bluuebunny/crossref_metadata_2025 huggingface dataset:
A computational method for optimising fuel treatment locations
Authors: Finney Mark A.
Published: December 2007

Modelling and experiments have suggested that spatial fuel treatment patterns can influence the movement of large fires. On simple theoretical landscapes consisting of two fuel types (treated and untreated), optimal patterns can be analytically derived that disrupt fire growth efficiently (i.e. with less area treated than random patterns). Although conceptually simple, the application of these theories to actual landscapes is made difficult by heterogeneity (fuels, weather, and topography). Here a computational method is described for heterogeneous landscapes that identifies efficient fuel treatment units and patterns for a selected fire weather scenario. The method requires input of two sets of spatial input data: (1) the current fuel conditions; and (2) the potential fuel conditions after a treatment is conducted (if treatment is permitted in a particular location). The contrast in fire spread rate between the two landscapes under the weather scenario conditions indicates where treatments are effective at delaying the growth of fires. Fire growth from the upwind edge of the landscape is then computed using a minimum travel time algorithm. This identifies major fire travel routes (areas needing treatment) and their intersections with the areas where treatments occurred and reduced the spread rate (opportunity for treatment). These zones of treatment ‘need and opportunity’ are iteratively delineated by contiguous patches of raster cells up to a user-supplied constraint on percentage of land area to be treated. This algorithm is demonstrated for simple and for complex landscapes.
EGF-induced PIP2 hydrolysis releases and activates cofilin locally in carcinoma cells
Authors: van Rheenen Jacco , Song Xiaoyan , van Roosmalen Wies , Cammer Michael , Chen Xiaoming , DesMarais Vera , Yip Shu-Chin , Backer Jonathan M. , Eddy Robert J. , Condeelis John S.
Published: December 2007

Lamellipodial protrusion and directional migration of carcinoma cells towards chemoattractants, such as epidermal growth factor (EGF), depend upon the spatial and temporal regulation of actin cytoskeleton by actin-binding proteins (ABPs). It is generally hypothesized that the activity of many ABPs are temporally and spatially regulated by PIP2; however, this is mainly based on in vitro–binding and structural studies, and generally in vivo evidence is lacking. Here, we provide the first in vivo data that directly visualize the spatial and temporal regulation of cofilin by PIP2 in living cells. We show that EGF induces a rapid loss of PIP2 through PLC activity, resulting in a release and activation of a membrane-bound pool of cofilin. Upon release, we find that cofilin binds to and severs F-actin, which is coincident with actin polymerization and lamellipod formation. Moreover, our data provide evidence for how PLC is involved in the formation of protrusions in breast carcinoma cells during chemotaxis and metastasis towards EGF.
Efficient peptide–MHC-I binding prediction for alleles with few known binders
Authors: Jacob Laurent , Vert Jean-Philippe
Published: December 2007

Motivation:  In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods in particular are widely used to score candidate binders based on their similarity with known binders and non-binders. The genes coding for the MHC molecules, however, are highly polymorphic, and statistical methods have difficulties building models for alleles with few known binders. In this context, recent work has demonstrated the utility of leveraging information across alleles to improve the performance of the prediction.

Results: We design a support vector machine algorithm that is able to learn peptide–MHC-I binding models for many alleles simultaneously, by sharing binding information across alleles. The sharing of information is controlled by a user-defined measure of similarity between alleles. We show that this similarity can be defined in terms of supertypes, or more directly by comparing key residues known to play a role in the peptide–MHC binding. We illustrate the potential of this approach on various benchmark experiments where it outperforms other state-of-the-art methods.

Availability: The method is implemented on a web server: http://cbio.ensmp.fr/kiss. All data and codes are freely and publicly available from the authors.

Contact:  laurent.jacob@ensmp.fr

Supplementary information: Supplementary data are available at Bioinformatics online.
Noradrenergic control of odor recognition in a nonassociative olfactory learning task in the mouse
Authors: Veyrac Alexandra , Nguyen Véronique , Marien Marc , Didier Anne , Jourdan François
Published: December 2007

The present study examined the influence of pharmacological modulations of the locus coeruleus noradrenergic system on odor recognition in the mouse. Mice exposed to a nonrewarded olfactory stimulation (training) were able to memorize this odor and to discriminate it from a new odor in a recall test performed 15 min later. At longer delays (30 or 60 min), the familiar odor was no longer retained, and both stimuli were perceived as new ones. Following a post-training injection of the α2-adrenoceptor antagonist dexefaroxan, the familiar odor was still remembered 30 min after training. In contrast, both the α2-adrenoceptor agonist UK 14304 and the noradrenergic neurotoxin DSP-4 prevented the recognition of the familiar odor 15 min after the first exposure. Noradrenaline release in the olfactory bulb, assessed by measurement of the extracellular noradrenaline metabolite normetanephrine, was increased by 62% following dexefaroxan injection, and was decreased by 38%–44% after treatment with UK 14304 and DSP-4. Performance of mice in the recall test was reduced by a post-training injection of the β-adrenoceptor antagonist propranolol or the α1-antagonist prazosin, thus implicating a role for β- and α1-adrenoceptors in the facilitating effects of noradrenaline on short-term olfactory recognition in this model.
Stress administered prior to encoding impairs neutral but enhances emotional long-term episodic memories
Authors: Payne Jessica D. , Jackson Eric D. , Hoscheidt Siobhan , Ryan Lee , Jacobs W. Jake , Nadel Lynn
Published: December 2007

