bluuebunny/crossref_metadata_2025 huggingface dataset:
Micromechanical function of myofibrils isolated from skeletal and cardiac muscles of the zebrafish
Authors: Iorga Bogdan , Neacsu Cristian Dan , Neiss Wolfram Friedrich , Wagener Raimund , Paulsson Mats , Stehle Robert , Pfitzer Gabriele
Published: March 2011

The zebrafish is a potentially important and cost-effective model for studies of development, motility, regeneration, and inherited human diseases. The object of our work was to show whether myofibrils isolated from zebrafish striated muscle represent a valid subcellular contractile model. These organelles, which determine contractile function in muscle, were used in a fast kinetic mechanical technique based on an atomic force probe and video microscopy. Mechanical variables measured included rate constants of force development (kACT) after Ca2+ activation and of force decay (τREL−1) during relaxation upon Ca2+ removal, isometric force at maximal (Fmax) or partial Ca2+ activations, and force response to an external stretch applied to the relaxed myofibril (Fpass). Myotomal myofibrils from larvae developed greater active and passive forces, and contracted and relaxed faster than skeletal myofibrils from adult zebrafish, indicating developmental changes in the contractile organelles of the myotomal muscles. Compared with murine cardiac myofibrils, measurements of adult zebrafish ventricular myofibrils show that kACT, Fmax, Ca2+ sensitivity of the force, and Fpass were comparable and τREL−1 was smaller. These results suggest that cardiac myofibrils from zebrafish, like those from mice, are suitable contractile models to study cardiac function at the sarcomeric level. The results prove the practicability and usefulness of mechanical and kinetic investigations on myofibrils isolated from larval and adult zebrafish muscles. This novel approach for investigating myotomal and myocardial function in zebrafish at the subcellular level, combined with the powerful genetic manipulations that are possible in the zebrafish, will allow the investigation of the functional primary consequences of human disease–related mutations in sarcomeric proteins in the zebrafish model.
Remote and direct plasma regions for low-temperature growth of carbon nanotubes on glass substrates for display applications
Authors: Tabatabaei M K , Ghafouri fard H , Koohsorkhi J , Khatami S , Mohajerzadeh S
Published: March 2011

A novel method for growing carbon nanotubes (CNTs) on glass substrates is introduced in this study. A two-stage plasma was used to achieve low-temperature and vertically aligned CNTs. Ni deposited on indium tin oxide/glass substrate was used as the catalyst and hydrogen and acetylene were used as gas feeds. In this investigation a new technique was developed to grow vertically aligned CNTs at temperatures below 400 °C while CNT growth by plasma-enhanced chemical vapour deposition required high temperatures. Low-temperature growth of vertically aligned CNTs was suitable for the fabrication of micro-lens and self-oriented displays on glass substrates. Also, we have reported a new configuration for CNT-based display by means of controlling the refractive index of liquid crystal around the CNT by applying a proper voltage to the top and bottom array.
Separable subgroups have bounded packing
Authors: Yang Wen-yuan
Published: March 2011

In this paper, we prove that separable subgroups have bounded packing in ambient groups. The notion bounded packing was introduced by Hruska and Wise, and, in particular, our result confirms a conjecture of theirs which states that each subgroup of a virtually polycyclic group has the bounded packing property.
Boundaries of escaping Fatou components
Authors: Rippon P. , Stallard G.
Published: March 2011

Let

f
f

be a transcendental entire function and

U
U

be a Fatou component of

f
f

. We show that if

U
U

is an escaping wandering domain of

f
f

, then most boundary points of

U
U

(in the sense of harmonic measure) are also escaping. In the other direction we show that if enough boundary points of

U
U

are escaping, then

U
U

is an escaping Fatou component. Some applications of these results are given; for example, if

I
(
f
)

I(f)

is the escaping set of

f
f

, then

I
(
f
)
∪
{
∞
}

I(f)\cup \{\infty \}

is connected.
Improvements to Turing’s method
Authors: Trudgian Timothy
Published: March 2011

This article improves the estimate of the size of the definite integral of

S
(
t
)

S(t)

, the argument of the Riemann zeta-function. The primary application of this improvement is Turing’s Method for the Riemann zeta-function. Analogous improvements are given for the arguments of Dirichlet

L
L

-functions and of Dedekind zeta-functions.
On Branson’s 𝑄-curvature of order eight
Authors: Juhl Andreas
Published: March 2011

We prove universal recursive formulas for Branson’s

Q
Q

-curvature of order eight in terms of lower-order

Q
Q

-curvatures, lower-order GJMS- operators and holographic coefficients. The results confirm a special case of a conjecture in [On conformally covariant powers of the Laplacian, arXiv:0905.3992v3].
Innovation in a Cold [War] Climate: Engineering Peace with the American Military–Industrial Complex
Authors: Wills Jocelyn
Published: March 2011

