bluuebunny/crossref_metadata_2025 huggingface dataset:
Ribosomal RNA gene sequence diversity in arbuscular mycorrhizal fungi (Glomeromycota)
Authors: RODRIGUEZ ALIA , CLAPP JUSTIN PETER , DODD JOHN CHARLES
Published: December 2004

The existence of multiple rRNA sequences within AMF single spores and the high levels of variability found in these symbionts for highly conserved genes with low copy numbers have provoked intense controversy over the genetic structure of the Glomeromycota. Lately, two hypotheses have been proposed to explain the source of such a variation, mainly either at internuclear (multigenomic) or intranuclear (polyploidy) levels.

Evidence reported by numerous authors suggests that the magnitude of sequence variation, and the presence in single spores of sequences from apparently unrelated taxa within the Glomeromycota, makes the use of one, or very few sequences, from only one or two isolates of AMF insufficient for taxonomic purposes in some species groups.

A large‐scale, collaborative study on genetic variation in AMF across different genes could help to address fundamental questions on the biology and genetic structure of these important symbionts.
Annual Variation of the Reproductive Activity of Three Exogoninae Species (Polychaeta: Syllidae) from the Western Mediterranean
Authors: Gallego Ramón , López Eduardo
Published: December 2004

Abstract.  During a 12‐month period (from May 2000 to the end of April 2001), the reproductive activity of three Exogoninae species was studied: Grubeosyllis clavata (Claparède, 1868), G. vieitezi (San Martín, 1984) and Sphaerosyllis (Sphaerosyllis) hystrix Claparède, 1863. A sample consisting of two replicates was collected every second month, and the individuals of each species were counted and assigned to different reproductive categories (immature, mature, and bearing eggs or embryos). The populations of the three species showed a dramatic decline in numbers during summer 2000. In regard to the reproductive activity, the two species of Grubeosyllis showed a continuous activity during the whole year, with a peak in July for G. vieitezi and in September and November for G. clavata. In contrast, S. (S.) hystrix had a pause in its reproductive activity in late summer when no mature or offspring‐carrying specimens were found. A relationship between the reproductive cycle and the brooding type (dorsal eggs versus ventral embryos) is likely, although further studies on other exogonin species are necessary to confirm the hypothesis suggested by the present results.
Surficial Hydrocarbon Seep Infauna from the Blake Ridge (Atlantic Ocean, 2150 m) and the Gulf of Mexico (690–2240 m)
Authors: Robinson Christie A. , Bernhard Joan M. , Levin Lisa A. , Mendoza Guillermo F. , Blanks Jessica K.
Published: December 2004

Abstract.  Infauna, including foraminifera and metazoans, were enumerated and identified from five types of seep habitats and two adjacent non‐seep habitats. Collections were made with the deep submergence research vessel ‘Alvin’ from three areas of active seepage in the Gulf of Mexico (Alaminos Canyon [2220 m], Atwater Canyon [1930 m], and Green Canyon lease block 272 [700 m]) and on the Blake Ridge Diapir [2250 m], which is located off the southeastern coast of the United States. The seep habitats sampled included four types of microbial mats (Beggiatoa, Thioploca, thin and thick Arcobacter) and the periphery of a large mussel bed. Sediments under large rhizopod protists, xenophyophores, were sampled adjacent to the mussel bed periphery. A non‐seep site, which was >1 km away from active seeps, was also sampled for comparison. Densities of most taxa were higher in the Gulf of Mexico seeps than in Blake Ridge samples, largely because densities in the thick microbial mats of Blake Ridge were significantly lower. Diversity was higher in the Thioploca mats compared to other microbial‐mat types. Within an ocean basin (i.e., Atlantic, Gulf of Mexico) we did not observe significant differences in meiofaunal or macrofaunal composition in Beggiatoa versus Thioploca mats or thin versus thick Arcobacter mats. Foraminifera represented up to 16% of the seep community, a proportion that is comparable to their contribution at adjacent non‐seep communities. In general, the observed densities and taxonomic composition of seep sites at the genus level was consistent with previous observations from seeps (e.g., the foraminifers Bolivina and Fursenkoina, the dorvilleid polychaete Ophryotrocha).
Frequency of intravascular catheter colonization by Malassezia spp. in adult patients
Authors: Curvale‐Fauchet Nathalie , Botterel Françoise , Legrand Patrick , Guillot Jacques , Bretagne Stéphane
Published: December 2004

Colonization of intravascular catheters (IVCs) with lipid‐dependent Malassezia spp. is rarely reported in adult patients probably because of the absence of additional lipids in routine culture media. Therefore, we systematically seeded 983 consecutive IVC onto Dixon medium compatible with the growth of Malassezia spp. Seven (0.7%) IVCs were positive. Six of them were from surgical patients. Four of them also yielded common bacteria. Identification using PCR‐RFLP and restriction enzymes yielded M. furfur and M. sympodialis. Colonization of IVCs with Malassezia spp. does not appear negligible and warrants additional studies to evaluate the clinical relevance of such findings and the role of this yeast in biofilm formation.
Understanding Economic Man
Authors: Steele G. R.
Published: December 2004

