bluuebunny/crossref_metadata_2025 huggingface dataset:
Deletion-Based Reverse Genetics in Medicago truncatula
Authors: Rogers Christian , Wen Jiangqi , Chen Rujin , Oldroyd Giles
Published: September 2009

The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA.
A Systems-Level Analysis of the Effects of Light Quality on the Metabolism of a Cyanobacterium
Authors: Singh Abhay K. , Bhattacharyya-Pakrasi Maitrayee , Elvitigala Thanura , Ghosh Bijoy , Aurora Rajeev , Pakrasi Himadri B.
Published: September 2009

Photosynthetic organisms experience changes in light quantity and light quality in their natural habitat. In response to changes in light quality, these organisms redistribute excitation energy and adjust photosystem stoichiometry to maximize the utilization of available light energy. However, the response of other cellular processes to changes in light quality is mostly unknown. Here, we report a systematic investigation into the adaptation of cellular processes in Synechocystis species PCC 6803 to light that preferentially excites either photosystem II or photosystem I. We find that preferential excitation of photosystem II and photosystem I induces massive reprogramming of the Synechocystis transcriptome. The rewiring of cellular processes begins as soon as Synechocystis senses the imbalance in the excitation of reaction centers. We find that Synechocystis utilizes the cyclic photosynthetic electron transport chain for ATP generation and a major part of the respiratory pathway to generate reducing equivalents and carbon skeletons during preferential excitation of photosystem I. In contrast, cytochrome c oxidase and photosystem I act as terminal components of the photosynthetic electron transport chain to produce sufficient ATP and limited amounts of NADPH and reduced ferredoxin during preferential excitation of photosystem II. To overcome the shortage of NADPH and reduced ferredoxin, Synechocystis preferentially activates transporters and acquisition pathways to assimilate ammonia, urea, and arginine over nitrate as a nitrogen source. This study provides a systematic analysis of cellular processes in cyanobacteria in response to preferential excitation and shows that the cyanobacterial cell undergoes significant adjustment of cellular processes, many of which were previously unknown.
Identification of an Arabidopsis Feruloyl-Coenzyme A Transferase Required for Suberin Synthesis
Authors: Molina Isabel , Li-Beisson Yonghua , Beisson Fred , Ohlrogge John B. , Pollard Mike
Published: September 2009

All plants produce suberin, a lipophilic barrier of the cell wall that controls water and solute fluxes and restricts pathogen infection. It is often described as a heteropolymer comprised of polyaliphatic and polyaromatic domains. Major monomers include ω-hydroxy and α,ω-dicarboxylic fatty acids, glycerol, and ferulate. No genes have yet been identified for the aromatic suberin pathway. Here we demonstrate that Arabidopsis (Arabidopsis thaliana) gene AT5G41040, a member of the BAHD family of acyltransferases, is essential for incorporation of ferulate into suberin. In Arabidopsis plants transformed with the AT5G41040 promoter:YFP fusion, reporter expression is localized to cell layers undergoing suberization. Knockout mutants of AT5G41040 show almost complete elimination of suberin-associated ester-linked ferulate. However, the classic lamellar structure of suberin in root periderm of at5g41040 is not disrupted. The reduction in ferulate in at5g41040-knockout seeds is associated with an approximate stoichiometric decrease in aliphatic monomers containing ω-hydroxyl groups. Recombinant AT5G41040p catalyzed acyl transfer from feruloyl-coenzyme A to ω-hydroxyfatty acids and fatty alcohols, demonstrating that the gene encodes a feruloyl transferase. CYP86B1, a cytochrome P450 monooxygenase gene whose transcript levels correlate with AT5G41040 expression, was also investigated. Knockouts and overexpression confirmed CYP86B1 as an oxidase required for the biosynthesis of very-long-chain saturated α,ω-bifunctional aliphatic monomers in suberin. The seed suberin composition of cyp86b1 knockout was surprisingly dominated by unsubstituted fatty acids that are incapable of polymeric linkages. Together, these results challenge our current view of suberin structure by questioning both the function of ester-linked ferulate as an essential component and the existence of an extended aliphatic polyester.
Turkey: Toward EU Accession
Authors: Togan Sübidey
Published: September 2009

