bluuebunny/crossref_metadata_2025 huggingface dataset:
THERMAL TRANSPORT IN A MULTIPLE JET IMPINGEMENT OVEN
Authors: KOCER D. , KARWE M.V.
Published: September 2005

Three‐dimensional numerical simulation of flow field and heat transfer in a jet impingement oven with multiple jets was carried out. Distribution of local heat transfer coefficient on a model cookie in the oven cavity was obtained from the predicted flow and temperature fields, and compared with the experimentally measured values. Effects of air temperature (400, 450K) and air velocity (2.5, 5, 10 m/s), on the surface heat transfer coefficient were studied. Numerical predictions showed good agreement with the experimental results.It was found that heat transfer coefficient was a strong function of air velocity while air temperature had no effect on the heat transfer coefficient. Local heat transfer coefficient values ranged between 11 and 66 W/m2K whereas average heat transfer coefficient values ranged between 24 and 42 W/m2K. Results also showed that because of the presence of the suction fan in the oven, flow field near the model cookie surface was quite different from that for a jet impinging on a flat surface.
ESTIMATION OF MOISTURE LOSS FROM THE COOLING DATA OF POTATOES
Authors: CHOURASIA M.K. , MAJI PRASENJIT , BASKEY AMIT , GOSWAMI T.K.
Published: September 2005

A procedure was developed to predict moisture loss from cooling data of potato packed in gunny bags and stacked on wooden platforms in commercial cold stores. To predict the moisture loss, mass transfer coefficients kcand kmwere estimated during the storage period, which were found to decrease with time. The calculated time average kcand kmvalues were 1.83 × 10−4 m/s and 2.31 × 10−10 kg/s·m2·Pa during the transient cooling period and 1.59 × 10−4 m/s and 2.27 × 10−10 kg/s·m2·Pa for the rest of the storage period, respectively. The estimated moisture losses were 4.8, 4.74 and 4.78%, at the center of three different stacks, for a storage period of 8 months. The corresponding experimentally measured weight losses at the center of the same stacks were 5.2, 5.1 and 5.26% with a variation of 11, 7.5 and 10.2%, respectively. Therefore, the procedure adopted in this study may be used to assess the moisture loss from potatoes under the different storage conditions. The effect of relative humidity (RH) and potato temperature on moisture loss was also predicted using the developed procedure. Decrease in RH of the storage air increased the moisture loss. The potatoes stored below 85% RH incurred more than 7% water loss. Therefore, 88–90% RH in the cold store may be used to limit the maximum moisture loss within the permissible limit of 5% even after 8 months of storage. It was also found that increasing the potato temperature exponentially increased the rate of moisture loss.
MODELING AND OPTIMIZATION OF OHMIC HEATING OF FOODS INSIDE A FLEXIBLE PACKAGE
Authors: JUN SOOJIN , SASTRY SUDHIR
Published: September 2005

A pulsed ohmic heating system and flexible package for food reheating and sterilization were developed to minimize Equivalent System Mass during long‐duration space missions. A package made of flexible pouch materials was powered through a pair of metal foil electrodes extending out. Preliminary tests of the package within an ohmic heating enclosure show that International Space Shuttle menu items such as chicken noodle soup and black beans could be heated using pulsed ohmic heating technology. The electrical conductivities of selected samples ranged between 0.01 and 0.03 S/cm. A 2‐D thermal‐electric model was developed using commercial CFD software Fluent to optimize the design and layout of electrodes to ensure uniform heating of the material. A static system under the assumption of there being no fluid motion in a microgravity environment was implemented. A package configuration with V‐shaped electrodes with dimensionless width of 0.147 was validated to be most appropriate for uniform heating while minimizing the cold zone to 2% of total area. The effect of field overshoot near the electrode edge is expected to be crucial to determine the uniformity of heating.
MOISTURE ADSORPTION ISOTHERMS AND ISOSTERIC ENERGY FOR ALMOND
Authors: PAHLEVANZADEH H. , YAZDANI M.
Published: September 2005

The equilibrium moisture contents of almond were determined using the gravimetric‐static method at 15, 30, 55 and 75C for powder and 15, 55 and 75C for nut state of almond for water activity (aw) ranging from 0.11 to 0.87. At a given aw, the results show that the moisture content decreases with increasing temperature. The experimental sorption curves are then described by the BET, GAB, Henderson, Oswin, Smith and Halsey models. A nonlinear regression‐analysis method was used to evaluate the constants of equations. The GAB model was found to be the most suitable for describing the sorption curves; the monolayer‐content values for the sorption at different temperatures are calculated. Also, the isosteric heats of adsorption of water were determined as a function of moisture content from the equilibrium data at different temperatures using the Clasius‐Clapeyron equation.
Multilayer Analytic Element Modeling of Radial Collector Wells
Authors: Bakker Mark , Kelson Victor A. , Luther Kenneth H.
Published: September 2005

