bluuebunny/crossref_metadata_2025 huggingface dataset:
Otomycosis: Clinical features and treatment implications
Authors: Ho Tang , Vrabec Jeffrey T. , Yoo Donald , Coker Newton J.
Published: October 2006

OBJECTIVES

To determine the clinical presentation, predisposing factors, complications, and treatment outcomes of otomycosis.

STUDY DESIGN AND SETTING

Retrospective review of 132 patients with a clinical diagnosis of otomycosis treated from 1998 to 2004 in an academic otology practice.

RESULTS

Otalgia and otorrhea were the most common presenting complaints (48%). Prior otologic procedures increase the risk of developing otomycosis. Residual disease was observed in 13% and recurrence in 15% of the subjects. The presence of a mastoid cavity was associated with higher recurrent and residual disease rates. Topical ketoconazole, cresylate otic drops, and aluminum acetate otic drops were all relatively effective with >80% resolution rate on initial application, although topical ketoconazole had a higher resolution rate and lower rate of disease recurrence.

CONCLUSIONS AND SIGNIFICANCE

Otomycosis can usually be diagnosed by clinical examination and often occurs in the setting of persistent otorrhea. Complications are not uncommon but usually resolve with application of appropriate topical antifungal agents. Eradication of disease is more difficult in the presence of a mastoid cavity.
Factors influencing intraoral removal of submandibular calculi
Authors: Park June Sik , Sohn Jin Ho , Kim Jeong Kyu
Published: October 2006

OBJECTIVES

To assess the effectiveness of intraoral removal of submandibular calculi based on several factors that may influence the results of surgery.

STUDY DESIGN AND SETTING

We retrospectively reviewed 172 patients who underwent intraoral removal of submandibular sialolithiasis. Results of surgery were divided into complete removal, partial removal, and failure. The effect of location, palpability, size, and presence of infection of the calculi on the results was estimated.

RESULTS

Univariate analysis showed that palpability and presence of infection were statistically significant factors affecting intraoral removal. Palpability was the only significant factor after multivariate analysis. Twelve of 13 patients with recurrent calculi underwent repeat intraoral removal successfully.

CONCLUSIONS

The palpability of submandibular calculi is the most important factor influencing their successful intraoral removal.

SIGNIFICANCE

Intraoral removal can be performed successfully regardless of location, size, presence of infection, or recurrence of calculi, if the calculi are palpable.
China’s economic integration into global regulatory frameworks: A study of government procurement
Authors: Chou Bill K.P.
Published: October 2006

This paper examines the extent of China’s integration in the global economy and its ability to implement the WTO commitments by using government procurement as a case study. This paper argues that the domestic framework of government procurement has been gradually harmonized with the WTO commitments. Full implementation of the commitments has been constrained by several factors: policy elites consider government procurement to be a drive of cost saving and against corruption instead of a policy of spurring trade liberalization. There are still significant discrepancies between the domestic and international regulatory frameworks. Besides that, the implementation contradicts the policy priorities of local state actors on whom the policy of elites heavily depend for success. The Chinese government’s capacity in enforcing international agreements has further been undermined by the structural problems of the administration.
Panel reviews NASA science plan
Authors: Kumar Mohi
Published: October 2006

The draft science plan of the NASA Science Mission Directorate lacks a clear strategy, and the agency may need to either abandon flagship missions or the ability to execute a balanced program due to rising costs, according to a 15 September report by the U.S. National Research Council.

Carl Wunsch, a member of the committee that authored the report and an oceanographer at the Massachusetts Institute of Technology, said that cutbacks and mission cancellations announced by NASA have led to “a general worry that the plan might be just a paper document. [The plan] does not really talk in any way about what implementation would cost or what has been dropped from earlier such plans.”
U.S. weather satellite program over budget
Authors: Zielinski Sarah
Published: October 2006

Because the next generation of U.S. weather satellites, the Geostationary Environmental Operational Satellite Series‐R (GOES‐R), would run several billion dollars over budget if constructed as originally planned, the U.S. National Oceanic and Atmospheric Administration (NOAA) will cancel development of at least one advanced sensor and is considering other options that would reduce costs, NOAA Administrator Conrad Lautenbacher, Jr., testified at a 29 September hearing before the U.S. House of Representatives Committee on Science.

GOES‐R would be the latest in a series of geostationary satellites that have been launched since the 1970s. NOAA currently operates two such satellites—one each over the U.S. east and west coasts—which provide images and oceanic, atmospheric, and climatic data over the continental United States and Hawaii. This information is used to forecast weather and provide warnings of severe weather.
Restoring Hetch Hetchy Valley: The role of modeling in policy
Authors: Null Sarah E. , Lund Jay R.
Published: October 2006

In 1923, following years of opposition and debate, the City of San Francisco, Calif., completed the O'Shaughnessy Dam, which flooded Hetch Hetchy Valley in California's Yosemite National Park. Today the future of Hetch Hetchy Valley is still debated.