On January 8, 2008, executives at MacDonald, Dettwiler and Associates (MDA), a systems engineering firm centered in Vancouver, British Columbia, triggered a political firestorm by announcing that, subject to regulatory approval by the governments of Canada and the United States, shareholders had approved the sale of the firm's space business to Alliant Techsystems (ATK), an aerospace company and manufacturer of land mines, cluster bombs, and missiles headquartered in Minneapolis, Minnesota. Daniel Friedmann, MDA's chief executive since 1995, argued the sale would “allow the company to focus management and financial resources exclusively on its rapidly growing information products business,” particularly the firm's property-information systems for those “involved in real estate-related transactions such as the buying, selling, conveyancing, mortgage financing, and insurance of properties.”
Analysis of 2‐Acetyl‐1‐Pyrroline in Rice by HSSE/GC/MS
Authors: Grimm Casey C. , Champagne Elaine T. , Lloyd Steven W. , Easson Michael , Condon Brian , McClung Anna
Published: March 2011

An extremely sensitive method for the analysis of 2‐acetyl‐1‐pyrroline (2AP) in rice, employing stir bar sorptive extraction (Twister) was studied. The Twister stir bar is placed in the headspace of a 20‐mL vial containing 1 g of rice kernels, 7.5 mL of 0.1M KOH, and 2.2 g of NaCl, along with a second Teflon‐coated stir bar for mixing. Analytes are adsorbed onto the Twister for 4 hr at 40°C and then desorbed at 270°C into a GC column while cryofocusing at –80°C. The headspace sorptive extraction (HSSE) method was able to detect <0.1 ppb of 2AP in rice. The precision of the HSSE method (>10%) was not as good as the GC/FID method (≈6%). Using HSSE, 2AP was observed in all samples generally considered to be aromatic and was not observed in any nonaromatic samples. Additionally, a modified method for the synthesis of 2‐acetyl‐1‐pyrroline was studied and the presence of a tautomer of 2‐acetyl‐1‐pyrroline was confirmed.
The Type VI Secretion System: A Multipurpose Delivery System with a Phage-Like Machinery
Authors: Records Angela R.
Published: March 2011

Whether they live in the soil, drift in the ocean, survive in the lungs of human hosts or reside on the surfaces of leaves, all bacteria must cope with an array of environmental stressors. Bacteria have evolved an impressive suite of protein secretion systems that enable their survival in hostile environments and facilitate colonization of eukaryotic hosts. Collectively, gram-negative bacteria produce six distinct secretion systems that deliver proteins to the extracellular milieu or directly into the cytosol of host cells. The type VI secretion system (T6SS) was discovered recently and is encoded in at least one fourth of all sequenced gram-negative bacterial genomes. T6SS proteins are evolutionarily and structurally related to phage proteins, and it is likely that the T6SS apparatus is reminiscent of phage injection machinery. Most studies of T6SS function have been conducted in the context of host-pathogen interactions. However, the totality of data suggests that the T6SS is a versatile tool with roles in virulence, symbiosis, interbacterial interactions, and antipathogenesis. This review gives a brief history of T6SS discovery and an overview of the pathway's predicted structure and function. Special attention is paid to research addressing the T6SS of plant-associated bacteria, including pathogens, symbionts and plant growth–promoting rhizobacteria.
First Report of Tomato spotted wilt virus on Tobacco in Campania, Italy
Authors: Carrieri R. , Sorrentino R. , Lahoz E. , Alioto D.
Published: March 2011

During the spring and summer of 2010, a survey for viruses was conducted in two tobacco field trials at the Agricultural Research and Experimentation Council in Scafati, Campania, Italy. A total of 1,392 symptomatic and asymptomatic tobacco plants (cv. Burley) were sampled, and leaves were analyzed by double-antibody sandwich-ELISA using polyclonal antisera against five tobacco-infecting viruses: Tobacco mosaic virus, Potato virus Y, Cucumber mosaic virus, Alfalfa mosaic virus, and Tomato spotted wilt virus (TSWV) (Loewe, Munich, Germany). Only one plant was positive to TSWV. Symptoms on this plant were severe necroses on the stem with a few chlorotic/necrotic leaflets on the top of the plant. This result was subsequently confirmed by reverse transcription (RT)-PCR. The primers (5′-ATGTCTAAGGTTAAGCTC-3′ forward and 5′-TTAAGCAAGTTCTGTGAG-3′ reverse) targeted the nucleocapsid gene of TSWV and amplified the expected product of approximately 800 bp (2). The resultant sequence (GenBank Accession No. JF290419) was aligned and edited using BlastN, displaying 99.9% identity with deposited TSWV nucleocapsid gene sequences in GenBank, with no similarity to any other targets, which confirmed the presence of TSWV in tobacco. Leaf homogenate from the tobacco symptomatic plants was inoculated onto three plants of Nicotiana benthamiana, N. glutinosa, and Datura metel. All plants developed a systemic necrosis after 7 days. Inoculation from N. glutinosa back to cv. White Burley tobacco produced symptoms similar to those observed in the field. Two plants from each species were used as noninoculated controls, which remained asymptomatic. TSWV infection has been responsible for severe epidemics on tobacco throughout the United States and Greece, with losses estimated as much as 85% (1,3). The presence of TSWV in Italy could therefore represent a serious threat for tobacco in the region, especially considering that it is prevalent in other crops in the area and vectors are widespread.