A new multilayer approach is presented for the modeling of ground water flow to radial collector wells. The approach allows for the inclusion of all aspects of the unique boundary condition along the lateral arms of a collector well, including skin effect and internal friction losses due to flow in the arms. The hydraulic conductivity may differ between horizontal layers within the aquifer, and vertical anisotropy can be taken into account. The approach is based on the multilayer analytic element method, such that regional flow and local three‐dimensional detail may be simulated simultaneously and accurately within one regional model. Horizontal flow inside a layer is computed analytically, while vertical flow is approximated with a standard finite‐difference scheme. Results obtained with the proposed approach compare well to results obtained with three‐dimensional analytic element solutions for flow in unconfined aquifers. The presented approach may be applied to predict the yield of a collector well in a regional setting and to compute the origin and residence time, and thus the quality, of water pumped by the collector well. As an example, the addition of three lateral arms to a collector well that already has three laterals is investigated. The new arms are added at an elevation of 2 m above the existing laterals. The yield increase of the collector well is computed as a function of the lengths of the three new arms.
Vehicle Acquisitions: Leasing or Financing?
Authors: FAN JESSIE X. , BURTON JOHN R.
Published: September 2005

In this study, we investigate household vehicle leasing versus financing behavior using the Interview Survey Portions of the 2001 Consumer Expenditure Survey. Two research questions are addressed in this study: (1) What are the demographics of those who lease as opposed to those who finance, and (2) What are the major factors affecting a consumer's probability of leasing versus financing when acquiring vehicles? Findings show that among income and demographic characteristics, being older, Caucasian or Hispanic, college educated, living in urban Northeast and Midwest, living in large Metropolitan Statistical Areas (MSAs), not having teenagers in the family, and having a higher income increase a consumer's probability to lease a vehicle. Most of these income and demographic effects either become smaller or disappear after the vehicle characteristics are controlled for. Among vehicle characteristics, being newer, Japanese or European made, luxury brand, with more cylinders, with power brakes, sunroof, and four‐wheel drive increase the probability of leasing. Purchasing the vehicle new instead of used, having a lower down payment and monthly payments, and having a smaller number of contracted payments also increase the probability of leasing.
Determinants of Household Expenditure on Computer Hardware and Software
Authors: YIN WEN , DEVANEY SHARON A. , STAHURA JOHN
Published: September 2005

This study investigated households’ expenditure on computer hardware and software using the 2000 Consumer Expenditure Survey. Based on neoclassical consumer theory, a conceptual model of computer expenditure was developed that included economic resources and consumer tastes and preferences. A double‐hurdle model was conducted to estimate whether or not households spent on computer hardware and software and the amount spent on computer hardware and software. Implications are offered for consumers and policy makers.
Use of Food Pantries and Food Stamps in Low‐Income Households in the United States
Authors: BHATTARAI GANDHI RAJ , DUFFY PATRICIA A , RAYMOND JENNIE
Published: September 2005

Using the Current Population Survey data for 1999, a bivariate probit model was estimated to determine food stamp and food pantries participation for low‐income households. Household income, the level of food insecurity, household structure, and metro versus nonmetro residence affected participation decisions in both programs. Shorter application forms for food stamp benefits encouraged food stamp participation. Food Stamp Program participation and food pantry use were found to be positively correlated.
Who Is in Control? The Role of Self‐Perception, Knowledge, and Income in Explaining Consumer Financial Behavior
Authors: PERRY VANESSA G , MORRIS MARLENE D
Published: September 2005

The current research examines the relationship between consumer financial knowledge, income, and locus of control on financial behavior. Ethnicity is included as a potential moderator of the effects of these three variables on financial behavior. Findings suggest that consumers’ propensity to save, budget, and control spending depends partly on their level of perceived control over outcomes as well as knowledge and financial resources. Evidence of race and ethnicity as moderators is mixed.
The Emergence of Biometrics and Its Effect on Consumers
Authors: LANGENDERFER JEFF , LINNHOFF STEFAN
Published: September 2005

Biometric authentication systems are becoming increasingly common. Though their use offers important advantages to governmental agencies, business, and consumers, the widespread use of biometric technology has the potential for serious negative consequences. In this paper, the authors explore the effects on consumers of the incorporation of biometric authentication into mainstream commerce, specifically focusing on privacy concerns of consumers in the context of the fair information practice principles of notice/awareness, choice/consent, access/participation, integrity/security, and enforcement/redress.
Your Privacy Is Sealed: Effects of Web Privacy Seals on Trust and Personal Disclosures
Authors: RIFON NORA J. , LaROSE ROBERT , CHOI SEJUNG MARINA
Published: September 2005

Online privacy is an issue of increasing national importance, and voluntary privacy seals provided by third‐party organizations such as TRUSTe and BBBOnline have been proposed as a means of assuring consumer privacy. Few studies have examined privacy seal effects. This study presents results of an online experiment that evaluated consumer response to privacy seals in a naturalistic exposure setting. Findings suggest that privacy seals enhance trust in the Web site and expectations that the site would inform the user of its information practices. While concern for privacy‐threatening information practices had no influence, privacy self‐efficacy, confidence in ability to protect one's privacy, moderated seal effects. Implications for the continued role of privacy seals are discussed.
Do Consumers Care about Ethics? Willingness to Pay for Fair‐Trade Coffee
Authors: DE PELSMACKER PATRICK , DRIESEN LIESBETH , RAYP GLENN
Published: September 2005