Current discussion of restoring the valley has arisen within the state, and the idea of restoration has been largely supported by the use of system optimization and simulation modeling. Mathematical modeling provides thorough and systematic analysis of water supply systems and can suggest improvements to incorporate additional water uses or changing priorities. CALVIN (California Value Integrated Network),an economic‐engineering optimization model, was one of two models used to evaluate the water supply and hydro‐power implications of removing the O'Shaughnessy Dam [Null, 2003; Null and Lund, 2006].
Postischemic Gene Transfer of Soluble Flt-1 Protects against Brain Ischemia with Marked Attenuation of Blood—Brain Barrier Permeability
Authors: Kumai Yasuhiro , Ooboshi Hiroaki , Ibayashi Setsuro , Ishikawa Eiichi , Sugimori Hiroshi , Kamouchi Masahiro , Kitazono Takanari , Egashira Kensuke , Iida Mitsuo
Published: October 2006

Brain edema is a major and often mortal complication of brain ischemia. Vascular endothelial growth factor (VEGF) is also known as a potent vascular permeability factor and may play detrimental roles at the acute stage of brain infarction. Our goal in this study was to explore protective effects of gene transfer of soluble flt-1 (sFlt-1), a natural inhibitor of VEGF, on focal brain ischemia. Adenoviral vector encoding sFlt-1 or β-galactosidase as control was injected into the lateral ventricle 90 mins after photochemical distal middle cerebral artery occlusion in male spontaneously hypertensive rats. The transduced sFlt-1 was released to the cerebrospinal fluid from the ventricular wall and significantly increased 6 h, 1 and 7 days after sFlt-1 transfection. One day after brain ischemia, sFlt-1 gene transfer significantly reduced infarct volume (by 35%), brain edema (by 35%), and blood—brain barrier permeability (Evans blue extravasation; by 69%) with diminished phosphorylation of focal adhesion kinase (FAKtyr397 and FAKtyr861) in the ischemic vessels. Seven days after ischemia, sFlt-1 gene transfer also significantly attenuated infarct volume (by 29%) and monocyte/macrophage infiltration (by 27%), although there were no reductions in angiogenesis by sFlt-1 overexpression. These results suggest that sFlt-1 gene therapy targeting brain edema in acute stage of brain ischemia may be useful for brain infarction.
CLA-1 and its splicing variant CLA-2 mediate bacterial adhesion and cytosolic bacterial invasion in mammalian cells
Authors: Vishnyakova Tatyana G. , Kurlander Roger , Bocharov Alexander V. , Baranova Irina N. , Chen Zhigang , Abu-Asab Mones S. , Tsokos Maria , Malide Daniela , Basso Federica , Remaley Alan , Csako Gyorgy , Eggerman Thomas L. , Patterson Amy P.
Published: October 2006

CD36 and LIMPII analog 1, CLA-1, and its splicing variant, CLA-2 (SR-BI and SR-BII in rodents), are human high density lipoprotein receptors with an identical extracellular domain which binds a spectrum of ligands including bacterial cell wall components. In this study, CLA-1- and CLA-2-stably transfected HeLa and HEK293 cells demonstrated several-fold increases in the uptake of various bacteria over mock-transfected cells. All bacteria tested, including both Gram-negatives (
Escherichia coli
K12, K1 and
Salmonella typhimurium
) and Gram-positives (
Staphylococcus aureus
and
Listeria monocytogenes
), demonstrated various degrees of lower uptake in control cells. This result is consistent with the presence of high-density lipoprotein-receptor-independent bacterial uptake that is enhanced by CLA-1/CLA-2 overexpression. Bacterial lipopolysaccharides, lipoteichoic acid, and synthetic amphipathic helical peptides (L-37pA and D-37pA) competed with
E. coli
K12 for CLA-1 and CLA-2 binding. Transmission electron microscopy and confocal microscopy revealed cytosolic accumulation of bacteria in CLA-1/CLA-2-overexpressing HeLa cells. The antibiotic protection assay confirmed that
E. coli
K12 was able to survive and replicate intracellularly in CLA-1- and CLA-2-overexpressing HeLa, but both L-37pA and D-37pA prevented
E. coli
K12 invasion. Peritoneal macrophages isolated from SR-BI/BII-knockout mice demonstrated a 30% decrease in bacterial uptake when compared with macrophages from normal mice. Knockout macrophages were also characterized by decreased bacterial cytosolic invasion, ubiquitination, and proteasome mobilization while retaining bacterial lysosomal accumulation. These results indicate that, by facilitating bacterial adhesion and cytosolic invasion, CLA-1 and CLA-2 may play an important role in infection and sepsis.
Identification of a starter unit acyl-carrier protein transacylase domain in an iterative type I polyketide synthase
Authors: Crawford Jason M. , Dancy Blair C. R. , Hill Eric A. , Udwary Daniel W. , Townsend Craig A.
Published: October 2006

Polyketides are a class of natural products that exhibit a wide range of functional and structural diversity. They include antibiotics, immunosuppressants, antifungals, antihypercholesterolemics, and cytotoxins. Polyketide synthases (PKSs) use chemistry similar to fatty acid synthases (FASs), although building block variation and differing extents of reduction of the growing polyketide chain underlie their biosynthetic versatility. In contrast to the well studied sequential modular type I PKSs, less is known about how the iterative type I PKSs carry out and control chain initiation, elongation, folding, and cyclization during polyketide processing. Domain structure analysis of a group of related fungal, nonreducing PKSs has revealed well defined N-terminal domains longer than commonly seen for FASs and modular PKSs. Predicted structure of this domain disclosed a region similar to malonyl-CoA:acyl-carrier protein (ACP) transacylases (MATs). MATs play a key role transferring precursor CoA thioesters from solution onto FASs and PKSs for chain elongation. On the basis of site-directed mutagenesis, radiolabeling, and kinetics experiments carried out with individual domains of the norsolorinic acid PKS, we propose that the N-terminal domain is a starter unit:ACP transacylase (SAT domain) that selects a C
6
fatty acid from a dedicated yeast-like FAS and transfers this unit onto the PKS ACP, leading to the production of the aflatoxin precursor, norsolorinic acid. These findings could indicate a much broader role for SAT domains in starter unit selection among nonreducing iterative, fungal PKSs, and they provide a biochemical rationale for the classical acetyl “starter unit effect.”
Molecular interactions between
Tbx3
and
Bmp4
and a model for dorsoventral positioning of mammary gland development
Authors: Cho Kyoung-Won , Kim Jae-Young , Song Soo-Jin , Farrell Elizabeth , Eblaghie Maxwell C. , Kim Hee-Jin , Tickle Cheryll , Jung Han-Sung
Published: October 2006