References: (1) E. K. Chatzivassiliou. Plant Dis. 92:1012, 2008. (2) R. K. Jain et al. Plant Dis. 82:900, 1998. (3) B. Mandal et al. Ann. Appl. Biol. 151:67, 2007.
Effects of Fuel Reduction Treatments on Incidence of Phytophthora Species in Soil of a Southern Appalachian Mountain Forest
Authors: Meadows I. M. , Zwart D. C. , Jeffers S. N. , Waldrop T. A. , Bridges W. C.
Published: March 2011

The National Fire and Fire Surrogate Study was initiated to study the effects of fuel reduction treatments on forest ecosystems. Four fuel reduction treatments were applied to three sites in a southern Appalachian Mountain forest in western North Carolina: prescribed burning, mechanical fuel reduction, mechanical fuel reduction followed by prescribed burning, and a nontreated control. To determine the effects of fuel reduction treatments on Phytophthora spp. in soil, incidences were assessed once before and twice after fuel reduction treatments were applied. Also, the efficiency of the baiting bioassay used to detect species of Phytophthora was evaluated, and the potential virulence of isolates of Phytophthora spp. collected from forest soils was determined. Phytophthora cinnamomi and P. heveae were the only two species recovered from the study site. Incidences of these species were not significantly affected by fuel reduction treatments, but incidence of P. cinnamomi increased over time. In the baiting bioassay, camellia leaf disks were better than hemlock needles as baits. P. cinnamomi was detected best in fresh soil, whereas P. heveae was detected best when soil was air-dried and remoistened prior to baiting. Isolates of P. heveae were weakly virulent and, therefore, potentially pathogenic—causing lesions only on wounded mountain laurel and rhododendron leaves; however, isolates of P. cinnamomi were virulent and caused root rot and mortality on mountain laurel and white pine plants.
Epidemiology of Soybean Rust in Soybean Sentinel Plots in Florida
Authors: Young Heather M. , Marois James J. , Wright David L. , Narváez Dario F. , O'Brien G. Kelly
Published: March 2011

Since its discovery in the southeastern United States in 2004, soybean rust (SBR) has been variable from year to year. Caused by Phakopsora pachyrhizi, SBR epidemics in Florida are important to understand, as they may serve as an inoculum source for other areas of the country. This study examined the first disease detection date, incidence, and severity of SBR in relation to environmental data, growth stage, and maturity group (MG3, MG5, MG7) in soybean sentinel plots (225 m2) across north Florida from 2005 through 2008. The majority (91%) of the initial infections were observed in MG5 and MG7 soybeans, with plots not becoming infected until growth stage R4 or later. Precipitation was the principle factor affecting disease progress, where disease increased rapidly after rain events and was suppressed during dry periods. On average, plots became infected 30 days earlier in 2008 than 2005. In 2008, there was a significant increase in disease incidence and severity associated with the occurrence of Tropical Storm Fay, which deposited up to 380 mm of rainfall in north Florida. The results of this study indicate that climatic and environmental factors are important in determining the development of SBR in north Florida.
Widespread Occurrence and Low Genetic Diversity ofColombian datura virusinBrugmansiaSuggest an Anthropogenic Role in Virus Selection and Spread
Authors: Chellemi Dan O. , Webster Craig G. , Baker Carlye A. , Annamalai Mani , Achor Diann , Adkins Scott
Published: March 2011

Brugmansia (Brugmansia spp.) is a perennial shrub in the Solanaceae, originating from South America, that is a popular landscape plant in the tropics and subtropics and container plant in temperate regions. Virus-like symptoms including mosaic, rugosity, and faint chlorotic spots were first observed on leaves of Brugmansia plants in a south Florida nursery in November 2003. Colombian datura virus (CDV) was identified in these initial plants and subsequent Brugmansia and Datura metel (a Brugmansia relative also grown as an ornamental) plants obtained from Florida, Connecticut, Wisconsin, and California. Overall, 77.5% of Brugmansia and two of four D. metel plants tested were infected with CDV. Partial NIb/CP sequences of 28 Brugmansia CDV isolates from this study were compared with all 16 CDV isolates in GenBank and found to share high levels of nucleotide and amino acid identity, with negative selection estimated to be occurring. A single Brugmansia plant was also infected with a recently described tobamovirus. The low genetic diversity of CDV observed, along with negative selection pressure on NIb/CP, suggests a recent ancestry (<400 years) of the worldwide population of CDV, coinciding with anthropogenic collection and dissemination of Brugmansia plants from their center of origin.
First Report of a Rhabdovirus Infecting Alfalfa in Argentina
Authors: Bejerman N. , Nome C. , Giolitti F. , Kitajima E. , de Breuil S. , Pérez Fernández J. , Basigalup D. , Cornacchione M. , Lenardon S.
Published: March 2011