Consumers’ buying behavior is not consistent with their positive attitude toward ethical products. In a survey of 808 Belgian respondents, the actual willingness to pay for fair‐trade coffee was measured. It was found that the average price premium that the consumers were willing to pay for a fair‐trade label was 10%. Ten percent of the sample was prepared to pay the current price premium of 27% in Belgium. Fair‐trade lovers (11%) were more idealistic, aged between 31 and 44 years and less “conventional.” Fair‐trade likers (40%) were more idealistic but sociodemographically not significantly different from the average consumer.
Portion Distortion: A Study of College Students
Authors: BRYANT RACHEL , DUNDES LAUREN
Published: September 2005

This study compared designated serving size to actual consumption (portion size). Forty‐two college students estimated portion size and serving size of cereal, candy, and punch. Most (81%) refer to package labels, and over a third of women identified serving size as “of major interest.” Only one‐third accurately estimated the serving size of cereal within 10% of the correct amount. The stated serving size of cereal and punch was less than half of the portion size. Increasing serving sizes to more closely correspond to portion sizes would benefit consumers by providing information more likely to represent the nutritional quantities commonly consumed.
A New Numerical Procedure for Coupling Radiation in Participating Media With Other Modes of Heat Transfer
Authors: Mazumder Sandip
Published: September 2005

Traditionally, radiation in participating media is coupled to other modes of heat transfer using an iterative procedure in which the overall energy equation (EE) and the radiative transfer equation (RTE) are solved sequentially and repeatedly until both equations converge. Although this explicit coupling approach is convenient from the point of view of computer code development, it is not necessarily the best approach for stability and convergence. A new numerical procedure is presented in which the EE and RTE are implicitly coupled and solved simultaneously, rather than as segregated equations. Depending on the average optical thickness of the medium, it is found that the coupled solution approach results in convergence that is between 2–100 times faster than the segregated solution approach. Several examples in one- and two-dimensional media, both gray and nongray, are presented to corroborate this claim.
A Compact Falling Film Absorber
Authors: Goel Nitin , Goswami D. Yogi
Published: September 2005

The paper presents a new design of a falling film absorber that could considerably reduce the absorber size without penalizing the vapor and coolant side pressure drops. The proposed design is based on the fundamental characteristics of an efficient absorber design: large liquid-vapor interfacial area and good wetting characteristics. A finite difference scheme is developed to numerically investigate the performance of the design. The results indicate that the proposed design is more compact and efficient than the horizontal tube-type falling film absorber.
Natural Convection in a Vertical Microchannel
Authors: Chen Cha’o-Kuang , Weng Huei Chu
Published: September 2005

It is highly desirable to understand the fluid flow and the heat transfer characteristics of buoyancy-induced micropump and microheat exchanger in microfluidic and thermal systems. In this study, we analytically investigate the fully developed natural convection in an open-ended vertical parallel-plate microchannel with asymmetric wall temperature distributions. Both of the velocity slip and the temperature jump conditions are considered because they have countereffects both on the volume flow rate and the heat transfer rate. Results reveal that in most of the natural convection situations, the volume flow rate at microscale is higher than that at macroscale, while the heat transfer rate is lower. It is, therefore, concluded that the temperature jump condition induced by the effects of rarefaction and fluid-wall interaction plays an important role in slip-flow natural convection.
New Method to Determine the Velocities of Particles on a Solid Propellant Surface in a Solid Rocket Motor
Authors: Xiao Yumin , Amano R. S. , Cai Timin , Li Jiang
Published: September 2005

Use of aluminized composite solid propellants and submerged nozzles are common in solid rocket motors (SRM). Due to the generation of slag, which injects into a combusted gas flow, a two-phase flow pattern is one of the main flow characteristics that need to be investigated in SRM. Validation of two-phase flow modeling in a solid rocket motor combustion chamber is the focus of this research. The particles’ boundary conditions constrain their trajectories, which affect both the two-phase flow calculations, and the evaluation of the slag accumulation. A harsh operation environment in the SRM with high temperatures and high pressure makes the measurement of the internal flow field quite difficult. The open literature includes only a few sets of experimental data that can be used to validate theoretical analyses and numerical calculations for the two-phase flow in a SRM. Therefore, mathematical models that calculate the trajectories of particles may reach different conclusions mainly because of the boundary conditions. A new method to determine the particle velocities on the solid propellant surface is developed in this study, which is based on the x-ray real-time radiography (RTR) technique, and is coupled with the two-phase flow numerical simulation. Other methods imitate the particle ejection from the propellant surface. The RTR high-speed motion analyzer measures the trajectory of the metal particles in a combustion chamber. An image processing software was developed for tracing a slug particle path with the RTR images in the combustion chamber, by which the trajectories of particles were successfully obtained.
Forced Convection Past an Oblate Spheroid at Low to Moderate Reynolds Numbers
Authors: Alassar Rajai S.
Published: September 2005