The purpose of this paper is to study selected aspects of Turkish accession to the EU. Joining the EU will require that Turkey attains macroeconomic stability, adopts the Common Agricultural Policy, and liberalizes its services and network industries. Furthermore, joining the EU will require Turkey to adopt and implement the whole body of EU legislation and standards – the acquis communautaire. According to the EU membership criteria, new members must be able to demonstrate the ‘ability to take on the obligations of membership including adherence to the aims of political, economic and monetary union’. Thus Turkey will be expected to adopt the euro when it is ready to do so, but not immediately upon accession. Integration will boost allocative efficiency in the Turkish economy which in turn will make the country a better place to invest. Furthermore, Turkey will reap the benefits from monetary integration and from migration of labour to the EU. But the welfare gains will have a price, and the price will be the adjustment costs associated with the adoption of the acquis communautaire. The final section of the paper considers the effects of accession on the EU in terms of migration and budgetary effects.
Forest eternal? Endemic butterflies of the Bamenda highlands, Cameroon, avoid close‐canopy forest
Authors: Tropek Robert , Konvicka Martin
Published: September 2009

The Gulf of Guinea Highlands, a centre of endemism and high conservation importance, represent the only large mountain system in West and Central Africa. We studied habitat use of three common endemic butterflies Colias electo manengoubensis, Bicyclus anisops and Mylothris jacksoni knutsoni, using time‐standardized surveys in four distinct habitats: close‐canopy forest, scrub and forest edges, bracken and grasslands. All three species avoided close‐canopy forests and bracken; the Colias preferring grassland, whereas Bicyclus and Mylothris scrub and forest edges. Ordination analyses of surrounding habitats indicated that all three taxa required heterogeneous landscape mosaics. We argue that the life history traits of taxa with limited geographic distribution may reflect past habitat conditions within their ranges, and that these habitat preferences can indicate the continuous existence of mosaic of forest and nonforest habitats in the West African mountains. Such a landscape was probably maintained by climatic fluctuation and large herbivores, further modified by human impact. This conclusion is consistent with the palaeoenvironmental record and with the requirements of Afromontane endemics from other groups. Recent conservation activities focus on patches of continuous forests, but the mosaic landscapes are no less threatened by intensive agriculture, and should be included to protected areas.
In vitro and in vivo stability of diluted recombinant factor VIII for continuous infusion use in haemophilia A
Authors: REVEL‐VILK S. , BLANCHETTE V. S. , SCHMUGGE M. , CLARK D. S. , LILLICRAP D. , RAND M. L.
Published: September 2009

Summary.  Factor VIII (FVIII) replacement by continuous infusion (CI) is used postoperatively or after significant bleeding. For young paediatric patients, CI may require FVIII dilution. Variable stabilities of diluted full‐length recombinant FVIII Kogenate® FS (KG‐FS) have been reported under different storage conditions. We investigated the recovery and stability of diluted KG‐FS in vitro and in vivo. Kogenate® FS was diluted to 50–120 U mL−1 and its recovery and stability in glass vials or polypropylene syringes was determined. Furthermore, stability of KG‐FS diluted to 80 U mL−1‘administered’ via single‐ and double‐pump mock CI systems was tested. Finally, the in vivo stability of KG‐FS diluted to ∼60 U mL−1 and administered postsurgically by CI with the double‐pump to a paediatric patient with severe haemophilia A undergoing implantable venous access device placement was investigated. Initial KG‐FS dilution resulted in a 10–20% FVIII loss; a further 25–30% loss occurred over 72 h in vials or syringes. With the double‐pump, 1 h recovery was 35%, increasing to 80% by 24 h; the initial losses were because of the Y‐infusion of a 10‐fold larger volume of saline concomitantly with the FVIII. In vivo, CI resulted in stable FVIII activity levels within the target range. These in vitro results are important for the generation of CI guidelines for diluted KG‐FS in the paediatric haemophilic population. That FVIII losses occur upon dilution and with the double‐pump does not preclude use of diluted KG‐FS. Indeed, stable FVIII levels were maintained when diluted KG‐FS was administered by CI with the double‐pump to a paediatric patient postsurgically.
Impact of processing treatments and packaging material on some properties of stored dehydrated cauliflower
Authors: Kadam Dattatreya M. , Samuel David V. K. , Chandra Pitam , Sikarwar Harman S.
Published: September 2009

