaneous formation of an aluminum germanate layer. In this paper, the effects that low-energy ions, supplied from a remote microwave plasma to the substrate along with the oxygen radicals, have on the surface reactions were studied. From a comparative study of aluminum oxide deposition under controlled ion flux irradiation on the deposition surface, it was found that the ions enhance the formation of the aluminum germanate layer. The plasma potential measured at the substrate position by the Langmuir probe method was 5.4 V. Assuming that the kinetic energy of ions arriving at the substrate surface is comparable to that gained by this plasma potential, such ions have sufficient energy to induce exchange reactions of surface-adsorbed Al atoms with the underlying Ge atoms without causing significant damage to the substrate. This ion-induced exchange reaction between Al and Ge atoms is inferred to be the background kinetics of the aluminum germanate formation by radical-enhanced atomic layer deposition.
A Comparison of the Media-Ideal and Athletic Internalization Between Young Female Gymnasts and Track and Field Sprinters
Authors: Fortes Leonardo de Sousa , Paes Santiago Tavares , Neves Clara Mockede , Meireles Juliana Fernandes Filgueiras , Ferreira Maria Elisa Caputo
Published: September 2015

The aim of this study was to compare the media-ideal and athletic internalization of gymnasts to track and field sprinters. Eighty-three female track and field sprinters and 50 female gymnasts participated. The subscales of the Sociocultural Attitudes Toward Appearance Questionnaire-3 were used to evaluate the influence of the media on body image. The Body Shape Questionnaire was used to assess body dissatisfaction. The results showed no difference between the groups in media-ideal internalization (p > .05); however, the results indicated differences in athletic internalization (p < .05) and body dissatisfaction (p < .05). We concluded that although media-ideal internalization was similar, gymnasts showed greater athletic internalization.
Mental Health Referral for Student-Athletes: Web-Based Education and Training
Authors: Van Raalte Judy L. , Cornelius Allen E. , Andrews Staci , Diehl Nancy S. , Brewer Britton W.
Published: September 2015

Physically and mentally healthy student-athletes are in a good position to thrive academically, socially, and athletically. Unfortunately, many student-athletes fail to get the mental health help they need due to factors such as lack of knowledge and mental health stigma. The purpose of this research was to create and evaluate a multimedia, interactive website (www.SupportForSport.org) to enable student-athletes to gain the necessary knowledge and confidence to make effective mental health referrals. Study 1 was conducted to determine if the website functioned as intended. In Study 2, 27 intercollegiate athletic directors and coaches evaluated the website. Their favorable evaluations led to Study 3, a controlled field trial with a national sample of 153 student-athletes. Results indicated that viewing the www.SupportForSport.org site resulted in enhanced mental health referral knowledge and efficacy relative to a control group. These results suggest that tailored online programming can affect outcomes for student-athletes across geographic regions and resource availability levels.
Science Signaling
Podcast for 29 September 2015: Glutamine and T cell differentiation
Authors: Dardalhon Valérie , Taylor Naomi , VanHook Annalisa M.
Published: September 2015

Availability of the nutrient glutamine influences the differentiation of T cells.
Antibiotics for sickle cell disease
Authors: Gough Nancy R.
Published: September 2015

Depletion of the microbiome with antibiotics may prevent neutrophil aging and improve circulation in patients with sickle cell disease.
Fitness Studies of Azole-Resistant Strains of Aspergillus fumigatus
Authors: Valsecchi Isabel , Mellado Emilia , Beau Rémi , Raj Shriya , Latgé Jean-Paul
Published: September 2015

Isogenic bar-coded strains of
Aspergillus fumigatus
carrying the G54W or M220K mutation in Cyp51A were constructed.
In vitro
, the growth and conidiation capacities of the mutants were similar to those of the parental strain. Competition studies in the absence of azoles showed that there was no adverse fitness cost for the azole-resistant
A. fumigatus
strains
in vitro
or
in vivo
compared to the parental strain.
Effects of Antiviral Drugs on Organic Anion Transport in Human Placental BeWo Cells
Authors: Nabekura Tomohiro , Kawasaki Tatsuya , Kamiya Yuki , Uwai Yuichi
Published: September 2015

