bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vitro Histone Methyltransferase Assay
Authors: Fingerman Ian M. , Du Hai-Ning , Briggs Scott D.
Published: February 2008

INTRODUCTION

Histone methyltransferases catalyze the addition of one or more methyl groups to a specific lysine or arginine residue within histones. Currently, there is a great deal of interest in histone methyltransferases, because mutations and misregulation of the genes encoding these proteins have been linked to various cancers and other diseases. Many genes encoding putative histone methyltransferases have been identified in eukaryotes, but the proteins they encode have not been functionally characterized. This protocol describes an in vitro assay for histone methyltransferase activity that uses bacterial cell extracts in which expression of a methyltransferase of interest is induced. In many cases, purification of the enzyme is unnecessary, making this experiment ideal for pilot studies. Bacterial cell extract containing the methyltransferase of interest is incubated with S-adenosyl-L-[methyl-3H]-methionine and various histone substrates, many of which are commercially available. Incorporation of the methyl-3H can be measured easily by scintillation counting. The labeled substrate is visualized by SDS-polyacrylamide gel electrophoresis (PAGE) followed by fluorography. This allows the substrate specificity and activity of a histone methyltransferase of interest to be readily characterized.
Stable Isotope Labeling of Mammals (SILAM)
Authors: McClatchy Daniel B. , Yates John R.
Published: February 2008

INTRODUCTION

A general approach in quantitative mass spectrometry is to mix a protein sample containing only natural-abundance isotopes with an identical protein sample containing proteins labeled with heavy stable isotopes (e.g., 2H, 13C, 15N, or 18O). Introduction of stable isotope labels into proteins alters their molecular weight and such changes can be observed on the mass spectrometer. The relative protein expression is calculated from the ion chromatograms of the labeled and unlabeled peptides. Introduction of stable isotopes via metabolic labeling is an efficient and quantitative method compared to in vitro covalent labeling strategies, because it ensures that every protein is enriched with a heavy stable isotope. Metabolic labeling is routinely performed with cultured cells, ranging from bacteria and yeast to mammalian cells. However, analysis of mammalian tissue allows greater insight into physiology compared to cultured cells. In this protocol, we describe a procedure to metabolically label Rattus norvegicus with 15N for quantitative mass spectrometry analysis. Stable isotope labeling of mammals (SILAM) allows the global quantitative analysis of any mammalian model of human disease.
Fixation, Embedding, and Sectioning of Plant Tissues
Authors: Weigel Detlef , Glazebrook Jane
Published: February 2008

INTRODUCTION

This protocol describes the preparation of plant tissues for sectioning and subsequent use in immunohistochemistry or in situ hybridization. Tissues of interest are fixed and embedded in Paraplast before sectioning.
Nonradioactive In Situ Hybridization of RNA Probes to Sections of Plant Tissues
Authors: Ferrandiz Cristina , Sessions Allen
Published: February 2008

INTRODUCTION

Both radioactive and nonradioactive probes can be used to detect RNA in situ. Radioactive in situ hybridizations are believed by many to be more sensitive, but the localization of signal is considerably less precise than for nonradioactive in situs, and each experiment takes much longer. Thus, nonradioactive in situ hybridization is generally preferred. Antisense RNA is typically labeled using digoxygenin (DIG), which is subsequently detected with an anti-DIG antibody coupled to alkaline phosphatase. This protocol describes in situ hybridization of a DIG-labeled probe to paraffin-embedded sections of plant tissue. Double labeling using both DIG- and fluorescein isothiocyanate (FITC)-conjugated ribonucleotides is also described.
Immunohistochemistry on Sections of Plant Tissues Using Enzyme-Coupled Avidin-Biotin Complex
Authors: Weigel Detlef , Glazebrook Jane
Published: February 2008

INTRODUCTION

Like RNA, proteins can be localized in situ on tissue sections. In situ localization or immunohistochemistry provides information on the cellular and subcellular distribution of proteins in different tissues. The technique described in this protocol employs a biotinylated secondary antibody in conjunction with a preformed Avidin:Biotinylated enzyme Complex (ABC) for immunohistochemistry. It allows for sensitive detection of antigens while avoiding fluorescent secondary antibodies, which produce a much less stable signal. Formation of the complex is achieved by mixing avidin and biotinylated enzyme in dilute solution and in defined amounts prior to use. The complex is then allowed to bind to biotinylated secondary antibodies, thus linking the antigen via primary and secondary antibodies to the enzyme used to generate the signal. Kits for this procedure are available from Vector Laboratories. The VECTASTAIN ABC kits are of three types, using the enzymes horseradish peroxidase, alkaline phosphatase, or glucose oxidase. This protocol assumes use of the peroxidase kit, but can be easily modified for the other kits.
Whole-Mount Fluorescence Immunocytochemistry on Xenopus Embryos
Authors: Lee Chanjae , Kieserman Esther , Gray Ryan S. , Park Tae Joo , Wallingford John
Published: February 2008

INTRODUCTION

Immunocytochemistry (ICC) is widely exploited in studying mammalian systems, but is underutilized among Xenopus developmental biologists. This stems, in part, from the relatively small number of Xenopus antibodies available for use in research. Common misconceptions about ICC in Xenopus embryos also prevail, discouraging researchers from trying the procedure. However, ICC with Xenopus is simple and effective. This article describes methods for whole-mount ICC in Xenopus embryos. Also included are simple procedures to quench autofluorescence of Xenopus and to remove surface pigment from embryos which may interfere with fluorescence imaging. The methods described here are useful for detecting tissue-specific probes (e.g., 12/101 to detect somites). They are also effective for imaging the cytoskeleton (e.g., α-tubulin to detect microtubules) or localizing specific proteins at the subcellular level (e.g., ZO-1 to detect tight junctions). In addition, combining ICC with in situ hybridization is simple and highly effective.
Rab-A2 and Rab-A3 GTPases Define atrans-Golgi Endosomal Membrane Domain inArabidopsisThat Contributes Substantially to the Cell Plate
Authors: Chow Cheung-Ming , Neto Hélia , Foucart Camille , Moore Ian
Published: February 2008

