bluuebunny/crossref_metadata_2025 huggingface dataset:
The tyrosine‐sulfated peptide receptors PSKR1 and PSY1R modify the immunity of Arabidopsis to biotrophic and necrotrophic pathogens in an antagonistic manner
Authors: Mosher Stephen , Seybold Heike , Rodriguez Patricia , Stahl Mark , Davies Kelli A. , Dayaratne Sajeewani , Morillo Santiago A. , Wierzba Michael , Favery Bruno , Keller Harald , Tax Frans E. , Kemmerling Birgit
Published: October 2012

The tyrosine‐sulfated peptides PSKα and PSY1 bind to specific leucine‐rich repeat surface receptor kinases and control cell proliferation in plants. In a reverse genetic screen, we identified the phytosulfokine (PSK) receptor PSKR1 as an important component of plant defense. Multiple independent loss‐of‐function mutants in PSKR1 are more resistant to biotrophic bacteria, show enhanced pathogen‐associated molecular pattern responses and less lesion formation after infection with the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. By contrast, pskr1 mutants are more susceptible to necrotrophic fungal infection with Alternaria brassicicola, show more lesion formation and fungal growth which is not observed on wild‐type plants. The antagonistic effect on biotrophic and necrotrophic pathogen resistance is reflected by enhanced salicylate and reduced jasmonate responses in the mutants, suggesting that PSKR1 suppresses salicylate‐dependent defense responses. Detailed analysis of single and multiple mutations in the three paralogous genes PSKR1, ‐2 and PSY1‐receptor (PSY1R) determined that PSKR1 and PSY1R, but not PSKR2, have a partially redundant effect on plant immunity. In animals and plants, peptide sulfation is catalyzed by a tyrosylprotein sulfotransferase (TPST). Mutants lacking TPST show increased resistance to bacterial infection and increased susceptibility to fungal infection, mimicking the triple receptor mutant phenotypes. Feeding experiments with PSKα in tpst‐1 mutants partially restore the defense‐related phenotypes, indicating that perception of the PSKα peptide has a direct effect on plant defense. These results suggest that the PSKR subfamily integrates growth‐promoting and defense signals mediated by sulfated peptides and modulates cellular plasticity to allow flexible adjustment to environmental changes.
Algebraic boundaries of Hilbert’s SOS cones
Authors: Blekherman Grigoriy , Hauenstein Jonathan , Ottem John Christian , Ranestad Kristian , Sturmfels Bernd
Published: October 2012

We study the geometry underlying the difference between non-negative polynomials and sums of squares (SOS). The hypersurfaces that discriminate these two cones for ternary sextics and quaternary quartics are shown to be Noether–Lefschetz loci of K3 surfaces. The projective duals of these hypersurfaces are defined by rank constraints on Hankel matrices. We compute their degrees using numerical algebraic geometry, thereby verifying results due to Maulik and Pandharipande. The non-SOS extreme rays of the two cones of non-negative forms are parametrized, respectively, by the Severi variety of plane rational sextics and by the variety of quartic symmetroids.
Advancements in pressure–volume catheter technology – stress remodelling after infarction
Authors: Clark James E. , Marber Michael S.
Published: October 2012

New Findings

What is the topic of this review?

The gold standards for assessing heart function in experimental animals are magnetic resonance imaging or high‐frequency ultrasound; however, these are not accessible in many laboratories. We review here the use of the new microconductance catheter technologies to assess cardiac function in rodent models of the diseased heart.

What advances does it highlight?

Recent advances in the technology of conductance and admittance catheter systems provide an inexpensive, readily available method to assess cardiac function in rodents. We discuss the common pitfalls in using this technique and present evidence showing that its reliability and reproducibility are similar to ultrasound.

Microconductance catheters have been successfully applied to measure left ventricular (LV) function in the mouse to assess cardiac or pharmacological interventions for a number of years. New complex admittance methods produce an estimate of the parallel admittance of cardiac muscle that can be used to correct the measurement in real time. This contrasts with existing conductance technologies that require in vivo calibration using a bolus of hypertonic saline. Here, we report the application of this emerging technology in the context of myocardial infarction and LV remodelling. Using a combination of high‐resolution ultrasound and LV conductance catheters, we compared measures of LV function using an admittance system and a traditional conductance‐derived pressure–volume (PV) system. We subjected C57BL/6 mice to focal myocardial ischaemia–reperfusion by transient ligation of the left anterior descending coronary artery and assessed cardiac function with different systems to determine the reliability and accuracy of these methods to distinguish between normal and dysfunctional ventricle. We demonstrate that the admittance PV system, in our hands, provides a straightforward solution for assessing LV function in mice. Using this technique in combination with other established methods, we measured LV dysfunction following coronary artery occlusion and reperfusion, which can be ameliorated using a known preconditioning agent (CORM‐3), and found that functional read‐outs are representative of other methods. We have found that, especially in diseased tissue, LV pressure–volume loops derived from complex admittance provide a reproducible and reliable method of determining LV function without the need for technically challenging calibration. Our data suggest that admittance records accurate/physiological LV cavity volumes when compared with other invasive methods in the same animal. This emerging technology is both effective and reproducible for measuring LV function and dysfunction in the mouse, without the need for complicated interventions to calibrate the measurements or training in a new technology. This may mark the way towards a fast and accurate assessment of murine cardiac function in normal animals and disease models.
The pulmonary vascular response to combined activation of the muscle metaboreflex and mechanoreflex
Authors: White Michael J. , Lykidis Christos K. , Balanos George M.
Published: October 2012

New Findings

What is the central question of this study?

