bluuebunny/crossref_metadata_2025 huggingface dataset:
Alteration of the N‐glycome of bovine milk glycoproteins during early lactation
Authors: Takimori Shota , Shimaoka Hideyuki , Furukawa Jun‐Ichi , Yamashita Tadashi , Amano Maho , Fujitani Naoki , Takegawa Yasuhiro , Hammarström Lennart , Kacskovics Imre , Shinohara Yasuro , Nishimura Shin‐Ichiro
Published: August 2011

Milk provides nutritional, immunological and developmental components for newborns. Whereas identification of such components has been performed by targeting proteins and free oligosaccharides, structural and functional analyses of the N‐glycome of milk glycoproteins are scarce. In this study, we investigated, for the first time, the alterations of the bovine milk N‐glycome during early lactation (1 day, 1, 2, 3 and 4 weeks postpartum), characterizing more than 80 N‐glycans. The glycomic profile of colostrum on day 1 after calving differed substantially from that in other periods during early lactation. The proteins in colostrum obtained 1 day postpartum were more highly sialylated than milk samples obtained at other time points, and the N‐glycolylneuraminic acid (Neu5Gc)/N‐acetylneuraminic acid (Neu5Ac) ratio was significantly higher on day 1, showing a gradual decline with time. In order to dissect the N‐glycome of colostrum, alterations of the N‐glycosylation profile of major bovine milk proteins during the early lactation stage were elucidated, revealing that the alteration is largely attributable to qualitative and quantitative N‐glycosylation changes of IgG, the major glycoprotein in colostrum. Furthermore, by preparing and analyzing IgGs in which the N‐glycan structure and subtypes were well characterized, we found that the interaction between IgG and FcRn was not affected by the structure of the N‐glycans attached to IgG. We also found that bovine FcRn binds IgG2 better than IgG1, strongly suggesting that the role of FcRn in the bovine mammary gland is to recycle IgG2 from the udder to blood, rather than to secrete IgG1 into colostrum.
Improved Sexual Function with Testosterone Replacement Therapy in Hypogonadal Men: Real-World Data from the Testim Registry in the United States (TRiUS)
Authors: Khera Mohit , Bhattacharya Rajib K. , Blick Gary , Kushner Harvey , Nguyen D.t. , Miner Martin M.
Published: August 2011

Introduction

Up to 30% of erectile dysfunction (ED) patients treated with phosphodiesterase type 5 (PDE5) inhibitors do not show improved sexual function, which may be due in part to low serum testosterone. Hypogonadal patients already receiving testosterone replacement therapy (TRT) likewise can still suffer from symptoms of sexual dysfunction. In these patient populations, augmenting with, or switching, TRT treatment may improve sexual function.

Aim

To determine if 12-month treatment with a testosterone gel improves sexual function in hypogonadal men, as measured by the Brief Male Sexual Function Inventory (BMSFI), and in subgroups defined by low testosterone, PDE5 inhibitor use, and prior TRT.

Methods

The Testim Registry in the United States (TRiUS) was a large (N = 849) multicenter registry of hypogonadal men treated with Testim (testosterone 1%) topical gel and followed for 12 months.

Main Outcome Measures

Data collected at suggested visits (baseline; 1, 3, 6, and 12 months) included total testosterone (TT), free testosterone (FT), BMSFI scores, physical exam, and body measurements.

Results

TRiUS had 271 patients with baseline testosterone and BMSFI measurements. At 12 months of TRT, TT and FT levels significantly increased from baseline (P < 0.001), with mean ± standard deviation final TT = 17.37 ± 8.61 nmol/L (500.6 ± 248.2 ng/dL) and FT = 240.1 ± 296.0 pmol/L (69.2 ± 85.3 pg/mL). The mean total BMSFI score significantly increased from baseline at 12 months (27.4 ± 10.3 to 33.8 ± 9.8, P < 0.001) and at each visit in all domains (sex drive/libido, erectile function, ejaculatory function, level of bother), overall and for all subgroups. Regression analysis indicated that increased total BMSFI score was significantly associated with increased TT levels at 6 months.

Conclusions

In hypogonadal patients, 12-month administration of topical testosterone gel resulted in increased TT and FT levels and significantly improved sexual function. All subgroups studied, including men taking PDE5 inhibitors for ED and those previously on TRT, demonstrated significant improvement in sexual function from baseline scores.
Women's Bike Seats: A Pressing Matter for Competitive Female Cyclists
Authors: Guess Marsha K. , Partin Sarah N. , Schrader Steven , Lowe Brian , LaCombe Julie , Reutman Susan , Wang Andrea , Toennis Christine , Melman Arnold , Mikhail Madgy , Connell Kathleen A.
Published: August 2011

Introduction

There are numerous genital complaints in women cyclists, including pain, numbness, and edema of pelvic floor structures. Debate ensues about the best saddle design for protection of the pelvic floor.

Aim

To investigate the relationships between saddle design, seat pressures, and genital nerve function in female, competitive cyclists.

Methods

We previously compared genital sensation in healthy, premenopausal, competitive women bicyclists and runners. The 48 cyclists from our original study comprise the study group in this subanalysis.

Main Outcome Measures

Main outcome measures were: (i) genital vibratory thresholds (VTs) determined using the Medoc Vibratory Sensation Analyzer 3000 and (ii) saddle pressures as determined using a specially designed map sensor.