The Ypt3/Rab11/Rab25 subfamily of Rab GTPases has expanded greatly in Arabidopsis thaliana, comprising 26 members in six provisional subclasses, Rab-A1 to Rab-A6. We show that the Rab-A2 and Rab-A3 subclasses define a novel post-Golgi membrane domain in Arabidopsis root tips. The Rab-A2/A3 compartment was distinct from but often close to Golgi stacks and prevacuolar compartments and partly overlapped the VHA-a1 trans-Golgi compartment. It was also sensitive to brefeldin A and accumulated FM4-64 before prevacuolar compartments did. Mutations in RAB-A2a that were predicted to stabilize the GDP- or GTP-bound state shifted the location of the protein to the Golgi or plasma membrane, respectively. In mitosis, KNOLLE accumulated principally in the Rab-A2/A3 compartment. During cytokinesis, Rab-A2 and Rab-A3 proteins localized precisely to the growing margins of the cell plate, but VHA-a1, GNOM, and prevacuolar markers were excluded. Inducible expression of dominant-inhibitory mutants of RAB-A2a resulted in enlarged, polynucleate, meristematic cells with cell wall stubs. The Rab-A2/A3 compartment, therefore, is a trans-Golgi compartment that communicates with the plasma membrane and early endosomal system and contributes substantially to the cell plate. Despite the unique features of plant cytokinesis, membrane traffic to the division plane exhibits surprising molecular similarity across eukaryotic kingdoms in its reliance on Ypt3/Rab11/Rab-A GTPases.
Epigenetic Modification of Centromeric Chromatin: Hypomethylation of DNA Sequences in the CENH3-Associated Chromatin inArabidopsis thalianaand Maize
Authors: Zhang Wenli , Lee Hye-Ran , Koo Dal-Hoe , Jiang Jiming
Published: February 2008

The centromere in eukaryotes is defined by the presence of a special histone H3 variant, CENH3. Centromeric chromatin consists of blocks of CENH3-containing nucleosomes interspersed with blocks of canonical H3-containing nucleosomes. However, it is not known how CENH3 is precisely deposited in the centromeres. It has been suggested that epigenetic modifications of the centromeric chromatin may play a role in centromere identity. The centromeres of Arabidopsis thaliana are composed of megabase-sized arrays of a 178-bp satellite repeat. Here, we report that the 178-bp repeats associated with the CENH3-containing chromatin (CEN chromatin) are hypomethylated compared with the same repeats located in the flanking pericentromeric regions. A similar hypomethylation of DNA in CEN chromatin was also revealed in maize (Zea mays). Hypomethylation of the DNA in CEN chromatin is correlated with a significantly reduced level of H3K9me2 in Arabidopsis. We demonstrate that the 178-bp repeats from CEN chromatin display a distinct distribution pattern of the CG and CNG sites, which may provide a foundation for the differential methylation of these repeats. Our results suggest that DNA methylation plays an important role in epigenetic demarcation of the CEN chromatin.
Expressive vocabulary in 18‐month‐old children in relation to demographic factors, mother and child characteristics, communication style and shared reading
Authors: Westerlund M. , Lagerberg D.
Published: February 2008

Background  Previous research has elucidated the associations between children's language development and reading habits, and maternal education, communication style, gender and birth order. Research including maternal age and child temperament is more scarce. We studied the associations of all these factors with children's expressive vocabulary and reading habits. We also analysed the relationships of reading with expressive vocabulary, and effect sizes associated with frequent reading.

Methods  Questionnaires were completed by mothers of 1091 children aged 17–19 months visiting the Swedish Child Health Services. Expressive vocabulary was assessed by the Swedish Communication Screening at 18 months, a screening version of McArthur‐Bates Communicative Development Inventories. Mother's perception of ability to communicate was measured by a scale constructed ad hoc from the International Child Development Programmes, a parent education curriculum. Bates' ‘difficultness’ scale was used to assess temperament.

Results  Good communication, low maternal age, female gender and frequent reading were significantly associated with expressive vocabulary. High maternal education, good communication, higher maternal age, female gender and being a first‐born child were significantly associated with frequent reading. Reading at least 6 times/week added more than 0.3 SD in vocabulary regardless of gender and communication.

Conclusions  The findings support the importance of reading and communication quality to early language development. Knowledge of the relationship between children's vocabulary and book reading in a context of joint attention is both theoretically and practically valuable to speech and language pathologists, pre‐school teachers, child health workers and other professionals.
Symptomatic nutritional rickets in a teenager with autistic spectrum disorder
Authors: Stewart C. , Latif A.
Published: February 2008

Selectivity with food and food related behavioural difficulties are relatively common in children on the Autistic Spectrum. This may result in an inadequate nutritional status. Integration of sensory signals in the brain associated with textures, tastes and smells has been postulated as a possible cause.
Objectively monitored patching regimens for treatment of amblyopia: randomised trial
Authors: Reading Richard
Published: February 2008

.
 
Stewart C.E.,
Stephens D.A.,
Fielder A.R. &
Moseley M.J.
(
2007
)

,
335
,
707
–
711
.
DOI: 10.1136/bmj.39301.460150.55.

Objectives  To compare visual outcome in response to two prescribed rates of occlusion (6 h a day and 12 h a day).