It is currently unknown whether there is a pulmonary vascular response to the combined activation of the muscle and the muscle mechanoreflex in man.

What is the main finding and its importance?

For the first time, we show that activation of the muscle mechanoreflex attenuated the increases in pulmonary vascular resistance caused by metaboreflex activation.

Muscle metabo‐ and mechanoreflexes are known to influence systemic cardiovascular responses to exercise. Whether interplay between these reflexes is operant in the control of the pulmonary vascular response to exercise is unknown. The aim of this study was to assess the pulmonary vascular response to the combined activation of the two muscle reflexes. Nine healthy subjects performed a bout of isometric calf plantarflexion exercise during local circulatory occlusion, which was continued for 9 min postexercise (PECO). At 5 min into PECO the calf muscle was passively stretched for 180 s. A control (no exercise) protocol was also undertaken. Heart rate, blood pressure measurements and echocardiographically determined estimates of systolic pulmonary artery pressure (SPAP) and cardiac output () were obtained at intervals throughout the two protocols. Elevations in SPAP (by 22.51 ± 2.61%), (by 26.92 ± 2.99%) and mean arterial pressure (by 15.38 ± 2.29%) were noted during isometric exercise in comparison to baseline (all P < 0.05). Increases in SPAP and mean arterial pressure persisted during PECO (All P < 0.05), whereas returned to resting levels. These increases in mean arterial pressure and SPAP were sustained during stretch which significantly elevated (All P < 0.05). These data suggest that activation of the muscle mechanoreflex attenuated the increases in pulmonary vascular resistance caused by metaboreflex activation. This finding has important implications for the regulation of pulmonary haemodynamics during human exercise.
Impact of Interstitial Mass Transport Resistance on Water Vapor Diffusion Through Fabric Layers
Authors: Sharma Anshul , Boetcher Sandra K. S. , Aissa Walid A. , Traum Matthew J.
Published: October 2012

Textiles maintain wearer comfort by allowing evaporated sweat to permeate through, providing thermal management and keeping skin dry. For single layers, resistance to mass transport is relatively straightforward. However, when textiles are layered, water vapor transport becomes more complex because diffusing molecules must traverse interstitial spaces between layers. Interstitial mass transport resistances of significant magnitude can reduce rates of water vapor transport through layered textile stacks. The prevailing textile mass transport resistance interrogation method is ASTM F1868: “Standard Test Method for Thermal and Evaporative Resistance of Clothing Materials Using a Sweating Hot Plate.” Four improvements to ASTM F1868 are recommended: (1) gravimetric mass transport measurement, (2) evaluating transport using the Stefan flow model, (3) correct accounting for apparatus mass transport resistances, and (4) recognizing and measuring interstitial mass transport resistances. These improvements were implemented and evaluated by running tests using Southern Mills Defender™ 750 fabric, the calibration standard used for ASTM F1868, on a new gravimetric experimental apparatus. For a single layer of calibration fabric, the gravimetric approach is consistent with the prescribed result from ASTM F1868; however, for stacks of two or more calibration fabric layers, the gravimetric approach does not agree with the prescribed ASTM F1868 result due to interstitial mass transport resistance between fabric layers.
Step Response of a Single-Pass Crossflow Heat Exchanger With Variable Inlet Temperatures and Mass Flow Rates
Authors: Silaipillayarputhur Karthik , Idem Stephen A.
Published: October 2012

The step response of a single-pass crossflow heat exchanger with variable inlet temperatures and mass flow rates was determined. In every instance, the energy balance equations were solved using an implicit central finite difference method. Numerical predictions were obtained for cases where both the minimum or maximum capacity rate fluids were subjected to step changes in inlet temperature, coupled with step mass flow rate changes of the fluids. Likewise, performance calculations were conducted for heat exchangers operating initially at steady state, where step flow rate changes of the minimum and maximum capacity rate fluids were imposed in the absence of any temperature perturbations. Because of the storage of energy in the heat exchanger wall, and finite propagation times associated with the inlet perturbations, the outlet temperatures of both fluids do not respond instantaneously. A parametric study was conducted by varying the dimensionless parameters governing the transient response of the heat exchanger over a representative range of values.
Numerical Simulation of a Turbulent Flow Over a Backward Facing Step With Heated Wall: Effect of Pulsating Velocity and Oscillating Wall
Authors: Pozarlik A. K. , Kok J. B. W.
Published: October 2012