Abstract.  The deficiencies of economic science are examined against its historical development: the utilitarian concentration upon individual choice conflates preferences and values and the hedonistic calculus is inoperable in the presence of incommensurability. In restricting explanations of behavioral patterns to changes in prices, incomes, and other “economic” variables, neoclassical analysis was destined to draw implausible conclusions. While the uniqueness of man rests in a highly developed self‐consciousness, his rationality need not imply conscious reason. Decisions and actions that are made in response to inputs from all of the sensory modalities are led by conventions and traditions that give structure to every response. Biological, psychological, social, and ethical constraints so limit purposeful action, that a complete economist (pace G. L. S. Shackle) is one who has mastered mathematics, philosophy, psychology, anthropology, history, geography, and political science.
Comments on “Echoes of Henry George in Modern Analysis”
Authors: Foldvary Fred E.
Published: December 2004

Abstract.  These comments were presented at a session entitled “Echoes of Henry George in Modern Analysis” held at the 2002 meetings of the Southern Economic Association.
A theoretical study of special acoustic effects caused by the staircase of the El Castillo pyramid at the Maya ruins of Chichen-Itza in Mexico
Authors: Declercq Nico F. , Degrieck Joris , Briers Rudy , Leroy Oswald
Published: December 2004

It is known that a handclap in front of the stairs of the great pyramid of Chichen Itza produces a chirp echo which sounds more or less like the sound of a Quetzal bird. The present work describes precise diffraction simulations and attempts to answer the critical question what physical effects cause the formation of the chirp echo. Comparison is made with experimental results obtained from David Lubman. Numerical simulations show that the echo shows a strong dependence on the kind of incident sound. Simulations are performed for a (delta function like) pulse and also for a real handclap. The effect of reflections on the ground in front of the pyramid is also discussed. The present work also explains why an observer seated on the lowest step of the pyramid hears the sound of raindrops falling in a water filled bucket instead of footstep sounds when people, situated higher up the pyramid, climb the stairs.
Annoyance of bandpass-filtered noises in relation to the factor extracted from autocorrelation function (L)
Authors: Soeta Yoshiharu , Maruo Takuya , Ando Yoichi
Published: December 2004

This study examines the annoyance of pure-tone and bandpass noises with center frequencies of 1000 and 2000 Hz under the condition of equal sound-pressure level. The bandwidths of the source signal were 0, 40, 80, 160, and 320 Hz, with a 2068-dB/octave sharp filter to control the autocorrelation function (ACF) of the source signal. Scale values of annoyance were obtained using a paired-comparison method. The results show that the annoyance of pure-tone and bandpass noises inside the critical band is not constant. The annoyance of pure tones is greater than that of sharply filtered noises within the critical band. The annoyance of bandpass noises increases with increasing effective duration of the ACF, τe, which represents the repetitive feature or tonal component of the source signal within the critical band.
On the kinematics of broadband multipath scintillation and the approach to saturation
Authors: Colosi John A. , Baggeroer Arthur B.
Published: December 2004

Utilizing a simple model in which the acoustic wave function is a sum of independent Gaussian wave packets, the relative intensity variance or scintillation index (SI) is analytically calculated. The model has an unspecified probability density function (PDF) for wave packet amplitudes and Gaussian PDFs for travel-time-induced and non-travel-time-induced phase shifts; amplitudes and both phase shifts are assumed to be mutually uncorrelated. It is shown that a proper treatment of the mean field is required to obtain the saturation value, SI=1, in the limit of a large number of interfering wave packets. The analytic formulas for SI allow identification of important wave packet parameters in the approach to saturation. Criteria are identified for both broadband and narrow-band cases for which the approach to saturation is from above and below 1. It is demonstrated that the broadband approach to saturation is much slower than the narrow-band cases, since wave packets separated in time by more than an inverse bandwidth do not strongly contribute to interference. This effect is quantified by the time–bandwidth product. The model is also used to obtain an analytic expression for pulse time spread; it is shown that multipath conditions which favor a rapid approach to saturation do not favor large pulse spread.
An iterative effective medium approximation (IEMA) for wave dispersion and attenuation predictions in particulate composites, suspensions and emulsions
Authors: Aggelis D. G. , Tsinopoulos S. V. , Polyzos D.
Published: December 2004

In the present work we deal with the scattering dispersion and attenuation of elastic waves in different types of nonhomogeneous media. The iterative effective medium approximation based on a single scattering consideration, for the estimation of wave dispersion and attenuation, proposed in Tsinopoulos et al., [Adv. Compos. Lett. 9, 193–200 (2000)] is examined herein not only for solid components but for liquid suspensions as well. The iterations are conducted by means of the classical relation of Waterman and Truell, while the self-consistent condition proposed by Kim et al. [J. Acoust. Soc. Am. 97, 1380–1388 (1995)] is used for the convergence of the iterative procedure. The single scattering problem is solved using the Ying and Truell formulation, which with a minor modification can accommodate the solution of scattering on inclusions in liquid. Theoretical results for several different systems of particulates and suspensions are presented being in excellent agreement with experimental data taken from the literature.
Investigation of the validity of radiosity for sound-field prediction in cubic rooms
Authors: Nosal Eva-Marie , Hodgson Murray , Ashdown Ian
Published: December 2004

This paper explores acoustical (or time-dependent) radiosity using predictions made in four cubic enclosures. The methods and algorithms used are those presented in a previous paper by the same authors [Nosal, Hodgson, and Ashdown, J. Acoust. Soc. Am. 116(2), 970–980 (2004)]. First, the algorithm, methods, and conditions for convergence are investigated by comparison of numerous predictions for the four cubic enclosures. Here, variables and parameters used in the predictions are varied to explore the effect of absorption distribution, the necessary conditions for convergence of the numerical solution to the analytical solution, form-factor prediction methods, and the computational requirements. The predictions are also used to investigate the effect of absorption distribution on sound fields in cubic enclosures with diffusely reflecting boundaries. Acoustical radiosity is then compared to predictions made in the four enclosures by a ray-tracing model that can account for diffuse reflection. Comparisons are made of echograms, room-acoustical parameters, and discretized echograms.
Direct measurement of onset and offset phonation threshold pressure in normal subjects
Authors: Plant Randall L. , Freed Gary L. , Plant Richard E.
Published: December 2004