Design  Unmasked randomized trial.

Setting  Research clinics in two London hospitals.

Participants  In total, 97 children with a confirmed diagnosis of amblyopia associated with strabismus, anisometropia, or both.

Interventions  An 18‐week period of wearing glasses (refractive adaptation) followed by occlusion prescribed (‘patching’) for 6 or 12 h a day.

Main outcome measures  Visual acuity measured by logMAR letter recognition, objectively monitored rate of occlusion (hours a day).

Results  The mean age of children at study entry was 5.6 (SD 1.5) years. Ninety were eligible for occlusion but 10 dropped out in this phase, leaving 80 children who were randomized to a prescribed dose rate of 6 (n = 40) or 12 (n = 40) h a day. The mean change in visual acuity of the amblyopic eye was not significantly different (P = 0.64) between the two groups [0.26 (95% confidence interval 0.21–0.31) log units in 6‐h group; 0.24 (0.19–0.29) log units in 12‐h group]. The mean dose rates (hours a day) actually received, however, were also not significantly different [4.2 (3.7–4.7) in 6‐h group vs. 6.2 (5.1–7.3) in 12‐h group; P = 0.06]. The visual outcome was similar for those children who received 3 to 6 h a day or more than 6 to 12 h a day, but significantly better than that in children who received less than 3 h a day. Children aged under 4 years required significantly less occlusion than older children. Visual outcome was not influenced by type of amblyopia.

Conclusions  Substantial (6 h a day) and maximal (12 h a day) prescribed occlusion results in similar visual outcome. On average, the occlusion dose received in the maximal group was only 50% more than in the substantial group and in both groups was much less than that prescribed. Younger children required the least occlusion.
Realist review to understand the efficacy of school feeding programmes
Authors: Reading Richard
Published: February 2008

.
 
Greenhalgh T.,
Kristjansson E. &
Robinson V.
(
2007
)

,
335
,
858
–
861
.
DOI: 10.1136/bmj.39359.525174.AD.
The serum levels of the EGF‐like homeotic protein dlk1 correlate with different metabolic parameters in two hormonally different children populations in Spain*
Authors: Hermida Carmen , Garcés Carmen , De Oya Manuel , Cano Beatriz , Martínez‐Costa Oscar H. , Rivero Samuel , García‐Ramírez José J. , Laborda Jorge , Aragón Juan J.
Published: February 2008

Background  The Dlk1 gene encodes for dlk1, a transmembrane protein belonging to the EGF‐like repeat‐containing family. Dlk1 has been shown to act as a regulator of adipogenesis. Fc‐dlk1 transgenic mice show a decrease in adipose tissue and glucose tolerance, hypertriglyceridaemia and lower insulin sensitivity. Dlk1‐deficient mice show growth retardation, increased serum lipid metabolites and develop obesity. These data advocate for a role of dlk1 in the maintenance of lipid homeostasis, and suggest that dlk1 levels may influence the development of cardiovascular disease.

Aim and methods  In this study, we analysed whether dlk1 serum levels could be indicative of the different hormonal or metabolic status shown by two Spanish children populations (6–8 years‐old), Orense and Murcia. We determined dlk1 serum levels by ELISA assay, using an antibody raised against the recombinant protein, and performed a correlation analysis against measurements of several hormonal and biochemical parameters in samples from 494 subjects.

Results  We found a statistically significant positive correlation between serum levels of dlk1 and those of glucose (P < 0·05), total cholesterol (P < 0·01) and high‐density lipoprotein‐cholesterol (HDL‐C) (P < 0·01) in children from Murcia, but not from Orense's population, where dehydroepiandrosterone‐sulphate (DHEA‐S) levels were significantly higher (P < 0·01) and dlk1 correlated positively with insulin (P < 0·01), homeostasis model assessment (HOMA) (P < 0·01) and free fatty acids (FFA) (P < 0·05).

Conclusions  dlk1 serum levels appear related to the anabolic status of the children in association with changes in the levels of DHEA‐S, which have been associated with hyperinsulinaemia and diabetes. Monitoring dlk1 levels may be important to evaluate the metabolic and hormonal stage of child development.
Control of IGF‐I levels with titrated dosing of lanreotide Autogel over 48 weeks in patients with acromegaly
Authors: Chanson Philippe , Borson‐Chazot Françoise , Kuhn Jean‐Marc , Blumberg Joëlle , Maisonobe Pascal , Delemer Brigitte ,   the Lanreotide Acromegaly Study Group
Published: February 2008

Background  An essential criterion for control of acromegaly is normalization of IGF‐I levels. Somatostatin analogues act to suppress IGF‐I and GH levels.

Objective  To assess the efficacy and safety of 48 weeks titrated dosing of lanreotide Autogel.

Design  Open‐label, multicentre, phase III, 48‐week trial.

Methods  Patients with active acromegaly (IGF‐I levels > 1·3 times upper limit of age‐adjusted normal range) were recruited. Twelve injections of lanreotide Autogel were given at 28‐day intervals: during the 16‐week fixed‐dose phase, patients received 90 mg; in the 32‐week dose‐titration phase, patients received 60, 90 or 120 mg according to GH and IGF‐I levels. Intention‐to‐treat analysis was performed to determine the proportion of patients with normalized age‐adjusted IGF‐I levels at study end. Secondary evaluations included GH levels, clinical acromegaly signs and safety.