Placental drug transfer is important for achieving better pharmacotherapy in pregnant women and in fetuses. In the present study, we examined the effects of anti-hepatitis C virus (HCV) and anti-HIV drugs on organic anion transport in human placental BeWo cells. The cellular uptake of two fluorescence organic anions, 8-(2-[fluoresceinyl]aminoethylthio)adenosine-3′,5′-cyclic monophosphate (8-FcAMP) and fluorescein, was temperature and concentration dependent. The Michaelis constant (

K
m

) and the maximum uptake rate (
V
max
) for 8-FcAMP transport in BeWo cells were estimated to be 6.45 ± 0.75 μM and 25.55 ± 5.93 pmol/mg protein/10 min, respectively. The

K
m

and
V
max
values for fluorescein uptake were estimated to be 31.2 ± 11.8 μM and 510.9 ± 90.6 pmol/mg protein/10 min, respectively. Several known substrates of organic anion transporters in human placenta, including atorvastatin, glibenclamide, estrone-3-sulfate, and rifampin, inhibited cellular uptake of 8-FcAMP and fluorescein in BeWo cells. Transport of 8-FcAMP and fluorescein was inhibited by the antiviral drugs boceprevir, telaprevir, elvitegravir, and maraviroc. These findings suggest that some antiviral drugs are sufficiently potent to influence placental drug transfer and cause drug-drug interactions.
Two Simple Rules for Improving the Accuracy of Empiric Treatment of Multidrug-Resistant Urinary Tract Infections
Authors: Linsenmeyer Katherine , Strymish Judith , Gupta Kalpana
Published: September 2015

The emergence of multidrug-resistant (MDR) uropathogens is making the treatment of urinary tract infections (UTIs) more challenging. We sought to evaluate the accuracy of empiric therapy for MDR UTIs and the utility of prior culture data in improving the accuracy of the therapy chosen. The electronic health records from three U.S. Department of Veterans Affairs facilities were retrospectively reviewed for the treatments used for MDR UTIs over 4 years. An MDR UTI was defined as an infection caused by a uropathogen resistant to three or more classes of drugs and identified by a clinician to require therapy. Previous data on culture results, antimicrobial use, and outcomes were captured from records from inpatient and outpatient settings. Among 126 patient episodes of MDR UTIs, the choices of empiric therapy against the index pathogen were accurate in 66 (52%) episodes. For the 95 patient episodes for which prior microbiologic data were available, when empiric therapy was concordant with the prior microbiologic data, the rate of accuracy of the treatment against the uropathogen improved from 32% to 76% (odds ratio, 6.9; 95% confidence interval, 2.7 to 17.1;
P
< 0.001). Genitourinary tract (GU)-directed agents (nitrofurantoin or sulfa agents) were equally as likely as broad-spectrum agents to be accurate (
P
= 0.3). Choosing an agent concordant with previous microbiologic data significantly increased the chance of accuracy of therapy for MDR UTIs, even if the previous uropathogen was a different species. Also, GU-directed or broad-spectrum therapy choices were equally likely to be accurate. The accuracy of empiric therapy could be improved by the use of these simple rules.
Novel Type XII Staphylococcal Cassette Chromosome
mec
Harboring a New Cassette Chromosome Recombinase, CcrC2
Authors: Wu Zhaowei , Li Fan , Liu Dongliang , Xue Huping , Zhao Xin
Published: September 2015

Excision and integration of staphylococcal cassette chromosome
mec
(SCC
mec
) are mediated by cassette chromosome recombinases (Ccr), which play a crucial role in the worldwide spread of methicillin resistance in staphylococci. We report a novel
ccr
gene,
ccrC2
, in the SCC
mec
of a
Staphylococcus aureus
isolate, BA01611, which showed 62.6% to 69.4% sequence identities to all published
ccrC1
sequences. A further survey found that the
ccrC2
gene was mainly located among coagulase-negative staphylococci (CoNS) and could be found in staphylococcal isolates from China, the United States, France, and Germany. The
ccr
gene complex harboring the
ccrC2
gene was designated a type 9 complex, and the SCC
mec
of BA01611 was considered a novel type and was designated type XII (9C2). This novel SCC
mec
element in BA01611 was flanked by a pseudo-SCC element (ΨSCC
BA01611
) carrying a truncated
ccrA1
gene. Both individual SCC elements and a composite SCC were excised from the chromosome based on detection of extrachromosomal circular intermediates. We advocate inclusion of the c
crC2
gene and type 9
ccr
gene complex during revision of the SCC
mec
typing method.
Fitness Cost of Rifampin Resistance in Neisseria meningitidis:
In Vitro
Study of Mechanisms Associated with
rpoB
H553Y Mutation
Authors: Colicchio Roberta , Pagliuca Chiara , Pastore Gabiria , Cicatiello Annunziata Gaetana , Pagliarulo Caterina , Talà Adelfia , Scaglione Elena , Sammartino Josè Camilla , Bucci Cecilia , Alifano Pietro , Salvatore Paola
Published: September 2015