Results

More than half of the participants (54.8%) used traditional saddles, and the remainder (45.2%) rode with cut-out saddles. On bivariate analysis, use of traditional saddles was associated with lower mean perineal saddle pressures (MPSP) than riding on cut-out saddles. Peak perineal saddle pressures (PPSP) were also lower; however, the difference did not reach statistical significance. Saddle design did not affect mean or peak total saddle pressures (MTSP, PTSP). Saddle width was significantly associated with PPSP, MTSP, and PTSP but not with MPSP. Women riding cut-out saddles had, on average, a 4 and 11 kPa increase in MPSP and PPSP, respectively, compared with women using traditional saddles (P = 0.008 and P = 0.010), after adjustment for other variables. Use of wider saddles was associated with lower PPSP and MTSP after adjustment. Although an inverse correlation was seen between saddle pressures and VTs on bivariate analysis, these differences were not significant after adjusting for age.

Conclusion

Cut-out and narrower saddles negatively affect saddle pressures in female cyclists. Effects of saddle design on pudendal nerve sensory function were not apparent in this cross-sectional analysis. Longitudinal studies evaluating the long-term effects of saddle pressure on the integrity of the pudendal nerve, pelvic floor, and sexual function are warranted.
Relationship between reduced lower abdominal blood flows and heart rate in recovery following cycling exercise
Authors: Osada T. , Iwane H. , Katsumura T. , Murase N. , Higuchi H. , Sakamoto A. , Hamaoka T. , Shimomitsu T.
Published: August 2011

Aim:  To examine the blood flow (BF) response in the lower abdomen (LAB) in recovery following upright cycling exercise at three levels of relative maximum pulmonary oxygen consumption () and the relationship of BFLAB to heart rate (HR) and target intensity.

Methods:  For 11 healthy subjects, BF (Doppler ultrasound) in the upper abdominal aorta (Ao) above the coeliac trunk and in the right femoral artery (RFA) was measured repeatedly for 720 s after the end of cycling exercises at target intensities of 30%, 50% and 85%, respectively. Blood flow in the lower abdomen (BFLAB) can be measured by subtracting bilateral BFFAs (≈twofolds of BFRFA) from BFAo. Change in BFLAB (or BFLAB volume) at any point was evaluated by difference between change in BFAo and in BFFAs. Heart rate and blood pressure were also measured.

Results:  At 85%, significant reduction in BFLAB by approx. 89% was shown at 90 s and remained until 360 s. At 50%, reduction in BFLAB by approx. 33% was found at 90 s although it returned to pre‐exercise value at 120 s. On the contrary at 30%, BFLAB showed a light increase (<20%) below 70 bpm of HR. There was a close negative relationship (P < 0.05) between change in BFLAB and recovery HR, as well as between change in BFLAB volume and both recovery HR and %.

Conclusion:  This study suggests that the lower abdominal BF in recovery may be influenced by sympathetic‐vagus control, and dynamics of BFLAB may be closely related to the level of relative exercise intensities.
Wheat Germ Agglutinin Modified Liposomes for the Photodynamic Inactivation of Bacteria†
Authors: Yang Kewei , Gitter Burkhard , Rüger Ronny , Albrecht Volker , Wieland Gerhard D. , Fahr Alfred
Published: August 2011

Photodynamic inactivation (PDI) of bacteria is a promising approach for combating the increasing emergence of antibiotic resistance in pathogenic bacteria. To further improve the PDI efficiency on bacteria, a bacteria‐targeting liposomal formulation was investigated. A generation II photosensitizer (temoporfin) was incorporated into liposomes, followed by conjugation with a specific lectin (wheat germ agglutinin, WGA) on the liposomal surface. WGA was successfully coupled to temoporfin‐loaded liposomes using an activated phospholipid containing N‐hydroxylsuccinimide residue. Methicillin‐resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa were selected to evaluate the WGA modified liposomes in terms of bacteria targeted delivery and in vitro PDI test. Fluorescence microscopy revealed that temoporfin was delivered to both kinds of bacteria, while flow cytometry demonstrated that WGA‐ modified liposomes delivered more temoporfin to bacteria compared to nonmodified liposomes. Consequently, the WGA‐ modified liposomes eradicated all MRSA and significantly enhanced the PDI of P. aeruginosa. In conclusion, the WGA‐ modified liposomes are a promising formulation for bacteria targeted delivery of temoporfin and for improving the PDI efficiency of temoporfin on both Gram‐positive and Gram‐negative bacterial cells.
An In Vitro Comparison of the Effects of the Iron‐Chelating Agents, CP94 and Dexrazoxane, on Protoporphyrin IX Accumulation for Photodynamic Therapy and/or Fluorescence Guided Resection
Authors: Blake Emma , Allen James , Curnow Alison
Published: August 2011

Photodynamic therapy (PDT) utilizes the combined interaction of a photosensitizer, light and molecular oxygen to ablate tumor tissue. Maximizing the accumulation of the photosensitizer protoporphyrin IX (PpIX) within different cell types would be clinically useful. Dermatological PpIX‐induced PDT regimes produce good clinical outcomes but this currently only applies when the lesion remains superficial. Also, as an adjuvant therapy for the treatment of primary brain tumors, fluorescence guided resection (FGR) and PDT can be used to highlight and destroy tumor cells unreachable by surgical resection. By employing iron chelators PpIX accumulation can be enhanced. Two iron‐chelating agents, 1,2‐diethyl‐3‐hydroxypyridin‐4‐one hydrochloride (CP94) and dexrazoxane, were individually combined with the porphyrin precursors aminolevulinic acid (ALA), methyl aminolevulinate (MAL) and hexyl aminolevulinate (HAL). Efficacies of the iron‐chelating agents were compared by recording the PpIX fluorescence in human squamous epithelial carcinoma cells (A431) and human glioma cells (U‐87 MG) every hour for up to 6 h. Coincubation of ALA/MAL/HAL with CP94 resulted in a greater accumulation of PpIX compared to that produced by coincubation of these congeners with dexrazoxane. Therefore the clinical employment of iron chelation, particularly with CP94 could potentially increase and/or accelerate the accumulation of ALA/MAL/HAL‐induced PpIX for PDT or FGR.
Differentiating between intra‐ and extracellular chemiluminescence in diluted whole‐blood samples
Authors: RÁJECKÝ M. , LOJEK A. , ČÍŽ M.
Published: August 2011