Results  Fifty‐seven of 63 patients completed the study. Lanreotide Autogel resulted in normalized age‐adjusted IGF‐I levels in 27 patients (43%, 95% CI 31–55). Mean GH levels decreased from 6·2 to 1·5 µg/l at study end, with 53 of 62 patients (85%) having GH levels ≤ 2·5 µg/l (95% CI 76·7–94·3) and 28 of 62 patients (45%) with levels < 1 µg/l (95% CI 32·8–57·6). Twenty‐four (38%) had both normal IGF‐I levels and GH levels ≤ 2·5 µg/l. Acromegaly symptoms reduced significantly in most patients throughout the study. The most common adverse events were gastrointestinal, as expected for somatostatin analogues.

Conclusions  Using IGF‐I as primary end‐point, 48 weeks lanreotide Autogel treatment, titrated for optimal hormonal control, controlled IGF‐I and GH levels effectively, reduced acromegaly symptoms and was well tolerated.
Metabolic characteristics of subjects with normal glucose tolerance and 1‐h hyperglycaemia
Authors: Qian Lei , Fu Xuelian , Xu Lihong , Zheng Sheng , Zhou Weibin , Wang Xiao , Gu Yanyun , Lin Fan , Luo Min
Published: February 2008

Objective  Nondiabetic subjects with a 1‐h plasma glucose ≥ 11·1 mmol/l during an oral glucose tolerance test (OGTT) drew our attention to their somewhat confusing status and relative frequency among Chinese patients. The aim of this study was to clarify the metabolic characteristics of these subjects.

Design and patients  A total of 2549 Chinese subjects were included in this study. Based on results of OGTT, these subjects were classified into three groups: normal glucose tolerance (NGT), impaired glucose regulation (IGR) and diabetes mellitus (DM). Then, according to the level of 1‐h plasma glucose, the NGT and IGR groups were subclassified, respectively, as: NGT without 1‐h hyperglycaemia (NGTN), NGT with hyperglycaemia at 1 h (NGT1H), IGR without 1‐h hyperglycaemia (IGRN), and IGR with hyperglycaemia at 1 h (IGR1H).

Results  After adjustments for age and gender, the insulinogenic index (IGI) of NGT1H and IGR1H was found to be lower than for those with NGTN and of IGRN, respectively (P < 0·05). No statistical differences, however, were found in oral glucose insulin sensitivity (OGIS) between either of the 1‐h hyperglycaemic groups or of the corresponding NGTN or IGRN groups. Homeostasis model assessment for β‐cell function (HOMA‐B) of NGT1H was lower than that of NGTN (P < 0·05), while IGRN and IGR1H showed no difference. No differences in homeostasis model assessment for insulin resistance (HOMA‐IR) were found among NGTN, NGT1H, IGRN and IGR1H groups. The levels of triglycerides (TG) were not significantly different among NGT1H, IGRN and IGR1H, while TG in these groups were significantly higher than in NGTN (P < 0·05). LDL‐C was significantly higher and HDL significantly lower in NGT1H than in all other groups (P < 0·05).The IGR group was also subclassified as: isolated impaired fasting glucose (IFG), isolated impaired glucose tolerance (IGT) and combined glucose intolerance (CGI). The IGI of the NGT1H group was similar to the IGI that of combined glucose intolerance group but lower than those of IFG and IGT (P < 0·05).The OGIS of the NGT1H group was the highest among all groups (P < 0·05). HOMA‐B of IGT and NGT1H were higher than that of IFG (P < 0·05). There was no difference among all groups in HOMA‐IR. Plasma lipid levels were not significantly different between NGT1H and any other group.

Conclusions  Chinese NGT subjects with a 1‐h plasma glucose ≥ 11·1 mmol/l are characterized by metabolic abnormalities, which may be caused by the impairment of early insulin release rather than aggravated insulin resistance.
Double‐stranded RNA mediates interferon regulatory factor 3 activation and interleukin‐6 production by engaging Toll‐like receptor 3 in human brain astrocytes
Authors: Kim Hyemi , Yang Eunjung , Lee Jeonggi , Kim Se‐Hoon , Shin Jeon‐Soo , Park Joo Young , Choi Sun Ju , Kim Se Jong , Choi In‐Hong
Published: February 2008

Toll‐like receptor 3 (TLR3) participates in the innate immune response by recognizing viral pathogens. In this study, human brain astrocytes were found to constitutively express TLR3, and this expression was increased by interferon‐γ (IFN‐γ) or double‐stranded RNA (dsRNA). Treatment employing dsRNA in astrocytes induced IFN regulatory factor 3 (IRF3) phosphorylation, dimer formation and nuclear translocation followed by STAT1 activation. This treatment also activated nuclear factor‐κB, p38 and c‐Jun N‐terminal kinase significantly, while activating extracellular signal‐regulated kinase to a lesser extent. Treatment with anti‐TLR3 antibody inhibited dsRNA‐mediated interleukin‐6 (IL‐6) production. In the presence of mitogen‐activated protein kinase inhibitors, astrocytes failed to secrete IL‐6 in response to dsRNA treatment. Therefore, dsRNA‐induced IL‐6 production is dependent on mitogen‐activated protein kinases and type I IFN production is dependent on IRF3 in brain astrocytes. These results suggest that brain inflammation, which produces inflammatory cytokines and type I IFNs, may enhance TLR3 expression in astrocytes. Additionally, upregulated TLR3 might modulate inflammatory processes by producing proinflammatory cytokines.
The periodontal pathogen Porphyromonas gingivalis cleaves apoB‐100 and increases the expression of apoM in LDL in whole blood leading to cell proliferation
Authors: Bengtsson T. , Karlsson H. , Gunnarsson P. , Skoglund C. , Elison C. , Leanderson P. , Lindahl M.
Published: February 2008

Objective.  Several studies support an association between periodontal disease and atherosclerosis with a crucial role for the pathogen Porphyromonas gingivalis. This study aims at investigating the proteolytic and oxidative activity of P. gingivalis on LDL in a whole blood system using a proteomic approach and analysing the effects of P. gingivalis‐modified LDL on cell proliferation.