Rifampin chemoprophylaxis against
Neisseria meningitidis
infections led to the onset of rifampin resistance in clinical isolates harboring point mutations in the
rpoB
gene, coding for the RNA polymerase β chain. These resistant strains are rare in medical practice, suggesting their decreased fitness in the human host. In this study, we isolated rifampin-resistant
rpoB
mutants from hypervirulent serogroup C strain 93/4286 and analyzed their different properties, including the ability to grow/survive in different culture media and in differentiated THP-1 human monocytes and to compete with the wild-type strain
in vitro
. Our results demonstrate that different
rpoB
mutations (H553Y, H553R, and S549F) may have different effects, ranging from low- to high-cost effects, on bacterial fitness
in vitro
. Moreover, we found that the S549F mutation confers temperature sensitivity, possibly explaining why it is observed very rarely in clinical isolates. Comparative high-throughput RNA sequencing analysis of bacteria grown in chemically defined medium demonstrated that the low-cost H553Y substitution resulted in global transcriptional changes that functionally mimic the stringent response. Interestingly, many virulence-associated genes, including those coding for meningococcal type IV pili, porin A, adhesins/invasins, IgA protease, two-partner secretion system HrpA/HrpB, enzymes involved in resistance to oxidative injury, lipooligosaccharide sialylation, and capsular polysaccharide biosynthesis, were downregulated in the H553Y mutant compared to their level of expression in the wild-type strain. These data might account for the reduced capacity of this mutant to grow/survive in differentiated THP-1 cells and explain the rarity of H553Y mutants among clinical isolates.
In Vitro
Activities of Primaquine-Schizonticide Combinations on Asexual Blood Stages and Gametocytes of Plasmodium falciparum
Authors: Cabrera Mynthia , Cui Liwang
Published: September 2015

Currently, the World Health Organization recommends addition of a 0.25-mg base/kg single dose of primaquine (PQ) to artemisinin combination therapies (ACTs) for
Plasmodium falciparum
malaria as a gametocytocidal agent for reducing transmission. Here, we investigated the potential interactions of PQ with the long-lasting components of the ACT drugs for eliminating the asexual blood stages and gametocytes of
in vitro
-cultured
P. falciparum
strains. Using the SYBR green I assay for asexual parasites and a flow cytometry-based assay for gametocytes, we determined the interactions of PQ with the schizonticides chloroquine, mefloquine, piperaquine, lumefantrine, and naphthoquine. With the sums of fractional inhibitory concentrations and isobolograms, we were able to determine mostly synergistic interactions for the various PQ and schizonticide combinations on the blood stages of
P. falciparum
laboratory strains. The synergism in inhibiting asexual stages and gametocytes was highly evident with PQ-naphthoquine, whereas synergism was moderate for the PQ-piperaquine, PQ-chloroquine, and PQ-mefloquine combinations. We have detected potentially antagonistic interactions between PQ and lumefantrine under certain drug combination ratios, suggesting that precautions might be needed when PQ is added as the gametocytocide to the artemether-lumefantrine ACT (Coartem).
Guanylate Binding Proteins Enable Rapid Activation of Canonical and Noncanonical Inflammasomes in Chlamydia-Infected Macrophages
Authors: Finethy Ryan , Jorgensen Ine , Haldar Arun K. , de Zoete Marcel R. , Strowig Till , Flavell Richard A. , Yamamoto Masahiro , Nagarajan Uma M. , Miao Edward A. , Coers Jörn
Published: September 2015