Introduction:  The differentiation between extra‐ and intracellular production of reactive oxygen species (ROS) in whole blood was measured by luminol‐ and isoluminol‐enhanced chemiluminescence (CL).

Methods:  Azide (total CL inhibition), azide + horseradish peroxidase (HRP, restoring extracellular CL), superoxide dismutase + catalase (depleting extracellular ROS) and HRP (enhancing extracellular CL) were used to modulate luminol‐ and isoluminol‐enhanced CL (10−6–10−3 m luminophores) of 125× diluted whole blood which was activated by both calcium ionophore A23187 (Ca‐I) and opsonized zymosan particles (OZP) separately.

Results:  Both activators stimulated intra‐ and extracellular production of ROS. Luminol‐enhanced CL of Ca‐I‐activated samples detected the intracellular ROS, and with the addition of HRP detected the extracellular CL as well. CL enhanced with isoluminol in concentrations of 10−4 m or less was mostly extracellular. There was a mixture of intra‐ and extracellular CL in OZP‐activated samples, probably because of the ingestion of luminophore molecules.

Conclusion:  Measurement of Ca‐I‐activated CL enhanced with 10−4 m luminol is recommended for the detection of intracellular ROS. The addition of HRP leads to the detection of overall ROS production while the OZP‐activated system with its addition of HRP can only be used to detect overall ROS production. Ca‐I‐activated CL enhanced with 10−4 m isoluminol and with addition of HRP is recommended for the detection of extracellular CL.
Individual Psychological Assessment: A Core Competency for Industrial–Organizational Psychology
Authors: Jeanneret Richard , Silzer Rob
Published: August 2011

Individual Psychological Assessment is widely practiced among I–O psychologists and supported as a core competency by a majority of the commentaries. Our response addresses some of the key points made in the commentaries, such as issues related to the definition, contextual and criterion variables, interpretation and integration methods, validity evidence, professional matters, and future research directions. We also respond to a few critics who want to entirely eliminate expert assessor judgment in IPAs. Models are presented for using assessor judgment and mechanical methods in IPAs and for distinguishing naïve and sophisticated IPA researchers and practitioners. We conclude that IPA is now widely accepted as a core part of I–O psychology.
Kinds of Learning and the Likelihood of Future True Beliefs: Reply to Jäger on Reliabilism and the Value Problem
Authors: OLSSON ERIK J. , JÖNSSON MARTIN L.
Published: August 2011

We reply to Christoph Jäger's criticism of the conditional probability solution (CPS) to the value problem for reliabilism due to Goldman and Olsson (2009). We argue that while Jäger raises some legitimate concerns about the compatibility of CPS with externalist epistemology, his objections do not in the end reduce the plausibility of that solution.
Brazilian Clinical Trials Registry and the challenges for clinical research governance
Authors: Laguardia Josué , Piolli Alessandro Luís , Prevot Margareth , Ramalho Luciano , Gamarski Ricardo , Nishizawa Claudio
Published: August 2011

Over the past five years, efforts to set up a Brazilian clinical trials registry have progressed from early discussions in academic forums through to the establishment of the registry as a web‐based computer platform. This article describes the process of developing and introducing the Brazilian Clinical Trials Registry (ReBEC), and its relationship with the authorities that regulate clinical research in Brazil. The Brazilian Clinical Trials Registry and the multilingual, free and open source, internet‐based software developed to manage it are outcomes of partnerships among Brazilian federal and international health agencies. Information for describing the technical and operational dimensions of Rebec was drawn from technical documents and the records of the OpenTrials software development team and the ReBEC executive and advisory committees, which are available in free‐access repositories. The Brazilian Clinical Trials Registry was launched in December 2010, and approved as a primary registry of the WHO ICTRP network in April 2011. ReBEC's arrival on‐line and its acceptance as an ICTRP primary registry is a significant step in consolidating a policy of free access to information on clinical research in Brazil.
Detection of Atherosclerosis Through Mapping Skin Temperature Variation Caused by Carotid Atherosclerosis Plaques
Authors: Yang Yang , Liu Jing
Published: August 2011

This paper reports the effects of atherosclerosis plaque on the human cervicum skin surface temperature. The classical Pennes bioheat equation and a 3-D model consisting of cervical vertebra, muscle, and skin layer is adopted to characterize the heat transfer in the cervicum. Since the formation of atherosclerotic plaque is random, several parametric analyses are conducted to simulate actual situations. A medical far-infrared thermal imaging system is employed on two healthy human subjects to evaluate the feasibility of this technique. According to the simulations, there are variations in the temperature contours on the surface of the skin due to the axial variations in thermal parameters between healthy arterial intimae and atherosclerosis plaque. This suggests that far-infrared thermal imaging can be used to detect the marker safely via a noncontact way. Additional parametric studies indicated that the cervicum skin surface temperature distribution discloses the information regarding the plaque such as position, depth, pattern, quantity, and metabolic heat generation, etc. Furthermore, the external thermal conditions and calm physiological state can be implemented to enhance the detection of the plaque via mapping skin temperature. To test this strategy, a far-infrared imaging system was applied to record the dynamic thermal pictures on the cervicum of two human subjects, and the intentional cooling by the alcohol was proposed to improve detection. The thermograph reveals the surface effects of the main blood vessel and organs in the cervicum. The present study sets up a theoretical foundation for using noncontact far-infrared imaging method for a reliable assessment of atherosclerosis plaque without causing any wound or radiation to human body.
A Novel Paradigm for the Qualitative Synthesis of Simple Kinematic Chains Based on Complexity Measures
Authors: Khan Waseem A. , Angeles Jorge
Published: August 2011