The formation of the dorsoventral (DV) boundary is central to establishing the body plan in embryonic development. Although there is some information about how limbs are positioned along the DV axis and how DV skin color pattern is determined, the way in which mammary glands are positioned is unknown. Here we focus on
Bmp4
and
Tbx3
, a gene associated with ulnar-mammary syndrome, and compare their expression along the DV axis in relation to mammary gland initiation in mouse embryos.
Tbx3
is expressed in the mammary gland-forming region with
Tbx15
, a gene involved in a DV coat color being expressed more dorsally and
Bmp4
being expressed more ventrally. When
Tbx3
was overexpressed, formation of mammary gland epithelium was extended along the DV axis. In contrast, overexpression of
Bmp4
inhibited both
Tbx3
and
Tbx15
expression. In addition, when BMP signaling was inhibited by NOGGIN,
Lef1
expression was lost. Thus, we propose that mutual interactions between
Bmp4
and
Tbx3
determine the presumptive DV boundary and formation of mammary glands in early mouse embryogenesis. 1,19-Dioctadecyl-3,3,39,39-tetramethyl indocarbocyanine perchloride labeling experiments showed that cells associated with mammary glands originate more dorsally and then move ventrally. This finding, together with previous findings, suggests that the same DV boundary may not only position limbs and determine coat color but also position mammary glands. Furthermore,
Bmp
signaling appears to be a fundamental feature of DV patterning.
Disulfide cross-linking indicates that FlgM-bound and free σ
28
adopt similar conformations
Authors: Sorenson Margareta K. , Darst Seth A.
Published: October 2006

The dissociable σ subunit of bacterial RNA polymerase is required for the promoter-specific initiation of transcription. When bound to RNA polymerase, σ makes sequence-specific promoter contacts and plays a crucial role in DNA melting. In isolation, however, σ lacks significant promoter binding activity. In the crystal structure of the flagellar σ factor, σ
28
, bound to the anti-σ factor, FlgM, σ
28
adopts a compact conformation in which the promoter binding surfaces are occluded by interdomain contacts. To test whether σ
28
adopts this conformation in the absence of FlgM, we engineered a set of double cysteine mutants predicted to form interdomain disulfides in the conformation observed in the FlgM complex. We show that these disulfides form in both the presence and absence of FlgM. For two of the mutants, quantitative measurements of disulfide formation under equilibrium conditions suggest that the major solution conformation favors disulfide formation. The results indicate that the compact conformation of σ
28
observed in the σ
28
/FlgM structure is similar to the predominant conformation of free σ
28
in solution. This finding suggests that autoinhibition of DNA binding in free σ
28
is accomplished by steric occlusion of the promoter binding surfaces by interdomain interactions within the σ factor as well as by a suboptimal distance between the promoter −10 and −35 element binding determinants in σ
2
and σ
4
, respectively.
Mutation of TweedleD, a member of an unconventional cuticle protein family, alters body shape in
Drosophila
Authors: Guan Xiao , Middlebrooks Brooke W. , Alexander Sherry , Wasserman Steven A.
Published: October 2006

Body shape determination represents a critical aspect of morphogenesis. In the course of investigating body shape regulation in
Drosophila
, we have identified a dominant mutation,

TweedleD
1

(

TwdlD
1

), that alters overall dimensions at the larval and pupal stages. Characterization of the affected locus led to the discovery of a gene family that has 27 members in
Drosophila
and is found only among insects. Analysis of gene expression at the RNA and protein levels revealed gene-specific temporal and spatial patterns in ectodermally derived tissues. In addition, light microscopic studies of fluorescently tagged proteins demonstrated that Tweedle proteins are incorporated into larval cuticular structures. This demonstration that a mutation in a
Drosophila
cuticular protein gene alters overall morphology confirms a role for the fly exoskeleton in determining body shape. Furthermore, parallels between these findings and studies of cuticle collagen genes in
Caenorhabditis elegans
suggest that the exoskeleton influences body shape in diverse organisms.
Combinatorial methods for small-molecule placement in computational enzyme design
Authors: Lassila Jonathan Kyle , Privett Heidi K. , Allen Benjamin D. , Mayo Stephen L.
Published: October 2006