Forced convection past a heated oblate spheroid is studied in an attempt to investigate the effect of the axis ratio on the heat transfer rate. The time-dependent full Navier–Stokes and energy equations are solved using a series truncation method. The axis ratios considered range from 1∕2 to 1 (a perfect sphere). The results for the flow and thermal fields are satisfactorily compared with relevant published research. The results are presented in the form of streamlines, isotherms, and the local and averaged Nusselt number distributions.
Numerical Simulation of Mixed Convective Flow Over a Three-Dimensional Horizontal Backward Facing Step
Authors: Saldana J. G. Barbosa , Anand N. K. , Sarin V.
Published: September 2005

Laminar mixed convective flow over a three-dimensional horizontal backward-facing step heated from below at a constant temperature was numerically simulated using a finite volume technique and the most relevant hydrodynamic and thermal features for air flowing through the channel are presented in this work. The channel considered in this work has an aspect ratio AR=4, and an expansion ratio ER=2, while the total length in the streamwise direction is 52 times the step height (L=52s) and the step length is equal to 2 times the step height (l=2s). The flow at the duct entrance was considered to be hydrodynamically fully developed and isothermal. The bottom wall of the channel was subjected to a constant high temperature while the other walls were treated to be adiabatic. The step was considered to be a thermally conducting block.
Modeling and Experiments of Laser Cladding With Droplet Injection
Authors: Choi J. , Han L. , Hua Y.
Published: September 2005

Laser aided Directed Material Deposition (DMD) is an additive manufacturing process based on laser cladding. A full understanding of laser cladding is essential in order to achieve a steady state and robust DMD process. A two dimensional mathematical model of laser cladding with droplet injection was developed to understand the influence of fluid flow on the mixing, dilution depth, and deposition dimension, while incorporating melting, solidification, and evaporation phenomena. The fluid flow in the melt pool that is driven by thermal capillary convection and an energy balance at the liquid–vapor and the solid–liquid interface was investigated and the impact of the droplets on the melt pool shape and ripple was also studied. Dynamic motion, development of melt pool and the formation of cladding layer were simulated. The simulated results for average surface roughness were compared with the experimental data and showed a comparable trend.
Thermal Behavior and Geometry Model of Melt Pool in Laser Material Process
Authors: Han Lijun , Liou Frank W. , Musti Srinivas
Published: September 2005

Melt pool geometry and thermal behavior control are essential in obtaining consistent building performances, such as geometrical accuracy, microstructure, and residual stress. In this paper, a three dimensional model is developed to predict the thermal behavior and geometry of the melt pool in the laser material interaction process. The evolution of the melt pool and effects of the process parameters are investigated through the simulations with stationary and moving laser beam cases. The roles of the convection and surface deformation on the heat dissipation and melt pool geometry are revealed by dimensionless analysis. The melt pool shape and fluid flow are considerably affected by interfacial forces such as thermocapillary force, surface tension, and recoil vapor pressure. Quantitative comparison of interfacial forces indicates that recoil vapor pressure is dominant under the melt pool center while thermocapillary force and surface tension are more important at the periphery of the melt pool. For verification purposes, the complementary metal oxide semiconductor camera has been utilized to acquire the melt pool image online and the melt pool geometries are measured by cross sectioning the samples obtained at various process conditions. Comparison of the experimental data and model prediction shows a good agreement.
Heat
Transfer and Pressure Drop Characteristics of Laminar Flow in Rectangular and Square Plain Ducts and
Ducts With Twisted-Tape Inserts
Authors: Saha S.
K. , Mallick D.
N.
Published: September 2005

The present paper reports the results of an experimental investigation of the heat transfer and pressure drop characteristics of laminar flow of viscous oil through horizontal rectangular and square plain ducts and ducts inserted with full-length twisted tapes, short-length twisted tapes, and regularly spaced twisted-tape elements. Isothermal pressure drop measurements were taken in acrylic ducts. Heat transfer measurements were taken in electrically heated stainless-steel ducts imposing uniform wall heat flux boundary conditions. The duct aspect ratios AR were 1, 0.5, and 0.333. The twist ratios of the twisted tapes were y=2.692, 5.385, 2.597, 5.193, 2.308, and 4.615. Short-length tapes were 0.9, 0.7, and 0.5 times the duct length. The space ratios were s=2.692, 5.385, 2.597, 5.193, 2.308, and 4.615. Both friction factor and Nusselt number increase with decreasing y and AR for AR⩽1 and increasing Re, Sw, and Pr. As the tape-length decreases, both friction factor and Nusselt number decrease. Friction factor increases as s decreases, and Nusselt number increases as s increases. Isothermal friction factor correlation and comprehensive Nusselt number correlation have been developed to predict data reasonably well in the entire range of parameters. Performance evaluation says that short-length twisted tapes are worse and regularly spaced twisted-tape elements are better than the full-length twisted tapes.
A Two-Temperature Model for Solid-Liquid Phase Change in Metal Foams
Authors: Krishnan Shankar , Murthy Jayathi Y. , Garimella Suresh V.
Published: September 2005