Interferon (IFN)-inducible guanylate binding proteins (GBPs) mediate cell-autonomous host resistance to bacterial pathogens and promote inflammasome activation. The prevailing model postulates that these two GBP-controlled activities are directly linked through GBP-dependent vacuolar lysis. It was proposed that the rupture of pathogen-containing vacuoles (PVs) by GBPs destroyed the microbial refuge and simultaneously contaminated the host cell cytosol with microbial activators of inflammasomes. Here, we demonstrate that GBP-mediated host resistance and GBP-mediated inflammatory responses can be uncoupled. We show that PVs formed by the rodent pathogenChlamydia muridarum, so-called inclusions, remain free of GBPs and thatC. muridarumis impervious to GBP-mediated restrictions on bacterial growth. Although GBPs neither bind toC. muridaruminclusions nor restrictC. muridarumgrowth, we find that GBPs promote inflammasome activation inC. muridarum-infected macrophages. We demonstrate thatC. muridaruminfections induce GBP-dependent pyroptosis through both caspase-11-dependent noncanonical and caspase-1-dependent canonical inflammasomes. Among canonical inflammasomes, we find thatC. muridarumand the human pathogenChlamydia trachomatisactivate not only NLRP3 but also AIM2. Our data show that GBPs support fast-kinetics processing and secretion of interleukin-1β (IL-1β) and IL-18 by the NLRP3 inflammasome but are dispensable for the secretion of the same cytokines at later times postinfection. Because IFN-γ fails to induce IL-1β transcription, GBP-dependent fast-kinetics inflammasome activation can drive the preferential processing of constitutively expressed IL-18 in IFN-γ-primed macrophages in the absence of prior Toll-like receptor stimulation. Together, our results reveal that GBPs control the kinetics of inflammasome activation and thereby shape macrophage responses toChlamydiainfections.
Vigilant Keratinocytes Trigger Pathogen-Associated Molecular Pattern Signaling in Response to Streptococcal M1 Protein
Authors: Persson Sandra T. , Wilk Laura , Mörgelin Matthias , Herwald Heiko
Published: September 2015

The human skin exerts many functions in order to maintain its barrier integrity and protect the host from invading microorganisms. One such pathogen isStreptococcus pyogenes, which can cause a variety of superficial skin wounds that may eventually progress into invasive deep soft tissue infections. Here we show that keratinocytes recognize soluble M1 protein, a streptococcal virulence factor, as a pathogen-associated molecular pattern to release alarming inflammatory responses. We found that this interaction initiates an inflammatory intracellular signaling cascade involving the activation of the mitogen-activated protein kinases extracellular signal-regulated kinase (ERK), p38, and Jun N-terminal protein kinase and the subsequent induction and mobilization of the transcription factors NF-κB and AP-1. We also determined the imprint of the inflammatory mediators released, such as interleukin-8 (IL-8), growth-related oncogene alpha, migration inhibitory factor, extracellular matrix metalloproteinase inducer, IL-1α, IL-1 receptor a, and ST2, in response to streptococcal M1 protein. The expression of IL-8 is dependent on Toll-like receptor 2 activity and subsequent activation of the mitogen-activated protein kinases ERK and p38. Notably, this signaling seems to be distinct for IL-8 release, and it is not shared with the other inflammatory mediators. We conclude that keratinocytes participate in a proinflammatory manner in streptococcal pattern recognition and that expression of the chemoattractant IL-8 by keratinocytes constitutes an important protective mechanism against streptococcal M1 protein.
Expression and Localization of Predicted Inclusion Membrane Proteins in Chlamydia trachomatis
Authors: Weber Mary M. , Bauler Laura D. , Lam Jennifer , Hackstadt Ted
Published: September 2015