Stressful events frequently comprise both neutral and emotionally arousing information, yet the impact of stress on emotional and neutral events is still not fully understood. The hippocampus and frontal cortex have dense concentrations of receptors for stress hormones, such as cortisol, which at high levels can impair performance on hippocampally dependent memory tasks. Yet, the same stress hormones can facilitate memory for emotional information, which involves interactions between the hippocampus and amygdala. Here, we induced psychosocial stress prior to encoding and examined its long-term effects on memory for emotional and neutral episodes. The stress manipulation disrupted long-term memory for a neutral episode, but facilitated long-term memory for an equivalent emotional episode compared with a control condition. The stress manipulation also increased salivary cortisol, catecholamines as indicated by the presence of α-amylase, heart rate, and subjectively reported stress. Stressed subjects reported more false memories than nonstressed control subjects, and these false memories correlated positively with cortisol levels, providing evidence for a relationship between stress and false memory formation. Our results demonstrate that stress, when administered prior to encoding, produces different patterns of long-term remembering for neutral and emotional episodes. These differences likely emerge from differential actions of stress hormones on memory-relevant regions of the brain.
Natural Variation inRPS2-Mediated Resistance amongArabidopsisAccessions: Correlation between Gene Expression Profiles and Phenotypic Responses
Authors: Van Poecke Remco M.P. , Sato Masanao , Lenarz-Wyatt Lisa , Weisberg Sanford , Katagiri Fumiaki
Published: December 2007

Natural variation in gene expression (expression traits or e-traits) is increasingly used for the discovery of genes controlling traits. An important question is whether a particular e-trait is correlated with a phenotypic trait. Here, we examined the correlations between phenotypic traits and e-traits among 10 Arabidopsis thaliana accessions. We studied defense against Pseudomonas syringae pv tomato DC3000 (Pst), with a focus on resistance gene–mediated resistance triggered by the type III effector protein AvrRpt2. As phenotypic traits, we measured growth of the bacteria and extent of the hypersensitive response (HR) as measured by electrolyte leakage. Genetic variation among accessions affected growth of Pst both with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector. Variation in HR was not correlated with variation in bacterial growth. We also collected gene expression profiles 6 h after mock and Pst avrRpt2 inoculation using a custom microarray. Clusters of genes whose expression levels are correlated with bacterial growth or electrolyte leakage were identified. Thus, we demonstrated that variation in gene expression profiles of Arabidopsis accessions collected at one time point under one experimental condition has the power to explain variation in phenotypic responses to pathogen attack.
FABRIC ALIGNMENT USING A ROBOTIC VISION SYSTEM
Authors: Iype C. , Porat I.
Published: December 2007

Two solid state cameras are used in conjunction with an IBM personal computer and a PUMA 560 robot operating under VAL I to align accurately a fabric deposited on an aluminium work surface. The method adopted and the software used is of a modular design so as to use the end‐effector of the robot to achieve the aligning of the fabric or alternatively to use a dedicated device such as an aligning table. Lighting is by ordinary fluorescent light. The software filters out noise such as the frayed edges of a fabric.
THE DESIGN OF EFFECTIVE CLOTHING FOR USE IN WINDY CONDITIONS
Authors: Fan J. , Keighley J.H.
Published: December 2007

The traditional way of wind protection is to use wind‐proof fabrics as outer covers of clothing systems which resist moisture vapour transfer from the inner body, and this can cause associated discomfort. To solve this problem, three design methods are proposed in this paper. These are: (1) to cover the windward areas of the clothing systems with impermeable fabrics and the leeward areas with permeable fabrics; (2) to block the air movement within the insulating materials of the clothing systems, and (3) to have even air pressure distributions over the circumference of a clothing system. The practical value of these designs is evaluated by testing clothing assemblies on a cylindrical togmeter located in a wind tunnel.
AN ENERGY APPROACH TO THE INSTABILITY PROBLEM OF OVERFED SEAMS
Authors: Amirbayat J.
Published: December 2007

Different factors affecting seam instability are discussed and major energy terms involved and their order of magnitude are recognised. By comparing pre‐buckling and post‐buckling energies, four dimensionless groups were derived which are responsible for seam instability and can be used as independent variables in analysing the experimental results. The paper goes further and compares the analytical conclusions with the results of other investigators.
THE USE OF KES AND FAST INSTRUMENTS
Authors: Barndt Herbert , Fortess Fred , Wiener Mel , Cyril Furniss J.
Published: December 2007