Alfalfa (Medicago sativa L.) is a major forage crop in Argentina with an estimated cultivated area of 4 million ha in the 2009–2010 season, which constitutes a primary component for the animal production chain. In early summer of 2010, alfalfa plants showing virus-like symptoms were identified in 20 commercial fields in La Pampa Province with 95% disease prevalence. Diseased plants had shortened internodes, a bushy appearance, deformations, puckering, epinasty of leaflet blades, vein enations, and varying sized papillae on the adaxial leaflet surfaces. Similar symptoms were observed in alfalfa crops in Buenos Aires, Cordoba, Santa Fe, and Santiago del Estero provinces. Electron microscopy (EM) and molecular assays were performed on leaf tissue from one asymptomatic and two symptomatic plants. EM of ultrathin sections revealed membrane-bound bullet-shaped particles associated with the endoplasmic reticulum of phloem cells from symptomatic plants only. Total RNA was extracted from symptomatic and asymptomatic plants with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) for a template in one-step reverse transcription (RT)-PCR assays with the Access RT-PCR Kit (Promega, Madison, WI). RT-PCR assays employed degenerate primers targeting conserved regions of plant rhabdovirus polymerase (L) genes (2). An amplicon of approximately 1 kilobase pairs (detected only from symptomatic plants) was gel purified with the Wizard SV Gel and PCR Clean-Up System (Promega), cloned into pGEM-T Easy Vector System (Promega), and sequenced. Three independents clones were sequenced in both directions at Macrogen Inc. (Korea Republic) to generate a consensus sequence (GenBank Accession No. HQ380230) and compared to sequences of other plant rhabdoviruses available on GenBank. The partial L gene sequence of the alfalfa-infecting rhabdovirus shared highest nucleotide (68.0%) and amino acid (76.5%) sequence identity with the cytorhabdovirus Strawberry crinkle virus (Accession No. AY331390). A phylogenetic tree based on partial amino acid sequences of the polymerase gene indicated the alfalfa-infecting virus was more closely related to cytorhabdoviruses than to nucleorhabdoviruses. Symptoms observed resembled those reported for alfalfa plants infected with a plant rhabdovirus named Alfalfa enation virus (1), which has never been fully characterized. Collectively, the data implicate the observed rhabdovirus as the etiological agent. To our knowledge, this is the first report in Argentina (and South America) of a rhabdovirus infecting alfalfa. Additional field surveys and monitoring of vector/s and yield losses need to be conducted.

References: (1) B. Alliot and P. A. Signoret. Phytopathol. Z. 74:69, 1972. (2) R. L. Lamprecht et al. Eur. J. Plant Pathol. 123:105, 2009.
Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2009
Authors: Kolmer J. A. , Long D. L. , Hughes M. E.
Published: March 2011

Collections of Puccinia triticina were obtained from rust-infected leaves provided by cooperators throughout the United States and from surveys of wheat (Triticum aestivum) fields and wheat breeding plots by United States Department of Agriculture–Agricultural Research Service personnel in the Great Plains, Ohio River Valley, southeast, California, and Washington State in order to determine the virulence of the wheat leaf rust population in 2009. Single uredinial isolates (591 in total) were derived from the collections and tested for virulence phenotype on lines of Thatcher wheat that are near-isogenic for leaf rust resistance genes Lr1, Lr2a, Lr2c, Lr3a, Lr9, Lr16, Lr24, Lr26, Lr3ka, Lr11, Lr17a, Lr30, LrB, Lr10, Lr14a, Lr18, Lr21, and Lr28 and a winter wheat line with Lr39/41. Forty-one virulence phenotypes were described. Virulence phenotypes MLDSD, TCRKG, and TDBGG were the three most common phenotypes. Phenotype MLDSD is virulent to Lr17 and Lr39/Lr41 and was widely distributed throughout the United States. Phenotype TCRKG is virulent to Lr11, Lr18, and Lr26 and is found mostly in the soft red winter wheat region in the eastern United States. TDBGG is virulent to Lr24 and was found in both the soft red winter wheat and hard red winter wheat regions. Virulence to Lr21 was not found in any of the tested isolates. Virulence to Lr11, Lr18, and Lr26 increased in 2009 in the soft red winter wheat regions. Virulence to Lr17 and Lr39/Lr41 increased in the Great Plains region. Two separate epidemiological zones of P. triticina in the soft red winter wheat region of the southern and eastern states and in the hard red wheat region of the Great Plains were described.
Sources of Resistance to Stem Rust Race Ug99 in Spring Wheat Germplasm
Authors: Rouse M. N. , Wanyera R. , Njau P. , Jin Y.
Published: March 2011

Wheat stem rust (Puccinia graminis f. sp. tritici) race TTKSK (Ug99), with virulence to the majority of the world's wheat (Triticum aestivum) cultivars, has spread from Uganda throughout eastern Africa, Yemen, and Iran. The identification and spread of variants of race TTKSK with virulence to additional stem rust resistance genes has reminded breeders and pathologists of the danger of deploying major resistance genes alone. In order to protect wheat from this rapidly spreading and adapting pathogen, multiple resistance genes are needed, preferably from improved germplasm. Preliminary screening of over 700 spring wheat breeding lines and cultivars developed at least 20 years ago identified 88 accessions with field resistance to Ug99. We included these resistant accessions in the stem rust screening nursery in Njoro, Kenya for two additional seasons. The accessions were also screened with a bulk of North American isolates of P. graminis f. sp. tritici in the field in St. Paul, MN. In order to further characterize the resistance in these accessions, we obtained seedling phenotypes for 10 races of P. graminis f. sp. tritici, including two races from the race TTKSK complex. This phenotyping led to the identification of accessions with either adult-plant or all-stage resistance to race TTKSK, and often North American races of P. graminis f. sp. tritici as well. These Ug99 resistant accessions can be obtained by breeders and introgressed into current breeding germplasm.
Synthetic circuit identifies subpopulations with sustained memory of DNA damage
Authors: Burrill Devin R. , Silver Pamela A.
Published: March 2011

