bluuebunny/crossref_metadata_2025 huggingface dataset:
Control Laws Based on Parameter Observation
Authors: Tornambe` A.
Published: March 2008

This paper deals with the use of asymptotic observers in the parameter estimation. Exact and approximate procedures are proposed taking into account the nonlinear behaviour of the dynamic systems considered. It is shown that a separation property holds for sufficiently fast observers and, therefore, that parameter estimates obtained by asymptotic observers are useful for the implementation of feedback control laws. The paper is completed with an application to flexible robot arms for the estimation of the elastic constant. Simulation tests are included.
Minimization of Power Losses in Cooperating Manipulators
Authors: Nahon M. , Angeles J.
Published: March 2008

The control of multiple manipulators handling a common object entails the solution of an underdetermined system of linear equations which represents the system’s dynamics. In order to choose an optimal solution to this problem, various approaches have been proposed: minimum internal force and minimum power, among others. The present work investigates an approach for minimizing the power losses in these systems. It is shown that the power imparted to the manipulator/payload system cannot be optimized once the system’s motion is prescribed. However, assuming certain loss characteristics for the dc servomotors commonly used on robotic manipulators, it is shown that the minimization of power losses can be cast as a linear-quadratic optimization problem. Local and global performance indices are introduced to allow comparison of the minimum power loss and the minimum internal force approaches. An example of two Puma 560 robots handling a common payload is shown to demonstrate the proposed technique.
Point-to-Point Positioning of Flexible Structures Using a Time Domain LQ Smoothness Constraint
Authors: Bhat S. P. , Miu D. K.
Published: March 2008

An analytical procedure to implement optimal smoothing of the finite-time control waveform for point-to-point control problem is presented, which minimizes an optimality constraint consisting of a linear combination of the quadratic norms of its time derivatives. It is shown that the resulting control input is essentially the minimum norm solution augmented to satisfy some additional continuity requirements in the time domain. Application of the proposed technique to finite-time maneuvering of flexible structures is experimentally demonstrated and performances are compared using control torques evaluated based on different order of the smoothness constraint and order of the truncated plant model.
Reconstructing Tethered Satellite Skiprope Motion by Bandpass Filtering Magnetometer Measurements
Authors: Polites M. E.
Published: March 2008

This paper presents a unique scheme for reconstructing tethered satellite skiprope motion by ground processing satellite magnetometer measurements. The measurements are modified based on ground knowledge of the Earth’s magnetic field and passed through bandpass filters tuned to the skiprope frequency. Skiprope motion is then deduced from the steady-state outputs of the filters. Simulation results are presented which verify the scheme and show it to be robust. The concept is not just limited to tethered satellites. Indeed, it can be applied whenever there is a need to reconstruct the coning motion of a body about a known axis, given measurements of a known vector in body-fixed axes.
Deadtime Compensation and Zero Frequency Decoupling of a Thermal Hydraulic Process
Authors: Liu J. Z. , Pieper J. K. , Surgenor B. W.
Published: March 2008

This brief details the design and experimental implementation of a practical multivariable controller applied to a thermal hydraulic process. Features of the design include a first-order plus deadtime process model, zero frequency decoupling, and multivariable deadtime compensation. The deadtime compensator allowed higher loop gains and consequently improved overall performance. Practical first order prediction based on an estimated delay and process time constant achieved the deadtime compensation. The high gain controller effectively handled both setpoint changes and disturbance rejection. An intelligent choice of estimation schemes yielded a simple but accurate model.
Modeling and Dynamic Characterization of the Czochralski Crystal Growth Process
Authors: Gevelber M. A. , Stephanopoulos G.
Published: March 2008

A lumped parameter model of the Czochralski crystal growth process is proposed that captures the dominant nonlinear dynamics, internal coupling, and disturbance structure. Conventional and advanced actuators are modeled. The dynamic characteristics of the interface shape and input/outputs that limit the achievable controller performance are identified.
Learning Algorithms for Neural Networks Based on Quasi-Newton Methods With Self-Scaling
Authors: Beigi H. S. M. , Li C. J.
Published: March 2008