The incorporation of small-molecule transition state structures into protein design calculations poses special challenges because of the need to represent the added translational, rotational, and conformational freedoms within an already difficult optimization problem. Successful approaches to computational enzyme design have focused on catalytic side-chain contacts to guide placement of small molecules in active sites. We describe a process for modeling small molecules in enzyme design calculations that extends previously described methods, allowing favorable small-molecule positions and conformations to be explored simultaneously with sequence optimization. Because all current computational enzyme design methods rely heavily on sampling of possible active site geometries from discrete conformational states, we tested the effects of discretization parameters on calculation results. Rotational and translational step sizes as well as side-chain library types were varied in a series of computational tests designed to identify native-like binding contacts in three natural systems. We find that conformational parameters, especially the type of rotamer library used, significantly affect the ability of design calculations to recover native binding-site geometries. We describe the construction and use of a crystallographic conformer library and find that it more reliably captures active-site geometries than traditional rotamer libraries in the systems tested.
The 39-kDa poly(ADP-ribose) glycohydrolase ARH3 hydrolyzes
O-
acetyl-ADP-ribose, a product of the Sir2 family of acetyl-histone deacetylases
Authors: Ono Tohru , Kasamatsu Atsushi , Oka Shunya , Moss Joel
Published: October 2006

The silent information regulator 2 (Sir2) family of NAD-dependent
N
-acetyl-protein deacetylases participates in the regulation of gene silencing, chromatin structure, and longevity. In the Sir2-catalyzed reaction, the acetyl moiety of
N
-acetyl-histone is transferred to the ADP-ribose of NAD, yielding
O
-acetyl-ADP-ribose and nicotinamide. We hypothesized that, if
O
-acetyl-ADP-ribose were an important signaling molecule, a specific hydrolase would cleave the (
O
-acetyl)–(ADP-ribose) linkage. We report here that the poly(ADP-ribose) glycohydrolase ARH3 hydrolyzed
O
-acetyl-ADP-ribose to produce ADP-ribose in a time- and Mg
2+
-dependent reaction and thus could participate in two signaling pathways. This
O
-acetyl-ADP-ribose hydrolase belongs to a family of three structurally related 39-kDa ADP-ribose-binding proteins (ARH1–ARH3). ARH1 was reported to hydrolyze ADP-ribosylarginine, whereas ARH3 degraded poly(ADP-ribose). ARH3-catalyzed generation of ADP-ribose from
O
-acetyl-ADP-ribose was significantly faster than from poly(ADP-ribose). Like the degradation of poly(ADP-ribose) by ARH3, hydrolysis of
O
-acetyl-ADP-ribose was abolished by replacement of the vicinal aspartates at positions 77 and 78 of ARH3 with asparagine. The rate of
O
-acetyl-ADP-ribose hydrolysis by recombinant ARH3 was 250-fold that observed with ARH1; ARH2 and poly(ADP-ribose) glycohydrolase were inactive. All data support the conclusion that the Sir2 reaction product
O
-acetyl-ADP-ribose is degraded by ARH3.
Sjögren's syndrome-like disease in mice with T cells lacking class 1A phosphoinositide-3-kinase
Authors: Oak Jean S. , Deane Jonathan A. , Kharas Michael G. , Luo Ji , Lane Thomas E. , Cantley Lewis C. , Fruman David A.
Published: October 2006

Sjögren's syndrome (SS) is an autoimmune disease that is characterized by infiltration of exocrine tissues, resulting in xerostomia (dry mouth) and keratoconjunctivitis sicca (dry eyes). Here, we show that mice with T cell-specific loss of class IA phosphoinositide 3-kinase function develop organ-specific autoimmunity that resembles the human disease SS. Most mutant mice aged 3–8 months develop corneal opacity and eye lesions due to irritation and constant scratching. These mice display cardinal signs of primary SS such as marked lymphocytic infiltration of the lacrimal glands, antinuclear antibodies in the serum, and elevated titer of anti-SS-A antibody, in the absence of kidney pathology. Immunofluorescence studies show the presence of numerous CD4+T cells with a smaller number of CD8+T cells and B cells in the lacrimal glands. CD4+T cells from these mice exhibit aberrant differentiationin vitro. These results indicate that aberrant T cells with impaired class IA phosphoinositide 3-kinase signaling can lead to organ-specific autoimmunity. In addition, the mouse model described here represents a tool to study the pathogenesis and treatment of SS.
Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen in
Arabidopsis thaliana
Authors: Danon Antoine , Sánchez Coll Núria , Apel Klaus
Published: October 2006

Programmed cell death (PCD) plays an important role during the life cycle of higher organisms. Although several regulatory mechanisms governing PCD are thought to be conserved in animals and plants, light-dependent cell death represents a form of PCD that is unique to plants. The light requirement of PCD has often been associated with the production of reactive oxygen species during photosynthesis. In support of this hypothesis, hydrogen peroxide and superoxide have been shown to be involved in triggering a PCD response. In the present work, we have used the conditional
flu
mutant of
Arabidopsis
to analyze the impact of another reactive oxygen species, singlet oxygen, on cell death. Unexpectedly, the light-dependent release of singlet oxygen alone is not sufficient to induce PCD of
flu
seedlings but has to act together with a second concurrent blue light reaction. This blue-light-specific trigger of PCD could not be attributed to a photosynthetic reaction or redox change within the chloroplast but to the activation of the blue light/UVA-specific photoreceptor cryptochrome. The singlet oxygen-mediated and cryptochrome-dependent cell death response differs in several ways from PCD triggered by hydrogen peroxide/superoxide.
Coupling of STIM1 to store-operated Ca
2+
entry through its constitutive and inducible movement in the endoplasmic reticulum
Authors: Baba Yoshihiro , Hayashi Kenji , Fujii Yoko , Mizushima Akiko , Watarai Hiroshi , Wakamori Minoru , Numaga Takuro , Mori Yasuo , Iino Masamitsu , Hikida Masaki , Kurosaki Tomohiro
Published: October 2006