Differential responses to stimuli can affect how cells succumb to disease. In yeast, DNA damage can create heterogeneous responses. To delineate how a response contributes to a cell's future behavior, we constructed a transcription-based memory circuit that detects DNA repair to isolate subpopulations with heritable damage responses. Strongly responsive cells show multigenerational effects, including growth defects and iron-associated gene expression. Less-responsive cells exhibit increased mutation frequencies but resume wild-type behavior. These two subpopulations remain distinct for multiple generations, indicating a transmissible memory of damage. Collectively, this work demonstrates the efficacy of using synthetic biology to define how environmental exposure contributes to distinct cell fates.
An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression
Authors: Pferdehirt Rebecca R. , Kruesi William S. , Meyer Barbara J.
Published: March 2011

Here we analyze the essential process of X-chromosome dosage compensation (DC) to elucidate mechanisms that control the assembly, genome-wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of Caenorhabditis elegans MLL/COMPASS, a gene activation complex, acts within the DC complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites for chromosome-wide reduction of gene expression. The DCC binds to two categories of sites on X: rex (recruitment element on X) sites that recruit the DCC in an autonomous, sequence-dependent manner, and dox (dependent on X) sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DC mutations that abolish rex site binding greatly reduce dox site binding but do not eliminate it. Instead, binding is diminished to the low level observed at autosomal sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate directly with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites have similar binding potential but are distinguished by linkage to rex sites. We propose a model for DCC binding in which low-level DCC binding at dox sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then enhances the magnitude of DCC binding to dox sites in cis, which lack high affinity for the DCC on their own. We also show that the DCC balances X-chromosome gene expression between sexes by controlling transcription.
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
Authors: Alsford Sam , Turner Daniel J. , Obado Samson O. , Sanchez-Flores Alejandro , Glover Lucy , Berriman Matthew , Hertz-Fowler Christiane , Horn David
Published: March 2011

African trypanosomes are major pathogens of humans and livestock and represent a model for studies of unusual protozoal biology. We describe a high-throughput phenotyping approach termed RNA interference (RNAi) target sequencing, or RIT-seq that, using Illumina sequencing, maps fitness-costs associated with RNAi. We scored the abundance of >90,000 integrated RNAi targets recovered from trypanosome libraries before and after induction of RNAi. Data are presented for 7435 protein coding sequences, >99% of a non-redundant set in the Trypanosoma brucei genome. Analysis of bloodstream and insect life-cycle stages and differentiated libraries revealed genome-scale knockdown profiles of growth and development, linking thousands of previously uncharacterized and “hypothetical” genes to essential functions. Genes underlying prominent features of trypanosome biology are highlighted, including the constitutive emphasis on post-transcriptional gene expression control, the importance of flagellar motility and glycolysis in the bloodstream, and of carboxylic acid metabolism and phosphorylation during differentiation from the bloodstream to the insect stage. The current data set also provides much needed genetic validation to identify new drug targets. RIT-seq represents a versatile new tool for genome-scale functional analyses and for the exploitation of genome sequence data.
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
Authors: Xi Yuanxin , Yao Jianhui , Chen Rui , Li Wei , He Xiangwei
Published: March 2011

The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity—nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed “fragile nucleosomes” throughout the yeast genome, nearly 1000 of which were at previously determined “nucleosome-free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation, and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
Type III secretion‐dependent host defence elicitation and type III secretion‐independent growth within leaves by Xanthomonas campestris pv. campestris
Authors: SUN WENXIAN , LIU LIJUAN , BENT ANDREW F.
Published: March 2011

In many plant–bacterial interactions, loss of the type III secretion system (T3SS) severely reduces bacterial growth, symptom causation and suppression of defences in host plants. In the present study of Xanthomonas campestris pv. campestris (Xcc), Xcc strain B305 grew better than strain B186 in Arabidopsis thaliana after hydathode inoculation, and B305 strains mutated to the loss of T3SS (ΔhrcC and/or ΔhrpE; also ΔhrcCΔflgBC) grew similarly to wild‐type B305 in Arabidopsis leaves. Unlike Xcc strain B186, wild‐type B305 was relatively inefficient in secreting the exogenous T3S effector AvrBsT, but ΔhrcC and/or ΔhrpE attenuated the disease symptoms caused by Xcc B305, showing that the partially compromised T3SS of this strain still promotes necrotic leaf symptoms. In contrast with the T3SS‐dependent defence suppression that has been observed for some other plant pathogenic bacteria, the Xcc B186 and B305 wild‐type strains (which are virulent on Arabidopsis) caused greater elicitation of host PR‐1 and PR‐5 expression and callose deposition in comparison with their respective T3SS mutants. A defence‐suppressing/virulence‐enhancing activity of the Xcc T3SS effector suite was detectable when co‐inoculation with wild‐type Xcc B186 increased the growth of ΔhrcC Xcc, but this activity did not prevent the above defence elicitation. Experiments using T3SS mutants and Arabidopsis fls2 mutants suggested that FLS2 does not play a prominent role in restriction of the examined Xcc strains. However, ectopic overexpression of the Pseudomonas syringae effector AvrPto promoted in planta growth of wild‐type and ΔhrcC Xcc. In summary, the T3SS components or effector suite from virulent Xcc strains elicit some host defence responses, but suppress other defences and stimulate more severe disease symptoms, AvrPto‐disruptable elements other than FLS2 apparently contribute to the host restriction of Xcc, and in some virulent Xcc strains the T3SS is not absolutely required for wild‐type levels of bacterial growth within the plant.
Negative regulation of defence signalling pathways by the EDR1 protein kinase
Authors: CHRISTIANSEN KATY M. , GU YANGNAN , RODIBAUGH NATALIE , INNES ROGER W.
Published: March 2011