Proposed in this paper is a paradigm for the qualitative synthesis of simple kinematic chains that is based on the concept of complexity. Qualitative synthesis is understood here as the number and the type stages of the kinematic-synthesis process. The formulation hinges on the geometric complexity of the surface associated with lower kinematic pairs. First, the geometric complexity of curves and surfaces is recalled, as defined via the loss of regularity (LOR). The LOR, based in turn on the concept of diversity, measures the spectral richness of the curvature of either the curve or the surface under study. The paper closes with a complexity analysis of all six lower kinematic pairs, as a means to guide the mechanical designer into the conceptual stage of the design process. The paradigm is illustrated with the computation of the complexity of the four-bar linkage in all its versions, planar, spherical, and spatial, as well as that of a transmission for the conversion of a rotation about a vertical axis into one about a horizontal axis.
Clinical accuracy of ExacTrac intracranial frameless stereotactic system
Authors: Ackerly T. , Lancaster C. M. , Geso M. , Roxby K. J.
Published: August 2011

Purpose:

In this paper, the authors assess the accuracy of the Brainlab ExacTrac system for frameless intracranial stereotactic treatments in clinical practice.

Methods:

They recorded couch angle and image fusion results (comprising lateral, longitudinal, and vertical shifts, and rotation corrections about these axes) for 109 stereotactic radiosurgery and 166 stereotactic radiotherapy patient treatments. Frameless stereotactic treatments involve iterative 6D image fusion corrections applied until the results conform to customizable pass criteria, theirs being 0.7 mm and 0.5° for each axis. The planning CT slice thickness was 1.25 mm. It has been reported in the literature that the CT slices' thickness impacts the accuracy of localization to bony anatomy. The principle of invariance with respect to patient orientation was used to determine spatial accuracy.

Results:

The data for radiosurgery comprised 927 image pairs, of which 532 passed (pass ratio of 57.4%). The data for radiotherapy comprised 15983 image pairs, of which 10 050 passed (pass ratio of 62.9%). For stereotactic radiotherapy, the combined uncertainty of ExacTrac calibration, image fusion, and intrafraction motion was (95% confidence interval) 0.290–0.302 and 0.306–0.319 mm in the longitudinal and lateral axes, respectively. The combined uncertainty of image fusion and intrafraction motion in the anterior‐posterior coordinates was 0.174–0.182 mm. For stereotactic radiosurgery, the equivalent ranges are 0.323–0.393, 0.337–0.409, and 0.231–0.281 mm. The overall spatial accuracy was 1.24 mm for stereotactic radiotherapy (SRT) and 1.35 mm for stereotactic radiosurgery (SRS).

Conclusions:

The ExacTrac intracranial frameless stereotactic system spatial accuracy is adequate for clinical practice, and with the same pass criteria, SRT is more accurate than SRS. They now use frameless stereotaxy exclusively at their center.
Role for the Membrane Receptor Guanylyl Cyclase-C in Attention Deficiency and Hyperactive Behavior
Authors: Gong Rong , Ding Cheng , Hu Ji , Lu Yao , Liu Fei , Mann Elizabeth , Xu Fuqiang , Cohen Mitchell B. , Luo Minmin
Published: August 2011

A receptor for gut hormones also functions in the brain, where its loss affects attention.
Coherent Two-Dimensional Nanoscopy
Authors: Aeschlimann Martin , Brixner Tobias , Fischer Alexander , Kramer Christian , Melchior Pascal , Pfeiffer Walter , Schneider Christian , Strüber Christian , Tuchscherer Philip , Voronine Dmitri V.
Published: August 2011

Coherent electronic states excited by ultrafast laser pulses were imaged at subwavelength resolution with photoelectrons.
Effect of Light Intensity on the Relative Dominance of Toxigenic and Nontoxigenic Strains of Microcystis aeruginosa
Authors: LeBlanc Renaud Susan , Pick Frances R. , Fortin Nathalie
Published: August 2011

In aquatic ecosystems, the factors that regulate the dominance of toxin-producing cyanobacteria over non-toxin-producing strains of the same species are largely unknown. One possible hypothesis is that limiting resources lead to the dominance of the latter because of the metabolic costs associated with toxin production. In this study, we tested the effect of light intensity on the performance of a microcystin-producing strain of
Microcystis aeruginosa
(UTCC 300) when grown in mixed cultures with non-microcystin-producing strains with similar intrinsic growth rates (UTCC 632 and UTCC 633). The endpoints measured included culture growth rates, microcystin concentrations and composition, and
mcyD
gene copy numbers determined using quantitative PCR (Q-PCR). In contrast to the predicted results, under conditions of low light intensity (20 μmol·m
−2
·s
−1
), the toxigenic strain became dominant in both of the mixed cultures based on gene copy numbers and microcystin concentrations. When grown under conditions of high light intensity (80 μmol·m
−2
·s
−1
), the toxigenic strain still appeared to dominate over nontoxigenic strain UTCC 632 but less so over strain UTCC 633. Microcystins may not be so costly to produce that toxigenic cyanobacteria are at a disadvantage in competition for limiting resources.
flaB
Gene as a Molecular Marker for Distinct Identification of Borrelia Species in Environmental Samples by the PCR-Restriction Fragment Length Polymorphism Method
Authors: Wodecka Beata
Published: August 2011