Depletion of intracellular calcium (Ca
2+
) stores induces store-operated Ca
2+
(SOC) entry across the plasma membrane (PM). STIM1, a putative Ca
2+
sensor in the endoplasmic reticulum (ER), has been recently shown to be necessary for SOC channel activation. Here we show that STIM1 dynamically moves in tubulovesicular shape on the ER and its subcompartment in resting living cells, whereas, upon Ca
2+
store depletion, it is rapidly redistributed into discrete puncta that are located underneath, but not inserted into the PM. Normal constitutive movement of STIM1 is mediated through the coiled-coil and Ser/Thr-rich C-terminal domains in the cytoplasmic region of STIM1, whereas subsequent inducible puncta formation further requires the sterile α motif domain protruding into the ER lumen. Each of these three domains (coiled-coil, Ser/Thr-rich, and sterile α motif) was essential for activating SOC channels. Hence, our findings based on structure–function experiments suggest that constitutive dynamic movement of STIM1 in the ER and its subcompartment is obligatory for subsequent depletion-dependent redistribution of STIM1 into puncta underneath the PM and activation of SOC channels.
The Contributions of Strategy Use to Working Memory Span: A Comparison of Strategy Assessment Methods
Authors: Dunlosky John , Kane Michael J.
Published: October 2006

In two experiments, we tested whether individual differences in strategy production account for individual differences in performance on a working memory span task. We measured the strategies used during a standard experimenter-paced operation span (OSPAN) task by having participants make both set-by-set reports of strategy use for individual item sets and global reports of strategy use. In Experiment 1, although normatively effective strategies were self-reported on only a small proportion of OSPAN sets, individual differences in effective strategy use correlated with span performance. Experiment 2 replicated this outcome using a sample of 100 participants but, as important, it demonstrated that individual differences in effective strategy use did not mediate the relationship between OSPAN and measures of verbal ability. Discussion focuses on the interpretation of strategy–span relationships and the relative utility of general reports of strategy use versus the set-by-set reports introduced here for the OSPAN task.
Distractor Repetitions Retrieve Previous Responses to Targets
Authors: Frings Christian , Rothermund Klaus , Wentura Dirk
Published: October 2006

Response retrieval theories assume that stimuli and responses become integrated into “event files” (Hommel, 1998) in memory so that a second encounter with a specific stimulus automatically retrieves the response that was previously associated with this stimulus. In this article, we tested a specific prediction of a recent variant of stimulus retrieval theories as introduced by Rothermund, Wentura, and De Houwer (2005): In selection tasks where target stimuli are accompanied by distractors, responses to target stimuli are automatically bound to distractor stimuli as well; repeating the distractor should retrieve the response to the target that formerly accompanied the distractor. In three experiments we confirmed this prediction: Distractor repetition facilitated responding in the probe in the case of response repetition whereas repeating the distractor delayed responding in the case of response change.
Masked onset priming effect for high-frequency words: Further support for the speech-planning account
Authors: Malouf Tania , Kinoshita Sachiko
Published: October 2006

Two experiments investigated whether priming due to a match in just the onset between a masked prime and target is found with high-frequency target words. Forster and Davis (1991, Exp. 5) reported that the masked onset priming effect was absent for high-frequency words and used the finding to argue that the effect has its locus in the grapheme–phoneme mapping process that operates serially within the nonlexical route. Experiment 1 used primes that were unrelated to targets and found a masked onset priming effect of equal size for high-frequency and low-frequency target words. Experiment 2 used form-related primes as used by Forster and Davis, and again found that the effect of onset mismatch was not dependent on target word frequency. These results are interpreted in terms of an alternative view that the masked onset priming effect has its origin in the process of preparing a speech response.
A novel histone exchange factor, protein phosphatase 2Cγ, mediates the exchange and dephosphorylation of H2A–H2B
Authors: Kimura Hiroshi , Takizawa Nanako , Allemand Eric , Hori Tetsuya , Iborra Francisco J. , Nozaki Naohito , Muraki Michiko , Hagiwara Masatoshi , Krainer Adrian R. , Fukagawa Tatsuo , Okawa Katsuya
Published: October 2006

In eukaryotic nuclei, DNA is wrapped around a protein octamer composed of the core histones H2A, H2B, H3, and H4, forming nucleosomes as the fundamental units of chromatin. The modification and deposition of specific histone variants play key roles in chromatin function. In this study, we established an in vitro system based on permeabilized cells that allows the assembly and exchange of histones in situ. H2A and H2B, each tagged with green fluorescent protein (GFP), are incorporated into euchromatin by exchange independently of DNA replication, and H3.1-GFP is assembled into replicated chromatin, as found in living cells. By purifying the cellular factors that assist in the incorporation of H2A–H2B, we identified protein phosphatase (PP) 2C γ subtype (PP2Cγ/PPM1G) as a histone chaperone that binds to and dephosphorylates H2A–H2B. The disruption of PP2Cγ in chicken DT40 cells increased the sensitivity to caffeine, a reagent that disturbs DNA replication and damage checkpoints, suggesting the involvement of PP2Cγ-mediated histone dephosphorylation and exchange in damage response or checkpoint recovery in higher eukaryotes.
Administration of Ratanhia‐Based Herbal Oral Care Products for the Prophylaxis of Oral Mucositis in Cancer Chemotherapy Patients: A Clinical Trial
Authors: Tiemann Patric , Toelg Michael , Ramos F. Mac H.
Published: October 2006