An accurate prediction of the flow and the thermal boundary layer is required to properly simulate gas to wall heat transfer in a turbulent flow. This is studied with a view to application to gas turbine combustors. A typical gas turbine combustion chamber flow presents similarities with the well-studied case of turbulent flow over a backward facing step, especially in the near-wall regions where the heat transfer phenomena take place. However, the combustion flow in a gas turbine engine is often of a dynamic nature and enclosed by a vibrating liner. Therefore apart from steady state situations, cases with an oscillatory inlet flow and vibrating walls are investigated. Results of steady state and transient calculations for the flow field, friction coefficient, and heat transfer coefficient, with the use of various turbulence models, are compared with literature data. It has been observed that the variations in the excitation frequency of the inlet flow and wall vibrations have an influence on the instantaneous heat transfer coefficient profile. However, significant effect on the time mean value and position of the heat transfer peak is only visible for the inlet velocity profile fluctuations with frequency approximately equal to the turbulence bursting frequency.
Relationship between film thickness loss and polymer deprotection for extreme ultraviolet and ArF photoresists
Authors: Winroth Gustaf , Younkin Todd R. , Blackwell James M. , Gronheid Roel
Published: October 2012

The authors report on the relationship between the film thickness loss (FTL) and the polymer deprotection of chemically amplified resists with chemistries for ArF and extreme ultraviolet lithography. FTL curves are quickly and easily accessed experimentally through in-line ellipsometry measurements. They also provide affordable and valuable input for the description of acid generation and polymer deprotection kinetics for resist modeling. Unlike 248 nm resist platforms, where a linear relationship has been observed between the polymer deprotection and the FTL, they observe that for 193 and 13.5 nm technologies, the polymer composition induces a deviation from this linearity. In particular, the authors use Fourier transform infrared spectroscopy for the evaluation of the polymer deprotection in both model resists (with known chemical properties) and state-of-the-art commercial resists. With the corresponding FTL, chemical components that contribute to the nonlinearity are identified.
Effect of MoO3 doping power on the electrical, optical, and structural properties of MoO3-doped In2O3 anodes for organic solar cells
Authors: Shin Yong-Hee , Kim Han-Ki , Na Seok-In
Published: October 2012

The authors investigated the effects of MoO3 doping power on the electrical, optical, and structural properties of MoO3-doped In2O3 (IMO) films for use as transparent electrodes in organic solar cells (OSCs). By optimizing the RF power of the MoO3 target (30 W), they obtained IMO films with sheet resistance of 24.57 Ω/sq and optical transmittance of 81.57%, comparable to conventional Sn-doped In2O3 (ITO) electrodes. In particular, the IMO film exhibited a high optical transmittance in the near-infrared (NIR) wavelength region due to the effects of Mo dopant with high Lewis acid strength and high mobility. In addition, strongly oriented (222) grains led to a smooth surface of the IMO electrode with root mean square roughness of 2.344 nm. The OSC fabricated on the optimized IMO electrode showed cell performances with a fill factor of 64.66%, a short circuit current of 8.058 mA/cm2, an open circuit voltage of 0.611 V, and a power conversion efficiency of 3.186%, which are nearly identical to OSCs with an ITO reference. This indicates that the IMO film is a promising alternative to the ITO electrode for the tandem OSC absorbing NIR wavelength region.
Vocalization of echolocation-like pulses for interindividual interaction in horseshoe bats (Rhinolophus ferrumequinum)
Authors: Kobayasi Kohta I. , Hiryu Shizuko , Shimozawa Ryota , Riquimaroux Hiroshi
Published: October 2012

Although much is known about the echolocation of horseshoe bats (Rhinolophus spp.), little is known about the characteristics and function of their communication calls. This study focused on a stereotyped behavior of a bat approaching a companion animal in the colony, and examined their interaction and vocalization during this behavior. The bats emit echolocation-like vocalizations when approaching each other and these vocalizations contain a “buildup” pulse sequence, in which the frequency of the pulse increases gradually to normal echolocation pulse frequencies. The results suggest that the echolocation-like pulses serve an important role in communication within the colony.
Tissint Martian Meteorite: A Fresh Look at the Interior, Surface, and Atmosphere of Mars
Authors: Aoudjehane H. Chennaoui , Avice G. , Barrat J.-A. , Boudouma O. , Chen G. , Duke M. J. M. , Franchi I. A. , Gattacceca J. , Grady M. M. , Greenwood R. C. , Herd C. D. K. , Hewins R. , Jambon A. , Marty B. , Rochette P. , Smith C. L , Sautter V. , Verchovsky A. , Weber P. , Zanda B.
Published: October 2012

A New Rock from Mars

On 18 July 2011 a meteorite originating from Mars fell on the moroccan desert.

Chennaoui Aoudjehane
et al.