A new protocol employing nested PCR-restriction fragment length polymorphism (RFLP) based on the
flaB
gene and two restriction enzymes was worked out. This protocol allows the identification of all
Borrelia
species transmitted by
Ixodes ricinus
in Europe, including
Borrelia miyamotoi
and 3 genetic variants of
B. garinii
. A dendrogram of
flaB
sequence similarity was in accordance with RFLP variants.
Biodiversity of Active and Inactive Bacteria in the Gut Flora of Wood-Feeding Huhu Beetle Larvae (Prionoplus reticularis)
Authors: Reid Nicola M. , Addison Sarah L. , Macdonald Lucy J. , Lloyd-Jones Gareth
Published: August 2011

Huhu grubs (Prionoplus reticularis) are wood-feeding beetle larvae endemic to New Zealand and belonging to the family Cerambycidae. Compared to the wood-feeding lower termites, very little is known about the diversity and activity of microorganisms associated with xylophagous cerambycid larvae. To address this, we used pyrosequencing to evaluate the diversity of metabolically active and inactive bacteria in the huhu larval gut. Our estimate, that the gut harbors at least 1,800 phylotypes, is based on 33,420 sequences amplified from genomic DNA and reverse-transcribed RNA. Analysis of genomic DNA- and RNA-derived data sets revealed that 71% of all phylotypes (representing 95% of all sequences) were metabolically active. Rare phylotypes contributed considerably to the richness of the community and were also largely metabolically active, indicating their participation in digestive processes in the gut. The dominant families in the active community (RNA data set) includedAcidobacteriaceae(24.3%),Xanthomonadaceae(16.7%),Acetobacteraceae(15.8%),Burkholderiaceae(8.7%), andEnterobacteriaceae(4.1%). The most abundant phylotype comprised 14% of the active community and affiliated withDyella ginsengisoli(Gammaproteobacteria), suggesting that aDyella-related organism is a likely symbiont. This study provides new information on the diversity and activity of gut-associated microorganisms that are essential for the digestion of the nutritionally poor diet consumed by wood-feeding larvae. Many huhu gut phylotypes affiliated with insect symbionts or with bacteria present in acidic environments or associated with fungi.
Molecular Enumeration of an Ecologically Important Cyanophage in a Laurentian Great Lake
Authors: Matteson Audrey R. , Loar Star N. , Bourbonniere Richard A. , Wilhelm Steven W.
Published: August 2011

Considerable research has shown that cyanobacteria and the viruses that infect them (cyanophage) are pervasive and diverse in global lake populations. Few studies have seasonally analyzed freshwater systems, and little is known about the bacterial and viral communities that coexist during the harsh winters of the Laurentian Great Lakes. Here, we employed quantitative PCR to estimate the abundance of cyanomyoviruses in this system, using the portal vertex
g20
gene as a proxy for cyanophage abundance and to determine the potential ecological relevance of these viruses. Cyanomyoviruses were abundant in both the summer and the winter observations, with up to 3.1 × 10
6
copies of
g20
genes ml
−1
found at several stations and depths in both seasons, representing up to 4.6% of the total virus community. Lake Erie was productive during both our observations, with high chlorophyll
a
concentrations in the summer (up to 10.3 μg liter
−1
) and winter (up to 5.2 μg liter
−1
). Both bacterial and viral abundances were significantly higher during the summer than during the winter (
P
< 0.05). Summer bacterial abundances ranged from 3.3 × 10
6
to 1.6 × 10
7
ml
−1
while winter abundances ranged between ∼3.4 × 10
5
and 1.2 × 10
6
ml
−1
. Total virus abundances were high during both months, with summer abundances significantly higher at most stations, ranging from 6.5 × 10
7
to 8.8 × 10
7
ml
−1
, and with winter abundances ranging from 3.4 × 10
7
to 6.6 × 10
7
ml
−1
. This work confirms that putative cyanomyoviruses are ubiquitous in both summer and winter months in this large freshwater lake system and that they are an abundant component of the virioplankton group.
Toward Improvement of Erythromycin A Production in an IndustrialSaccharopolyspora erythraea Strain via Facilitation of Genetic Manipulation with an Artificial
attB
Site for Specific Recombination
Authors: Wu Jiequn , Zhang Qinglin , Deng Wei , Qian Jiangchao , Zhang Siliang , Liu Wen
Published: August 2011

Large-scale production of erythromycin A (Er-A) relies on the organism
Saccharopolyspora erythraea
, in which lack of a typical
attB
site largely impedes the application of phage ΦC31 integrase-mediated recombination into site-specific engineering. We herein report construction of an artificial
attB
site in an industrial
S. erythraea
strain, HL3168 E3, in an effort to break the bottleneck previously encountered during genetic manipulation mainly from homologous or unpredictable nonspecific integration. Replacement of a cryptic gene,
nrps1-1
, with a cassette containing eight
attB
DNA sequences did not affect the high Er-producing ability, setting the stage for precisely engineering the industrial Er-producing strain for foreign DNA introduction with a reliable conjugation frequency. Transfer of either exogenous or endogenous genes of importance to Er-A biosynthesis, including the
S
-adenosylmethionine synthetase gene for positive regulation,
vhb
for increasing the oxygen supply, and two tailoring genes,
eryK
and
eryG
, for optimizing the biotransformation at the late stage, was achieved by taking advantage of this facility, allowing systematic improvement of Er-A production as well as elimination of the by-products Er-B and Er-C in fermentation. The strategy developed here can generally be applicable to other strains that lack the
attB
site.
Unexpected Role for a Serine/Threonine-Rich Domain in the Candida albicans Iff Protein Family
Authors: Boisramé Anita , Cornu Amandine , Da Costa Grégory , Richard Mathias L.
Published: August 2011