The enhanced disease resistance 1 (edr1) mutant of Arabidopsis confers enhanced resistance to bacterial and fungal pathogens. To better understand how edr1‐mediated resistance occurs, we performed transcriptome analyses on wild‐type and edr1 plants inoculated with the fungal pathogen Golovinomyces cichoracearum (powdery mildew). The expression of many known and putative defence‐associated genes was more rapidly induced, and to higher levels, in edr1 plants relative to the wild‐type. Many of the genes with elevated expression encoded WRKY transcription factors and there was enrichment for their binding sites in promoters of the genes upregulated in edr1. Confocal microscopy of transiently expressed EDR1 protein showed that a significant fraction of EDR1 was localized to the nucleus, suggesting that EDR1 could potentially interact with transcription factors in the nucleus. Analysis of gene ontology annotations revealed that genes associated with the endomembrane system, defence, reactive oxygen species (ROS) production and protein kinases were induced early in the edr1 mutant, and that elevated expression of the endomembrane system, defence and ROS‐related genes was maintained for at least 4 days after infection.
The pharmacokinetics of PF‐734200, a DPP‐IV inhibitor, in subjects with renal insufficiency
Authors: Dai Haiqing , Johnson Susan L. , Terra Steven G. , Marbury Thomas C. , Smith William B. , Alcorn Harry , Boyd Rebecca A. , Wang Rong , Nguyen Tu T.
Published: March 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Data demonstrating the pharmacokinetics (PK), efficacy and tolerability of PF‐734200, a potent DPP‐IV inhibitor in subjects with normal renal function, have been published or presented.

WHAT THIS STUDY ADDS

• This study provides better data on the PK of PF‐734200 in subjects with varying degrees of renal insufficiency and in subjects with end‐stage renal disease undergoing haemodialysis. In assessing the effects of renal impairment on the PK of PF‐734200, this study provides evidence for potential dose adjustment of PF‐734200 in patients with certain categories of renal impairment.

AIMS PF‐734200 is a potent, selective inhibitor of DPP‐IV. This two‐part study evaluated the pharmacokinetics (PK) of oral 20 mg PF‐734200 in subjects with varying degrees of renal insufficiency or with end‐stage renal disease (ESRD) requiring chronic haemodialysis (HD). The study also assessed the HD clearance of PF‐734200 in ESRD.

METHODS Part 1 included subjects with normal renal function or renal insufficiency but not on HD. Subjects received a single dose of 20 mg PF‐734200 while fasting and serum and urine samples were collected. In part 2, period 1, 1 h after HD, a single 20‐mg dose was given to subjects with ESRD and serum samples were collected. After a 7‐day washout, subjects received another dose followed by collection of serum samples (period 2), during which HD was initiated 4 h after dosing. Dialysate samples were collected to quantify amount of drug removed, from which HD clearance was calculated. The fraction of drug dialysed was calculated using an AUC‐based method.

RESULTS Systemic exposures of PF‐734200 increased approximately 1.5‐, 2.2‐, 2.1‐ and 2.8‐fold in subjects with mild, moderate, or severe renal insufficiency or ESRD, respectively, compared with subjects with normal renal function. The terminal half‐life increased from 16.2 h in subjects with normal renal function to 36.6 h in subjects with ESRD. Approximately, 29% of PF‐734200 in the body after a single‐dose administration was dialysed by 4 h HD.

CONCLUSIONS Systemic exposure of PF‐734200 increases with decreasing renal function. The effect of HD on drug removal is modest.
Monitoring the effectiveness of antiplatelet therapy: opportunities and limitations
Authors: Sambu Nalyaka , Curzen Nick
Published: March 2011

Previous clinical studies have shown heterogeneity in individual patient responses to antiplatelet therapy and high residual platelet reactivity is associated with increased risk of adverse clinical events. Monitoring response to antiplatelet therapy and tailoring treatment accordingly is currently not recommended in routine clinical practice largely due to the lack of a standardized definition of antiplatelet therapy hyporesponse and the need for a widely accepted point‐of‐care platelet function test that can be reliably utilized in frontline clinical practice. Recent data have shown that titrating the dose of clopidogrel in patients undergoing percutaneous coronary intervention significantly reduces the incidence of major adverse cardiovascular events and large‐scale clinical trials are currently underway to investigate whether individually tailored treatment based on results of platelet function testing leads to improved clinical outcome. Furthermore, genetic testing has demonstrated a link between CYP2C19 genetic polymorphisms, altered clopidogrel metabolite concentrations and adverse clinical events. Clinical studies are currently underway to investigate the potential clinical benefit associated with genotype‐guided tailoring of antiplatelet therapy. With the advent of newer, more potent antiplatelet agents and their associated increased bleeding risks, it will become imperative in the future to select the most appropriate, safe and effective drug.
CD16+ monocytes in breast cancer patients: expanded by monocyte chemoattractant protein-1 and may be useful for early diagnosis
Authors: Feng A-L , Zhu J-K , Sun J-T , Yang M-X , Neckenig M R , Wang X-W , Shao Q-Q , Song B-F , Yang Q-F , Kong B-H , Qu X
Published: March 2011