Chlamydia trachomatis
is an obligate intracellular pathogen that replicates in a membrane-bound vacuole termed the inclusion. Early in the infection cycle, the pathogen extensively modifies the inclusion membrane through incorporation of numerous type III secreted effector proteins, called inclusion membrane proteins (Incs). These proteins are characterized by a bilobed hydrophobic domain of 40 amino acids. The presence of this domain has been used to predict up to 59 putative Incs for
C. trachomatis
; however, localization to the inclusion membrane with specific antibodies has been demonstrated for only about half of them. Here, we employed recently developed genetic tools to verify the localization of predicted Incs that had not been previously localized to the inclusion membrane. Expression of epitope-tagged putative Incs identified 10 that were previously unverified as inclusion membrane localized and thus authentic Incs. One novel Inc and 3 previously described Incs were localized to inclusion membrane microdomains, as evidenced by colocalization with phosphorylated Src (p-Src). Several predicted Incs did not localize to the inclusion membrane but instead remained associated with the bacteria. Using
Yersinia
as a surrogate host, we demonstrated that many of these are not secreted via type III secretion, further suggesting they may not be true Incs. Collectively, our results highlight the utility of genetic tools for demonstrating secretion from chlamydia. Further mechanistic studies aimed at elucidating effector function will advance our understanding of how the pathogen maintains its unique intracellular niche and mediates interactions with the host.
An Electrostatic Net Model for the Role of Extracellular DNA in Biofilm Formation by Staphylococcus aureus
Authors: Dengler Vanina , Foulston Lucy , DeFrancesco Alicia S. , Losick Richard
Published: September 2015

Staphylococcus aureus
is an important human pathogen that can form biofilms on various surfaces. These cell communities are protected from the environment by a self-produced extracellular matrix composed of proteins, DNA, and polysaccharide. The exact compositions and roles of the different components are not fully understood. In this study, we investigated the role of extracellular DNA (eDNA) and its interaction with the recently identified cytoplasmic proteins that have a moonlighting role in the biofilm matrix. These matrix proteins associate with the cell surface upon the drop in pH that naturally occurs during biofilm formation, and we found here that this association is independent of eDNA. Conversely, the association of eDNA with the matrix was dependent on matrix proteins. Both proteinase and DNase treatments severely reduced clumping of resuspended biofilms; highlighting the importance of both proteins and eDNA in connecting cells together. By adding an excess of exogenous DNA to DNase-treated biofilm, clumping was partially restored, confirming the crucial role of eDNA in the interconnection of cells. On the basis of our results, we propose that eDNA acts as an electrostatic net, interconnecting cells surrounded by positively charged matrix proteins at a low pH.

IMPORTANCE
Extracellular DNA (eDNA) is an important component of the biofilm matrix of diverse bacteria, but its role in biofilm formation is not well understood. Here we report that in
Staphylococcus aureus
, eDNA associates with cells in a manner that depends on matrix proteins and that eDNA is required to link cells together in the biofilm. These results confirm previous studies that showed that eDNA is an important component of the
S. aureus
biofilm matrix and also suggest that eDNA acts as an electrostatic net that tethers cells together via the proteinaceous layer of the biofilm matrix.
Sequential transcription-translation of simian virus 40 by using mammalian cell extracts.
Authors: Cepko C L , Hansen U , Handa H , Sharp P A
Published: September 2015

Ribonucleic acids (RNAs) transcribed in vitro by using the whole-cell extract system of Manley et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3855-3859, 1980) were tested for their efficiency and fidelity in directing protein synthesis in reticulocyte lysates. Simian virus 40 deoxyribonucleic acid (DNA), cleaved by various restriction endonucleases, was used as the template. Successful translation of the small tumor antigen t, as well as the capsid proteins VP1, VP2, and VP3, was detected by immunoprecipitation analysis. Although no synthesis of large T antigen was detected, use of this technology allows detection of large T synthesis resulting from the correct splicing of as little as 0.2% of the in vitro RNA transcripts, making it ideal for use as an in vitro splicing assay. Transcripts synthesized in vitro were used as messages at least as efficiently as were viral messenger RNA's (mRNA's) synthesized in vivo; and in the case of small t, there was more efficient translation of small t mRNA synthesized in vitro than of small t mRNA synthesized in vivo. The transcripts that served as mRNA's for the various polypeptides were identified by using the following two criteria. (i) The sensitivity of synthesis of a given protein to digestion of the template DNA with restriction enzymes allowed the localization of the promoter and coding regions. (ii) Translation of size-fractionated RNA allowed confirmation of the transcript-mRNA assignments. With these techniques we found that VP2, VP3 and, in some cases, VP1 synthesis resulted from the initiation of translation at internal AUG codons. In fact, families of polypeptides were produced by initiation of translation at AUG codons within sequences coding for VP1 and T, presumably as a result of transcription initiation events that generated 5' ends immediately upstream from these AUGs. Application of this technology for the identification of coding regions within cloned DNA fragments is discussed.
Induction of cellular deoxyribonucleic acid synthesis in butyrate-treated cells by simian virus 40 deoxyribonucleic acid.
Authors: Kawasaki S , Diamond L , Baserga R
Published: September 2015