(p.
785
, published online 11 October) show that this meteorite was ejected from the surface of Mars 700,000 years ago and contains components derived from the interior, surface, and atmosphere of the red planet. Previous to this fall, only four other martian meteorites have been collected after being witnessed falling to Earth. All the other martian meteorites that are represented in collections around the world, have been found long after their arrival on Earth, and thus have suffered from exposure to the terrestrial environment.
Tug-of-War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold
Authors: Derr N. D. , Goodman B. S. , Jungmann R. , Leschziner A. E. , Shih W. M. , Reck-Peterson S. L.
Published: October 2012

Push Me, Release, Pull You

In eukaryotic cells, nearly all long-distance transport of cargos is carried out by the microtubule-based motors kinesin and dynein. These opposite-polarity motors move cargos bidirectionally so that they reach their cellular destinations with spatial and temporal specificity. To understand transport by motor ensembles,

Derr
et al.

(p.
662
, published online 11 October; see the Persective by

Diehl

) used a DNA scaffold for building an artificial cargo that could be programmed to bind different numbers and types of molecular motors with defined geometry. A cargo with multiple copies of the same motor was transported with minimal interference, suggesting that similar-polarity motors can coordinate without the need for additional cellular factors. However, ensembles of opposite-polarity motors frequently engaged in a sort of “tug of war,” which could only be resolved by releasing one motor from the microtubule track. Thus, within the cell, it is likely that regulation is required for bidirectional transport.
Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns
Authors: Calcagno V. , Demoinet E. , Gollner K. , Guidi L. , Ruths D. , de Mazancourt C.
Published: October 2012

Fathoming Publication Strategies

While many studies have tracked numbers of citations after publication, such studies cannot reveal how prepublication dynamics affects subsequent citation history.

Calcagno
et al.

(p.
1065
, published online 11 October) surveyed the submission history of more than 80,000 articles published in 16 fields of biology in 2006–2008 and constructed a social network based on manuscript flows among scientific journals. High-impact journals occupied central positions in the network. A majority of manuscripts were published in the first journal to which they were submitted. However, submission history affected the post-publication impact (citation count) of articles, with manuscripts requiring resubmission eventually receiving more citations.
Copy Number Variation of Multiple Genes at
Rhg1
Mediates Nematode Resistance in Soybean
Authors: Cook David E. , Lee Tong Geon , Guo Xiaoli , Melito Sara , Wang Kai , Bayless Adam M. , Wang Jianping , Hughes Teresa J. , Willis David K. , Clemente Thomas E. , Diers Brian W. , Jiang Jiming , Hudson Matthew E. , Bent Andrew F.
Published: October 2012

Resistance to a damaging disease of soybean is conferred by a cluster of linked genes present in multiple copies.
Financial Costs of Meeting Global Biodiversity Conservation Targets: Current Spending and Unmet Needs
Authors: McCarthy Donal P. , Donald Paul F. , Scharlemann Jörn P. W. , Buchanan Graeme M. , Balmford Andrew , Green Jonathan M. H. , Bennun Leon A. , Burgess Neil D. , Fishpool Lincoln D. C. , Garnett Stephen T. , Leonard David L. , Maloney Richard F. , Morling Paul , Schaefer H. Martin , Symes Andy , Wiedenfeld David A. , Butchart Stuart H. M.
Published: October 2012

Costs of Conservation

In 2010, world governments agreed to a strategic plan for biodiversity conservation, including 20 targets to be met by 2020, through the Convention on Biological Diversity. Discussions on financing the plan have still not been resolved, partly because there is little information on the likely costs of meeting the targets.

McCarthy
et al.

(p.
946
, published online 11 October) estimate the financial costs for two of the targets relating to protected areas and preventing extinctions. Using data from birds, they develop models that can be extrapolated to the costs for biodiversity more broadly. Reducing extinction risk for all species is estimated to require in the region of U.S. $4 billion annually, while the projected costs of establishing and maintaining protected areas may be as much as U.S. $58 billion—although both sums are small, relative to the economic costs of ecosystem losses.
Environment-Dependent Distribution of the Sediment
nifH
-Harboring Microbiota in the Northern South China Sea
Authors: Dang Hongyue , Yang Jinying , Li Jing , Luan Xiwu , Zhang Yunbo , Gu Guizhou , Xue Rongrong , Zong Mingyue , Klotz Martin G.
Published: October 2012

The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N
2
fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting
nifH
and some other functional biomarker genes. Diverse and novel
nifH
sequences were obtained, significantly extending the evolutionary complexity of extant
nifH
genes. Statistical analyses indicate that sediment
in situ
temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment
nifH
-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH
4
+
concentration with the
nifH
gene abundance suggests that the nSCS sediment
nifH
-harboring microbiota is active in N
2
fixation and NH
4
+
production. Several other environmental factors, including sediment pore water PO
4
3−
concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the
nifH
-harboring microbial assemblages. We also confirmed that the
nifH
genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c
nifH
genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.
Expression and Characterization of a Bifidobacterium adolescentis Beta-Mannanase Carrying Mannan-Binding and Cell Association Motifs
Authors: Kulcinskaja Evelina , Rosengren Anna , Ibrahim Romany , Kolenová Katarína , Stålbrand Henrik
Published: October 2012