Human peripheral blood monocytes are a heterogeneous population, including CD14+CD16- ‘classical’ monocytes and CD14+CD16+‘proinflammatory’ monocytes. CD16+ monocytes are expanded in various inflammatory conditions. However, little is known about the CD14+CD16+ monocytes in patients with breast cancer. We detected CD14+CD16+ monocytes in 96 patients with breast cancer and 54 control subjects using flow cytometry. Receiver-operating characteristic (ROC) curve analysis was used to determine the feasibility of CD14+CD16+ monocytes as an indicator for diagnosis of breast cancer. We found that the frequency of CD14+CD16+ monocytes showed a significantly greater increase in breast cancer patients than in controls (16·96% versus 10·84%, P < 0·0001). The area under the ROC curve for CD14+CD16+ monocytes was 0·805 [95% confidence interval (95% CI): 0·714–0·877, P = 0·0001]. Furthermore, the levels of CD16+ monocytes were significantly negatively associated with the tumour size and pathological staging. In vitro, we showed that CD14+CD16+ monocytes were expanded significantly when the purified CD14+ monocytes were exposed to Michigan Cancer Foundation (MCF)-7 cells-conditioned medium (MCF-CM) or, separately, to monocyte chemotactic protein 1 (MCP-1). Neutralizing antibodies against MCP-1 inhibited the expansion of CD14+CD16+ monocytes by MCF-CM. Collectively, our findings indicated that MCP-1 can expand CD14+CD16+ monocytes in patients with breast cancer. Furthermore, the CD14+CD16+ monocyte may be a useful indicator in early diagnosis of breast cancer.
Stimulation of a shorter duration in the state of anergy by an invariant natural killer T cell agonist enhances its efficiency of protection from type 1 diabetes
Authors: Tohn R , Blumenfeld H , Haeryfar S M M , Veerapen N , Besra G S , Porcelli S A , Delovitch T L
Published: March 2011

We have reported previously that treatment of non-obese diabetic (NOD) mice with the invariant natural killer T (iNK T) cell agonist α-galactosylceramide C26:0 (α-GalCer) or its T helper type 2 (Th2)-biasing derivative α-GalCer C20:2 (C20:2) protects against type 1 diabetes (T1D), with C20:2 yielding greater protection. After an initial response to α-GalCer, iNK T cells become anergic upon restimulation. While such anergic iNK T cells can induce tolerogenic dendritic cells (DCs) that mediate protection from T1D, chronic administration of α-GalCer also results in long-lasting anergy accompanied by significantly reduced iNK T cell frequencies, which raises concerns about its long-term therapeutic use. In this study, our objective was to understand more clearly the roles of anergy and induction of tolerogenic DCs in iNK T cell-mediated protection from T1D and to circumvent potential complications associated with α-GalCer. We demonstrate that NOD iNK T cells activated during multi-dose (MD) treatment in vivo with C20:2 enter into and exit from anergy more rapidly than after activation by α-GalCer. Importantly, this shorter duration of iNK T cells in the anergic state promotes the more rapid induction of tolerogenic DCs and reduced iNK T cell death, and enables C20:2 stimulated iNK T cells to elicit enhanced protection from T1D. Our findings further that suggest C20:2 is a more effective therapeutic drug than α-GalCer for protection from T1D. Moreover, the characteristics of C20:2 provide a basis of selection of next-generation iNK T cell agonists for the prevention of T1D.
Uncertainty analysis for the integration of seismic and controlled source electro‐magnetic data
Authors: Kwon Myoung Jae , Snieder Roel
Published: March 2011

We study the appraisal problem for the joint inversion of seismic and controlled source electro‐magnetic (CSEM) data and utilize rock‐physics models to integrate these two disparate data sets. The appraisal problem is solved by adopting a Bayesian model and we incorporate four representative sources of uncertainty. These are uncertainties in 1) seismic wave velocity, 2) electric conductivity, 3) seismic data and 4) CSEM data. The uncertainties in porosity and water saturation are quantified by a posterior random sampling in the model space of porosity and water saturation in a marine one‐dimensional structure. We study the relative contributions from the four individual sources of uncertainty by performing several statistical experiments. The uncertainties in the seismic wave velocity and electric conductivity play a more significant role on the variation of posterior uncertainty than do the seismic and CSEM data noise. The numerical simulations also show that the uncertainty in porosity is most affected by the uncertainty in the seismic wave velocity and that the uncertainty in water saturation is most influenced by the uncertainty in electric conductivity. The framework of the uncertainty analysis presented in this study can be utilized to effectively reduce the uncertainty of the porosity and water saturation derived from the integration of seismic and CSEM data.
Allogeneic apoptotic thymocyte‐stimulated dendritic cells expand functional regulatory T cells
Authors: da Costa Thaís Boccia , Sardinha Luiz R. , Larocca Rafael , Peron Jean P. S. , Rizzo Luiz V.
Published: March 2011