Methods.  The cellular effects of P. gingivalis in human whole blood were assessed using lumi‐aggregometry analysing reactive oxygen species production and aggregation. Blood was incubated for 30 min with P. gingivalis, whereafter LDL was isolated and a proteomic approach was applied to examine protein expression. LDL‐oxidation was determined by analysing the formation of protein carbonyls. The effects of P. gingivalis‐modified LDL on fibroblast proliferation were studied using the MTS assay.

Results.  Incubation of whole blood with P. gingivalis caused an extensive aggregation and ROS production, indicating platelet and leucocyte activation. LDL prepared from bacteria‐exposed blood showed an increased protein oxidation, elevated levels of apoM and formation of two apoB‐100 N‐terminal fragments. Porphyromonas gingivalis‐modified LDL markedly increased the growth of fibroblasts. Inhibition of gingipain R suppressed the modification of LDL by P. gingivalis.

Conclusions.  The ability of P. gingivalis to change the protein expression and proliferative capacity of LDL may represent a crucial event in periodontitis‐associated atherosclerosis.
PYK10, a β‐glucosidase located in the endoplasmatic reticulum, is crucial for the beneficial interaction between Arabidopsis thaliana and the endophytic fungus Piriformospora indica
Authors: Sherameti Irena , Venus Yvonne , Drzewiecki Corinna , Tripathi Swati , Dan Vipin Mohan , Nitz Inke , Varma Ajit , Grundler Florian M. , Oelmüller Ralf
Published: February 2008

Piriformospora indica, an endophyte of the Sebacinaceae family, promotes growth and seed production of many plant species, including Arabidopsis. Growth of a T‐DNA insertion line in PYK10 is not promoted and the plants do not produce more seeds in the presence of P. indica, although their roots are more colonized by the fungus than wild‐type roots. Overexpression of PYK10 mRNA did not affect root colonization and the response to the fungus. PYK10 codes for a root‐ and hypocotyl‐specific β‐glucosidase/myrosinase, which is implicated to be involved in plant defences against herbivores and pathogens. Expression of PYK10 is activated by the basic helix‐loop‐helix domain containing transcription factor NAI1, and two Arabidopsis lines with mutations in the NAI1 gene show the same response to P. indica as the PYK10 insertion line. PYK10 transcript and PYK10 protein levels are severely reduced in a NAI1 mutant, indicating that PYK10 and not the transcription factor NAI1 is responsible for the response to the fungus. In wild‐type roots, the message level for a leucine‐rich repeat protein LRR1, but not for plant defensin 1.2 (PDF1.2), is upregulated in the presence of P. indica. In contrast, in lines with reduced PYK10 levels the PDF1.2, but not LRR1, message level is upregulated in the presence of the fungus. We propose that PYK10 restricts root colonization by P. indica, which results in the repression of defence responses and the upregulation of responses leading to a mutualistic interaction between the two symbiotic partners.
Sequential glucosylation of a furofuran lignan, (+)‐sesaminol, by Sesamum indicum UGT71A9 and UGT94D1 glucosyltransferases
Authors: Noguchi Akio , Fukui Yuko , Iuchi‐Okada Asako , Kakutani Saki , Satake Honoo , Iwashita Takashi , Nakao Masahiro , Umezawa Toshiaki , Ono Eiichiro
Published: February 2008

(+)‐Sesaminol 2‐O‐triglucoside is the most abundant water‐soluble furofuran lignan in sesame seeds (Sesamum indicum) and is considered to be a beneficial compound for human health. The biosyntheses and physiological roles of lignan glycosides, however, remain elusive. Here we report the molecular identification and biochemical characterization of two Sesamum uridine diphosphate (UDP) glucose:lignan glucosyltransferases. Sesamum indicum UGT71A9 preferentially glucosylated at the 2‐hydroxyl group of (+)‐sesaminol, resulting in (+)‐sesaminol 2‐O‐glucoside. Similarly, two UGT71A9 homologs from Sesamum radiatum (UGT71A10) and Sesamum alatum (UGT71A8) also showed (+)‐sesaminol glucosylating activity, evidencing the functional conservation of (+)‐sesaminol 2‐O‐glucosyltransferases in the Sesamum genus. In addition, S. indicum UGT94D1 specifically glucosylated at the 6′‐hydroxyl group of the sugar moiety of (+)‐sesaminol 2‐O‐glucoside but not at that of flavonoid glucosides. The gene expression patterns of UGT71A9 and UGT94D1 during seed development were correlated with the glucosylating activities toward (+)‐sesaminol in planta, suggesting that the two lignan UDP‐glycosyltransferases participate in the sequential glucosylation steps in the biosynthesis of (+)‐sesaminol 2‐O‐triglucoside.
A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes
Authors: Xie Zhengzhi , Kapteyn Jeremy , Gang David R.
Published: February 2008