Oral complications are a common side effect of cancer chemotherapy, as antineoplastic agents affect both the immune system and the oral mucosa. This study demonstrates preventive and therapeutic effects of dental treatment and regular use of Weleda Ratanhia‐Mundwasser® (herbal mouthwash) and Weleda Pflanzen‐Zahngel® (herbal toothgel) on oral mucositis during chemotherapy. Thirty‐two female patients with breast cancer starting on chemotherapy were evaluated in this study. Plaque index, gingival index, degree of mucositis and 10 single symptoms were monitored once weekly for four consecutive weeks. After four weeks, plaque and gingival indexes were slightly decreased compared to baseline values. The degree of mucositis was increased by one grade in 15.6 % of the patients and over 70 % remained without symptoms. On the whole, single symptoms decreased from day 7 since beginning of chemotherapy to day 28. Mucositis symptoms were moderate in severity, and the results indicate a positive influence of using Weleda Ratanhia-Mundwasser and Weleda Pflanzen-Zahngel. Further studies might be promising.
Improvement of Memory by Means of Ultra‐Low Doses of Antibodies to S‐100B Antigen
Authors: Epstein O. I. , Pavlov I. F. , Shtark M. B.
Published: October 2006

Antigen S‐100B of nervous tissue, according to the data of numerous studies, affects the mechanisms of nervous system plasticity and memory. The influence of ultralow doses of antibodies to S‐100B (6C dilution, according to the homeopathic pharmacopoeia) has been studied on three learning behavioral models on Wistar rats, which were inhibitory avoidance, choosing of bowls with sucrose and feeding behavior cessation after auditory signal. For all three tasks, parameters of reproduction of the learned skills improved after per oral administration of potentiated antibodies to S‐100B antigen immediately after learning. Possible mechanisms of the anti‐S‐100B antibodies influence on memory formation are discussed.
Evaluation of Source Leaf Responses to Water-Deficit Stresses in Cotton Using a Novel Stress Bioassay
Authors: Burke John J.
Published: October 2006

Water-deficit stresses preferentially reduce shoot growth, thereby disrupting the flow of carbohydrates from source leaves to the developing sinks. Here, we use a novel stress bioassay to dissect responses of field and greenhouse-grown cotton (Gossypium hirsutum) source leaves to water-deficit stresses. Fifth main stem leaf samples were harvested at sunrise and subjected to a prolonged elevated respiratory demand in the dark. Sucrose levels are lower in nonstressed cotton at sunrise compared to water-deficit stressed cotton, potentially predisposing the nonstressed tissue to succumb more rapidly. Tissue death was determined initially using the cell viability stain 2,3,5-triphenyltetrazolium chloride, but was determined in subsequent experiments by monitoring the decline in chlorophyll fluorescence yield. Fluorescence yield measurements were obtained within minutes of harvesting and individual samples were monitored over the time course of the treatment. Analyses of the time course and magnitude of chlorophyll fluorescence yield decline in samples from irrigated and dryland plots permitted the detection of stress responses within 24 h of the cessation of irrigation. The rate of fluorescence yield decline during the elevated respiratory demand treatment slowed as the water-deficit stress increased. Upon irrigation, the source leaves of the water-stressed plants recovered to prestress values within 4 d. Well-watered cotton overexpressing heat shock protein 101 had identical rates of fluorescence yield decline as nontransgenic cotton. These results suggest that the delayed decline in fluorescence yield of water-stressed tissue exposed to prolonged elevated respiratory demand can be used as a sensitive indicator of water-deficit stress responses.
Arabidopsis Orthologs of Maize Chloroplast Splicing Factors Promote Splicing of Orthologous and Species-Specific Group II Introns
Authors: Asakura Yukari , Barkan Alice
Published: October 2006

Chloroplast genomes in plants and green algae contain numerous group II introns, large ribozymes that splice via the same chemical steps as spliceosome-mediated splicing in the nucleus. Most chloroplast group II introns are degenerate, requiring interaction with nucleus-encoded proteins to splice in vivo. Genetic approaches in maize (Zea mays) and Chlamydomonas reinhardtii have elucidated distinct sets of proteins that assemble with chloroplast group II introns and facilitate splicing. Little information is available, however, concerning these processes in Arabidopsis (Arabidopsis thaliana). To determine whether the paucity of data concerning chloroplast splicing factors in Arabidopsis reflects a fundamental difference between protein-facilitated group II splicing in monocot and dicot plants, we examined the mutant phenotypes associated with T-DNA insertions in Arabidopsis genes encoding orthologs of the maize chloroplast splicing factors CRS1, CAF1, and CAF2 (AtCRS1, AtCAF1, and AtCAF2). We show that the splicing functions and intron specificities of these proteins are largely conserved between maize and Arabidopsis, indicating that these proteins were recruited to promote the splicing of plastid group II introns prior to the divergence of monocot and dicot plants. We show further that AtCAF1 promotes the splicing of two group II introns, rpoC1 and clpP-intron 1, that are found in Arabidopsis but not in maize; AtCAF1 is the first splicing factor described for these introns. Finally, we show that a strong AtCAF2 allele conditions an embryo-lethal phenotype, adding to the body of data suggesting that cell viability is more sensitive to the loss of plastid translation in Arabidopsis than in maize.
A Sodium Transporter (HKT7) Is a Candidate forNax1, a Gene for Salt Tolerance in Durum Wheat
Authors: Huang Shaobai , Spielmeyer Wolfgang , Lagudah Evans S. , James Richard A. , Platten J. Damien , Dennis Elizabeth S. , Munns Rana
Published: October 2006