Phonation threshold pressures were directly measured in five normal subjects in a variety of voicing conditions. The effects of fundamental frequency, intensity, closure speed of the vocal folds, and laryngeal airway resistance on phonation threshold pressures were determined. Subglottic air pressures were measured using percutaneous puncture of the cricothyroid membrane. Both onset and offset of phonation were studied to see if a hysteresis effect produced lower offset pressures than onset pressures. Univariate analysis showed that phonation threshold pressure was influenced most strongly by fundamental frequency and intensity. Multiple linear regression showed that these two variables, as well as laryngeal airway resistance, most strongly predicted phonation threshold pressure. Two of the five subjects demonstrated a significant hysteresis effect, but one subject actually had higher offset pressures than onset pressures.
Nonlinear acoustic techniques for landmine detection
Authors: Korman Murray S. , Sabatier James M.
Published: December 2004

Measurements of the top surface vibration of a buried (inert) VS 2.2 anti-tank plastic landmine reveal significant resonances in the frequency range between 80 and 650 Hz. Resonances from measurements of the normal component of the acoustically induced soil surface particle velocity (due to sufficient acoustic-to-seismic coupling) have been used in detection schemes. Since the interface between the top plate and the soil responds nonlinearly to pressure fluctuations, characteristics of landmines, the soil, and the interface are rich in nonlinear physics and allow for a method of buried landmine detection not previously exploited. Tuning curve experiments (revealing “softening” and a back-bone curve linear in particle velocity amplitude versus frequency) help characterize the nonlinear resonant behavior of the soil-landmine oscillator. The results appear to exhibit the characteristics of nonlinear mesoscopic elastic behavior, which is explored. When two primary waves f1 and f2 drive the soil over the mine near resonance, a rich spectrum of nonlinearly generated tones is measured with a geophone on the surface over the buried landmine in agreement with Donskoy [SPIE Proc. 3392, 221–217 (1998); 3710, 239–246 (1999)]. In profiling, particular nonlinear tonals can improve the contrast ratio compared to using either primary tone in the spectrum.
An alternate approach to constructing distortion product otoacoustic emission (DPOAE) suppression tuning curves
Authors: Johnson Tiffany A. , Neely Stephen T. , Dierking Darcia M. , Hoover Brenda M. , Gorga Michael P.
Published: December 2004

Distortion product otoacoustic emission (DPOAE) suppression tuning curves (STCs) typically are constructed using suppression criteria of 3 or 6 dB. This paper describes a technique for generating DPOAE STCs using criteria ranging from 3 dB to complete suppression. The criterion effect was examined at various primary levels (f2=4 kHz) in normal-hearing ears. As expected, QERB and tip-to-tail differences decreased as probe level (L2) increased. QERB values were not systematically dependent on criterion. For low L2’s, tip-to-tail differences decreased as criterion increased. Given similarities in methodology, DPOAE STCs constructed from completely suppressed responses might be most appropriate for comparison to psychophysical tuning curves.
Insertion loss of an acoustic enclosure
Authors: Ming Ruisen , Pan Jie
Published: December 2004

Acoustical enclosures are the common arrangements in reducing airborne noise from shipboard machinery such as engines and generators. In this paper the theoretical models, established based on statistical energy analysis, are presented for predicting the insertion loss of acoustical enclosures in different frequency ranges. In addition to the consideration of resonant modal coupling between internal sound field and enclosure structural vibration, the nonresonant transmission though and the interaction between enclosure walls in the models are also included. It is shown that the insertion loss of enclosures is mainly controlled by the nonresonant modes in the intermediate frequency range. At high frequencies, the insertion loss of enclosures can be improved by increasing the sound absorption at the internal boundaries of enclosures. Experiments were carried out on two enclosures made of different materials. The measured results are compared with the predicted values and the good agreement between them is the initial demonstration of the validity and feasibility of the theoretical models.
Bubble dynamics and size distributions during focused ultrasound insonation
Authors: Yang Xinmai , Roy Ronald A. , Holt R. Glynn
Published: December 2004

The deposition of ultrasonic energy in tissue can cause tissue damage due to local heating. For pressures above a critical threshold, cavitation will occur, inducing a much larger thermal energy deposition in a local region. The present work develops a nonlinear bubble dynamics model to numerically investigate bubble oscillations and bubble-enhanced heating during focused ultrasound (HIFU) insonation. The model is applied to calculate two threshold-dependent phenomena occurring for nonlinearly oscillating bubbles: Shape instability and growth by rectified diffusion. These instabilities in turn are shown to place physical boundaries on the time-dependent bubble size distribution, and thus the thermal energy deposition.
Modifications of acoustic modes and coupling due to a leaning wall in a rectangular cavity
Authors: Li Y. Y. , Cheng L.
Published: December 2004