Glycosylphosphatidylinositol (GPI)-anchored proteins are an important class of cell wall proteins in
Candida albicans
because of their localization and their function, even if more than half of them have no characterized homolog in the databases. In this study, we focused on the IFF protein family, investigating their exposure on the cell surface and the sequences that determine their subcellular localization. Protein localization and surface exposure were monitored by the addition of a V5 tag on all members of the family. The data obtained using the complete proteins showed for Iff3 (or -9), Iff5, Iff6, and Iff8 a covalent linkage to the β-1,6-glucan network but, remarkably, showed that Iff2/Hyr3 was linked through disulfide bridges or NaOH-labile bonds. However, since some proteins of the Iff family were undetectable, we designed chimeric constructions using the last 60 amino acids of these proteins to test the localization signal. These constructions showed a β-1,6-glucan linkage for Iff1/Rbr3, Iff2/Hyr3, Iff4 and Iff7/Hyr4 C-terminal–Iff5 fusion proteins, and a membrane localization for the Iff10/Flo9 C terminus-Iff5 fusion protein. Immunofluorescence analyses coupled to these cell fraction data confirmed the importance of the length of the central serine/threonine-rich region for cell surface exposure. Further analysis of the Iff2/Hyr3 linkage to the cell surface showed for the first time that a serine/threonine central region of a GPI-anchored protein may be responsible for the disulfide and the NaOH bonds to the glucan and glycoproteins network and may also override the signal of the proximal ω site region.
Mitochondrial Genomic Dysfunction Causes Dephosphorylation of Sch9 in the Yeast Saccharomyces cerevisiae
Authors: Kawai Shigeyuki , Urban Jörg , Piccolis Manuele , Panchaud Nicolas , De Virgilio Claudio , Loewith Robbie
Published: August 2011

TORC1-dependent phosphorylation of
Saccharomyces cerevisiae
Sch9 was dramatically reduced upon exposure to a protonophore or in respiration-incompetent ρ
0
cells but not in respiration-incompetent
pet
mutants, providing important insight into the molecular mechanisms governing interorganellar signaling in general and retrograde signaling in particular.
Candida albicans
SRR1
, a Putative Two-Component Response Regulator Gene, Is Required for Stress Adaptation, Morphogenesis, and Virulence
Authors: Desai Chirayu , Mavrianos John , Chauhan Neeraj
Published: August 2011

We report here the identification and characterization of a previously uncharacterized, two-component response regulator gene (orf19.5843) from
Candida albicans
. Because of its apparent functions in stress adaptation, we have named this gene
SRR1
(
s
tress
r
esponse
r
egulator 1). Disruption of
SRR1
causes defects in hyphal development, reduced resistance to stress, and severe virulence attenuation in the mouse model of disseminated candidiasis.
Gulosibacter molinativorax ON4
T
Molinate Hydrolase, a Novel Cobalt-Dependent Amidohydrolase
Authors: Duarte Márcia , Ferreira-da-Silva Frederico , Lünsdorf Heinrich , Junca Howard , Gales Luís , Pieper Dietmar H. , Nunes Olga C.
Published: August 2011

A new pathway of molinate mineralization has recently been described. Among the five members of the mixed culture able to promote such a process,
Gulosibacter molinativorax
ON4
T
has been observed to promote the initial breakdown of the herbicide into ethanethiol and azepane-1-carboxylate. In the current study, the gene encoding the enzyme responsible for molinate hydrolysis was identified and heterologously expressed, and the resultant active protein was purified and characterized. Nucleotide sequence analysis revealed that the gene encodes a 465-amino-acid protein of the metal-dependent hydrolase A subfamily of the amidohydrolase superfamily with a predicted molecular mass of 50.9 kDa. Molinate hydrolase shares the highest amino acid sequence identity (48 to 50%) with phenylurea hydrolases of
Arthrobacter globiformis
and
Mycobacterium brisbanense
. However, in contrast to previously described members of the metal-dependent hydrolase A subfamily, molinate hydrolase contains cobalt as the only active-site metal.
Lipoarabinomannan Localization and Abundance during Growth of Mycobacterium smegmatis
Authors: Dhiman Rakesh K. , Dinadayala Premkumar , Ryan Gavin J. , Lenaerts Anne J. , Schenkel Alan R. , Crick Dean C.
Published: August 2011