The gene encoding β-mannanase (EC 3.2.1.78) BaMan26A from the bacteriumBifidobacterium adolescentis(living in the human gut) was cloned and the gene product characterized. The enzyme was found to be modular and to contain a putative signal peptide. It possesses a catalytic module of the glycoside hydrolase family 26, a predicted immunoglobulin-like module, and two putative carbohydrate-binding modules (CBMs) of family 23. The enzyme is likely cell attached either by the sortase mechanism (LPXTG motif) or via a C-terminal transmembrane helix. The gene was expressed inEscherichia coliwithout the native signal peptide or the cell anchor. Two variants were made: one containing all four modules, designated BaMan26A-101K, and one truncated before the CBMs, designated BaMan26A-53K. BaMan26A-101K, which contains the CBMs, showed an affinity to carob galactomannan having a dissociation constant of 0.34 μM (8.8 mg/liter), whereas BaMan26A-53K did not bind, showing that at least one of the putative CBMs of family 23 is mannan binding. For BaMan26A-53K,kcatwas determined to be 444 s−1andKm21.3 g/liter using carob galactomannan as the substrate at the optimal pH of 5.3. Both of the enzyme variants hydrolyzed konjac glucomannan, as well as carob and guar gum galactomannans to a mixture of oligosaccharides. The dominant product from ivory nut mannan was found to be mannotriose. Mannobiose and mannotetraose were produced to a lesser extent, as shown by high-performance anion-exchange chromatography. Mannobiose was not hydrolyzed, and mannotriose was hydrolyzed at a significantly lower rate than the longer oligosaccharides.
Functional γ-Aminobutyrate Shunt in Listeria monocytogenes: Role in Acid Tolerance and Succinate Biosynthesis
Authors: Feehily Conor , O'Byrne Conor P. , Karatzas Kimon Andreas G.
Published: October 2012

Listeria monocytogenes
, the causative agent of human listeriosis, is known for its ability to withstand severe environmental stresses. The glutamate decarboxylase (GAD) system is one of the principal systems utilized by the bacterium to cope with acid stress, a reaction that produces γ-aminobutyrate (GABA) from glutamate. Recently, we have shown that GABA can accumulate intracellularly under acidic conditions, even under conditions where no extracellular glutamate-GABA exchange is detectable. The GABA shunt, a pathway that metabolizes GABA to succinate, has been described for several other bacterial genera, and the present study sought to determine whether
L. monocytogenes
has this metabolic capacity, which, if present, could provide a possible route for succinate biosynthesis in
L. monocytogenes
. Using crude protein extracts from
L. monocytogenes
EGD-e, we show that this strain exhibits activity for the two main enzyme reactions in the GABA shunt, GABA aminotransferase (GABA-AT) and succinic semialdehyde dehydrogenase (SSDH). Two genes were identified as candidates for encoding these enzyme activities,
argD
(GABA-AT) and
lmo0913
(SSDH). Crude protein extracts prepared from a mutant lacking a functional
argD
gene significantly reduced GABA-AT activity, while an
lmo0913
mutant lost all detectable SSDH activity. The deletion of
lmo0913
increased the acid tolerance of EGD-e and showed an increased accumulation of intracellular GABA, suggesting that this pathway plays a significant role in the survival of this pathogen under acidic conditions. This is the first report of such a pathway in the genus
Listeria
, which highlights an important link between metabolism and acid tolerance and also presents a possible compensatory pathway to partially overcome the incomplete tricarboxylic acid cycle of
Listeria
.
Lineage-Specific Responses of Microbial Communities to Environmental Change
Authors: Youngblut Nicholas D. , Shade Ashley , Read Jordan S. , McMahon Katherine D. , Whitaker Rachel J.
Published: October 2012

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene
ccoN
, to provide additional taxonomic resolution for the common freshwater genus
Polynucleobacter
. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant
Polynucleobacter
lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant
Actinobacteria
OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.
Tetrathionate-Forming Thiosulfate Dehydrogenase from the Acidophilic, Chemolithoautotrophic Bacterium Acidithiobacillus ferrooxidans
Authors: Kikumoto Mei , Nogami Shohei , Kanao Tadayoshi , Takada Jun , Kamimura Kazuo
Published: October 2012