Acoustic modes and the coupling characteristics of a rectangular-like cavity with a slight geometrical distortion introduced through a leaning wall are investigated in this paper. A pressure variation index is proposed to quantify the global changes in acoustic modes caused by the inclination of the wall. Effects on the coupling between acoustic modes and structural modes are investigated using coupling coefficients. Numerical results show a simple relationship between the distortion effect and the acoustic wavelength. The effect is most significant when the distortion approaches the half wavelength. Compared with a rectangular enclosure, the existence of the leaning wall gives rise to a much more effective coupling between the structure and the enclosure.
Role of
Candida albicans
Transcription Factor Upc2p in Drug Resistance and Sterol Metabolism
Authors: Silver Peter M. , Oliver Brian G. , White Theodore C.
Published: December 2004

In
Candida albicans
, drug resistance to clinically important antifungal drugs may be regulated through the action of transcription factors in a manner that may or may not be similar to regulation in
Saccharomyces cerevisiae
. A search of the
C. albicans
genome identified a single homolog of the
S. cerevisiae
transcription factor genes
UPC2
(
ScUPC2
) and
ECM22
(
ScECM22
) that have been associated with regulation of ergosterol biosynthesis. Sequence analysis of this
C. albicans UPC2
(
CaUPC2
) gene identifies two domains, an anchoring transmembrane domain and a transcription factor region containing multiple nuclear localization signals and a fungal Zn(2)-Cys(6) binuclear cluster domain. Heterozygous deletion, homozygous deletion, and reconstructed strains of
CaUPC2
as well as the parental strain were tested against several antifungal drugs, including ergosterol biosynthesis inhibitors. The
CaUPC2
homozygous deletion strain showed marked hypersusceptibility to most drugs, compared to the parental and reconstructed strains. The deletion strains accumulate significantly less radiolabeled cholesterol, suggesting reduced ergosterol scavenging in those strains. When grown under azole drug pressure, the parental, heterozygous deletion and reconstructed strains of
CaUPC2
upregulate the
ERG2
and
ERG11
ergosterol biosynthesis genes, while the homozygous deletion strain shows no such upregulation. Consistent with these results,
CaUPC2
deletion strains show reduced ergosterol levels, which may explain the increased susceptibilities of the
CaUPC2
deletion strains. Thus, it appears that
CaUPC2
acts as a transcription factor involved in the regulation of ergosterol biosynthetic genes and as a regulator of sterol uptake across the plasma membrane.
FoSTUA, Encoding a Basic Helix-Loop-Helix Protein, Differentially Regulates Development of Three Kinds of Asexual Spores, Macroconidia, Microconidia, and Chlamydospores, in the Fungal Plant PathogenFusarium oxysporum
Authors: Ohara Toshiaki , Tsuge Takashi
Published: December 2004

The soil-borne fungusFusarium oxysporumcauses vascular wilt of a wide variety of plant species.F. oxysporumproduces three kinds of asexual spores, macroconidia, microconidia, and chlamydospores. Falcate macroconidia are formed generally from terminal phialides on conidiophores and rarely from intercalary phialides on hyphae. Ellipsoidal microconidia are formed from intercalary phialides on hyphae. Globose chlamydospores with thick walls are developed by the modification of hyphal and conidial cells. Here we describeFoSTUAofF. oxysporum, which differentially regulates the development of macroconidia, microconidia, and chlamydospores.FoSTUAencodes a basic helix-loop-helix protein with similarity toAspergillus nidulansStuA, which has been identified as a transcriptional regulator controlling conidiation. Nuclear localization of FoStuA was verified by using strains expressing FoStuA-green fluorescent protein fusions. TheFoSTUA-targeted mutants exhibited normal microconidium formation in cultures. However, the mutants lacked conidiophores and produced macroconidia at low frequencies only from intercalary phialides. Thus,FoSTUAappears to be necessary to induce conidiophore differentiation. In contrast, chlamydospore formation was dramatically promoted in the mutants. These data demonstrate that FoStuA is a positive regulator and a negative regulator for the development of macroconidia and chlamydospores, respectively, and is dispensable for microconidium formation in cultures. The disease-causing ability ofF. oxysporumwas not affected by mutations inFoSTUA. However, the mutants produced markedly fewer macroconidia and microconidia in infected plants than the wild type. These results suggest thatFoSTUAalso has an important role for microconidium formation specifically in infected plants.
Deletion of the Three Distal S1 Motifs of
Saccharomyces cerevisiae
Rrp5p Abolishes Pre-rRNA Processing at Site A
2
without Reducing the Production of Functional 40S Subunits
Authors: Vos Harmjan R. , Faber Alex W. , de Gier Maaike D. , Vos Jan C. , Raué Hendrik A.
Published: December 2004