Transient solid-liquid phase change occurring in a phase-change material (PCM) embedded in a metal foam is investigated. Natural convection in the melt is considered. Volume-averaged mass and momentum equations are employed, with the Brinkman-Forchheimer extension to the Darcy law to model the porous resistance. Owing to the difference in the thermal diffusivities between the metal foam and the PCM, local thermal equilibrium between the two is not assured. Assuming equilibrium melting at the pore scale, separate volume-averaged energy equations are written for the solid metal foam and the PCM and are closed using an interstitial heat transfer coefficient. The enthalpy method is employed to account for phase change. The governing equations are solved implicitly using the finite volume method on a fixed grid. The influence of Rayleigh, Stefan, and interstitial Nusselt numbers on the temporal evolution of the melt front location, wall Nusselt number, temperature differentials between the solid and fluid, and the melting rate is documented and discussed. The merits of incorporating metal foam for improving the effective thermal conductivity of thermal storage systems are discussed.
Effectiveness-NTU Relationship for a Counterflow Heat Exchanger Subjected to an External Heat Transfer
Authors: Nellis Gregory F. , Pfotenhauer John M.
Published: September 2005

This paper presents the analytical solution for the effectiveness of a counterflow heat exchanger subjected to a uniformly distributed, external heat flux. The solution is verified against conventional ε-NTU relations in the limit of zero external heat flux. This situation is of interest in applications such as cryogenic and process engineering, and the analytical solution provides a convenient method for treating differential elements of a heat exchanger in a numerical model.
Ribo-gnome: The Big World of Small RNAs
Authors: Zamore Phillip D. , Haley Benjamin
Published: September 2005

Small RNA guides—microRNAs, small interfering RNAs, and repeat-associated small interfering RNAs, 21 to 30 nucleotides in length—shape diverse cellular pathways, from chromosome architecture to stem cell maintenance. Fifteen years after the discovery of RNA silencing, we are only just beginning to understand the depth and complexity of how these RNAs regulate gene expression and to consider their role in shaping the evolutionary history of higher eukaryotes.
RNA Structure: Reading the Ribosome
Authors: Noller Harry F.
Published: September 2005

The crystal structures of the ribosome and its subunits have increased the amount of information about RNA structure by about two orders of magnitude. This is leading to an understanding of the principles of RNA folding and of the molecular interactions that underlie the functional capabilities of the ribosome and other RNA systems. Nearly all of the possible types of RNA tertiary interactions have been found in ribosomal RNA. One of these, an abundant tertiary structural motif called the A-minor interaction, has been shown to participate in both aminoacyl-transfer RNA selection and in peptidyl transferase; it may also play an important role in the structural dynamics of the ribosome.
Antisense Transcription in the Mammalian Transcriptome
Authors: Katayama S. , Tomaru Y. , Kasukawa T. , Waki K. , Nakanishi M. , Nakamura M. , Nishida H. , Yap C. C. , Suzuki M. , Kawai J. , Suzuki H. , Carninci P. , Hayashizaki Y. , Wells C. , Frith M. , Ravasi T. , Pang K. C. , Hallinan J. , Mattick J. , Hume D. A. , Lipovich L. , Batalov S. , Engström P. G. , Mizuno Y. , Faghihi M. A. , Sandelin A. , Chalk A. M. , Mottagui-Tabar S. , Liang Z. , Lenhard B. , Wahlestedt C.
Published: September 2005

Antisense transcription (transcription from the opposite strand to a protein-coding or sense strand) has been ascribed roles in gene regulation involving degradation of the corresponding sense transcripts (RNA interference), as well as gene silencing at the chromatin level. Global transcriptome analysis provides evidence that a large proportion of the genome can produce transcripts from both strands, and that antisense transcripts commonly link neighboring “genes” in complex loci into chains of linked transcriptional units. Expression profiling reveals frequent concordant regulation of sense/antisense pairs. We present experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.
Inositol Hexakisphosphate Is Bound in the ADAR2 Core and Required for RNA Editing
Authors: Macbeth Mark R. , Schubert Heidi L. , VanDemark Andrew P. , Lingam Arunth T. , Hill Christopher P. , Bass Brenda L.
Published: September 2005

We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP
6
) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP
6
is required for activity. Amino acids that coordinate IP
6
in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP
6
is also essential for in vivo and in vitro deamination of adenosine 37 of tRNA
ala
by ADAT1.
Modulation of Hepatitis C Virus RNA Abundance by a Liver-Specific MicroRNA
Authors: Jopling Catherine L. , Yi MinKyung , Lancaster Alissa M. , Lemon Stanley M. , Sarnow Peter
Published: September 2005

MicroRNAs are small RNA molecules that regulate messenger RNA (mRNA) expression. MicroRNA 122 (miR-122) is specifically expressed and highly abundant in the human liver. We show that the sequestration of miR-122 in liver cells results in marked loss of autonomously replicating hepatitis C viral RNAs. A genetic interaction between miR-122 and the 5′ noncoding region of the viral genome was revealed by mutational analyses of the predicted microRNA binding site and ectopic expression of miR-122 molecules containing compensatory mutations. Studies with replication-defective RNAs suggested that miR-122 did not detectably affect mRNA translation or RNA stability. Therefore, miR-122 is likely to facilitate replication of the viral RNA, suggesting that miR-122 may present a target for antiviral intervention.
Elucidation of the Small RNA Component of the Transcriptome
Authors: Lu Cheng , Tej Shivakundan Singh , Luo Shujun , Haudenschild Christian D. , Meyers Blake C. , Green Pamela J.
Published: September 2005