The experience of the Philadelphia College of Textiles and Science with the use of Kawabata Evaluation System for Fabrics (KES‐F) since 1984 and more recently, 1988, with the Fabric Assurance by Simple Testing (FAST) is described. Although previous projects have involved the effect of chemical and mechanical finishing and sponging on the hand and mechanical properties of fabrics, the major emphasis here correlates the processability of fabrics in tailored clothing manufacturing, especially in manually operated overfeed sewing, with the tensile‐elongation and shear properties of these fabrics. It is anticipated that programmable sewing machines will require instructions based on the mechanical properties of the fabrics being processed.
RELATION BETWEEN FABRIC MECHANICAL PROPERTIES AND GARMENT DESIGN AND TAILORABILITY
Authors: Shishoo R.L.
Published: December 2007

Future automation and robotisation of apparel manufacturing processes will undoubtedly require that the machines and systems are selected based on the specific properties of the fabric being processed. Thus it is essential to develop and use objective evaluation methods for producing fabric compatibility data which are necessary for control of material handling, sewing and other processes involved in the conversion of fabrics into garments. The qualitative and quantitative analyses of relationships between properties of apparel fabrics and garment making‐up processes are focused on. Studies of mechanical properties of fabrics such as extension, shear and bending and their relationship to objective tailorability determinations constitute the main part of this research work
THE PREDICTION OF GARMENT APPEARANCE FROM MEASURED FABRIC PROPERTIES
Authors: Biglia U. , Roczniok A.F. , Fassina C. , Ly N.G.
Published: December 2007

A simple measurement of fabric pressing performance as indicated by crease angle has been developed and applied to the prediction of appearance of wool and wool blend tailored jackets. Industrial and laboratory trials have measured by the FAST system to give an assessment of garment appearance of lightweight fabrics after they are pressed.
PLACING FABRIC ONTO MOVING SURFACES
Authors: Gunner M.B. , Taylor P.M.
Published: December 2007

There are many instances in automated garment manufacture where static fabric panels have to be picked up and placed onto a moving surface such as a conveyor. The techniques used and, in particular, the effects of lowering a fabric held by its upper edge, onto a moving horizontal surface are described. The particular case of a non‐symmetrical piece is analysed in detail.
REDUCTION IN THREAD STRENGTH AS A CAUSE OF LOADING IN THE SEWING PROCESS
Authors: Geršak Jelka , Knez Blaž
Published: December 2007

Discusses reduction of thread strength as a cause of loading in sewing. Investigates measurements of dynamic loads of the thread during seam formation and reduction of thread strength after loading in sewing. Analysis of results shows that the reduction in thread strength after loading in sewing is a function of dynamic strains of the thread and frictional forces created therein.
PATTERN CONSTRUCTION RULES FOR DOWN'S SYNDROME FEMALES
Authors: Wong Hung Yeh Tam
Published: December 2007

Down's syndrome females generally have non‐standard body features. A database of dimensions is established for 200 Down's syndrome females in Hong Kong aged 15 years and over; the effect of mental retardation upon their ability to dress/undress and deal successfully with a range of fastenings is investigated; studies of posture and ergonomic factors were undertaken. From the information collected it has been possible to establish mannequins and size tables. Important outer garment types have been identified and pattern construction rules developed for five major garment categories: skirt; culottes; slacks; blouses and casual jackets. Recommendations for future development work are made.
THE STIFFNESS OF KNITTED FABRICS:
Authors: Cassidy T. , Cassidy C. , Cassie S. , Arkison M.
Published: December 2007

Gives a review of the various methods which have been developed to measure the stiffness of fabric and describes a new method. This new approach enables the testing of knitted fabrics which are difficult to test using the cantilever system. The inter‐operative reproducibility of the new instrument is compared with that of the cantilever method and the drape meter. Also reports inter‐laboratory comparisons on woven fabric and on knitted fabric, the latter having been measured on a KES‐F system.
PERCEPTION OF FABRICS
Authors: Laughlin Joan
Published: December 2007

The texturalcentric model of non‐attribute‐based visual and tactile response to textural fabric surfaces was used to elicit definitive qualities or dimensions of textural fabric surfaces. Multidimensional scaling analysis permitted subjects to provide numeric judgements of fabrics rather than using words with individuals' historic definitions of those terms, or without understanding some terms. Objectives of the study included validating the attributes identified by college students, and ascertaining the persistence of attributes that contribute to visual and tactile perception of adult women (25–45 years of age) and older women (60 years of age and older). One‐hundred‐and‐twenty subjects (50 per cent adult, 50 per cent older) provided visual or tactile ratings of the similarities of 30 fabrics. Data were subjected to multidimensional scaling analysis and coefficients of congruence were calculated. Dimensions or characteristics of fabrics were named using bipolar adjectives: rough to smooth, plane to depth, irregular to regular surface units, shiny to matt, fine to coarse, lightweight to heavyweight, simple to complex, hard to soft compressibility, pliable to stiff, harsh to slippery, small units to large units, open to compact, and soft to bumpy‐rough. From these, a schema for the textural perception of fabric surfaces, was modelled.
Automated Lace Measurement
Authors: Brown K. , Lunney T.
Published: December 2007