Yeast Rrp5p, one of the few
trans-
acting proteins required for the biogenesis of both ribosomal subunits, has a remarkable two-domain structure. Its C-terminal region consists of seven tetratricopeptide motifs, several of which are crucial for cleavages at sites A
0
to A
2
and thus for the formation of 18S rRNA. The N-terminal region, on the other hand, contains 12 S1 RNA-binding motifs, most of which are required for processing at site A
3
and thus for the production of the short form of 5.8S rRNA. Yeast cells expressing a mutant Rrp5p protein that lacks S1 motifs 10 to 12 (mutant
rrp5Δ6
) have a normal growth rate and wild-type steady-state levels of the mature rRNA species, suggesting that these motifs are irrelevant for ribosome biogenesis. Here we show that, nevertheless, in the
rrp5Δ6
mutant, pre-rRNA processing follows an alternative pathway that does not include the cleavage of 32S pre-rRNA at site A
2
. Instead, the 32S precursor is processed directly at site A
3
, producing exclusively 21S rather than 20S pre-rRNA. This is the first evidence that the 21S precursor, which was observed previously only in cells showing a substantial growth defect or as a minor species in addition to the normal 20S precursor, is an efficient substrate for 18S rRNA synthesis. Maturation of the 21S precursor occurs via the same endonucleolytic cleavage at site D as that used for 20S pre-rRNA maturation. The resulting D
-
A
3
fragment, however, is degraded by both 5′→3′ and 3′→5′ exonuclease digestions, the latter involving the exosome, in contrast to the exclusively 5′→3′ exonucleolytic digestion of the D
-
A
2
fragment. We also show that
rrp5Δ6
cells are hypersensitive to both hygromycin B and cycloheximide, suggesting that, despite their wild-type growth rate, their preribosomes or ribosomes may be structurally abnormal.
Role for the Ran Binding Protein, Mog1p, in
Saccharomyces cerevisiae
SLN1-SKN7 Signal Transduction
Authors: Lu Jade Mei-Yeh , Deschenes Robert J. , Fassler Jan S.
Published: December 2004

Yeast Sln1p is an osmotic stress sensor with histidine kinase activity. Modulation of Sln1 kinase activity in response to changes in the osmotic environment regulates the activity of the osmotic response mitogen-activated protein kinase pathway and the activity of the Skn7p transcription factor, both important for adaptation to changing osmotic stress conditions. Many aspects of Sln1 function, such as how kinase activity is regulated to allow a rapid response to the continually changing osmotic environment, are not understood. To gain insight into Sln1p function, we conducted a two-hybrid screen to identify interactors. Mog1p, a protein that interacts with the yeast Ran1 homolog, Gsp1p, was identified in this screen. The interaction with Mog1p was characterized in vitro, and its importance was assessed in vivo.
mog1
mutants exhibit defects in SLN1-SKN7 signal transduction and mislocalization of the Skn7p transcription factor. The requirement for Mog1p in normal localization of Skn7p to the nucleus does not fully account for the
mog1
-related defects in SLN1-SKN7 signal transduction, raising the possibility that Mog1p may play a role in Skn7 binding and activation of osmotic response genes.
Gid8p (Dcr1p) and Dcr2p Function in a Common Pathway To Promote START Completion in
Saccharomyces cerevisiae
Authors: Pathak Ritu , Bogomolnaya Lydia M. , Guo Jinbai , Polymenis Michael
Published: December 2004

How cells determine when to initiate DNA replication is poorly understood. Here we report that in
Saccharomyces cerevisiae
overexpression of the dosage-dependent cell cycle regulator genes
DCR2
(
YLR361C
) and
GID8
(
DCR1/YMR135C
) accelerates initiation of DNA replication. Cells lacking both
GID8
and
DCR2
delay initiation of DNA replication. Genetic analysis suggests that Gid8p functions upstream of Dcr2p to promote cell cycle progression.
DCR2
is predicted to encode a gene product with phosphoesterase activity. Consistent with these predictions, a
DCR2
allele carrying a His338 point mutation, which in known protein phosphatases prevents catalysis but allows substrate binding, antagonized the function of the wild-type
DCR2
allele. Finally, we report genetic interactions involving
GID8
,
DCR2
, and
CLN3
(which encodes a G
1
cyclin) or
SWI4
(which encodes a transcription factor of the G
1
/S transcription program). Our findings identify two gene products with a probable regulatory role in the timing of initiation of cell division.
Status of the Microbial Census
Authors: Schloss Patrick D. , Handelsman Jo
Published: December 2004

Over the past 20 years, more than 78,000 16S rRNA gene sequences have been deposited in GenBank and the Ribosomal Database Project, making the 16S rRNA gene the most widely studied gene for reconstructing bacterial phylogeny. While there is a general appreciation that these sequences are largely unique and derived from diverse species of bacteria, there has not been a quantitative attempt to describe the extent of sequencing efforts to date. We constructed rarefaction curves for each bacterial phylum and for the entire bacterial domain to assess the current state of sampling and the relative taxonomic richness of each phylum. This analysis quantifies the general sense among microbiologists that we are a long way from a complete census of the bacteria on Earth. Moreover, the analysis indicates that current sampling strategies might not be the most effective ones to describe novel diversity because there remain numerous phyla that are globally distributed yet poorly sampled. Based on the current level of sampling, it is not possible to estimate the total number of bacterial species on Earth, but the minimum species richness is 35,498. Considering previous global species richness estimates of 10
7
to 10
9
, we are certain that this estimate will increase with additional sequencing efforts. The data support previous calls for extensive surveys of multiple chemically disparate environments and of specific phylogenetic groups to advance the census most rapidly.
Process of Protein Transport by the Type III Secretion System
Authors: Ghosh Partho
Published: December 2004