Small RNAs play important regulatory roles in most eukaryotes, but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant
Arabidopsis thaliana
. Known and new microRNAs (miRNAs) were among the most abundant of the nonredundant set of more than 75,000 sequences, whereas more than half represented lower abundance small interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs.
A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT
Authors: Willingham A. T. , Orth A. P. , Batalov S. , Peters E. C. , Wen B. G. , Aza-Blanc P. , Hogenesch J. B. , Schultz P. G.
Published: September 2005

Noncoding RNA molecules (ncRNAs) have been implicated in numerous biological processes including transcriptional regulation and the modulation of protein function. Yet, in spite of the apparent abundance of ncRNA, little is known about the biological role of the projected thousands of ncRNA genes present in the human genome. To facilitate functional analysis of these RNAs, we have created an arrayed library of short hairpin RNAs (shRNAs) directed against 512 evolutionarily conserved putative ncRNAs and, via cell-based assays, we have begun to determine their roles in cellular pathways. Using this system, we have identified an ncRNA repressor of the nuclear factor of activated T cells (NFAT), which interacts with multiple proteins including members of the importin-beta superfamily and likely functions as a specific regulator of NFAT nuclear trafficking.
Recombination Regulation by Transcription-Induced Cohesin Dissociation in rDNA Repeats
Authors: Kobayashi Takehiko , Ganley Austen R. D.
Published: September 2005

Organisms maintain ribosomal RNA gene repeats (rDNA) at stable copy numbers by recombination; the loss of repeats results in gene amplification. Here we report a mechanism of amplification regulation. We show that amplification is dependent on transcription from a noncoding bidirectional promoter (E-pro) within the rDNA spacer. E-pro transcription stimulates the dissociation of cohesin, a DNA binding protein complex that suppresses sister-chromatid-based changes in rDNA copy number. This transcription is regulated by the silencing gene,
SIR2
, and by copy number. Transcription-induced cohesin dissociation may be a general mechanism of recombination regulation.
200 Years of Accommodation
Authors: Cutler Alan
Published: September 2005

Before Darwin
. Reconciling God and Nature.
Keith Thomson
. Yale University Press, New Haven, CT, 2005. 328 pp. $27. ISBN 0-300-10793-5.

The Watch on the Heath
. Science and Religion Before Darwin. HarperCollins, London, 2005. £20. ISBN 0-00-713313-8.

The author explores aspects and effects of the clash between the developing scientific study of Earth and beliefs based on literal readings of the Bible in England from the 1650s through to 1860.
Major Biocontrol of Plant Tumors Targets tRNA Synthetase
Authors: Reader John S. , Ordoukhanian Phillip T. , Kim Jung-Gun , de Crécy-Lagard Valerie , Hwang Ingyu , Farrand Stephen , Schimmel Paul
Published: September 2005

Crops can be devastated by pathogenic strains of
Agrobacterium tumefaciens
that cause crown gall tumors. This devastation can be prevented by the nonpathogenic biocontrol agent
A. radiobacter
K84, which prevents disease by production of the "Trojan horse" toxin agrocin 84, which is specifically imported into tumorgenic
A. tumefaciens
strains to cause cell death. We demonstrate that this biocontrol agent targets
A. tumefaciens
leucyl-tRNA synthetase (LeuRS), an essential enzyme for cell viability, while the agent itself survives by having a second, self-protective copy of the synthetase. In principle, this strategy from nature could be applied to other crop diseases by direct intervention.
The Functional Genomics of Noncoding RNA
Authors: Mattick John S.
Published: September 2005

Large numbers of noncoding RNA transcripts (ncRNAs) are being revealed by complementary DNA cloning and genome tiling array studies in animals. The big and as yet largely unanswered question is whether these transcripts are relevant. A paper by Willingham
et al
. shows the way forward by developing a strategy for large-scale functional screening of ncRNAs, involving small interfering RNA knockdowns in cell-based screens, which identified a previously unidentified ncRNA repressor of the transcription factor NFAT. It appears likely that ncRNAs constitute a critical hidden layer of gene regulation in complex organisms, the understanding of which requires new approaches in functional genomics.
Activity of the Mason-Pfizer Monkey Virus Fusion Protein Is Modulated by Single Amino Acids in the Cytoplasmic Tail
Authors: Song Chisu , Micoli Keith , Hunter Eric
Published: September 2005