In today's competitive world with reduced profit margins it is important for manufacturers accurately to monitor incoming raw material to ensure that there is no shortfall in terms of quantity and quality (i.e. “what you buy is what you get”). Addresses the quantity aspect by considering the design and development of an automated lace‐measuring system. Considers the design aspect of the system and reports on the operational feedback and results used to evaluate the system in the context of its operating environment.
Detection and Removal of Fabric Defects in Apparel Production
Authors: Tincher Wayne C. , Daley Wayne , Holcomb Wiley
Published: December 2007

Defects in fabric have been and continue to be a major source of seconds in finished garments. These defects persist despite several visual inspections and intensive efforts to remove defective parts during sewing operations. The increased use of automation in assembly steps will intensify the problem of detection and removal of fabric defects in cut‐parts. Describes a workstation utilizing machine vision which has been designed and constructed to detect and remove defective cut‐parts prior to the initiation of assembly operations. The workstation employs two vision systems — an area camera and a line camera — to inspect parts on a conveyor belt both statically and dynamically. The colour of the parts is also determined and the area and perimeter are measured to detect improperly cut parts. The acceptable parts are then stacked in a manner suitable for input to an automated sewing station. The workstation should permit placing into the assembly operations a set of defect‐free, properly‐cut and colour‐matched parts. It is estimated that this cut‐part inspection system will reduce defects in finished garments by approximately 50 per cent and should greatly simplify the labour‐intensive and costly fabric defect control systems currently in place in most apparel plants.
A Methodological Approach to the Study of Ergonomic Loads in the Clothing Industry
Authors: Verhovnik Vekoslav , Polajnar Andrej
Published: December 2007

Presents a special methodological approach to the study of stress and strain at work, in order to reduce excessive workload by allowing extra time for the operation. In the study three methods were used: activity sampling; job analysis and evaluation; and measurement of workplace conditions. Also, a method was used which gives criteria and grades for research and evaluation of stresses at the workplace. These are physical stress (dynamical and statical); thermal; visual; noise stress; stress caused by contact with aerosols; gases; vapours; stress caused by monotony. They are measured as ecological, physiological and comfort indexes. It is clear that stress factors enable the evaluation of most physical work. The application scope for our model of defining the ergonomic coefficient was the clothing industry. The defined ergonomic coefficient represents a smaller addition to standard time than the strain and the environmental coefficients used at present.
An Optical Technique to Detect Miss Stitch in Real Time
Authors: Porat I. , Alagha M.J.
Published: December 2007

Miss stitch is a known fault which can unravel the properly formed stitches in single needle, chain‐stitch seams. Describes a new technique based on optical arrangement to detect miss stitch on high speed sewing machines. A bifurcated fibre optic in an electro‐optical system in conjunction with monitoring circuitry and microprocessor have been developed to stop the sewing operation as miss stitch occurs. The system proved reliable and commercial exploitation will shortly be pursued.
Objective Evaluation of the Quality of Ladies' Garments
Authors: Kawabata S. , Niwa Masako
Published: December 2007

Discusses the quality of fabrics and garment technology. Looks at the various types of material focusing particularly on the female market. Shows how new synthetic fibres have improved the feel of garments and that consumers, fashion designers and experts in finishing have all reached the same conclusion, that quality judgement is still possible, even with today's exacting standards.
Report on Scoping the Apparel Manufacturing Enterprise
Authors: Moncarz Howard T. , Tina Lee Y.
Published: December 2007

Identifies a set of manufacturing data interfaces that could be standardized for the effective computer integration of the information required to operate an apparel manufacturing enterprise. The interfaces are called Application Protocols. Describes a method using pieces of information, referred to as Units of Functionality, as building blocks for designing Application Protocols.
Manufacturing Technology for Apparel Automation — Lay up Module
Authors: Seyam A. , Sun F. , McPherson E. , Clapp T. , Little T.
Published: December 2007

Describes a novel principle of the automatic cloth layup module. Discusses the optimum design requirement of the slat, and the main element of the cloth stacking conveyor. Using Bernoulli‐Euler beam theory, calculates the maximum deflection of the slat for different materials and different cross‐sections of various dimensions. For the range of dimensions studied under the constraints set by the requirement of the slat, concludes that C or a hollow rectangular beam made of aluminium is the optimum selection among the cases considered.
Optimization of the Design of a Ply Separation Device
Authors: Beaton John R. , Clapp Timothy G.
Published: December 2007

Describes the redesign of the Clupicker, a ply separation device used in the textile industry, based on design for assembly techniques. Presents design for assembly (DFA) guidelines. Describes Boothroyd's Systematic DFA Methodology and Zorowski's PDM program, and analyses the design of the Clupicker using both of these methods. Presents and analyses a proposed redesign of the Clupicker based on DFA techniques.
A Theoretical Study on Convective Condensation of Water Vapor From Humid Air in Turbulent Flow in a Vertical Duct
Authors: Dharma Rao V. , Murali Krishna V. , Sharma K. V. , Sarma P. K.
Published: December 2007