Dendritic cells (DCs) play an important role in the clearance of apoptotic cells. The removal of apoptotic cells leads to peripheral tolerance, although their role is still not clear. We show that the uptake of apoptotic thymocytes by DCs converts these cells into tolerogenic DCs resistant to maturation by lipopolysaccharide, modulating the production of interleukin‐12 and up‐regulating the expression of transforming growth factor‐β1 latency associated peptide. We also observed that DCs pulsed with apoptotic cells in the allogeneic context were more efficient in the expansion of regulatory T cells (Tregs), and that this expansion requires contact between DCs and the T cell. The Tregs sorted from in vitro culture suppressed the proliferation of splenocytes in vitro in a specific and non‐specific manner. In the in vivo model, the transfer of CD4+ CD25− cells to Nude mice induced autoimmunity, with cell infiltrate found in the stomach, colon, liver and kidneys. The co‐transfer of CD4+ CD25− and CD4+ CD25+ prevented the presence of cell infiltrates in several organs and increased the total cell count in lymph nodes. Our data indicate that apoptotic cells have an important role in peripheral tolerance via induction of tolerogenic DCs and CD4+ CD25+ Foxp3+ cells that present regulatory functions.
The quorum‐hindered transcription factor YenR of Yersinia enterocolitica inhibits pheromone production and promotes motility via a small non‐coding RNA
Authors: Tsai Ching‐Sung , Winans Stephen C.
Published: March 2011

The YenR and YenI proteins of Yersinia enterocolitica resemble the quorum sensing proteins LuxR and LuxI of Vibrio fischeri. Apo‐YenR activated a gene, designated yenS, that lies adjacent to and divergent from yenR. YenR‐dependent expression of yenS was inhibited by endogenous or exogenous 3‐oxohexanoylhomoserine lactone (OHHL) a pheromone made by YenI. Purified apo‐YenR bound non‐cooperatively to two 20‐nucleotide sites that lie upstream of yenS. Binding occurred in the absence of (OHHL), and YenR was largely released from the DNA by this pheromone. yenS encoded two non‐translated RNAs 169 and 105 nucleotides long that share the same 5′ end but have different 3′ ends. One or both RNAs inhibited the translation and accumulation of the yenI mRNA by binding to a region that overlaps the YenI start codon. A mutation in yenI strongly stimulated swarming motility on the surface of semi‐solid agar, while exogenous OHHL completely suppressed this phenotype. Hypermotility in yenI mutants was also suppressed by mutations in yenR or yenS, suggesting that YenS plays a direct, stimulatory role in swarming motility.
Many ways to build an actin filament
Authors: Popp David , Robinson Robert C.
Published: March 2011

Cells rely on extensive networks of protein fibres to help maintain their proper form and function. For species ranging from bacteria to humans, this ‘cytoskeleton’ is integrally involved in diverse processes including movement, DNA segregation, cell division and transport of molecular cargoes. The most abundant cytoskeletal filament‐forming protein, F‐actin, is remarkably well conserved across eukaryotic species. From yeast to human – an evolutionary distance of over one billion years – only about 10% of residues in actin have changed and the filament structure has been highly conserved. Surprisingly, recent structural data show this to be not the case for filamentous bacterial actins, which exhibit highly divergent helical symmetries in conjunction with structural plasticity or polymorphism, and dynamic properties that may make them uniquely suited for the specific cellular processes in which they participate. Bacterial actin filaments often organize themselves into complex structures within the prokaryotic cell, driven by molecular crowding and cation association, to form bundles (ParM) or interwoven sheets (MreB). The formation of supramolecular structures is essential for bacterial cytoskeleton function. We discuss the underlying physical principles that lead to complex structure formation and the implications these have on the physiological functions of cytoskeletal proteins.
Unravelling the regulatory twist – regulation of CO2 fixation in Rhodopseudomonas palustris CGA010 mediated by atypical response regulator(s)†
Authors: Joshi Gauri S. , Bobst Cedric E. , Tabita F. Robert
Published: March 2011

In Rhodopseudomonas palustris CGA010, the LysR type regulator, CbbR, specifically controls transcription of the cbbLS genes encoding form I RubisCO. Previous genetic and physiological studies had indicated that a unique two‐component (CbbRRS) system influences CbbR‐mediated cbbLS transcription under conditions where CO2 is the sole carbon source. In this study, we have established direct protein–protein interactions between the response regulators of the CbbRRS system and CbbR, using a variety of techniques. The bacterial two‐hybrid system established a specific interaction between CbbR and CbbRR1 (response regulator 1 of the CbbRRS system), confirmed in vitro by chemical cross‐linking. In addition, both response regulators (CbbRR1 and CbbRR2) played distinct roles in influencing the CbbR–cbbLS promoter interactions in gel mobility shift assays. CbbRR1 increased the binding affinity of CbbR at the cbbI promoter three‐ to fivefold while CbbRR2 appeared to stabilize CbbR binding. Specific interactions were further supported by surface plasmon resonance (SPR) analyses. In total, the results suggested that both response regulators, with no discernible DNA‐binding domains, must interact with CbbR to influence cbbLS expression. Thus the CbbRRS system provides an additional level of transcriptional control beyond CbbR alone, and appears to be significant for potentially fine‐tuning cbbLS expression in Rps. palustris.