Lipoarabinomannan (LAM) is a structurally heterogeneous amphipathic lipoglycan present inMycobacteriumspp. and other actinomycetes, which constitutes a major component of the cell wall and exhibits a wide spectrum of immunomodulatory effects. Analysis ofMycobacterium smegmatissubcellular fractions and spheroplasts showed that LAM and lipomannan (LM) were primarily found in a cell wall-enriched subcellular fraction and correlated with the presence (or absence) of the mycolic acids in spheroplast preparations, suggesting that LAM and LM are primarily associated with the putative outer membrane of mycobacteria. During the course of these studies significant changes in the LAM/LM content of the cell wall were noted relative to the age of the culture. The LAM content of theM. smegmatiscell wall was dramatically reduced as the bacilli approached stationary phase, whereas LM, mycolic acid, and arabinogalactan content appeared to be unchanged. In addition, cell morphology and acid-fast staining characteristics showed variations with growth phase of the bacteria. In the logarithmic phase, the bacteria were found to be classic rod-shaped acid-fast bacilli, while in the stationary phaseM. smegmatislost the characteristic rod shape and developed a punctate acid-fast staining pattern with carbolfuchsin. The number of viable bacteria was independent of LAM content and phenotype. Taken together, the results presented here suggest that LAM is primarily localized with the mycolic acids in the cell wall and that the cellular concentration of LAM inM. smegmatisis selectively modulated with the growth phase.
Negative Effect of Glucose onompAmRNA Stability: a Potential Role of Cyclic AMP in the Repression ofhfqin Escherichia coli
Authors: Lin Hsiao-Hsien , Hsu Chi-Cheng , Yang Chi-Dung , Ju Yih-Wei , Chen Yi-Pei , Tseng Ching-Ping
Published: August 2011

Glucose is a carbon source that is capable of modulating the level of cyclic AMP (cAMP)-regulated genes. In the present study, we found that the stability ofompAmRNA was reduced inEscherichia coliwhen glucose (40 mM) was present in Luria-Bertani (LB) medium. This effect was associated with a low level of cAMP induced by the glucose. The results were confirmed with an adenylyl cyclase mutant with low levels of cAMP that are not modulated by glucose. Northern blot and Western blot analyses revealed that the host factor I (Hfq) (both mRNA and protein) levels were downregulated in the presence of cAMP. Furthermore, we showed that a complex of cAMP receptor protein (CRP) and cAMP binds to a specific P3hfqpromoter region ofhfqand regulateshfqexpression. The regulation of thehfqgene was confirmedin vivousing anhfq-deficient mutant transformed with an exogenoushfqgene containing the promoter. These results demonstrated that expression ofhfqwas repressed by the CRP-cAMP complex. The presence of glucose resulted in increased Hfq protein levels, which decreasedompAmRNA stability. An additional experiment showed that cAMP also increased the stability offurmRNA. Taken together, these results suggested that the repression of Hfq by cAMP may contribute to the stability of other mRNA inE. coli.
The Biofilm Inhibitor Carolacton Disturbs Membrane Integrity and Cell Division of Streptococcus mutans through the Serine/Threonine Protein Kinase PknB
Authors: Reck Michael , Rutz Katrin , Kunze Brigitte , Tomasch Jürgen , Surapaneni Subhash Kumar , Schulz Stefan , Wagner-Döbler Irene
Published: August 2011

Carolacton, a secondary metabolite isolated from the myxobacterium
Sorangium cellulosum
, disturbs
Streptococcus mutans
biofilm viability at nanomolar concentrations. Here we show that carolacton causes leakage of cytoplasmic content (DNA and proteins) in growing cells at low pH and provide quantitative data on the membrane damage. Furthermore, we demonstrate that the biofilm-specific activity of carolacton is due to the strong acidification occurring during biofilm growth. The chemical conversion of the ketocarbonic function of the molecule to a carolacton methylester did not impact its activity, indicating that carolacton is not functionally activated at low pH by a change of its net charge. A comparative time series microarray analysis identified the VicKRX and ComDE two-component signal transduction systems and genes involved in cell wall metabolism as playing essential roles in the response to carolacton treatment. A sensitivity testing of mutants with deletions of all 13 viable histidine kinases and the serine/threonine protein kinase PknB of
S. mutans
identified only the Δ
pknB
deletion mutant as being insensitive to carolacton treatment. A strong overlap between the regulon of PknB in
S. mutans
and the genes affected by carolacton treatment was found. The data suggest that carolacton acts by interfering with PknB-mediated signaling in growing cells. The resulting altered cell wall morphology causes membrane damage and cell death at low pH.
Long-Chain
N
-Acyl Amino Acid Synthases Are Linked to the Putative PEP-CTERM/Exosortase Protein-Sorting System in Gram-Negative Bacteria
Authors: Craig Jeffrey W. , Cherry Marisa A. , Brady Sean F.
Published: August 2011

Clones that encode the biosynthesis of long-chain
N
-acyl amino acids are frequently recovered from activity-based screens of soil metagenomic libraries. Members of a diverse set of enzymes referred to as
N
-acyl amino acid synthases are responsible for the production of all metagenome-derived
N
-acyl amino acids characterized to date. Based on the frequency at which
N
-acyl amino acid synthase genes have been identified from metagenomic samples, related genes are expected to be common throughout the global bacterial metagenome. Homologs of metagenome-derived
N
-acyl amino acid synthase genes are scarce, however, within the sequenced genomes of cultured bacterial species. Toward the goal of understanding the role(s) played by
N
-acyl amino acids in environmental bacteria, we looked for conserved genetic features that are positionally linked to metagenome-derived
N
-acyl amino acid synthase genes. This analysis revealed that
N
-acyl amino acid synthase genes are frequently found adjacent to genes predicted to encode PEP-CTERM motif-containing proteins and, in some cases, other conserved elements of the PEP-CTERM/exosortase system. Although relatively little is known about the PEP-CTERM/exosortase system, its core components are believed to represent the putative Gram-negative equivalent of the LPXTG/sortase protein-sorting system of Gram-positive bacteria. During the course of this investigation, we were able to provide evidence that an uncharacterized family of hypothetical acyltransferases, which had previously been linked to the PEP-CTERM/exosortase system by bioinformatics, is a new family of
N
-acyl amino acid synthases that is widely distributed among the PEP-CTERM/exosortase system-containing
Proteobacteria
.
Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough
Authors: Price Morgan N. , Deutschbauer Adam M. , Kuehl Jennifer V. , Liu Haichuan , Witkowska H. Ewa , Arkin Adam P.
Published: August 2011