The problem of condensation of water vapor from humid air flowing in a duct in turbulent flow is formulated theoretically. Vapor condensing at the dew-point temperature of the vapor-air mixture diffuses to the wall of the duct through an air film. The flow of the condensate is laminar. The condensing vapor releases both convection and latent heats to the wall of the duct. Thus, it is treated as a combined heat and mass transfer problem. The mass, momentum, and energy balance equations for the vapor-air mixture flowing in the duct and the diffusion equation for the vapor species are considered. Ti, the temperature at gas-to-liquid interface, at which condensation takes place, is estimated with the help of the heat balance and mass balance equations at interface. The local and average values of the condensation Nusselt number, condensate Reynolds number, gas-liquid interface temperature, and pressure drop are estimated from the numerical results for different values of the system parameters, such as relative humidity and temperature of air at inlet, gas phase Reynolds number, and total pressure at inlet. The gas phase convection Nusselt and Sherwood numbers are also computed. A comparison of the present work with experimental data, for the case of in-tube condensation of vapor from humid air, shows satisfactory agreement.
Magnetohydrodynamic Flow Past a Vertical Plate With Radiative Heat Transfer
Authors: Shateyi S. , Sibanda P. , Motsa S. S.
Published: December 2007

The problem of steady, laminar, magnetohydrodynamic flow past a semi-infinite vertical plate is studied. The primary purpose of this study was to characterize the effects of thermal radiative heat transfer, magnetic field strength, and Hall currents on the flow properties. The governing nonlinear coupled differential equations comprising the laws of mass, linear momentum, and energy modified to include magnetic and radiative effects were solved numerically. The effects of the Hall current, the Hartmann number, and the radiative parameter on the velocity and temperature profiles are presented graphically. Large Hall currents and radiation effects cause the fluid to heat up and the velocity to increase in the lateral direction but decrease in the tangential direction. This study showed inter alia that reducing Hall currents and increasing the strength of the magnetic field lead to a reduction in the temperature and, consequently, in the thermal boundary layer, and so confirming that heat transfer mitigation through magnetic control is possible.
Effect of the Temperature Difference Aspect Ratio on Natural Convection in a Square Cavity for Nonuniform Thermal Boundary Conditions
Authors: Sathiyamoorthy M. , Basak Tanmay , Roy S. , Mahanti N. C.
Published: December 2007

The present numerical investigation deals with steady natural convection flow in a closed square cavity when the bottom wall is sinusoidal heated and vertical walls are linearly heated, whereas the top wall is well insulated. In the nonuniformly heated bottom wall maximum temperature TH attains at the center of the bottom wall. The sidewalls are linearly heated, maintained at minimum temperature Tc at top edges of the sidewalls and at temperature Th at the bottom edges of the sidewalls, i.e., Tc≤Th≤TH. Nonlinear coupled PDEs governing the flow have been solved by the penalty finite element method with biquadratic rectangular elements. Numerical results are obtained for various values of Prandtl number (Pr)(0.01≤Pr≤10) and temperature difference aspect ratio A=[(Th−Tc)∕(TH−Tc)](0≤A≤1) for higher Raleigh number Ra=105. Results are presented in the form of streamlines, isotherm contours, local Nusselt number, and the average Nusselt number as a function of temperature difference aspect ratio A. The overall heat transfer process is shown to be tuned efficiently with suitable selection of A.
A Methodology for Blast Furnace Hearth Inner Profile Analysis
Authors: Zhang Yu , Deshpande Rohit , Huang D. , Chaubal Pinakin , Zhou Chenn Q.
Published: December 2007

The wear of a blast furnace hearth and the hearth inner profile are highly dependent on the liquid iron flow pattern, refractory temperatures, and temperature distributions at the hot face. In this paper, the detailed methodology is presented along with the examples of hearth inner profile predictions. A new methodology along with new algorithms is proposed to calculate the hearth erosion and its inner profile. The methodology is to estimate the hearth primary inner profile based on 1D heat transfer and to compute the hot-face temperature using the 3D CFD hearth model according to the 1D preestimated and reestimated profiles. After the hot-face temperatures are converged, the hot-face positions are refined by a new algorithm, which is based on the difference between the calculated and measured results, for the 3D computational fluid dynamics (CFD) hearth model further computations, until the calculated temperatures well agree with those measured by the thermocouples.
Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the
13
C Content of Bacterial rRNA
Authors: Pearson Ann , Kraunz Kimberly S. , Sessions Alex L. , Dekas Anne E. , Leavitt William D. , Edwards Katrina J.
Published: December 2007