The glandular trichome is an excellent model system for investigating plant metabolic processes and their regulation within a single cell type. We utilized a proteomics‐based approach with isolated trichomes of four different sweet basil (Ocimum basilicum L.) lines possessing very different metabolite profiles to clarify the regulation of metabolism in this single cell type. Significant differences in the distribution and accumulation of the 881 highly abundant and non‐redundant protein entries demonstrated that although the proteomes of the glandular trichomes of the four basil lines shared many similarities they were also each quite distinct. Correspondence between proteomic, expressed sequence tag, and metabolic profiling data demonstrated that differential gene expression at major metabolic branch points appears to be responsible for controlling the overall production of phenylpropanoid versus terpenoid constituents in the glandular trichomes of the different basil lines. In contrast, post‐transcriptional and post‐translational regulation of some enzymes appears to contribute significantly to the chemical diversity observed within compound classes for the different basil lines. Differential phosphorylation of enzymes in the 2‐C‐methyl‐d‐erythritol 4‐phosphate (MEP)/terpenoid and shikimate/phenylpropanoid pathways appears to play an important role in regulating metabolism in this single cell type. Additionally, precursors for different classes of terpenoids, including mono‐ and sesquiterpenoids, appear to be almost exclusively supplied by the MEP pathway, and not the mevalonate pathway, in basil glandular trichomes.
AtMKK1 mediates ABA‐induced CAT1 expression and H2O2 production via AtMPK6‐coupled signaling in Arabidopsis
Authors: Xing Yu , Jia Wensuo , Zhang Jianhua
Published: February 2008

Catalase controls cellular H2O2 and plays important roles in the adaptation of plants to various stresses, but little is known about the signaling events that lead to the expression of CAT1 and the production of H2O2. Here we report the dependence of CAT1 expression and H2O2 production on a mitogen‐activated protein kinase (MAPK) cascade. CAT1 transcript was induced in an ABA‐dependent way and the induction was abolished in the T‐DNA insertion mutant mkk1 (SALK_015914), while AtMKK1 overexpression significantly enhanced the ABA‐induced CAT1 expression and H2O2 production. AtMPK6, another component in the MAPK cascade, was also involved: mpk6 mutant blocked and overexpressing AtMPK6 enhanced the ABA‐dependent expression of CAT1 and H2O2 production. The activity of AtMPK6 was increased by ABA in an AtMKK1‐dependent manner. These data clearly suggest an ABA‐dependent signaling pathway connecting CAT1 expression through a phosphorelay including AtMKK1 and AtMPK6. In further support of this view, mkk1 mutant reduced both the sensitivity to ABA during germination and the drought tolerance of seedlings, whereas the AtMKK1 overexpression line showed the opposite responses when compared with the wild type. The data suggest AtMKK1–AtMPK6 to be a key module in an ABA‐dependent signaling cascade causing H2O2 production and stress responses.
Cloning the wild mouflon
Authors: Heatherington Tracey
Published: February 2008

In 2001, a collaboration between Edinburgh scientists and a research team in Teramo, Italy, made the first surviving clone of an endangered mammal: a wild sheep species called the mouflon, indigenous to the Mediterranean islands of Sardinia, Corsica and Cyprus. Amidst fierce debates on the ethics of cloning, this application of biotechnology to wildlife conservation appeared relatively felicitous. Will cloning techniques bring redemption for the immanent loss of genetic resources? How would this alter the very nature and culture of biodiversity protection? On an island of notorious shepherds, wilderness and wildlife are increasingly valued over the objects of traditional pastoral work. Set against the background of ongoing tensions over the creation of a new national park in Sardinia, the story of the cloned mouflon signified the power of new science to redefine the politics of biodiversity, undermining the cultural authority of shepherd towns over human‐animal relations.
Flights of passion
Authors: Falzon Mark‐Anthony
Published: February 2008

The hunting of wild birds is practised intensively in the Mediterranean region generally and in particular the islands. This article looks at the dynamics of shooting and trapping in the archipelago‐state of Malta. Hunting passion, land transformations, and interactions with a number of key actors are discussed with reference to local politics and EU legislation. It is also suggested that Mediterranean bird hunting might be understood as a legacy of deep rooted practices of food production in the region.
Evolution of bone mineral density in AIDS patients on treatment with zidovudine/lamivudine plus abacavir or lopinavir/ritonavir
Authors: Rivas P , Górgolas M , García‐Delgado R , Díaz‐Curiel M , Goyenechea A , Fernández‐Guerrero ML
Published: February 2008

Objectives

The aim of the study was to determine the factors that may contribute to decreases in bone mineral density (BMD) in patients with AIDS.

Methods

This was a prospective, non‐randomized study. Dual X‐ray absorptiometry (DXA) was used to determine the BMD of the lumbar spine, femoral neck and distal radius in treatment‐naïve HIV‐infected male patients with AIDS before and after 1 year of treatment with zidovudine (ZDV)/lamivudine (3TC) plus abacavir (ABC) or lopinavir/ritonavir (LPV/r).

Results

Basal DXA was performed in 50 patients with CD4 counts <200 cells/μL and/or any AIDS‐defining condition. Thirty‐two patients completed 1 year with full adherence (17 on ABC and 15 on LPV/r) and a second DXA was then performed. At baseline, 19% had osteopenia at the lumbar spine and 19% at the femoral neck. Low body weight was related to low BMD. After 48 weeks, BMD loss was significant at the three locations. The percentage of BMD loss at the femoral neck tended to be greater in the lopinavir group (5.3 vs. 3.2%, P=0.058). The differences became significant at the lumbar spine (5.7 vs. 2.7%, P=0.044). In the multivariate analysis, the treatment with LPV/r remained associated with bone loss at the lumbar spine.

Conclusions

Osteopenia is frequent in treatment‐naïve HIV‐infected men with AIDS. Bone loss is higher with LPV/r‐based regimens compared with triple nucleoside reverse transcriptase inhibitors.
Early changes in adipokine levels and baseline limb fat may predict HIV lipoatrophy over 2 years following initiation of antiretroviral therapy*
Authors: Calmy A , Carey D , Mallon PWG , Wand H , Law M , Cooper DA , Carr A ,   on behalf of the INITIO Trial International Co‐ordinating Committee,   HAMA study coordination team
Published: February 2008

Background

No biological marker has been identified that predicts the development of lipodystrophy (LD). We investigated whether metabolic and body composition parameters could predict the development of LD over 2 years in adults initiating antiretroviral therapy (ART).