The type III secretion system (TTSS) of gram-negative bacteria is responsible for delivering bacterial proteins, termed effectors, from the bacterial cytosol directly into the interior of host cells. The TTSS is expressed predominantly by pathogenic bacteria and is usually used to introduce deleterious effectors into host cells. While biochemical activities of effectors vary widely, the TTSS apparatus used to deliver these effectors is conserved and shows functional complementarity for secretion and translocation. This review focuses on proteins that constitute the TTSS apparatus and on mechanisms that guide effectors to the TTSS apparatus for transport. The TTSS apparatus includes predicted integral inner membrane proteins that are conserved widely across TTSSs and in the basal body of the bacterial flagellum. It also includes proteins that are specific to the TTSS and contribute to ring-like structures in the inner membrane and includes secretin family members that form ring-like structures in the outer membrane. Most prominently situated on these coaxial, membrane-embedded rings is a needle-like or pilus-like structure that is implicated as a conduit for effector translocation into host cells. A short region of mRNA sequence or protein sequence in effectors acts as a signal sequence, directing proteins for transport through the TTSS. Additionally, a number of effectors require the action of specific TTSS chaperones for efficient and physiologically meaningful translocation into host cells. Numerous models explaining how effectors are transported into host cells have been proposed, but understanding of this process is incomplete and this topic remains an active area of inquiry.
Bovine serum albumin adsorption on passivated porous silicon layers
Authors: Tay L , Rowell N L , Poitras D , Fraser J W , Lockwood D J , Boukherroub R
Published: December 2004

Hydrogen-terminated porous silicon (pSi-H) films were fabricated through electrochemical anodization of crystalline silicon in hydrofluoric-acid-based solutions. The pSi-H surface was chemically functionalized by thermal reaction with undecylenic acid to produce an organic monolayer covalently attached to the silicon surface through SiC bonds and bearing an acid terminal group. Bovine serum albumin (BSA) was adsorbed onto such surface-modified pSi structures. The resulting surfaces were characterized using scanning electron microscopy (SEM), reflection FT-IR spectroscopy, and ellipsometry. SEM showed that the porous films were damaged and partially lifted off the silicon substrate after a prolonged BSA adsorption. Ellipsometry analysis revealed that the BSA penetrated ∼1.3 µm into the porous structure. The film damage is likely a result of BSA anchoring itself tightly through strong electrostatic interaction with the acid-covered Si sidewalls. A change in surface tension during BSA film formation then causes the pSi layer to buckle and lift off the underlying Si substrate. FT-IR results from the undecylenic-acid-modified pSi surfaces before and after BSA adsorption showed the presence of strong characteristic amide I, II, and III vibrational bands after BSA adsorption. The surface properties of the pSi matrix and its interactions with BSA are examined in this study.Key words: ellipsometry, porous silicon, protein adsorption, surface passivation.
Genetic improvement of kraft pulp yield in Eucalyptus nitens using cellulose content determined by near infrared spectroscopy
Authors: Schimleck Laurence R , Kube Peter D , Raymond Carolyn A
Published: December 2004

Eucalyptus nitens (Deane & Maiden) Maiden (shining gum) is widely grown for kraft pulp production in many cool temperate regions of the world. Improving the kraft pulp yield of this species is important for increasing plantation profitability, but traditional assessment is slow and expensive. Cellulose content, which is strongly correlated with pulp yield, has been used as an alternative in tree breeding programs. However, a direct measure of cellulose content still relies on wet chemistry, limiting the number of samples that can be processed and the subsequent gains that can be made in a tree breeding program. An indirect method such as near infrared (NIR) spectroscopy provides a large increase in the numbers of samples that can be analysed. In this study, the genetic gains in cellulose content of E. nitens were compared using cellulose content, determined using wet chemistry and predicted by NIR calibrations based on different sampling intensities. Genetic gains based on NIR-predicted cellulose content were high, and a large proportion of the gain was achievable using a direct measure of cellulose. Calibrations were robust and generally could be reliably used across sites. NIR-predicted cellulose is highly heritable, with heritabilities comparable to or better than direct measures of cellulose.
Si(100) WAFERS CLEANED BY LASER ABLATION
Authors: CRUZ M. P. , DÍAZ J. A. , SIQUEIROS J. M.
Published: December 2004

A quick and relatively simple technique for stripping off Si wafers of its native oxide and carbon impurities, using pulsed laser ablation at room temperature, is presented. In a chamber at 10-10 Torr, an oxidized Si (100) surface is ablated with 248 nm UV radiation from a KrF excimer laser. Experiments using 200 pulses of different laser energy densities were performed until a clean surface, at 600 mJ/cm 2, was obtained as determined by Auger electron spectroscopy and ellipsometry measurements. The slightly out of focus laser beam is scanned over the selected area leaving an atomically 1×1 feceted Si surface, as shown by RHEED. The familiar 1×2 reconstructed Si surface may be obtained through a post annealing process.
PREPARATION AND PROPERTIES OF A NOVEL EPOXIDIZED CASTOR OIL/CLAY NANOCOMPOSITES
Authors: PARK S.-J. , JIN F.-L. , LEE J.-R.
Published: December 2004

A novel nanocomposites of modified clay in a glassy epoxy were prepared using a direct melt intercalation technique. The contents of oganoclay were varied with 0, 1, 2, and 3 wt% and N-benzylpyrazinium hexafluoroantimonate (BPH) was used for curing of epoxy matrix as a cationic latent catalyst. Dynamic mechanical analysis (DMA) measurement was performed to examine the glass transition temperature of the nanocomposites. As a result, X-ray diffraction indicated the intercalation of the epoxy chains happening inside the gallery of clay. The nanocomposites showed a higher glass transition temperature and storage modulus than those of the pristine epoxy. The mechanical interfacial properties of the nanocomposites were also investigated and the improvement in tearing energy of 160% over pristine epoxy was obtained.
TEC FAMILY KINASES IN T LYMPHOCYTE DEVELOPMENT AND FUNCTION
Authors: Berg Leslie J. , Finkelstein Lisa D. , Lucas Julie A. , Schwartzberg Pamela L.
Published: December 2004