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the
13
C-enriched C
4
grass
Spartina alterniflora
and
13
C-depleted petroleum to monitor changes in the
13
C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the
13
C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of
Gamma
- and
Deltaproteobacteria
and
Firmicutes
in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the
13
C content of biomarker lipids.
N-Glycan Modification in
Aspergillus
Species
Authors: Kainz Elke , Gallmetzer Andreas , Hatzl Christian , Nett Juergen H. , Li Huijuan , Schinko Thorsten , Pachlinger Robert , Berger Harald , Reyes-Dominguez Yazmid , Bernreiter Andreas , Gerngross Tillmann , Wildt Stefan , Strauss Joseph
Published: December 2007

The production by filamentous fungi of therapeutic glycoproteins intended for use in mammals is held back by the inherent difference in protein N-glycosylation and by the inability of the fungal cell to modify proteins with mammalian glycosylation structures. Here, we report protein N-glycan engineering in two
Aspergillus
species. We functionally expressed in the fungal hosts heterologous chimeric fusion proteins containing different localization peptides and catalytic domains. This strategy allowed the isolation of a strain with a functional α-1,2-mannosidase producing increased amounts of N-glycans of the Man
5
GlcNAc
2
type. This strain was further engineered by the introduction of a functional GlcNAc transferase I construct yielding GlcNAcMan
5
GlcNac
2
N-glycans. Additionally, we deleted
algC
genes coding for an enzyme involved in an early step of the fungal glycosylation pathway yielding Man
3
GlcNAc
2
N-glycans. This modification of fungal glycosylation is a step toward the ability to produce humanized complex N-glycans on therapeutic proteins in filamentous fungi.
Identification of a Putative Mexican Strain ofSerratia entomophilaPathogenic against Root-Damaging Larvae of Scarabaeidae (Coleoptera)
Authors: Nuñez-Valdez M. Eugenia , Calderón Marco A. , Aranda Eduardo , Hernández Luciano , Ramírez-Gama Rosa M. , Lina Laura , Rodríguez-Segura Zitlhally , Gutiérrez María del C. , Villalobos Francisco J.
Published: December 2007

The larvae of scarab beetles, known as “white grubs” and belonging to the generaPhyllophagaandAnomala(Coleoptera: Scarabaeidae), are regarded as soil-dwelling pests in Mexico. During a survey conducted to find pathogenic bacteria with the potential to control scarab larvae, a nativeSerratiasp. (strain Mor4.1) was isolated from a dead third-instarPhyllophaga blanchardilarva collected from a cornfield in Tres Marías, Morelos, Mexico. Oral bioassays using healthyP. blanchardilarvae fed with the Mor4.1 isolate showed that this strain was able to cause an antifeeding effect and a significant loss of weight. Mortality was observed forP. blanchardi,P. trichodes, andP. obsoletain a multidose experiment. The Mor4.1 isolate also caused 100% mortality 24 h after intracoelomic inoculation of the larvae ofP. blanchardi,P. ravida,Anomala donovaniand the lepidopteran insectManduca sexta. Oral and injection bioassays were performed with concentrated culture broths of the Mor4.1 isolate to search for disease symptoms and mortality caused by extracellular proteins. The results have shown that Mor4.1 broths produce significant antifeeding effects and mortality. Mor4.1 broths treated with proteinase K lost the ability to cause disease symptoms and mortality, in both the oral and the injection bioassays, suggesting the involvement of toxic proteins in the disease. The Mor4.1 isolate was identified as a putativeSerratia entomophilaMor4.1 strain based on numerical taxonomy and phylogenetic analyses done with the 16S rRNA gene sequence. The potential ofS. entomophilaMor4.1 and its toxins to be used in an integrated pest management program is discussed.
Identification of a Ciliate (Oligohymenophorea: Scuticociliatia) Associated with Brown Band Disease on Corals of the Great Barrier Reef
Authors: Bourne David G. , Boyett Holly V. , Henderson Meegan E. , Muirhead Andrew , Willis Bette L.
Published: December 2007

A ciliate associated with the coral disease brown band (BrB) was identified as a new species belonging to the class Oligohymenophorea, subclass Scuticociliatia. The ciliates were characterized by the presence of large numbers of intracellular dinoflagellates and displayed an elongated, tube-shaped body structure. They had uniform ciliature, except for three distinct cilia in the caudal region, and were typically 200 to 400 μm in length and 20 to 50 μm in width.
Heterologous Expression of the Pneumococcal Serotype 14 Polysaccharide inLactococcus lactisRequires LactococcalepsABCRegulatory Genes
Authors: Nierop Groot Masja N. , Godefrooij Jeroen , Kleerebezem Michiel
Published: December 2007

The pneumococcal serotype 14 polysaccharide was produced inLactococcus lactisby coexpressing pneumococcal polysaccharide type 14-specific genes (cpsFGHIJKL14) with the lactococcal regulatory and priming glucosyltransferase-encoding genes specific for B40 polysaccharide (epsABCDB40). The polysaccharide produced byLactococcuswas secreted in the medium, simplifying downstream processing and polysaccharide isolation from culture broth.
Recovery of Spores from Thermophilic Dairy Bacilli and Effects of Their Surface Characteristics on Attachment to Different Surfaces
Authors: Seale R. B. , Flint S. H. , McQuillan A. J. , Bremer P. J.
Published: December 2007