Methods

We used stored plasma collected at baseline and weeks 12, 24 and 48 from adults initiating combination ART. Adipocytokine, inflammatory cytokine, lipid and glycaemic parameters were measured and related to subsequent lipoatrophy (loss of limb fat mass of at least 2 kg from weeks 24 to 96 by dual‐energy X‐ray absorptiometry) and an increase in visceral adipose tissue (VAT; an increase of at least 18 cm2 from baseline to week 48 by abdominal computed tomography). Risk factors associated with limb fat loss and VAT gain were analysed by logistic regression.

Results

Fifty‐four HIV‐infected, treatment‐naïve adults were included in the study: 53 (98%) of them were men, and they had a median age of 39 years [interquartile range (IQR) 34–48 years] and a median body mass index of 22.6 kg/m2 (IQR 20–24.8 kg/m2). In multivariate analysis, a higher baseline limb fat percentage, and a 1 mmol/L increase in plasma leptin levels during the first 6 months of ART, independently predicted a peripheral fat loss of ≥2 kg [odds ratio (OR) 2.58, 95% confidence interval (CI) 1.04–6.41; OR 3.15, 95% CI 1.34–7.35, respectively). VAT changes showed a borderline association with high baseline tumour necrosis factor‐α levels and hip circumference (OR 1.04, 95% CI 1.00–1.07; OR 1.44, 95% CI 1.07–1.95, respectively).

Conclusions

In ART‐naïve men, higher baseline limb fat and an early increase in leptin concentrations may predict the subsequent development of lipoatrophy. We did not find the same risk factors in the two different groups of patients with peripheral fat loss and central fat gain, suggesting a partially independent pathogenesis.
CD38 expression on CD8 T cells has a weak association with CD4 T‐cell recovery and is a poor marker of viral replication in HIV‐1‐infected patients on antiretroviral therapy
Authors: Steel A , John L , Shamji MH , Henderson DC , Gotch FM , Gazzard BG , Kelleher P
Published: February 2008

Objective

The aim of the study was to determine whether the expression of CD38 on CD8 T cells can identify patients with virological failure on antiretroviral therapy (ART).

Design

This was a cross‐sectional study of patients attending a single HIV clinic in London.

Methods

The expression of CD38 on CD8 T cells was assessed using a biologically calibrated flow cytometry protocol. Patients were characterized by lymphocyte subset and viral load measurements. Characteristics including historical CD4 T cell counts, therapeutic history, co‐infections and demographics were obtained from medical records.

Results

Elevated levels of CD8 CD38high T cells were found in HIV‐1‐infected patients who failed to suppress viral replication with ART; however, this parameter lacked sufficient sensitivity and specificity to replace viral load testing in assessing the efficacy of ART. Increased levels of CD8 CD38high cells were associated with reduced CD4 T cell counts in HIV‐1‐infected patients on ART after correcting for known determinants of CD4 T‐cell recovery.

Conclusions

The expression of CD38 on CD8 T cells lacks sufficient sensitivity and specificity to be used as a surrogate marker for viral load to monitor HIV‐1 infection. T‐cell activation is associated with reduced CD4 T‐cell reconstitution in patients receiving ART.
HIV voluntary counselling and testing in Nakuru, Kenya: findings from a community survey
Authors: Irungu TK , Varkey P , Cha S , Patterson JM
Published: February 2008

Objectives

HIV voluntary counselling and testing (VCT) is important for prevention, detection and treatment of HIV infection. A study was conducted to determine the extent of utilization of VCT, and to study the attitudes and preferences of the community regarding VCT.

Methods

A total of 301 adults, aged 18–49 years, residing in Nakuru, Kenya were randomly selected using a two‐stage sampling process. A self‐administered questionnaire delivered during home visits was used to collect data over a 4‐week period.

Results

The majority of study participants (184 of 287; 64.1%) had never been tested for HIV; 77 (26.8%) had received VCT, and 26 (9.1%) had received HIV testing without counselling. A total of 219 (78.2%) of the 280 responding participants expressed readiness to have VCT. The majority of participants (216 of 296; 73%) preferred VCT, while 46 (15.5%) preferred testing without counselling. The majority (227; 76.7%) preferred couple testing and dedicated clinics and private doctors' offices as testing facilities. The choice of a nearby facility was ranked above the provision of anonymity by most participants (162 of 298; 54.4%; vice versa for 136 of 298; 45.6%).

Conclusions

With HIV/AIDS continuing to be a major public health concern in Kenya, the issues surrounding acceptance and use of VCT need to be addressed. Enhancing community awareness of the benefits of early HIV diagnosis, providing couple‐based VCT as an integral part of VCT and increasing access to VCT testing sites may enhance utilization of VCT.
Beyond “Global Production Networks”: Australian Fashion Week's Trans‐Sectoral Synergies
Authors: WELLER SALLY
Published: February 2008

ABSTRACT When studies of industrial organisation are informed by commodity chain, actor network, or global production network theories and focus on tracing commodity flows, social networks, or a combination of the two, they can easily overlook the less routine trans‐sectoral associations that are crucial to the creation and realisation of value. This paper shifts attention to identifying the sites at which diverse specialisations meet to concentrate and amplify mutually reinforcing circuits of value. These valorisation processes are demonstrated in the case of Australian Fashion Week, an event in which multiple interests converge to synchronize different expressions of fashion ideas, actively construct fashion markets and enhance the value of a diverse range of fashionable commodities. Conceptualising these interconnected industries as components of a trans‐sectoral fashion complex has implications for understanding regional development, world cities, production location, and the manner in which production systems “touch down” in different places.
No Man's Brand—Brands, Institutions, and Fashion
Authors: POWER DOMINIC , HAUGE ATLE
Published: February 2008