Previous studies have suggested that, for moderate sized neural networks, the use of classical Quasi-Newton methods yields the best convergence properties among all the state-of-the-art [1]. This paper describes a set of even better learning algorithms based on a class of Quasi-Newton optimization techniques called Self-Scaling Variable Metric (SSVM) methods. One of the characteristics of SSVM methods is that they provide a set of search directions which are invariant under the scaling of the objective function. With an XOR benchmark and an encoder benchmark, simulations using the SSVM algorithms for the learning of general feedforward neural networks were carried out to study their performance. Compared to classical Quasi-Newton methods, it is shown that the SSVM method reduces the number of iterations required for convergence by 40 percent to 60 percent that of the classical Quasi-Newton methods which, in general, converge two to three orders of magnitude faster than the steepest descent techniques.
Dynamic Model and Response of Robot Manipulators With Joint Irregularities
Authors: Chang R. J. , Jiang T. C.
Published: March 2008

The dynamic equation of a robotic manipulator with joint irregularities is formulated and employed for the prediction of the positioning accuracy and precision of a robotic manipulator in high-speed operation. The mathematical model is derived by incorporating a dynamic model of irregular joints in an ideal robotic equation and employing the Lagrangian formulation. The joint irregularity is modelled as an elastic sliding pair which consists of a journal with an irregular surface sliding on the surface of an elastic bearing. By employing Gaussian linearization methods, the operational accuracy and precision of the robotic manipulator are obtained from mean and covariance propagation equations of the robotic system. The operation of a single-arm robotic manipulator with joint irregularities is investigated for demonstrating the applications of the present techniques.
Qualitative Template Matching Using Dynamic Process Models for State Transition Recognition of Robotic Assembly
Authors: McCarragher B. J. , Asada H.
Published: March 2008

This paper presents a model-based approach to the recognition of discrete state transitions for robotic assembly. Sensor signals, in particular, force and moment, are interpreted with reference to the physical model of an assembly process in order to recognize the state of assembly in real time. Assembly is a dynamic as well as a geometric process. Here, the model-based approach is applied to the unique problems of the dynamics generated by geometric interactions in an assembly process. First, a new method for the modeling of the assembly process is presented. In contrast to the traditional quasi-static treatment of assembly, the new method incorporates the dynamic nature of the process to highlight the discrete changes of state, e.g., gain and loss of contact. Second, a qualitative recognition method is developed to understand a time series of force signals. The qualitative technique allows for quick identification of the change of state because dynamic modelling provides much richer and more copious information than the traditional quasi-static modeling. A network representation is used to compactly present the modelling state transition information. Lastly, experimental results are given to demonstrate the recognition method. Successful transition recognition was accomplished in a very short period of time: 7-10 ms.
Experiments on the Tracking Control of a Flexible One-Link Manipulator
Authors: Menq Chia-Hsiang , Xia Jack Zhijie
Published: March 2008

Experimental study on the tracking control of a flexible onelink manipulator is reported in this paper. A tracking control scheme is developed based on the system transfer function. In the proposed control scheme, the desired control input for a given end-point trajectory is obtained by using a command feedforward controller instead of solving the inverse dynamic equations of the system. The proposed control scheme requires small amount of computations and can be easily implemented for real time control. The experimental results are presented, which shows very good tracking performance.
Active Control of Flexible Structures Subject to Distributed and Seismic Disturbances
Authors: Ohsumi Akira , Sawada Yuichi
Published: March 2008

The purpose of this paper is to present a method of active control for suppressing the vibration of a mechanically flexible cantilever beam which is subject to a distributed random disturbance and also a seismic input at the clamped end. First, the mathematical model of the flexible structure is established by a stochastic partial differential equation which describes the Euler-Bernoulli type distributed parameter system with internal viscous damping and subject to the seismic and distributed random inputs. Second, the distributed parameter model, which is considered as an infinite-dimensional system, is reduced to a finite-dimensional one by using the modal expansion, and split into the controlled part and the uncontrolled (residual) one. The principal approach is to regard the observation spillover due to uncontrolled part as a colored observation noise and construct an estimator, and then we construct the optimal control system. Finally, simulation studies are presented by using a real earthquake accelerogram data.
Active Versus Passive Vibration Absorbers
Authors: Herzog R.
Published: March 2008