Investigations were carried out to see the impact of blanching time, pretreatment and storage and packaging on the physico‐chemical properties of solar dehydrated cauliflower. The processing treatments selected for the study were blanching time of 3, 5, 7 and 9 min, potassium metabisulphite (KMS) pretreatment having 0.5%, 1.0% and 1.5% concentration level and storage in high‐density polyethylene, laminated aluminium foil and polypropylene. The cauliflowers were further processed and dehydrated in solar dryer before packing it into different packaging materials. Packed dehydrated cauliflower was stored for 6 months at room temperature. The stored cauliflower samples were tested periodically for their moisture content, rehydration ratio, rehydration coefficient, ascorbic acid and browning. Ranking of blanching time, chemical concentration level and packaging materials were statistically analysed by using SAS package. The samples with 9 min blanching time, followed by dipping in 1.0% KMS solution, and packed in laminated aluminium foil showed better results in comparison with other treatments.
Chemical composition and toxic trace element composition of some Nigerian edible wild mushrooms
Authors: Falade Olumuyiwa S. , Adepoju Oluwatoyin O. , Owoyomi Olanrewaja , Adewusi Steve R.
Published: September 2009

Two essential amino acids (methionine and tryptophan); anti‐nutritional factors (tannin and trypsin inhibitor) and toxic elements (Pb, Cd, Ni, As, Hg and Cr) were determined spectrophotometrically from five edible wild mushrooms. The tryptophan content was between 1.00 and 1.82 g (100 g)−1 but methionine was low at 0.26–1.38 g (100 g)−1. Tannin content was high (30.3–40.0 mg g−1) but trypsin inhibitor was low (22.0–39.5 TIU g−1). Trace elements analysis reviled Pb (0.34–5.06 mg kg−1) to be the highest of all the trace elements. Cd was (0.06–1.70 mg kg−1), Ni (0.26–2.08 mg kg−1), As (0.17–0.92 mg kg−1), Hg (0.01–0.05 mg kg−1) and Cr (0.04–0.22 mg kg−1). These mushrooms are nutritious but must be well processed to eliminate or at least reduce the levels of tannin and Pb to improve their nutritional values.
Heterocyclic amine formation during frying of frozen beefburgers
Authors: Persson Elna , Oroszvári Bea Kovácsné , Tornberg Eva , Sjöholm Ingegerd , Skog Kerstin
Published: September 2009

The formation of heterocyclic amines (HCAs) was studied during frying of beefburgers with different fat contents (6.7%, 16.1% and 39%). Beefburgers were fried from the frozen state for 60, 90, 120 s, and until the centre temperature had reached 72 °C (approximately 150 s) in a double‐sided pan fryer. The beefburgers were analysed for HCAs with solid‐phase extraction and LC/MS detection, and 2‐amino‐3,8‐dimethylimidazo[4,5‐f]quinoxaline (MeIQx), 2‐amino‐3,4,8‐trimethylimidazo[4,5‐f]quinoxaline (4,8‐DiMeIQx), 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine (PhIP), 1‐methyl‐9H‐pyrido[3,4‐b]indole (Harman) and 9H‐pyrido[3,4‐b]indole (Norharman) were detected in all samples. The concentrations of HCAs ranged between 0 and 2.3 ng g−1. The HCAs concentrations were fitted to a first‐order reaction model. The amounts of HCAs in beefburgers fried from the frozen state were in the same range as in beefburgers that have reached room temperature before frying. Furthermore, it was found that the formation of HCAs is not only concentration‐controlled but also mass transport‐controlled and that kinetic models stated in earlier studies fit relatively well our analysed values on HCAs in fried beefburgers.
Development of an indirect α‐actinin‐based immunoassay for the evaluation of protein breakdown and quality loss in fish species subjected to different chilling methods
Authors: Carrera Mónica , Losada Vanesa , Gallardo José Manuel , Aubourg Santiago P. , Piñeiro Carmen
Published: September 2009

α‐Actinin release from the myofibrillar protein fraction to the sarcoplasm can be considered as an accurate proteolysis index in seafood muscle. The main objective of the present study was to develop a specific enzyme‐linked immunosorbent assay (ELISA), based on the use of a monoclonal antibody against α‐actinin to evaluate the degree of proteolysis in two different chilled fish species – European hake (Merluccius merluccius) and turbot (Psetta maxima) – kept under two different storage systems: flake ice and slurry ice. Comparison with sensory assessment, K‐value and sarcoplasmic protein profiles was carried out. A different degree of proteolysis could be observed in both fish species; thus, the immunoassay was shown to be useful in monitoring the protein degradation events in hake muscle especially under flake ice storage. In the case of turbot, as very low proteolysis development could be obtained, the assay was not suitable for assessing quality changes. A different break point of immunoassay values for each fish species is suggested.
Effects of a bacteriocin‐like substance produced by Leuconostoc mesenteroides subsp. cremoris on spoilage strain Lactobacillus fructivorans and various pathogens
Authors: Yurdugül Seyhun , Bozoglu Faruk
Published: September 2009