Mason-Pfizer monkey virus (M-PMV) encodes a transmembrane glycoprotein with a 38-amino-acid-long cytoplasmic tail. After the release of the immature virus, a viral protease-mediated cleavage of the cytoplasmic tail (CT) results in the loss of 17 amino acids from the carboxy terminus and renders the envelope protein fusion competent. To investigate the role of individual amino acid residues in the CT in fusion, a series of mutations was introduced, and the effects of these mutations on glycoprotein biosynthesis and fusion were examined. Most of the alanine-scanning mutations in the CT had little effect on fusion activity. However, four amino acid substitutions (threonine 4, lysine 7, glutamine 9, and isoleucine 10) resulted in substantially increased fusogenicity, while six (leucine 2, phenylalanine 5, isoleucine 13, lysine 16, proline 17, and glycine 31) resulted in much-reduced fusion. Interestingly, the bulk of these mutations are located upstream of the CT cleavage site in a region that has the potential to form a coiled-coil in the Env trimer. Substitutions at glutamine 9 and isoleucine 10 with alanine had the most dramatic positive effect and resulted in the formation of large syncytia. Taken together, these data demonstrate that individual residues within the cytoplasmic domain of M-PMV Env can modulate, in both a positive and negative manner, biological functions that are associated with the extracellular domains of the glycoprotein complex.
Herpes Simplex Virus Glycoprotein B Binds to Cell Surfaces Independently of Heparan Sulfate and Blocks Virus Entry
Authors: Bender Florent C. , Whitbeck J. Charles , Lou Huan , Cohen Gary H. , Eisenberg Roselyn J.
Published: September 2005

Virion glycoproteins gB, gD, and gH/gL play essential roles for herpes simplex virus (HSV) entry. The function of gD is to interact with a cognate receptor, and soluble forms of gD block HSV entry by tying up cell surface receptors. Both gB and the nonessential gC interact with cell surface heparan sulfate proteoglycan (HSPG), promoting viral attachment. However, cells deficient in proteoglycan synthesis can still be infected by HSV. This suggests another function for gB. We found that a soluble truncated form of gB bound saturably to the surface of Vero, A431, HeLa, and BSC-1 cells, L-cells, and a mouse melanoma cell line expressing the gD receptor nectin-1. The HSPG analog heparin completely blocked attachment of the gC ectodomain to Vero cells. In contrast, heparin only partially blocked attachment of soluble gB, leaving 20% of the input gB still bound even at high concentrations of inhibitor. Moreover, heparin treatment removed soluble gC but not gB from the cell surface. These data suggest that a portion of gB binds to cells independently of HSPG. In addition, gB bound to two HSPG-deficient cell lines derived from L-cells. Gro2C cells are deficient in HSPG, and Sog9 cells are deficient in HSPG, as well as chondroitin sulfate proteoglycan (CSPG). To identify particular gB epitopes responsible for HSPG-independent binding, we used a panel of monoclonal antibodies (MAbs) to gB to block gB binding. Only those gB MAbs that neutralized virus blocked binding of soluble gB to the cells. HSV entry into Gro2C and Sog9 cells was reduced but still detectable relative to the parental L-cells, as previously reported. Importantly, entry into Gro2C cells was blocked by purified forms of either the gD or gB ectodomain. On a molar basis, the extent of inhibition by gB was similar to that seen with gD. Together, these results suggest that soluble gB binds specifically to the surface of different cell types independently of HSPG and CSPG and that by doing so, the protein inhibits entry. The results provide evidence for the existence of a cellular entry receptor for gB.
Antimicrobial Peptides from Amphibian Skin Potently Inhibit Human Immunodeficiency Virus Infection and Transfer of Virus from Dendritic Cells to T Cells
Authors: VanCompernolle Scott E. , Taylor R. Jeffery , Oswald-Richter Kyra , Jiang Jiyang , Youree Bryan E. , Bowie John H. , Tyler Michael J. , Conlon J. Michael , Wade David , Aiken Christopher , Dermody Terence S. , KewalRamani Vineet N. , Rollins-Smith Louise A. , Unutmaz Derya
Published: September 2005

Topical antimicrobicides hold great promise in reducing human immunodeficiency virus (HIV) transmission. Amphibian skin provides a rich source of broad-spectrum antimicrobial peptides including some that have antiviral activity. We tested 14 peptides derived from diverse amphibian species for the capacity to inhibit HIV infection. Three peptides (caerin 1.1, caerin 1.9, and maculatin 1.1) completely inhibited HIV infection of T cells within minutes of exposure to virus at concentrations that were not toxic to target cells. These peptides also suppressed infection by murine leukemia virus but not by reovirus, a structurally unrelated nonenveloped virus. Preincubation with peptides prevented viral fusion to target cells and disrupted the HIV envelope. Remarkably, these amphibian peptides also were highly effective in inhibiting the transfer of HIV by dendritic cells (DCs) to T cells, even when DCs were transiently exposed to peptides 8 h after virus capture. These data suggest that amphibian-derived peptides can access DC-sequestered HIV and destroy the virus before it can be transferred to T cells. Thus, amphibian-derived antimicrobial peptides show promise as topical inhibitors of mucosal HIV transmission and provide novel tools to understand the complex biology of HIV capture by DCs.
Decreased Virus Population Diversity in
p53
-Null Mice Infected with Weakly Oncogenic Abelson Virus
Authors: Marchlik Erica , Kalman Richard , Rosenberg Naomi
Published: September 2005