Passivity based control has several advantages, e.g., robustness and simplicity. However, the passivity constraint causes performance degradations. Specifically, the degree to which passively controlled absorber systems yield a flat response around the nominal absorber frequency is limited. An inherent flatness bound is derived using Nevanlinna-Pick boundary interpolation theory. For active vibration absorbers, this limitation cancels, and magnitude response can be made arbitrarily flat.
Incorporating Right Half-Plane Poles and Zeros in a Frequency Domain Design Technique
Authors: Sobhani Massoud , Jayasuriya Suhada
Published: March 2008

The frequency domain design methodology developed in Jayasuriya and Franchek (1988) for the synthesis of controllers that maximize the allowable size of an unknown-but-bounded disturbance in the presence of several time domain constraints is revisited. It is shown that (i) the basic ingredients of the methodology stays essentially the same for systems with nonminimum phase zeros and/or unstable poles, and (ii) two modifications can facilitate the loop shaping step. In particular, a nonminimum phase problem may be converted to one of frequency shaping a minimum phase loop; and a prestabilization scheme may be used for unstable systems. Two examples illustrate the proposed modifications with one compared to results obtained by the so called Set-Theoretic (ST) approach.
Impact and Force Control: Modeling and Experiments
Authors: Youcef-Toumi K. , Gutz D. A.
Published: March 2008

Robot manipulators and drive systems can experience instability or poor control performance after impacting with an environment. This paper presents an analytical model for impact which is experimentally validated step-by-step. Extensive simulations and experiments are conducted to explain impact phenomena for the case of a force feedback control of a drive system. The results are based on an energy method and presented concisely in dimensionless form. To this end, a small number of dimensionless groups are used to characterize the impact behavior through simulations and tests. The study shows that an integral force compensation with a velocity feedback improves force tracking and reject impacts. It is also revealed that impact response can be tuned by selecting a favorable dimensionless ratio of force to approach velocity.
Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil
Authors: Peng Jingjing , Lü Zhe , Rui Junpeng , Lu Yahai
Published: March 2008

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH
4
production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH
4
was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH
4
production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that
Methanosarcinaceae
developed early in the incubations, whereas
Methanosaetaceae
became more abundant in the later stages.
Methanosarcinaceae
and
Methanosaetaceae
seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic
Methanobacteriales
and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of
Methanosarcinaceae
, whereas the root residues favored
Methanosaetaceae
. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H
2
) seems to be the key factor that regulates the shift of methanogenic community.
Genomic Insights into Mn(II) Oxidation by the Marine Alphaproteobacterium
Aurantimonas
sp. Strain SI85-9A1
Authors: Dick Gregory J. , Podell Sheila , Johnson Hope A. , Rivera-Espinoza Yadira , Bernier-Latmani Rizlan , McCarthy James K. , Torpey Justin W. , Clement Brian G. , Gaasterland Terry , Tebo Bradley M.
Published: March 2008

Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium
Aurantimonas
sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O
2
concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca
2+
-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.
Microbes Enriched in Seawater after Addition of Coral Mucus
Authors: Allers Elke , Niesner Christina , Wild Christian , Pernthaler Jakob
Published: March 2008

We investigated which microbial taxa in coastal Red Sea water were stimulated by addition of mucus from the coral
Fungia
sp. Decreases in the concentration and C/N ratio of particulate organic material during short-term incubations (50 h) were paralleled by a steep rise in the number of
Gammaproteobacteria
, particularly
Alteromonadaceae
, followed by
Vibrionaceae
. Two almost identical genotypes affiliated with
Alteromonas macleodii
accounted for up to >85% of all
Alteromonadaceae
(45% of the total cells) in the mucus-amended enrichments but were rare in unamended control incubations and in ambient seawater.
A. macleodii
-like bacteria might thus be important in the transfer of organic carbon from coral mucus to the pelagic microbial food webs of coral reefs.
Identification and Onion Pathogenicity of
Burkholderia cepacia
Complex Isolates from the Onion Rhizosphere and Onion Field Soil
Authors: Jacobs Janette L. , Fasi Anthony C. , Ramette Alban , Smith James J. , Hammerschmidt Raymond , Sundin George W.
Published: March 2008