Durum wheat (Triticum turgidum subsp. durum) is more salt sensitive than bread wheat (Triticum aestivum). A novel source of Na+ exclusion conferring salt tolerance to durum wheat is present in the durum wheat Line 149 derived from Triticum monococcum C68-101, and a quantitative trait locus contributing to low Na+ concentration in leaf blades, Nax1, mapped to chromosome 2AL. In this study, we used the rice (Oryza sativa) genome sequence and data from the wheat expressed sequence tag deletion bin mapping project to identify markers and construct a high-resolution map of the Nax1 region. Genes on wheat chromosome 2AL and rice chromosome 4L had good overall colinearity, but there was an inversion of a chromosomal segment that includes the Nax1 locus. Two putative sodium transporter genes (TmHKT7) related to OsHKT7 were mapped to chromosome 2AL. One TmHKT7 member (TmHKT7-A1) was polymorphic between the salt-tolerant and -sensitive lines, and cosegregated with Nax1 in the high-resolution mapping family. The other TmHKT7 member (TmHKT7-A2) was located within the same bacterial artificial chromosome contig of approximately 145 kb as TmHKT7-A1. TmHKT7-A1 and -A2 showed 83% amino acid identity. TmHKT7-A2, but not TmHKT7-A1, was expressed in roots and leaf sheaths of the salt-tolerant durum wheat Line 149. The expression pattern of TmHKT7-A2 was consistent with the physiological role of Nax1 in reducing Na+ concentration in leaf blades by retaining Na+ in the sheaths. TmHKT7-A2 could control Na+ unloading from xylem in roots and sheaths.
Plant Glutathione Peroxidases Are Functional Peroxiredoxins Distributed in Several Subcellular Compartments and Regulated during Biotic and Abiotic Stresses
Authors: Navrot Nicolas , Collin Valérie , Gualberto José , Gelhaye Eric , Hirasawa Masakazu , Rey Pascal , Knaff David B. , Issakidis Emmanuelle , Jacquot Jean-Pierre , Rouhier Nicolas
Published: October 2006

We provide here an exhaustive overview of the glutathione (GSH) peroxidase (Gpx) family of poplar (Populus trichocarpa). Although these proteins were initially defined as GSH dependent, in fact they use only reduced thioredoxin (Trx) for their regeneration and do not react with GSH or glutaredoxin, constituting a fifth class of peroxiredoxins. The two chloroplastic Gpxs display a marked selectivity toward their electron donors, being exclusively specific for Trxs of the y type for their reduction. In contrast, poplar Gpxs are much less specific with regard to their electron-accepting substrates, reducing hydrogen peroxide and more complex hydroperoxides equally well. Site-directed mutagenesis indicates that the catalytic mechanism and the Trx-mediated recycling process involve only two (cysteine [Cys]-107 and Cys-155) of the three conserved Cys, which form a disulfide bridge with an oxidation-redox midpoint potential of −295 mV. The reduction/formation of this disulfide is detected both by a shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by measuring the intrinsic tryptophan fluorescence of the protein. The six genes identified coding for Gpxs are expressed in various poplar organs, and two of them are localized in the chloroplast, with one colocalizing in mitochondria, suggesting a broad distribution of Gpxs in plant cells. The abundance of some Gpxs is modified in plants subjected to environmental constraints, generally increasing during fungal infection, water deficit, and metal stress, and decreasing during photooxidative stress, showing that Gpx proteins are involved in the response to both biotic and abiotic stress conditions.
MIKC* MADS-Protein Complexes Bind Motifs Enriched in the Proximal Region of Late Pollen-Specific Arabidopsis Promoters
Authors: Verelst Wim , Saedler Heinz , Münster Thomas
Published: October 2006

The genome of Arabidopsis (Arabidopsis thaliana) encodes over 100 MADS-domain transcription factors, categorized into five phylogenetic subgroups. Most research efforts have focused on just one of these subgroups (MIKCc), whereas the other four remain largely unexplored. Here, we report on five members of the so-called Mδ or Arabidopsis MIKC* (AtMIKC*) subgroup, which are predominantly expressed during the late stages of pollen development. Very few MADS-box genes function in mature pollen, and from this perspective, the AtMIKC* genes are therefore highly exceptional. We found that the AtMIKC* proteins are able to form multiple heterodimeric complexes in planta, and that these protein complexes exhibit a for the MADS-family unusual and high DNA binding specificity in vitro. Compared to their occurrence in promoters genome wide, AtMIKC* binding sites are strongly overrepresented in the proximal region of late pollen-specific promoters. By combining our experimental data with in silico genomics and pollen transcriptomics approaches, we identified a considerable number of putative direct target genes of the AtMIKC* transcription factor complexes in pollen, many of which have known or proposed functions in pollen tube growth. The expression of several of these predicted targets is altered in mutant pollen in which all AtMIKC* complexes are affected, and in vitro germination of this mutant pollen is severely impaired. Our data therefore suggest that the AtMIKC* protein complexes play an essential role in transcriptional regulation during late pollen development.
tie-dyed1Regulates Carbohydrate Accumulation in Maize Leaves
Authors: Braun David M. , Ma Yi , Inada Noriko , Muszynski Michael G. , Baker R. Frank
Published: October 2006