Spores from four
Geobacillus
spp. were isolated from a milk powder manufacturing line in New Zealand. Liquid sporulation media produced spore yields of ∼10
7
spores ml
−1
; spores were purified using a two-phase system created with polyethylene glycol 4000 and 3 M phosphate buffer. The zeta potentials of the spores from the four isolates ranged from −10 to −20 mV at neutral pH, with an isoelectric point between pH 3 and 4. Through contact angle measurements, spores were found to be hydrophilic and had relative hydrophobicity values of 10 to 40%, as measured by the microbial adhesion to hexadecane assay. The most hydrophilic spore isolate with the smallest negative charge attached in the highest numbers to Thermanox and stainless steel (1 × 10
4
spores cm
−2
), with fewer spores attaching to glass (3 × 10
3
spores cm
−2
). However, spores produced by the other three strains attached in similar numbers (
P
> 0.05) to all substrata (∼1 × 10
3
spores cm
−2
), indicating that there was no simple relationship between individual physicochemical interactions and spore adherence. Therefore, surface modifications which limit the attachment of one strain may not be effective for all stains, and control regimens need to be devised with reference to the characteristics of the particular strains of concern.
Miniprimer PCR, a New Lens for Viewing the Microbial World
Authors: Isenbarger Thomas A. , Finney Michael , Ríos-Velázquez Carlos , Handelsman Jo , Ruvkun Gary
Published: December 2007

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and
Taq
polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.
Effect of Shadowing on Survival of Bacteria under Conditions Simulating the Martian Atmosphere and UV Radiation
Authors: Osman Shariff , Peeters Zan , La Duc Myron T. , Mancinelli Rocco , Ehrenfreund Pascale , Venkateswaran Kasthuri
Published: December 2007

Spacecraft-associated spores and four non-spore-forming bacterial isolates were prepared in Atacama Desert soil suspensions and tested both in solution and in a desiccated state to elucidate the shadowing effect of soil particulates on bacterial survival under simulated Martian atmospheric and UV irradiation conditions. All non-spore-forming cells that were prepared in nutrient-depleted, 0.2-μm-filtered desert soil (DSE) microcosms and desiccated for 75 days on aluminum died, whereas cells prepared similarly in 60-μm-filtered desert soil (DS) microcosms survived such conditions. Among the bacterial cells tested,
Microbacterium schleiferi
and
Arthrobacter
sp. exhibited elevated resistance to 254-nm UV irradiation (low-pressure Hg lamp), and their survival indices were comparable to those of DS- and DSE-associated
Bacillus pumilus
spores. Desiccated DSE-associated spores survived exposure to full Martian UV irradiation (200 to 400 nm) for 5 min and were only slightly affected by Martian atmospheric conditions in the absence of UV irradiation. Although prolonged UV irradiation (5 min to 12 h) killed substantial portions of the spores in DSE microcosms (∼5- to 6-log reduction with Martian UV irradiation), dramatic survival of spores was apparent in DS-spore microcosms. The survival of soil-associated wild-type spores under Martian conditions could have repercussions for forward contamination of extraterrestrial environments, especially Mars.
Root Exudates Regulate Soil Fungal Community Composition and Diversity
Authors: Broeckling Corey D. , Broz Amanda K. , Bergelson Joy , Manter Daniel K. , Vivanco Jorge M.
Published: December 2007

Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species (
Arabidopsis thaliana
and
Medicago truncatula
) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.
Anaerobic Conditions Promote Expression of Sfp Fimbriae and Adherence of Sorbitol-Fermenting Enterohemorrhagic
Escherichia coli
O157:NM to Human Intestinal Epithelial Cells
Authors: Müsken Anne , Bielaszewska Martina , Greune Lilo , Schweppe Christian H. , Müthing Johannes , Schmidt Herbert , Schmidt M. Alexander , Karch Helge , Zhang Wenlan
Published: December 2007

The
sfp
gene cluster, unique to sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157:NM strains, encodes fimbriae that mediate mannose-resistant hemagglutination in laboratory
E. coli
strains but are not expressed in wild-type SF EHEC O157:NM strains under standard laboratory conditions. We investigated whether Sfp fimbriae are expressed under conditions that mimic the intestinal environment and whether they contribute to the adherence of SF EHEC O157:NM strains to human intestinal epithelial cells. The transcription of
sfpA
(encoding the major fimbrial subunit) was upregulated in all strains investigated, and all expressed SfpA and possessed fimbriae that reacted with an anti-SfpA antibody when the strains were grown on solid media under anaerobic conditions. Sfp expression was absent under aerobic conditions and in liquid media. Sfp upregulation under anaerobic conditions was significantly higher on blood agar and a medium simulating the colonic environment than on a medium simulating the ileal environment (
P
< 0.05). The induction of Sfp fimbriae in SF
E. coli
O157:NM strains correlates with increased adherence to Caco-2 and HCT-8 cells. Our data indicate that the expression of Sfp fimbriae in SF
E. coli
O157:NM strains is induced under conditions resembling those of the natural site of infection and that Sfp fimbriae may contribute to the adherence of the organisms to human intestinal epithelium.
Effect of Hydroxyurea on Procyclic
Trypanosoma brucei
: an Unconventional Mechanism for Achieving Synchronous Growth
Authors: Chowdhury Arnab Roy , Zhao Zhixing , Englund Paul T.
Published: December 2007