Burkholderia cepacia
complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on
B. cepacia
complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative
B. cepacia
complex isolates were recovered on
Pseudomonas cepacia
azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative
B. cepacia
complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and
recA
sequences and restriction fragment length polymorphism analysis of the
recA
sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species
B. cepacia
(160),
B. cenocepacia
(480),
B. ambifaria
(623), and
B. pyrrocinia
(27). The majority of isolates identified as
B. cepacia
(85%),
B. cenocepacia
(90%), and
B. ambifaria
(76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of
recA
sequences from representative
B. cepacia
complex type and panel strains, along with isolates collected in this study, revealed that the
B. cenocepacia
isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple
B. cepacia
complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source of
B. cenocepacia
.
Impact of Nitrate on the Structure and Function of Bacterial Biofilm Communities in Pipelines Used for Injection of Seawater into Oil Fields
Authors: Schwermer Carsten U. , Lavik Gaute , Abed Raeid M. M. , Dunsmore Braden , Ferdelman Timothy G. , Stoodley Paul , Gieseke Armin , de Beer Dirk
Published: March 2008

We studied the impact of NO
3
−
on the bacterial community composition, diversity, and function in in situ industrial, anaerobic biofilms by combining microsensor profiling,
15
N and
35
S labeling, and 16S rRNA gene-based fingerprinting. Biofilms were grown on carbon steel coupons within a system designed to treat seawater for injection into an oil field for pressurized oil recovery. NO
3
−
was added to the seawater in an attempt to prevent bacterial H
2
S generation and microbially influenced corrosion in the field. Microprofiling of nitrogen compounds and redox potential inside the biofilms showed that the zone of highest metabolic activity was located close to the metal surface, correlating with a high bacterial abundance in this zone. Upon addition, NO
3
−
was mainly reduced to NO
2
−
. In biofilms grown in the absence of NO
3
−
, redox potentials of <−450 mV at the metal surface suggested the release of Fe
2+
. NO
3
−
addition to previously untreated biofilms induced a decline (65%) in bacterial species richness, with
Methylophaga
- and
Colwellia
-related sequences having the highest number of obtained clones in the clone library. In contrast, no changes in community composition and potential NO
3
−
reduction occurred upon subsequent withdrawal of NO
3
−
. Active sulfate reduction was below detection levels in all biofilms, but S isotope fractionation analysis of sulfide deposits suggested that it must have occurred either at low rates or episodically. Scanning electron microscopy revealed that pitting corrosion occurred on all coupons, independent of the treatment. However, uniform corrosion was clearly mitigated by NO
3
−
addition.
Estimates of Biogenic Methane Production Rates in Deep Marine Sediments at Hydrate Ridge, Cascadia Margin
Authors: Colwell F. S. , Boyd S. , Delwiche M. E. , Reed D. W. , Phelps T. J. , Newby D. T.
Published: March 2008

Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor,
Methanoculleus submarinus
produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (
mcrA
) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.
Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics
Authors: Sagova-Mareckova Marketa , Cermak Ladislav , Novotna Jitka , Plhackova Kamila , Forstova Jana , Kopecky Jan
Published: March 2008

Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO
3
or purification of extracted DNA by CaCl
2
. The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl
2
purification and in 93% of cases by the method based on CaCO
3
pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.
Rapid Differentiation of Phenotypically Similar Yeast Species by Single-Strand Conformation Polymorphism Analysis of Ribosomal DNA
Authors: Wang Qi-Ming , Li Juan , Wang Shi-An , Bai Feng-Yan
Published: March 2008

Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including
Saccharomyces
species, medically important
Candida
species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.
Ecological Dynamics of the Toxic Bloom-Forming Cyanobacterium
Microcystis aeruginosa
and Its Cyanophages in Freshwater
Authors: Yoshida Mitsuhiro , Yoshida Takashi , Kashima Aki , Takashima Yukari , Hosoda Naohiko , Nagasaki Keizo , Hiroishi Shingo
Published: March 2008

The abundance of potentially
Microcystis aeruginosa
-infectious cyanophages in freshwater was studied using
g91
real-time PCR. A clear increase in cyanophage abundance was observed when
M. aeruginosa
numbers declined, showing that these factors were significantly negatively correlated. Furthermore, our data suggested that cyanophage dynamics may also affect shifts in microcystin-producing and non-microcystin-producing populations.
Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow
Authors: Wakelin Steven A. , Colloff Matt J. , Kookana Rai S.
Published: March 2008

We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (
P
< 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including
Oceanospirillales
and
Methylococcaceae
. 16S rRNA gene sequences from less-disturbed sites had representatives of the
Caulobacteraceae
,
Sphingomonadaceae
, and
Nitrospirae
which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (
P
< 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (
P
< 0.05). The abundance of
amoA
,
narG
, and
nifH
genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N.
Metabolic Engineering of
Escherichia coli
for
l
-Tyrosine Production by Expression of Genes Coding for the Chorismate Mutase Domain of the Native Chorismate Mutase-Prephenate Dehydratase and a Cyclohexadienyl Dehydrogenase from
Zymomonas mobilis
Authors: Chávez-Béjar María I. , Lara Alvaro R. , López Hezraí , Hernández-Chávez Georgina , Martinez Alfredo , Ramírez Octavio T. , Bolívar Francisco , Gosset Guillermo
Published: March 2008

The expression of the feedback inhibition-insensitive enzyme cyclohexadienyl dehydrogenase (TyrC) from
Zymomonas mobilis
and the chorismate mutase domain from native chorismate mutase-prephenate dehydratase (PheA
CM
) from
Escherichia coli
was compared to the expression of native feedback inhibition-sensitive chorismate mutase-prephenate dehydrogenase (CM-TyrA
p
) with regard to the capacity to produce
l
-tyrosine in
E. coli
strains modified to increase the carbon flow to chorismate. Shake flask experiments showed that TyrC increased the yield of
l
-tyrosine from glucose (

Y

l
-Tyr/Glc

) by 6.8-fold compared to the yield obtained with CM-TyrA
p
. In bioreactor experiments, a strain expressing both TyrC and PheA
CM
produced 3 g/liter of
l
-tyrosine with a

Y

l
-Tyr/Glc

of 66 mg/g. These values are 46 and 48% higher than the values for a strain expressing only TyrC. The results show that the feedback inhibition-insensitive enzymes can be employed for strain development as part of a metabolic engineering strategy for
l
-tyrosine production.
Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis
Authors: He Zhili , Zhou Jizhong
Published: March 2008

Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect-match (PM) and mismatch (MM) probes based upon four genes from
Shewanella oneidensis
MR-1. A new SNR calculation, called the signal-to-both-standard-deviations ratio (SSDR), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (SSR) and the signal-to-background ratio (SBR). At a low stringency, the thresholds of the SSR, SBR, and SSDR were 2.5, 1.60, and 0.80 with an oligonucleotide and a PCR amplicon as target templates and 2.0, 1.60, and 0.70 with genomic DNAs as target templates. Slightly higher thresholds were obtained under high-stringency conditions. The thresholds of the SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types) and the presence of background DNA and a decrease in the compositions of targets, while the SBR remained unchanged in all situations. The lowest percentage of false positives and false negatives was observed with the SSDR calculation method, suggesting that it may be a better SNR calculation for more accurate determination of SNR thresholds. Positive spots identified by SNR thresholds were verified by the Student
t
test, and consistent results were observed. This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions.
Relative Abundance ofBacteroidesspp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension
Authors: Hong Pei-Ying , Wu Jer-Horng , Liu Wen-Tso
Published: March 2008

A molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominantBacteroidesspp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14Bacteroidesspp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species likeB. vulgatus,B. thetaiotaomicron,B. caccae,B. uniformis,B. fragilis,B. eggerthii, andB. massiliensiscould be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species likeB. pyogenes,B. salyersiae, andB. nordiiwere detected only collectively using a primer that targeted theB. fragilissubgroup (corresponding to ∼0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., mostBacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances ofBacteroidesspp. predominant in fecal samples.
Malic Acid Production by
Saccharomyces cerevisiae
: Engineering of Pyruvate Carboxylation, Oxaloacetate Reduction, and Malate Export
Authors: Zelle Rintze M. , de Hulster Erik , van Winden Wouter A. , de Waard Pieter , Dijkema Cor , Winkler Aaron A. , Geertman Jan-Maarten A. , van Dijken Johannes P. , Pronk Jack T. , van Maris Antonius J. A.
Published: March 2008

Malic acid is a potential biomass-derivable “building block” for chemical synthesis. Since wild-type
Saccharomyces cerevisiae
strains produce only low levels of malate, metabolic engineering is required to achieve efficient malate production with this yeast. A promising pathway for malate production from glucose proceeds via carboxylation of pyruvate, followed by reduction of oxaloacetate to malate. This redox- and ATP-neutral, CO
2
-fixing pathway has a theoretical maximum yield of 2 mol malate (mol glucose)
−1
. A previously engineered glucose-tolerant, C
2
-independent pyruvate decarboxylase-negative
S. cerevisiae
strain was used as the platform to evaluate the impact of individual and combined introduction of three genetic modifications: (i) overexpression of the native pyruvate carboxylase encoded by
PYC2
, (ii) high-level expression of an allele of the
MDH3
gene, of which the encoded malate dehydrogenase was retargeted to the cytosol by deletion of the C-terminal peroxisomal targeting sequence, and (iii) functional expression of the
Schizosaccharomyces pombe
malate transporter gene Sp
MAE1
. While single or double modifications improved malate production, the highest malate yields and titers were obtained with the simultaneous introduction of all three modifications. In glucose-grown batch cultures, the resulting engineered strain produced malate at titers of up to 59 g liter
−1
at a malate yield of 0.42 mol (mol glucose)
−1
. Metabolic flux analysis showed that metabolite labeling patterns observed upon nuclear magnetic resonance analyses of cultures grown on
13
C-labeled glucose were consistent with the envisaged nonoxidative, fermentative pathway for malate production. The engineered strains still produced substantial amounts of pyruvate, indicating that the pathway efficiency can be further improved.
High-Level Folate Production in Fermented Foods by the B
12
Producer
Lactobacillus reuteri
JCM1112
Authors: Santos Filipe , Wegkamp Arno , de Vos Willem M. , Smid Eddy J. , Hugenholtz Jeroen
Published: March 2008

We observed that
Lactobacillus reuteri
JCM1112 produces B
12
and folate. However, the folate/B
12
mass ratio found was far below that desired for human consumption (∼170:1). We used metabolic engineering applying genetic and physiological approaches to improve this ratio and developed a generic and natural process that significantly increases folate production.
Biogeographic and Phylogenetic Diversity of Thermoacidophilic Cyanidiales in Yellowstone National Park, Japan, and New Zealand
Authors: Toplin J. A. , Norris T. B. , Lehr C. R. , McDermott T. R. , Castenholz R. W.
Published: March 2008