Thiosulfate dehydrogenase is known to play a significant role in thiosulfate oxidation in the acidophilic, obligately chemolithoautotroph,
Acidithiobacillus ferrooxidans
. Enzyme activity measured using ferricyanide as the electron acceptor was detected in cell extracts of
A. ferrooxidans
ATCC 23270 grown on tetrathionate or sulfur, but no activity was detected in ferrous iron-grown cells. The enzyme was enriched 63-fold from cell extracts of tetrathionate-grown cells. Maximum enzyme activity (13.8 U mg
−1
) was observed at pH 2.5 and 70°C. The end product of the enzyme reaction was tetrathionate. The enzyme reduced neither ubiquinone nor horse heart cytochrome
c
, which serves as an electron acceptor. A major protein with a molecular mass of ∼25 kDa was detected in the partially purified preparation. Heme was not detected in the preparation, according to the results of spectroscopic analysis and heme staining. The open reading frame of AFE_0042 was identified by BLAST by using the N-terminal amino acid sequence of the protein. The gene was found within a region that was previously noted for sulfur metabolism-related gene clustering. The recombinant protein produced in
Escherichia coli
had a molecular mass of ∼25 kDa and showed thiosulfate dehydrogenase activity, with maximum enzyme activity (6.5 U mg
−1
) observed at pH 2.5 and 50°C.
Catalase Activity as a Biomarker for Mild-Stress-Induced Robustness in Bacillus weihenstephanensis
Authors: den Besten Heidy M. W. , Effraimidou Styliani , Abee Tjakko
Published: October 2012

Microorganisms are able to survive and grow in changing environments by activating stress adaptation mechanisms which may enhance bacterial robustness. Stress-induced enhanced robustness complicates the predictability of microbial inactivation. Using psychrotolerant
Bacillus weihenstephanensis
strain KBAB4 as a model, we investigated the impact of the culturing temperature on mild-oxidative-stress-induced (cross-)protection toward multiple stresses, including severe oxidative, heat, and acid stresses. Culturing at a refrigeration temperature (7°C) compared to the optimal growth temperature (30°C) affected both the robustness level of
B. weihenstephanensis
and the oxidative stress adaptive response. Scavengers of reactive oxygen species have a crucial role in adaptation to oxidative stresses, and this points to a possible predictive role in mild-oxidative-stress-induced robustness. Therefore, the catalase activity was determined upon mild oxidative stress treatment and was demonstrated to be significantly correlated with the robustness level of mild-stress-treated cells toward severe oxidative and heat stresses but not toward severe acid stress for cells grown at both refrigeration and optimal temperatures. The quantified correlations supported the predictive quality of catalase activity as a biomarker and also underlined that the predictive quality is stress specific. Biomarkers that are able to predict stress-induced enhanced robustness can be used to better understand stress adaptation mechanisms and might allow the design of effective combinations of hurdles to control microbial behavior.
Community and Proteomic Analysis of Methanogenic Consortia Degrading Terephthalate
Authors: Wu Jer-Horng , Wu Feng-Yau , Chuang Hui-Ping , Chen Wei-Yu , Huang Hung-Jen , Chen Shu-Hui , Liu Wen-Tso
Published: October 2012

Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122–130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that
Pelotomaculum
,
Methanosaeta
, and
Methanolinea
were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed
in situ
. The results confirmed that TA was degraded by
Pelotomaculum
spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H
2
/CO
2
, and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.
Isotope-Assisted Screening for Iron-Containing Metabolites Reveals a High Degree of Diversity among Known and Unknown Siderophores Produced by Trichoderma spp
Authors: Lehner Sylvia M. , Atanasova Lea , Neumann Nora K. N. , Krska Rudolf , Lemmens Marc , Druzhinina Irina S. , Schuhmacher Rainer
Published: October 2012

Due to low iron availability under environmental conditions, many microorganisms excrete iron-chelating agents (siderophores) to cover their iron demands. A novel screening approach for the detection of siderophores using liquid chromatography coupled to high-resolution tandem mass spectrometry was developed to study the production of extracellular siderophores of 10 wild-type
Trichoderma
strains. For annotation of siderophores, an in-house library comprising 422 known microbial siderophores was established. After 96 h of cultivation, 18 different iron chelators were detected. Four of those (dimerum acid, fusigen, coprogen, and ferricrocin) were identified by measuring authentic standards.
cis
-Fusarinine, fusarinine A and B, and des-diserylglycylferrirhodin were annotated based on high-accuracy mass spectral analysis. In total, at least 10 novel iron-containing metabolites of the hydroxamate type were found. On average
Trichoderma
spp. produced 12 to 14 siderophores, with 6 common to all species tested. The highest number (15) of siderophores was detected for the most common environmental opportunistic and strongly fungicidic species,
Trichoderma harzianum
, which, however, did not have any unique compounds. The tropical species
T. reesei
had the most distinctive pattern, producing one unique siderophore (
cis
-fusarinine) and three others that were present only in
T. harzianum
and not in other species. The diversity of siderophores did not directly correlate with the antifungal potential of the species tested. Our data suggest that the high diversity of siderophores produced by
Trichoderma
spp. might be the result of further modifications of the nonribosomal peptide synthetase (NRPS) products and not due to diverse NRPS-encoding genes.
Investigation of the Amycolatopsis sp. Strain ATCC 39116 Vanillin Dehydrogenase and Its Impact on the Biotechnical Production of Vanillin
Authors: Fleige Christian , Hansen Gunda , Kroll Jens , Steinbüchel Alexander
Published: October 2012