Sodium butyrate (3 mM) inhibited the entry into the S phase of quiescent 3T3 cells stimulated by serum, but had no effect on the accumulation of cellular ribonucleic acid. Simian virus 40 infection or manual microinjection of cloned fragments from the simian virus 40 A gene caused quiescent 3T3 cells to enter the S phase even in the presence of butyrate. NGI cells, a line of 3T3 cells transformed by simian virus 40, grew vigorously in 3 mM butyrate. Homokaryons were formed between G1 and S-phase 3T3 cells, Butyrate inhibited the induction of deoxyribonucleic acid synthesis that usually occurs in B1 nuclei when G1 cells are fused with S-phase cells. However, when G1 3T3 cells were fused with exponentially growing NGI cells, the 3T3 nuclei were induced to enter deoxyribonucleic acid synthesis. In tsAF8 cells, a ribonucleic acid polymerase II mutant that stops in the G1 phase of the cell cycle, no temporal sequence was demonstrated between the butyrate block and the temperature-sensitive block. These results confirm previous reports that certain virally coded proteins can induce cell deoxyribonucleic acid synthesis in the absence of cellular functions that are required by serum-stimulated cells. Our interpretation of these data is that butyrate inhibited cell growth by inhibiting the expression of genes required for the G0 leads to G1 leads to S transition and that the product of the simian virus 40 A gene overrode this inhibition by providing all of the necessary functions for the entry into the S phase.
Organization and closing of mitochondrial deoxyribonucleic acid from Paramecium tetraaurelia and Paramecium primaurelia.
Authors: Cummings D J , Laping J L
Published: September 2015

Previously we showed that the mitochondrial deoxyribonucleic acid (DNA) from Paramecium aurelia consists of a linear genome and that replication of this genome is initiated at one terminus and proceeds unidirectionally to the other terminus. Analyses of mitochondria from four closely related species (1, 4, 5, and 7) indicated that the species 1, 5, and 7 DNAs are essentially completely homologous but that the species 4 mitochondrial DNA is only 40 to 50% homologous with that from species 1. The major regions of homology are those containing the genes for ribosomal ribonucleic acid (RNA). To understand the replication and organization of the linear mitochondrial genome better, we compared species 1 (Paramecium primaurelia) and 4 (Paramecium tetraaurelia) DNAs with regard to restriction fragment mapping and homology between initiation regions; we also identified the sites of the genes for ribosomal RNA. In general, the structures of the species 1 and 4 mitochondrial genomes were quite similar. Each ribosomal RNA gene was present in one copy per genome, with the large ribosomal RNA gene located near the terminal region of replication and the small ribosomal RNA gene located more centrally. These two genes were separated by about 10 kilobases in the species 1 genome and by about 12 kilobases in the species 4 genome. In contrast to our previous findings, by using nonstringent hybridization conditions we detected homology between the species 1 and 4 DNA fragments containing the initiation regions. We constructed recombinant DNA clones for many fragments, especially those containing the initiation region and the ribosomal RNA genes. We also constructed restriction enzyme maps for six enzymes for both P. primaurelia and P. tetraaurelia.
Cellular titers and subcellular distributions of abundant polyadenylate-containing ribonucleic acid species during early development in the frog Xenopus laevis.
Authors: Dworkin M B , Hershey J W
Published: September 2015