Members of the rhodophytan order Cyanidiales are unique among phototrophs in their ability to live in extreme environments that combine low pH levels (∼0.2 to 4.0) and moderately high temperatures of 40 to 56°C. These unicellular algae occur in far-flung volcanic areas throughout the earth. Three genera (
Cyanidium
,
Galdieria
, and
Cyanidioschyzon
) are recognized. The phylogenetic diversity of culture isolates of the Cyanidiales from habitats throughout Yellowstone National Park (YNP), three areas in Japan, and seven regions in New Zealand was examined by using the chloroplast RuBisCO large subunit gene (
rbcL
) and the 18S rRNA gene. Based on the nucleotide sequences of both genes, the YNP isolates fall into two groups, one with high identity to
Galdieria sulphuraria
(type II) and another that is by far the most common and extensively distributed Yellowstone type (type IA). The latter is a spherical, walled cell that reproduces by internal divisions, with a subsequent release of smaller daughter cells. This type, nevertheless, shows a 99 to 100% identity to
Cyanidioschyzon merolae
(type IB), which lacks a wall, divides by “fission”-like cytokinesis into two daughter cells, and has less than 5% of the cell volume of type IA. The evolutionary and taxonomic ramifications of this disparity are discussed. Although the 18S rRNA and
rbcL
genes did not reveal diversity among the numerous isolates of type IA, chloroplast short sequence repeats did show some variation by location within YNP. In contrast, Japanese and New Zealand strains showed considerable diversity when we examined only the sequences of 18S and
rbcL
genes. Most exhibited identities closer to
Galdieria maxima
than to other strains, but these identities were commonly as low as 91 to 93%. Some of these Japanese and New Zealand strains probably represent undescribed species that diverged after long-term geographic isolation.
Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production
Authors: Kizer Lance , Pitera Douglas J. , Pfleger Brian F. , Keasling Jay D.
Published: March 2008

Producing complex chemicals using synthetic metabolic pathways in microbial hosts can have many advantages over chemical synthesis but is often complicated by deleterious interactions between pathway intermediates and the host cell metabolism. With the maturation of functional genomic analysis, it is now technically feasible to identify modes of toxicity associated with the accumulation of foreign molecules in the engineered bacterium. Previously,
Escherichia coli
was engineered to produce large quantities of isoprenoids by creating a mevalonate-based isopentenyl pyrophosphate biosynthetic pathway (V. J. J. Martin et al., Nat. Biotechnol.
21:
796-802, 2003). The engineered
E. coli
strain produced high levels of isoprenoids, but further optimization led to an imbalance in carbon flux and the accumulation of the pathway intermediate 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), which proved to be cytotoxic to
E. coli
. Using both DNA microarray analysis and targeted metabolite profiling, we have studied
E. coli
strains inhibited by the intracellular accumulation of HMG-CoA. Our results indicate that HMG-CoA inhibits fatty acid biosynthesis in the microbial host, leading to generalized membrane stress. The cytotoxic effects of HMG-CoA accumulation can be counteracted by the addition of palmitic acid (16:0) and, to a lesser extent, oleic acid (
cis
-Δ
9
-18:1) in the growth medium. This work demonstrates the utility of using transcriptomic and metabolomic methods to optimize synthetic biological systems.
Imaging of Long-Distance α-Aminoisobutyric Acid Translocation Dynamics during Resource Capture by
Serpula lacrymans
Authors: Tlalka Monika , Fricker Mark , Watkinson Sarah
Published: March 2008

α-Aminoisobutyric acid (AIB) is a nonmetabolized amino acid analogue of alanine, which at low (μM) concentrations acts as a tracer for amino acid movements. At high concentrations (mM), it competitively inhibits membrane transport and metabolism of protein amino acids and acts as a systemic translocated inhibitor of mycelial extension in fungi. AIB can control mycelial spread of the basidiomycete
Serpula lacrymans
, the cause of brown rot of wood in buildings. However, it is not known how effectively the inhibitor is distributed throughout the mycelium. Realistically heterogeneous microcosms, in which the fungus grew across nutritionally inert sand to colonize discrete wood resources, were used to investigate patterns of inhibition and translocation following local application of AIB. At a 0.1 M concentration, locally applied AIB caused immediate arrest of extension throughout the whole mycelium, maintained for a 6-week experimental period. The dynamics of translocation of subtoxic amounts of [1-
14
C]AIB ([
14
C]AIB) were mapped by photon-counting scintillation imaging in conjunction with destructive harvest to establish the velocity, direction, and rate of translocation and the extent of [
14
C]AIB reallocation accompanying the invasion of fresh wood. Locally applied [
14
C]AIB was distributed throughout complex mycelial networks within 2 h of application, becoming localized in growing margins by 12 h. Encounter with a fresh wood resource triggered a widespread response, causing withdrawal of [
14
C]AIB from throughout the network, accompanied by accumulation in the newly colonized wood and associated mycelium. The results are discussed in the context of nutrient dynamics in wood decomposer fungi and the mechanism of the amino acid reallocation response.
Efficient Production of
l
-Ribose with a Recombinant
Escherichia coli
Biocatalyst
Authors: Woodyer Ryan D. , Wymer Nathan J. , Racine F. Michael , Khan Shama N. , Saha Badal C.
Published: March 2008