▪ Abstract  The Tec family tyrosine kinases are now recognized as important mediators of antigen receptor signaling in lymphocytes. Three members of this family, Itk, Rlk, and Tec, are expressed in T cells and activated in response to T cell receptor (TCR) engagement. Although initial studies demonstrated a role for these proteins in TCR-mediated activation of phospholipase C-γ, recent data indicate that Tec family kinases also regulate actin cytoskeletal reorganization and cellular adhesion following TCR stimulation. In addition, Tec family kinases are activated downstream of G protein–coupled chemokine receptors, where they play parallel roles in the regulation of Rho GTPases, cell polarization, adhesion, and migration. In all these systems, however, Tec family kinases are not essential signaling components, but instead function to modulate or amplify signaling pathways. Although they quantitatively reduce proximal signaling, mutations that eliminate Tec family kinases in T cells nonetheless qualitatively alter T cell development and differentiation.
Overexpression of β2-adrenergic receptors in mouse liver alters the expression of gluconeogenic and glycolytic enzymes
Authors: Erraji-Benchekroun Loubna , Couton Dominique , Postic Catherine , Borde Isabelle , Gaston Jesintha , Guillet Jean-Gérard , André Claudine
Published: December 2004

In the livers of humans and many other mammalian species, β2-adrenergic receptors (β2-ARs) play an important role in the modulation of glucose production by glycogenolysis and gluconeogenesis. In male mice and rats, however, the expression and physiological role of hepatic β2-ARs are rapidly lost with development under normal physiological conditions. We previously described a line of transgenic mice, F28 (André C, Erraji L, Gaston J, Grimber G, Briand P, and Guillet JG. Eur J Biochem 241: 417–424, 1996), which carry the human β2-AR gene under the control of its own promoter. In these mice, hepatic β2-AR levels are shown to increase rapidly after birth and, as in humans, be maintained at an elevated level in adulthood. F28 mice display strongly enhanced adenylyl cyclase responses to β-AR agonists in their livers and, compared with normal mice, have increased basal hepatic adenylyl cyclase activity. In this report we demonstrate that, under normal physiological conditions, this increased β2-AR activity affects the expression of the gluconeogenic and glycolytic key enzymes phospho enolpyruvate carboxykinase, glucose-6-phosphatase, and l-pyruvate kinase and considerably decreases hepatic glycogen levels. Furthermore, we show that the effects of β-adrenergic ligands on liver glycogen observed in humans are reproduced in these mice: liver glycogen levels are strongly decreased by the β2-AR agonist clenbuterol and increased by the β-AR antagonist propranolol. These transgenic mice open new perspectives for studying in vivo the hepatic β2-AR system physiopathology and for testing the effects of β-AR ligands on liver metabolism.
Sympathetic nervous system activity in rat thyroid: potential role in goitrogenesis
Authors: Young James B. , Bürgi-Saville M. Elizabeth , Bürgi Ulrich , Landsberg Lewis
Published: December 2004

The role of sympathetic innervation in regulation of thyroid function is incompletely understood. We, therefore, carried out studies in rats utilizing techniques of norepinephrine turnover to assess thyroid sympathetic activity in vivo. Thyroidal sympathetic activity was increased 95% by exposure to cold (4°C), 42% by chronic ingestion of an iodine-deficient diet, and 32% in rats fed a goitrogenic diet (low-iodine diet supplemented with propylthiouracil). In addition, fasting for 2 days reduced sympathetic nervous system activity in thyroid by 38%. Thyroid growth and 125I uptake were also compared in intact and decentralized hemithyroids obtained from animals subjected to unilateral superior cervical ganglion decentralization. Unilateral superior cervical ganglion decentralization led to a reduction in thyroid weight, in 125I uptake by thyroid tissue, and in TSH-induced stimulation of 125I uptake in decentralized hemithyroids. These results suggest that sympathetic activity in thyroid contributes to gland enlargement and may modulate tissue responsiveness to TSH.
Activation of p38 MAP kinase enhances sensitivity of muscle glucose transport to insulin
Authors: Geiger Paige C. , Wright David C. , Han Dong-Ho , Holloszy John O.
Published: December 2004

Muscle contractile activity is followed by an increase in the sensitivity of glucose transport to insulin. There is evidence suggesting that activation of p38 MAP kinase (p38) is involved in the stimulation of glucose transport by insulin and contractions. Exercise results in an increase in p38 phosphorylation that lasts for hours. In this context, we tested the hypothesis that activation of p38 results in an increase in insulin sensitivity. Muscles were exposed to anisomycin for 30 min to activate p38. Anisomycin increased p38 phosphorylation ∼2.5-fold and glucose transport activity 2- to 3-fold. Three hours after anisomycin treatment, by which time the acute effect on glucose transport had partially worn off, sensitivity of muscle glucose transport to 60 μU/ml insulin was markedly increased. Both the activation of p38 and the increase in insulin sensitivity induced by anisomycin were completely prevented by pretreatment of muscles with the p38 inhibitor SB-202190. However, in contrast to the finding with anisomycin, inhibition of p38 activation did not prevent the contraction-induced increase in insulin sensitivity. Thus our results show that activation of p38 is followed by an increase in insulin sensitivity of muscle glucose transport. However, activation of p38 is not necessary for induction of an increase in muscle insulin sensitivity by contractions. This finding provides evidence that contractions have an additional effect that makes p38 activation unnecessary for enhancement of insulin sensitivity by contractile activity.
In vitro analysis of the effects of cholecystokinin on rat brain stem motoneurons
Authors: Zheng Zhongling , Lewis Mark W. , Travagli R. Alberto
Published: December 2004