The distribution of cytoplasmic messenger ribonucleic acids (RNAs) in translationally active polysomes and inactive ribonucleoprotein particles changes during early development. Cellular levels and subcellular distributions have been determined for most messenger RNAs, but little is known about how individual sequences change. In this study, we used hybridization techniques with cloned sequences to measure the titers of 23 mitochondrial and non-mitochondrial polyadenylate-containing [poly(A)+]RNA species during early development in the frog Xenopus laevis. These RNA species were some of the most abundant cellular poly(A)+ RNA species in early embryos. The concentrations of most of the non-mitochondrial (cytoplasmic) RNAs remained constant in embryos during the first 10 h of development, although the concentrations of a few species increased. During neurulation, we detected several new poly(A)+ RNA sequences in polysomes, and with one possible exception the accumulation of these sequences was largely the result of new synthesis or de novo polyadenylation and not due to the recruitment of nonpolysomal (free ribonucleoprotein) poly(A)+ RNA. We measured the subcellular distributions of these RNA species in polysomes and free ribonucleoproteins during early development. In gastrulae, non-mitochondrial RNAs were distributed differentially between the two cell fractions; some RNA species were represented more in free ribonucleoproteins, and others were represented less. By the neurula stage this differential distribution in polysomes and free ribonucleoproteins was less pronounced, and we found species almost entirely in polysomes. Some poly(A)+ RNA species transcribed from the mitochondrial genome were localized within the mitochondria and were mapped to discrete fragments of the mitochondrial genome. Much of this poly(A)+ RNA was transcribed from the ribosomal locus. Nonribosomal mitochondrial poly(A)+ RNA species became enriched in polysome-like structures after fertilization, with time courses similar to the time course of mobilization of cytoplasmic poly(A)+ RNA.
Nonlytic simian virus 40-specific 100K phosphoprotein is associated with anchorage-independent growth in simian virus 40-transformed and revertant mouse cell lines.
Authors: Chen S , Verderame M , Lo A , Pollack R
Published: September 2015

Normal fibroblasts display two distinct growth controls which can be assayed as requirements for serum or for anchorage. Interaction of mouse 3T3 fibroblasts with simian virus 40 (SV40) thus generates four classes of transformed cells. We have examined viral gene expression in these four classes of cell lines. Immunoprecipitation of [35S]methionine-labeled cell extracts with an antiserum obtained from tumor-bearing hamsters detected the SV40 large T and small t proteins (94,000 molecular weight [94K], 17K) and the nonviral host 54K protein in all cell lines tested. A tumor antigen with an apparent molecular weight of 100,000 was also found in some, but not all, lines. Similar "super T" molecules have been found by others in many rodent transformed lines. We carried out an analysis of the relation of phenotype to relative amounts of these proteins in cell lines of the four classes, using the Spearman rank correlation test. The amount of the 100K T antigen relative to the 94K T antigen or to total viral protein was well correlated with the ability to form colonies in semisolid medium. No significant correlation was found between quantities of labeled 94K T antigen, 54K host antigen, or 17K t antigen and either serum or anchorage independence. Mouse cells transformed with the small t SV40 deletion mutant 884 synthesized a 100K T antigen, suggesting that small t is not required for the production of this protein. The 100K T antigen migrated more slowly than lytic T. Since mixtures of extracts from cells expressing and lacking the 100K T antigen yielded the expected amount of this protein, it is unlikely that the 100K T derives from the 94K protein by a posttranslational modification.
Chemotactic responses of Chlamydomonas reinhardtii.
Authors: Sjoblad R D , Frederikse P H
Published: September 2015

A capillary chemotaxis assay revealed that among a wide range of inorganic and organic chemicals, only ammonium ion (NH4+) could serve as an attractant of Chlamydomonas reinhardtii. NH4+ (10(-2) M) gave the maximum response, with up to a 15-fold increase in accumulated algae being measured. No repellents for the chlorophyte were detected. The response to NH4+ was influenced by exogenous levels of calcium, but not by L-methionine. The optimal pH for positive chemotaxis was 7.0; however, attraction was measurable from pH 4.0 to 9.0. Positive chemotaxis was stimulated by performing the assay under fluorescent illumination rather than in the dark.
Adenovirus chromatin structure at different stages of infection.
Authors: Daniell E , Groff D E , Fedor M J
Published: September 2015

We investigated the structure of adenovirus deoxyribonucleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococcal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parenteral DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with [3H]thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure we identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. We found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.
Relation between the efficiency of homothallic switching of yeast mating type genes and the distribution of cell types.
Authors: Davidow L S , Haber J E
Published: September 2015