The actinomycete
Amycolatopsis
sp. strain ATCC 39116 is capable of synthesizing large amounts of vanillin from ferulic acid, which is a natural cell wall component of higher plants. The desired intermediate vanillin is subject to undesired catabolism caused by the metabolic activity of a hitherto unknown vanillin dehydrogenase (VDH
ATCC 39116
). In order to prevent the oxidation of vanillin to vanillic acid and thereby to obtain higher yields and concentrations of vanillin, the responsible vanillin dehydrogenase in
Amycolatopsis
sp. ATCC 39116 was investigated for the first time by using data from our genome sequence analysis and further bioinformatic approaches. The
vdh
gene was heterologously expressed in
Escherichia coli
, and the encoded vanillin dehydrogenase was characterized in detail. VDH
ATCC 39116
was purified to apparent electrophoretic homogeneity and exhibited NAD
+
-dependent activity toward vanillin, coniferylaldehyde, cinnamaldehyde, and benzaldehyde. The enzyme showed its highest level of activity toward vanillin at pH 8.0 and at a temperature of 44°C. In a next step, a precise
vdh
deletion mutant of
Amycolatopsis
sp. ATCC 39116 was generated. The mutant lost its ability to grow on vanillin and did not show vanillin dehydrogenase activity. A 2.3-times-higher vanillin concentration and a substantially reduced amount of vanillic acid occurred with the
Amycolatopsis
sp. ATCC 39116 Δ
vdh
::Km
r
mutant when ferulic acid was provided for biotransformation in a cultivation experiment on a 2-liter-bioreactor scale. Based on these results and taking further metabolic engineering into account, the
Amycolatopsis
sp. ATCC 39116 Δ
vdh
::Km
r
mutant represents an optimized and industrially applicable platform for the biotechnological production of natural vanillin.
Evaluation of Two Approaches for Assessing the Genetic Similarity of Virioplankton Populations as Defined by Genome Size
Authors: Jamindar Sanchita , Polson Shawn W. , Srinivasiah Sharath , Waidner Lisa , Wommack K. Eric
Published: October 2012

Viral production estimates show that virioplankton communities turn over rapidly in aquatic ecosystems. Thus, it is likely that the genetic identity of viral populations comprising the virioplankton also change over temporal and spatial scales, reflecting shifts in viral-host interactions. However, there are few approaches that can provide data on the genotypic identity of viral populations at low cost and with the sample throughput necessary to assess dynamic changes in the virioplankton. This study examined two of these approaches—T4-like major capsid protein (g23) gene polymorphism and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting—to ask how well each technique could track differences in virioplankton populations over time and geographic location. Seasonal changes in overall virioplankton composition were apparent from pulsed-field gel electrophoresis (PFGE) analysis. T4-like phages containing similar g23 proteins were found within both small- and large-genome populations, including populations from different geographic locations and times. The surprising occurrence of T4-like g23 within small genomic groups (23 to 64 kb) indicated that the genome size range of T4-like phages may be broader than previously believed. In contrast, RAPD-PCR fingerprinting detected high genotypic similarity within PFGE bands from the same location, time, and genome size class without the requirement for DNA sequencing. Unlike g23 polymorphism, RAPD-PCR fingerprints showed a greater temporal than geographic variation. Thus, while polymorphism in a viral signature gene, such as g23, can be a powerful tool for inferring evolutionary relationships, the degree to which this approach can capture fine-scale variability within virioplankton populations is less clear.
The Noncommensal Bacterium Methylococcus capsulatus (Bath) Ameliorates Dextran Sulfate (Sodium Salt)-Induced Ulcerative Colitis by Influencing Mechanisms Essential for Maintenance of the Colonic Barrier Function
Authors: Kleiveland Charlotte R. , Hult Lene T. Olsen , Spetalen Signe , Kaldhusdal Magne , Christofferesen Trine Eker , Bengtsson Oskar , Romarheim Odd Helge , Jacobsen Morten , Lea Tor
Published: October 2012