A new synthetic platform with potential for the production of several rare sugars, with
l
-ribose as the model target, is described. The gene encoding the unique NAD-dependent mannitol-
1
-dehydrogenase (MDH) from
Apium graveolens
(garden celery) was synthetically constructed for optimal expression in
Escherichia coli
. This MDH enzyme catalyzes the interconversion of several polyols and their
l
-sugar counterparts, including the conversion of ribitol to
l
-ribose. Expression of recombinant MDH in the active form was successfully achieved, and one-step purification was demonstrated. Using the created recombinant
E. coli
strain as a whole-cell catalyst, the synthetic utility was demonstrated for production of
l
-ribose, and the system was improved using shaken flask experiments. It was determined that addition of 50 to 500 μM ZnCl
2
and addition of 5 g/liter glycerol both improved production. The final levels of conversion achieved were >70% at a concentration of 40 g/liter and >50% at a concentration of 100 g/liter. The best conditions determined were then scaled up to a 1-liter fermentation that resulted in 55% conversion of 100 g/liter ribitol in 72 h, for a volumetric productivity of 17.4 g liter
−1
day
−1
. This system represents a significantly improved method for the large-scale production of
l
-ribose.
Novel Root Fungal Consortium Associated with a Dominant Desert Grass
Authors: Porras-Alfaro Andrea , Herrera Jose , Sinsabaugh Robert L. , Odenbach Kylea J. , Lowrey Timothy , Natvig Donald O.
Published: March 2008

The broad distribution and high colonization rates of plant roots by a variety of endophytic fungi suggest that these symbionts have an important role in the function of ecosystems. Semiarid and arid lands cover more than one-third of the terrestrial ecosystems on Earth. However, a limited number of studies have been conducted to characterize root-associated fungal communities in semiarid grasslands. We conducted a study of the fungal community associated with the roots of a dominant grass,
Bouteloua gracilis
, at the Sevilleta National Wildlife Refuge in New Mexico. Internal transcribed spacer ribosomal DNA sequences from roots collected in May 2005, October 2005, and January 2006 were amplified using fungal-specific primers, and a total of 630 sequences were obtained, 69% of which were novel (less than 97% similarity with respect to sequences in the NCBI database).
B. gracilis
roots were colonized by at least 10 different orders, including endophytic, coprophilous, mycorrhizal, saprophytic, and plant pathogenic fungi. A total of 51 operational taxonomic units (OTUs) were found, and diversity estimators did not show saturation. Despite the high diversity found within
B. gracilis
roots, the root-associated fungal community is dominated by a novel group of dark septate fungi (DSF) within the order Pleosporales. Microscopic analysis confirmed that
B. gracilis
roots are highly colonized by DSF. Other common orders colonizing the roots included Sordariales, Xylariales, and Agaricales. By contributing to drought tolerance and nutrient acquisition, DSF may be integral to the function of arid ecosystems.
Archaea
Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte
Littorella uniflora
Authors: Herrmann Martina , Saunders Aaron M. , Schramm Andreas
Published: March 2008

Archaeal and bacterial ammonia monooxygenase genes (
amoA
) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte
Littorella uniflora
, archaeal
amoA
was 500- to >8,000-fold enriched compared to bacterial
amoA
, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing
Archaea
.