Homothallic switching of yeast mating type genes occurs as often as each cell division, so that a colony derived from a single haploid spore soon contains an equal number of MATa and MAT alpha cells. Cells of opposite mating types conjugate, and eventually the colony contains only nonmating MATa/MAT alpha diploids. Mutations that reduce the efficiency of homothallic MAT conversions yield colonies that still contain many haploid cells of the original spore mating type plus a few recently generated cells of the opposite mating type. These (a greater than alpha)- or (alpha greater than a)-mating colonies also contain some nonmating diploid cells. As an alternative to microscopic pedigree analysis to determine the frequency of mating type conversions in a variety of mutant homothallic strains, we analyzed the proportions of MATa, MAT alpha, and MATa/MAT alpha cells in a colony by examining the mating phenotypes of subclones. We developed a mathematical model that described the proportion of cell types in a slow-switching colony. This model predicted that the proportion of nonmating cells would continually increase with the size (age) of a colony derived from a single cell. This prediction was confirmed by determining the proportion of cell types in colonies of an HO swi1 strain that was grown for different numbers of cell divisions. Data from subcloning (a greater than alpha) and (alpha greater than a) colonies from a variety of slow-switching mutations and chromosomal rearrangements were used to calculate the frequency of MAT conversions in these strains.
Globin synthesis in hybrid cells constructed by transplantation of dormant avian erythrocyte nuclei into enucleated fibroblasts.
Authors: Bruno J , Reich N , Lucas J J
Published: September 2015

The polypeptides synthesized by mature embryonic erythrocytes prepared from the peripheral blood of 14- to 15-day-old chicken embryos were analyzed by two-dimensional gel electrophoresis. Fewer than 200 species of polypeptides were detected; the major polypeptides made at this time were identified as the alpha A-, alpha D-, and beta-globin chains. The dormant erythrocyte nuclei were next reactivated to transcriptional competence by transplantation into enucleated mouse or chicken embryo fibroblasts, with frequencies of cytoplast renucleation of about 50 and 90%, respectively. Since large numbers of hybrid cells could be constructed, a biochemical analysis was possible. Electrophoretic analysis of the [35S]methionine-labeled polypeptides made in the hybrid cell types showed that polypeptides having the mobilities of only two (alpha A and alpha D) of the three major adult globin chains were made as major constituents of the hybrid cells. However, analysis of 14C-amino acid-labeled polypeptides revealed that a beta-like polypeptide that lacked methionine was also synthesized in large amounts. This polypeptide was tentatively identified as the early embryonic globin species rho. Globin synthesis was detected as early as 3 h after nuclear transplantation and as late as 18 h, the last time measured in these experiments. It appeared that globin polypeptides made at very early times were translated at least partially from chicken messenger ribonucleic acid introduced into the hybrid cells during fusion, whereas those made at later times were translated primarily from newly synthesized globin messenger ribonucleic acid. The potential usefulness of this hybrid cell system in analyzing mechanisms regulating globin gene expression is discussed.
Membrane phase state and the rearrangement of hematopoietic cell surface receptors.
Authors: Williamson P L , Massey W A , Phelps B M , Schlegel R A
Published: September 2015

Transformed murine hematopoietic cells of several lineages bound the fluorescent membrane probe merocyanine 540, whereas their normal counterparts did not. Similar selective binding was reproduced in artificial liposomes which bound this probe above their phase transition temperature, but not below it. The regions of the membrane to which merocyanine 540 binds along with the receptors for the lectin concanavalin A, but not the receptors for the lectin wheat germ agglutinin, were rearranged during the course of induced differentiation of erythroleukemia cells. Based on these findings, we propose a model of hematopoietic cell surface differentiation in which proteins such as concanavalin A receptors, which are destined for removal from the plasma membrane, are specifically associated with disordered, liquid-like lipid domains which can be visualized with merocyanine 540. For the specific case of erythroid differentiation, these domains and their associated proteins are collected at the region of the membrane where nuclear extrusion occurs and are eliminated from the reticulocyte plasma membrane by the enucleation event.
Electron microscopy of Achlya deoxyribonucleic acid sequence organization.
Authors: Pellegrini M , Timberlake W E , Goldberg R B
Published: September 2015

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.