ABSTRACT Branding has become so intertwined with consumption that today's consumers have often deeply personal relationships to brands and brand histories. Branding is an attempt to strategically “personify” products and to encapsulate a balance between different economic values: quality, utility, symbolic, and cultural worth. In this paper we argue that the relationship between the contemporary consumer and producer is mediated by and governed by a reflexive construction of brands. As such brands are best understood from an institutional perspective. The paper illustrates the institutional role of brands by using the example of the fashion industry. It is argued that in the fashion industry, a focus on consumer‐producer brand‐building and brand loyalty is central to the commodity and value chains built around products. We conclude by suggesting that economic geography has consistently undervalued brands as an area of study. By taking brands as a core product in industrial production rather than as an interesting aside for sociologists, historians, and cultural theorists, economic geography can better understand the institutions governing the economy. In particular, better understanding the institution of brands helps us better appreciate the dynamics systems within which commodities and commodity chains are formed.
THE MASS ON THE WORLD
Authors: PENDERGAST, S.J. RICHARD J.
Published: February 2008

The present article has three sections. The first one discusses the relationship of the theological theory of transubstantiation to that of transignification (change of meaning) and transfinalization (change of finality), ideas that were introduced just before the time of Vatican II by northern European theologians. The second section develops a holistic view of the nature of matter. Our present scientific knowledge seems to require that we abandon the Aristotelian theory of hylomorphism in favor of a theory in which real beings of a certain level ‘sublate’ real but subordinate beings of lower levels. For example, a human being is a substance that includes within itself many smaller substances. When he was in the flesh, the physical body of Christ included within itself a vast number of interconnected atoms and molecules. The third section discusses ideas of Teilhard de Chardin about the relationship of Christ to matter.
Age‐related intrinsic changes in human bone‐marrow‐derived mesenchymal stem cells and their differentiation to osteoblasts
Authors: Zhou Shuanhu , Greenberger Joel S. , Epperly Michael W. , Goff Julie P. , Adler Carolyn , LeBoff Meryl S. , Glowacki Julie
Published: February 2008

In vivo and in vitro studies indicate that a subpopulation of human marrow‐derived stromal cells (MSCs, also known as mesenchymal stem cells) has potential to differentiate into multiple cell types, including osteoblasts. In this study, we tested the hypothesis that there are intrinsic effects of age in human MSCs (17–90 years). We tested the effect of age on senescence‐associated β‐galactosidase, proliferation, apoptosis, p53 pathway genes, and osteoblast differentiation in confluent monolayers by alkaline phosphatase activity and osteoblast gene expression analysis. There were fourfold more human bone MSCs (hMSCs) positive for senescence‐associated β‐galactosidase in samples from older than younger subjects (P < 0.001; n = 17). Doubling time of hMSCs was 1.7‐fold longer in cells from the older than the younger subjects, and was positively correlated with age (P = 0.002; n = 19). Novel age‐related changes were identified. With age, more cells were apoptotic (P = 0.016; n = 10). Further, there were age‐related increases in expression of p53 and its pathway genes, p21 and BAX. Consistent with other experiments, there was a significant age‐related decrease in generation of osteoblasts both in the STRO‐1+ cells (P = 0.047; n = 8) and in adherent MSCs (P < 0.001; n = 10). In sum, there is an age‐dependent decrease in proliferation and osteoblast differentiation, and an increase in senescence‐associated β‐galactosidase‐positive cells and apoptosis in hMSCs. Up‐regulation of the p53 pathway with age may have a critical role in mediating the reduction in both proliferation and osteoblastogenesis of hMSCs. These findings support the view that there are intrinsic alterations in human MSCs with aging that may contribute to the process of skeletal aging in humans.
Neuropsychological Deficits in Alcoholics: Facts and Fancies
Authors: Parsons Oscar A.
Published: February 2008

Five facts and complementary “fancies” have been examined. Brain damage is found in alcoholics but whether alcohol directly causes the damage is not clear at this time. Cortical and subcortical atrophy is found in 50%‐70% of unselected alcoholics coming for treatment but a substantial minority of alcoholics do not have such changes. Brain changes in alcoholics are associated significantly with neuropsychological deficits but the magnitude of the correlations leaves much of the variance unexplained. Neuropsychological deficits in alcoholics (who do not have “mental deterioration”) are relatively specific and in most instances functions can be recovered but there are some suggestions of more permanent, if limited, deficits. While specific neuropsychological deficits in alcoholics have been recurrently established, their relationship to therapeutic strategies and therapeutic outcome remains to be explored. Finally, it is abundantly clear that implicit and explicit criteria for patient selection in neuropsychological studies are major, if not critical, variables in work in this field.
Biochemical Tests for the Detection of Alcoholism: Comparison of Plasma Alpha‐Amino‐n‐Butyric Acid with Other Available Tests
Authors: Shaw Spencer , Lue Shih‐Lin , Lieber Charles S.
Published: February 2008

The measurement of AANB relative to leucine was found to be a useful biochemical test for the detection of chronic alcohol consumption. This test, in combination with GGTP determinations, provided a sensitive means of detection (81% positive) for chronic alcohol consumption with a minimum of false positive determinations (2%).
Diagnosis and Treatment of the Elderly Alcoholic
Authors: Zimberg Sheldon
Published: February 2008

Treatment interventions will be much more effective when delivered through facilities serving the aged, such as senior citizen programs, outpatient, geriatric, medical or psychiatric programs, nursing homes, or home‐care programs. It is unlikely that significant numbers of elderly will be willing to go to alcoholism programs to deal with their problem drinking.