We used high-resolution tiling microarrays and 5′ RNA sequencing to identify transcripts inDesulfovibrio vulgarisHildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed thatD. vulgarisprefers −10 and −35 boxes different from those preferred byEscherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5′ ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available athttp://genomics.lbl.gov/supplemental/DvHtranscripts2011/.
The crystal and molecular structure of tris(pentamethylenedithiocarbamate) chromium(III)-chloroform (1 : 2)
Authors: Kettman Viktor , Garaj Ján , Majer Jaroslav
Published: August 2011

The crystal and molecular structure of [Cr(S2CN(CH2)5)3].2 CHCl3 was found by the X-ray structural analysis method. The value R 0.090 was found for 1 131 observed independent reflections. The substance crystallizes in a space group of symmetry P212121 with the following unit cell dimensions: a = 0.8675 (6), b = 1.815(2), c = 2.155(3) nm. The experimentally observed crustal density was 1.48 Mgm-3 and the value calculated for Z = 4 was 1.51 Mgm-3. The CrS6 coordination polyhedron has the shape of a trigonally distorted octahedron, where the D3 symmetry is a approximately retained. The degree of trigonal distortion expressed as the projection of the chelate S-Cr-S angle onto the plane perpendicular to the C3 pseudo axis is Φ = 41.7° (Φ = 60° for an octahedron). The skeleton of the structure formed by the complex molecules contains channels filled with chloroform molecules. The specific type of complex-chloroform interaction consists of the formation of hydrogen bonds of the chloroform protons with the fully occupied pπ-orbitals of the sulphur atoms in the coordination polyhedra. The low stability and crystal decomposition can be explained by loss of chloroform from the channels.
Coulometry in resonator cavity of EPR spectrometer: Electrochemical oxidation of carbazole methyl derivatives
Authors: Kubáček Pavel
Published: August 2011

Electrochemical reduction of carbazole, 3-methyl- and 3,9-dimethylcarbazole in acetonitrile leads to the formation of a layer of conductive, insoluble products on the electrode surface of a partially radical character. This phenomenon was studied by coulometry in the resonator cavity of an EPR spectrometer with simultaneous measuring of the spin concentration. With carbazole and 3-methylcarbazole, the radical particles are formed with a yield of about 2% with respect to the current passed, whereas with 3,9-dimethylcarbazole this yield is by an order or magnitude lower. The radical product adsorbed on the electrode is probably a sparingly soluble perchlorate of the cation radical of 3,3'- or 6,6'-bicarbazole. 3,6,9-Trimethylcarbazole gives on oxidation a relatively stable primary cation radical. Electrochemical oxidation of 9-methyl- and 3,6-dimethylcarbazole does not lead to radical products.
Gradual exposure of cystine side-chain residues during urea denaturation of human serum albumin
Authors: Chmelík Josef , Kadleček Jiří , Kalous Vítěz
Published: August 2011

Showing the accessibility of disulfide groups in the protein molecule, the polarographic catalytic hydrogen current (Brdicka current) was employed for the investigation of the urea denaturation of human serum albumin. The stepwise character of the denaturation curve was accounted for the gradual conformational changes of the protein molecule and related increasing accessibility of cystine side-chain residues.
Modelling of catalytic activity of transition metals in hydrogenolysis of ethane by the pattern recognition approach
Authors: Štrouf Oldřich , Fusek Jiří , Kuchynka Karel
Published: August 2011

For modelling the catalytic activity in hydrogenolysis of ethane, thirty transition metals were characterized by a set of fifteen fundamental physical variables for each of them. The dimensionality reduction of this physical model up to the dimensionality seven was carried out by the determination of seven linearly almost independent variables. This set was used for the definition of the class of catalytically active metals on the basis of their similarity using an asymmetric (one-class) pattern recognition approach. The values of similarity measure were approximated by the polynominal function of the second degree which is accounted for as a mathematical representation of the structure of the active class.
Mass transfer between a moving gas stream and single particles of some important sorbents for sulphur dioxide
Authors: Hartman Miloslav , Svoboda Karel
Published: August 2011

For the particles of calcium oxide and active sodium carbonate an effect of mass transfer is explored on the overall rate of their reactions with sulphur dioxide. The results of a simple analysis show that the mass transfer resistance in the gas phase cannot be neglected. The extraordinary reactivity of active sodium carbonate can be fully utilized only in such contactors where very high rates of mass transfer are ensured.
Kinetics of secondary nucleation with attrition and the mean size of product crystals from the continuous stirred crystalliser
Authors: Nývlt Jaroslav
Published: August 2011

A form of kinetic equation of nucleation has been proposed expressing also the mechanism of attrition of crystals. In limiting cases this equation expresses the secondary nucleation due to attrition or caused by other mechanisms while both limit expressions are quite different. The resulting relation enables correlation of experimental data also in the case when it is not possible to neglect any of the mentioned phenomena. Relation has been derived for the mean size of product crystals from the MSMPR (mixed suspension, mixed product removal) crystalliser showing that in cases with the prevailing attrition of crystals it might be advantageous to operate at a larger crystalliser output i.e. with a shorter residence time of crystals in the unit.