Using whole cell patch clamp in thin brain stem slices, we tested the effects of cholecystokinin (CCK) on identified gastric-projecting neurons of the rat dorsal motor nucleus of the vagus (DMV). Perfusion with the sulfated form of CCK octapeptide (CCK8s, 30 pM–300 nM, EC50 ∼4 nM) induced a concentration-dependent inward current in 35 and 41% of corpus- and antrum/pylorus-projecting DMV neurons, respectively. Conversely, none of the fundus-projecting DMV neurons responded to perfusion with CCK8s. The CCK8s-induced inward current was accompanied by a 65 ± 17% increase in membrane input resistance and reversed at 90 ± 4 mV, indicating that the excitatory effects of CCK8s were mediated by the closure of a potassium conductance. Pretreatment with the synaptic blocker TTX (0.3–1 μM) reduced the CCK8s-induced current, suggesting that a portion of the CCK8s-induced current was mediated indirectly via an action on presynaptic neurons apposing the DMV membrane. Pretreatment with the selective CCK-A receptor antagonist lorglumide (0.3–3 μM) attenuated the CCK8s-induced inward current in a concentration-dependent manner, with a maximum inhibition of 69 ± 12% obtained with 3 μM lorglumide. Conversely, pretreatment with the selective CCK-B antagonist triglumide did not attenuate the CCK8s-induced inward current; pretreatment with triglumide (3 μM) and lorglumide (1 μM) attenuated the CCK8s-induced current to the same extent as pretreatment with lorglumide alone. Immunohistochemical experiments showed that CCK-A receptors were localized on the membrane of 34, 65, and 60% of fundus-, corpus-, and antrum/pylorus-projecting DMV neurons, respectively. Our data indicate that CCK-A receptors are present on a subpopulation of gastric-projecting neurons and that their activation leads to excitation of the DMV membrane.
Branched-chain amino acids improve glucose metabolism in rats with liver cirrhosis
Authors: Nishitani Shinobu , Takehana Kenji , Fujitani Shoji , Sonaka Ichiro
Published: December 2004

It is well established that impaired glucose metabolism is a frequent complication in patients with hepatic cirrhosis. We previously showed that leucine, one of the branched-chain amino acids (BCAA), promotes glucose uptake under insulin-free conditions in isolated skeletal muscle from normal rats. The aim of the present study was to evaluate the effects of BCAA on glucose metabolism in a rat model of CCl4-induced cirrhosis (CCl4rats). Oral glucose tolerance tests were performed on BCAA-treated CCl4rats. In the CCl4rats, treatment with leucine or isoleucine, but not valine, improved glucose tolerance significantly, with the effect of isoleucine being greater than the effect of leucine. Glucose uptake experiments using isolated soleus muscle from the CCl4rats revealed that leucine and isoleucine, but not valine, promoted glucose uptake under insulin-free conditions. To clarify the mechanism of the blood glucose-lowering effects of BCAA, we collected soleus muscles from BCAA-treated CCl4rats with or without a glucose load. These samples were used to determine the subcellular location of glucose transporter proteins and glycogen synthase (GS) activity. Oral administration of leucine or isoleucine without a glucose load induced GLUT4 and GLUT1 translocation to the plasma membrane. GS activity was augmented only in leucine-treated rats and was completely inhibited by rapamycin, an inhibitor of mammalian target of rapamycin. In summary, we found that leucine and isoleucine improved glucose metabolism in CCl4rats by promoting glucose uptake in skeletal muscle. This effect occurred as a result of upregulation of GLUT4 and GLUT1 and also by mammalian target of rapamycin-dependent activation of GS in skeletal muscle. From these results, we consider that BCAA treatment may have beneficial effects on glucose metabolism in cirrhotic patients.
Gestational programming: population survival effects of drought and famine during pregnancy
Authors: Ross Michael G. , Desai Mina
Published: December 2004

The process whereby a stimulus or stress at a critical or sensitive period of development has long-term effects is termed “programming.” Studies in humans and animals convincingly demonstrate that environmental perturbations in utero may permanently change organ structure and metabolism and/or alter homeostatic regulatory mechanisms among the offspring. These programmed changes may be the origins of adult diseases, including cardiovascular disease, obesity, and diabetes. Throughout evolution and development, humans and animals have been exposed to two common environmental stresses, drought and famine. Notably, drought-induced water deprivation is associated with dehydration anorexia and thus a concomitant potential nutrient stress. Our laboratory has performed studies among pregnant rat and sheep in which we simulate drought conditions via maternal dehydration and famine conditions via nutrient restriction. Maternal dehydration results in low-birth-weight offspring, which demonstrate gender-specific plasma hypernatremia and hypertonicity and arterial hypertension. Gestational nutrient restriction also resulted in low-birth-weight offspring. If permitted rapid catch-up growth by nutrient availability, these offspring demonstrate evidence of increased body weight and body fat, and leptin resistance as adults. Conversely, if the catch-up growth is delayed by nutrition restriction, the offspring exhibit normal body weight, body fat, and plasma leptin levels as adults. These studies indicate that osmoregulatory and cardiovascular homeostasis and phenotypic predisposition to obesity may be programmed in utero. Importantly, these results suggest that programming effects may be either potentiated or prevented by interventions during the neonatal period.