Procyclic
Trypanosoma brucei
cells were synchronized with 0.2 mM hydroxyurea. The cells did not arrest at the G
1
/S boundary but proceeded through one round of replication and arrested near the end of S phase. The mitochondrial genome (kinetoplast DNA network) replicated, forming two progeny networks, but the repair of minicircle gaps was inhibited.
Escherichia coli
Cytosolic Glycerophosphodiester Phosphodiesterase (UgpQ) Requires Mg
2+
, Co
2+
, or Mn
2+
for Its Enzyme Activity
Authors: Ohshima Noriyasu , Yamashita Saori , Takahashi Naoko , Kuroishi Chizu , Shiro Yoshitsugu , Takio Koji
Published: December 2007

Escherichia coli
cytosolic glycerophosphodiester phosphodiesterase, UgpQ, functions in the absence of other proteins encoded by the
ugp
operon and requires Mg
2+
, Mn
2+
, or Co
2+
, in contrast to Ca
2+
-dependent periplasmic glycerophosphodiester phosphodiesterase, GlpQ. UgpQ has broad substrate specificity toward various glycerophosphodiesters, producing
sn
-glycerol-3-phosphate and the corresponding alcohols. UgpQ accumulates under conditions of phosphate starvation, suggesting that it allows the utilization of glycerophosphodiesters as a source of phosphate. These results clarify how
E. coli
utilizes glycerophosphodiesters using two homologous enzymes, UgpQ and GlpQ.
γ-Butyrolactone-Dependent Expression of theStreptomycesAntibiotic Regulatory Protein GenesrrYPlays a Central Role in the Regulatory Cascade Leading to Lankacidin and Lankamycin Production inStreptomyces rochei
Authors: Yamamoto Shouji , He Yuxi , Arakawa Kenji , Kinashi Haruyasu
Published: December 2007

Our previous studies revealed that thesrrXandsrrAgenes carried on the large linear plasmid pSLA2-L constitute a γ-butyrolactone-receptor system inStreptomyces rochei. Extensive transcriptional analysis has now showed that theStreptomycesantibiotic regulatory protein genesrrY, which is also carried on pSLA2-L, is a target of the receptor/repressor SrrA and plays a central role in lankacidin and lankamycin production. ThesrrYgene was expressed in a growth-dependent manner, slightly preceding antibiotic production. The expression ofsrrYwas undetectable in thesrrXmutant but was restored in thesrrX srrAdouble mutant. In addition, SrrA was bound specifically to the promoter region ofsrrY, and this binding was prevented by the addition of theS. rocheiγ-butyrolactone fraction, while the W119A mutant receptor SrrA was kept bound even in the presence ofS. rocheiγ-butyrolactone. Furthermore, the introduction of an intactsrrYgene under the control of a foreign promoter into thesrrXorsrrA(W119A) mutant restored antibiotic production. All of these results confirmed the signaling pathway fromsrrXthroughsrrAtosrrY, leading to lankacidin and lankamycin production.
A Mutational Analysis Defines
Vibrio fischeri
LuxR Binding Sites
Authors: Antunes Luis Caetano M. , Ferreira Rosana B. R. , Lostroh C. Phoebe , Greenberg E. Peter
Published: December 2007

Vibrio fischeri
quorum sensing involves the LuxI and LuxR proteins. The LuxI protein generates the quorum-sensing signal
N
-3-oxohexanoyl-
l
-homoserine lactone (3OC6-HSL), and LuxR is a signal-responsive transcriptional regulator which activates the luminescence (
lux
) genes and 17 other
V. fischeri
genes. For activation of the
lux
genes, LuxR binds to a 20-base-pair inverted repeat, the
lux
box, which is centered 42.5 base pairs upstream of the transcriptional start of the
lux
operon. Similar
lux
box-like elements have been identified in only a few of the LuxR-activated
V. fischeri
promoters. To better understand the DNA sequence elements required for LuxR binding and to identify binding sites in LuxR-regulated promoters other than the
lux
operon promoter, we have systematically mutagenized the
lux
box and evaluated the activity of many mutants. By doing so, we have identified nucleotides that are critical for promoter activity. Interestingly, certain
lux
box mutations allow a 3OC6-HSL-independent LuxR activation of the
lux
operon promoter. We have used the results of the mutational analysis to create a consensus
lux
box, and we have used this consensus sequence to identify LuxR binding sites in 3OC6-HSL-activated genes for which
lux
boxes could not be identified previously.