The Abelson murine leukemia virus (Ab-MLV), like other retroviruses that contain v-
onc
genes, arose following a recombination event between a replicating retrovirus and a cellular oncogene. Although experimentally validated models have been presented to address the mechanism by which oncogene capture occurs, very little is known about the events that influence emerging viruses following the recombination event that incorporates the cellular sequences. One feature that may play a role is the genetic makeup of the host in which the virus arises; a number of host genes, including oncogenes and tumor suppressor genes, have been shown to affect the pathogenesis of many murine leukemia viruses. To examine how a host gene might affect an emerging v-
onc
gene-containing retrovirus, we studied the weakly oncogenic Ab-MLV-P90A strain, a mutant that generates highly oncogenic variants in vivo, and compared the viral populations in normal mice and mice lacking the
p53
tumor suppressor gene. While variants arose in both
p53

+/+

and
p53
−
/
−
tumors, the samples from the wild-type animals contained a more diverse virus population. Differences in virus population diversity were not observed when wild-type and null animals were infected with a highly oncogenic wild-type strain of Ab-MLV. These results indicate that
p53
, and presumably other host genes, affects the selective forces that operate on virus populations in vivo and likely influences the evolution of oncogenic retroviruses such as Ab-MLV.
Influence of Fiber Detargeting on Adenovirus-Mediated Innate and Adaptive Immune Activation
Authors: Schoggins John W. , Nociari Marcelo , Philpott Nicola , Falck-Pedersen Erik
Published: September 2005

The major adenovirus (Ad) capsid proteins hexon, penton, and fiber influence the efficiency and tropism of gene transduction by Ad vectors. Fiber is the high-affinity receptor binding protein that serves to mediate cell attachment in vitro when using coxsackie-adenovirus receptor (CAR)-containing cell lines. This contrasts with transduction efficiency in macrophages or dendritic cells that lack high concentrations of CAR. To determine how fiber influences gene transduction and immune activation in a murine model, we have characterized Ad type 5 (Ad5) vectors with two classes of chimeric fiber, CAR binding and non-CAR binding. In a systemic infection, Ad5 fiber contributes to DNA localization and vector transduction in hepatic tissue. However, the majority of vector localization is due to Ad5 fiber-specific functions distinct from CAR binding. CAR-directed transduction occurs but at a modest level. In contrast to CAR binding vectors, the F7 and F7F41S non-CAR-binding vectors demonstrate a 2-log decrease in hepatic transduction, with a 10-fold decrease in the amount of vector DNA localizing to the hepatic tissue. To characterize the innate response to early infection using fiber chimeric vectors, intrahepatic cytokine and chemokine mRNAs were quantified 5 hours postinfection. Tumor necrosis factor alpha mRNA levels resulting from Ad5 fiber infections were elevated compared to viruses expressing serotype 7 or 41 fiber. Levels of chemokine mRNA (gamma interferon-inducible protein 10, T-cell activation gene 3, and macrophage inflammatory protein 1β) were 10- to 20-fold higher with CAR binding vectors (Ad5 and F41T) than with non-CAR-binding vectors (F7 and F7F41S). In spite of quantitative differences in vector localization and innate activation, fiber pseudotyping did not significantly change the outcome of anti-Ad adaptive immunity. All vectors were cleared with the same kinetics as wild-type Ad5 vectors, and each induced neutralizing antibody. Although non-CAR-binding vectors were impaired in transduction by nearly 2 orders of magnitude, the level of antitransgene immunity was the same for each of the vectors. Using primary bone marrow-derived macrophages and dendritic cells, we demonstrate that transduction, induction of cytokine/chemokine, and phenotypic maturation of these antigen-presenting cells are independent of fiber content. Our data support a model where fiber-mediated hepatic localization enhances innate responses to virus infection but minimally impacts on adaptive immunity.
Single Amino Acid Substitutions in the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Determine Viral Entry and Immunogenicity of a Major Neutralizing Domain
Authors: Yi Christopher E. , Ba Lei , Zhang Linqi , Ho David D. , Chen Zhiwei
Published: September 2005

Neutralizing antibodies (NAbs) against severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) spike (S) glycoprotein confer protection to animals experimentally infected with the pathogenic virus. We and others previously demonstrated that a major mechanism for neutralizing SARS-CoV was through blocking the interaction between the S glycoprotein and the cellular receptor angiotensin-converting enzyme 2 (ACE2). In this study, we used in vivo electroporation DNA immunization and a pseudovirus-based assay to functionally evaluate immunogenicity and viral entry. We characterized the neutralization and viral entry determinants within the ACE2-binding domain of the S glycoprotein. The deletion of a positively charged region SΔ(422-463) abolished the capacity of the S glycoprotein to induce NAbs in mice vaccinated by in vivo DNA electroporation. Moreover, the SΔ(422-463) pseudovirus was unable to infect HEK293T-ACE2 cells. To determine the specific residues that contribute to related phenotypes, we replaced eight basic amino acids with alanine. We found that a single amino acid substitution (R441A) in the full-length S DNA vaccine failed to induce NAbs and abolished viral entry when pseudoviruses were generated. However, another substitution (R453A) abolished viral entry while retaining the capacity for inducing NAbs. The difference between R441A and R453A suggests that the determinants for immunogenicity and viral entry may not be identical. Our findings provide direct evidence that these basic residues are essential for immunogenicity of the major neutralizing domain and for viral entry. Our data have implications for the rational design of vaccine and antiviral agents as well as for understanding viral tropism.