Dietary inclusion of a bacterial meal has recently been shown to efficiently abolish soybean meal-induced enteritis in Atlantic salmon. The objective of this study was to investigate whether inclusion of this bacterial meal in the diet could abrogate disease development in a murine model of epithelial injury and colitis and thus possibly have therapeutic potential in human inflammatory bowel disease. C57BL/6N mice were fedad libituma control diet or an experimental diet containing 254 g/kg of body weight BioProtein, a bacterial meal consisting ofMethylococcus capsulatus(Bath), together with the heterogenic bacteriaRalstoniasp.,Brevibacillus agri, andAneurinibacillussp. At day 8, colitis was induced by 3.5% dextran sulfate sodium (DSS)ad libitumin the drinking water for 6 days. Symptoms of DSS treatment were less profound after prophylactic treatment with the diet containing the BioProtein. Colitis-associated parameters such as reduced body weight, colon shortening, and epithelial damage also showed significant improvement. Levels of acute-phase reactants, proteins whose plasma concentrations increase in response to inflammation, and neutrophil infiltration were reduced. On the other, increased epithelial cell proliferation and enhanced mucin 2 (Muc2) transcription indicated improved integrity of the colonic epithelial layer. BioProtein mainly consists ofMethylococcus capsulatus(Bath) (88%). The results that we obtained when using a bacterial meal consisting ofM. capsulatus(Bath) were similar to those obtained when using BioProtein in the DSS model. Our results show that a bacterial meal of the noncommensal bacteriumM. capsulatus(Bath) has the potential to attenuate DSS-induced colitis in mice by enhancing colonic barrier function, as judged by increased epithelial proliferation and increased Muc2 transcription.
Exploration of the Genomic Diversity and Core Genome of the Bifidobacterium adolescentis Phylogenetic Group by Means of a Polyphasic Approach
Authors: Duranti Sabrina , Turroni Francesca , Milani Christian , Foroni Elena , Bottacini Francesca , Dal Bello Fabio , Ferrarini Alberto , Delledonne Massimo , van Sinderen Douwe , Ventura Marco
Published: October 2012

In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e.,
Bifidobacterium adolescentis
,
Bifidobacterium catenulatum
, and
Bifidobacterium pseudocatenulatum
, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.
Promoter Swapping Unveils the Role of the Citrobacter rodentium CTS1 Type VI Secretion System in Interbacterial Competition
Authors: Gueguen Erwan , Cascales Eric
Published: October 2012

The type VI secretion system (T6SS) is a versatile secretion machine dedicated to various functions in Gram-negative bacteria, including virulence toward eukaryotic cells and antibacterial activity. Activity of T6SS might be followed
in vitro
by the release of two proteins, Hcp and VgrG, in the culture supernatant.
Citrobacter rodentium
, a rodent pathogen, harbors two T6SS gene clusters,
cts1
and
cts2
. Reporter fusion and Hcp release assays suggested that the CTS1 T6SS was not produced or not active. The
cts1
locus is composed of two divergent operons. We therefore developed a new vector allowing us to swap the two divergent endogenous promoters by

P
tac

and

P
BAD

using the λ red recombination technology. Artificial induction of both promoters demonstrated that the CTS1 T6SS is functional as shown by the Hcp release assay and confers on
C. rodentium
a growth advantage in antibacterial competition experiments with
Escherichia coli
.
Identification and Characterization of a Bile Salt Hydrolase from Lactobacillus salivarius for Development of Novel Alternatives to Antibiotic Growth Promoters
Authors: Wang Zhong , Zeng Ximin , Mo Yiming , Smith Katie , Guo Yuming , Lin Jun
Published: October 2012

Antibiotic growth promoters (AGPs) have been used as feed additives to improve average body weight gain and feed efficiency in food animals for more than 5 decades. However, there is a worldwide trend to limit AGP use to protect food safety and public health, which raises an urgent need to discover effective alternatives to AGPs. The growth-promoting effect of AGPs has been shown to be highly correlated with the decreased activity of intestinal bile salt hydrolase (BSH), an enzyme that is produced by various gut microflora and involved in host lipid metabolism. Thus, BSH inhibitors are likely promising feed additives to AGPs to improve animal growth performance. In this study, the genome of
Lactobacillus salivarius
NRRL B-30514, a BSH-producing strain isolated from chicken, was sequenced by a 454 GS FLX sequencer. A BSH gene identified by genome analysis was cloned and expressed in an
Escherichia coli
expression system for enzymatic analyses. The BSH displayed efficient hydrolysis activity for both glycoconjugated and tauroconjugated bile salts, with slightly higher catalytic efficiencies (
k
cat
/

K
m

) on glycoconjugated bile salts. The optimal pH and temperature for the BSH activity were 5.5 and 41°C, respectively. Examination of a panel of dietary compounds using the purified BSH identified some potent BSH inhibitors, in which copper and zinc have been recently demonstrated to promote feed digestion and body weight gain in different food animals. In sum, this study identified and characterized a BSH with broad substrate specificity from a chicken
L. salivarius
strain and established a solid platform for us to discover novel BSH inhibitors, the promising feed additives to replace AGPs for enhancing the productivity and sustainability of food animals.
Protective Role of Spore Structural Components in Determining Bacillus subtilis Spore Resistance to Simulated Mars Surface Conditions
Authors: Moeller Ralf , Schuerger Andrew C. , Reitz Günther , Nicholson Wayne L.
Published: October 2012

Spores of wild-type and mutant
Bacillus subtilis
strains lacking various structural components were exposed to simulated Martian atmospheric and UV irradiation conditions. Spore survival and mutagenesis were strongly dependent on the functionality of all of the structural components, with small acid-soluble spore proteins, coat layers, and dipicolinic acid as key protectants.