Acquisition of cell identity requires communication among neighboring cells. To dissect the genetic pathways regulating cell signaling in later leaf development, a screen was performed to identify mutants with chloroplast pigmentation sectors that violate cell lineage boundaries in maize (Zea mays) leaves. We have characterized a recessive mutant, tie-dyed1 (tdy1), which develops stable, nonclonal variegated yellow and green leaf sectors. Sector formation requires high light, occurs during a limited developmental time, and is restricted to leaf blade tissue. Yellow tdy1 sectors accumulate excessive soluble sugars and starch, whereas green sectors appear unaffected. Significantly, starch accumulation precedes chlorosis in cells that will become a yellow sector. Retention of carbohydrates in tdy1 leaves is associated with a delay in reproductive maturity, decreased stature, and reduced yield. To explain the tdy1 sectoring pattern, we propose a threshold model that incorporates the light requirement and the hyperaccumulation of photoassimilates. A possible function consistent with this model is that TDY1 acts as a sugar sensor to regulate an inducible sugar export pathway as leaves develop under high light conditions.
Backbone dynamics of SDF‐1α determined by NMR: Interpretation in the presence of monomer–dimer equilibrium
Authors: Baryshnikova Olga K. , Sykes Brian D.
Published: October 2006

SDF‐1α is a member of the chemokine family implicated in various reactions in the immune system. The interaction of SDF‐1α with its receptor, CXCR4, is responsible for metastasis of a variety of cancers. SDF‐1α is also known to play a role in HIV‐1 pathogenesis. The structures of SDF‐1α determined by NMR spectroscopy have been shown to be monomeric while X‐ray structures are dimeric. Biochemical data and in vivo studies suggest that dimerization is likely to be important for the function of chemokines. We report here the dynamics of SDF‐1α determined through measurement of main chain 15N NMR relaxation data. The data were obtained at several concentrations of SDF‐1α and used to determine a dimerization constant of ∼5 mM for a monomer–dimer equilibrium. The dimerization constant was subsequently used to extrapolate values for the relaxation data corresponding to monomeric SDF‐1α. The experimental relaxation data and the extrapolated data for monomeric SDF‐1α were analyzed using the model free approach. The model free analysis indicated that SDF‐1α is rigid on the nano‐ to picosecond timescale with flexible termini. Several residues involved in the dimer interface display slow micro‐ to millisecond timescale motions attributable to chemical exchange such as monomer–dimer equilibrium. NMR relaxation measurements are shown to be applicable for studying oligomerization processes such as the dimerization of SDF‐1α.
Solution structure of the kinase‐associated domain 1 of mouse microtubule‐associated protein/microtubule affinity‐regulating kinase 3
Authors: Tochio Naoya , Koshiba Seizo , Kobayashi Naohiro , Inoue Makoto , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Matsuda Takayoshi , Tomo Yasuko , Motoda Yoko , Kobayashi Atsuo , Tanaka Akiko , Hayashizaki Yoshihide , Terada Takaho , Shirouzu Mikako , Kigawa Takanori , Yokoyama Shigeyuki
Published: October 2006

Microtubule‐associated protein/microtubule affinity‐regulating kinases (MARKs)/PAR‐1 are common regulators of cell polarity that are conserved from nematode to human. All of these kinases have a highly conserved C‐terminal domain, which is termed the kinase‐associated domain 1 (KA1), although its function is unknown. In this study, we determined the solution structure of the KA1 domain of mouse MARK3 by NMR spectroscopy. We found that ∼50 additional residues preceding the previously defined KA1 domain are required for its proper folding. The newly defined KA1 domain adopts a compact α+β structure with a βαββββα topology. We also found a characteristic hydrophobic, concave surface surrounded by positively charged residues. This concave surface includes the highly conserved Glu‐Leu‐Lys‐Leu motif at the C terminus, indicating that it is important for the function of the KA1 domain.
Inter‐ and intra‐population morphological differences between wild and farmed Atlantic salmon juveniles
Authors: Solem Ø. , Berg O. K. , Kjøsnes A. J.
Published: October 2006

Whether population‐specific morphological differences were detectable in small (26–52 mm) Atlantic salmon Salmo salar parr reared under similar conditions was tested. Discrimination based on morphological characters was total (100%) between the fish of farmed origin (from AquaGen) and four wild fish populations. Between the four wild populations the corresponding discrimination was 59·8–86·3%. The inter‐population variation in morphological characters was larger than the intra‐population variation. The fish originating from the local populations at Driva and Innfjord were narrower in body form, whereas fish from the AquaGen and Innfjord populations had smaller and less pointed heads with smaller eyes. The Driva population fish had the smallest mouth while the longest pectoral fin was found in the Bjoreio population, the river that also has the largest fall gradient. Population‐specific morphological characters were thus detectable among Atlantic salmon parr relatively rapidly after yolk absorption.
On the occurrence of the Asiatic cyprinid Pseudorasbora parva in the Netherlands
Authors: Pollux B. J. A. , Korosi A.
Published: October 2006

A large scale inventory along the Meuse River (the Netherlands), showed that floodplain lakes function as spawning, nursery and adult habitats, while the main river channel merely serves as a dispersal corridor for adult Pseudorasbora parva, one of the most successful invasive fish species that have colonized Europe.