Certain lactic acid bacteria present in the natural flora of the wine fermentation medium perform the malolactic fermentation process and other biochemical activities which lead to the formation of the outstanding aroma and bouquet of wine. However, because of the spoilage phenomena caused also by certain lactic cultures, off‐odours formed via metabolic side reactions cause severe economic losses in the wine industry. Several control mechanisms were introduced in order to eliminate these spoilage cultures, but none of these has been implemented as an efficient and healthy process. A partially purified bacteriocin‐like inhibitory substance (BLIS) with a molecular weight of 32 000 Da, obtained from a Leuconostoc mesenteroides subsp. cremoris isolate belonging to the native flora of wines of the Cappadocia region, was studied for its inhibitory activity on the spoilage strain, Lactobacillus fructivorans, isolated from the same wine flora and several other pathogens, and was found to be efficient in eliminating both the spoilage strain and the pathogens.
Some properties of polyphenol oxidase from lily
Authors: Yang Ying , Wang Zhang
Published: September 2009

A study of crude polyphenol oxidase (PPO) from lily bulbs was carried out to provide information useful for guiding food processing operations. Optimum pH for the enzyme activity in the presence of catechol, were 4.0 and 7.0 at room temperature(approximately 20 °C) and the enzyme was stable in the pH range from 5.0 to 6.5 at 4 °C for 10 h. Its optimum temperature was 40 °C and the heat inactivation of the enzyme followed first‐order kinetics. Lily PPO possessed a diphenolase activity toward catechol, catechin and gallic acid; catechin was the best substrate for the enzyme considering the Vmax/Km ratio. The most effective enzyme inhibitor was sodium sulphite, although ascorbic acid, l‐cysteine and thiourea were also effective inhibitors at high concentration. But NaCl and citric acid were poor inhibitors of the enzyme. Data generated by this study might help to better prevent lily bulbs browning.
A rapid direct solvent extraction method for the extraction of cyclobutanones from irradiated chicken and liquid whole egg
Authors: Tewfik Ihab
Published: September 2009

2‐Alkylcyclobutanones (cyclobutanones) are accepted as radiolytic markers in lipid‐containing foods (LCF). To date, cyclobutanones have not been detected in non‐irradiated foods. Their identification is the basis of a standardised detection test for irradiated LCF (BS EN 1785, 2003). This paper reports work to develop and refine a new rapid method for the analysis of cyclobutanones in irradiated LCF (e.g. chicken meat and liquid whole egg). Direct solvent extraction (DSE) enables the efficient screening of large numbers of food samples and is not as resource intensive as the BS EN 1785 (2003) method. The new DSE appears to be a promising, rapid, simple and robust method for the analysis of irradiated lipid‐containing foods.
Measurement of odour after in vitro or in vivo ingestion of raw or heated garlic, using electronic nose, gas chromatography and sensory analysis
Authors: Tamaki Kazuhiko , Sonoki Shigenori , Tamaki Takeshi , Ehara Katsuo
Published: September 2009

The possibility of characterising the garlic odour in in vitro and in vivo was demonstrated using the newly developed electronic nose, based on an array of metal oxide semiconductor sensors. Two grams of raw and heat‐treated garlic, and breath odour after eating 2 g of raw garlic and heat‐treated garlic were analysed with an electronic nose. Furthermore, calculation of F‐value (odour quality) and S‐value (odour strength) demonstrated distinct odour differences between the samples, and that the electronic nose could differentiate between the various garlic associated odours corresponding to the different origins (in vivo or in vitro), or to the different processing (raw or heat‐treated). The correlation between gas chromatography and sensory analysis was also discussed in order to identify the volatile compounds in the sample, and to investigate the association with the response of human perception to the samples. Results showed that odour sensor data were easier to obtain and were well correlated with both types of instrument.
A fuzzy comprehensive evaluation for selecting yeast for cider making
Authors: Peng Bangzhu , Yue Tianli , Yuan Yahong
Published: September 2009

In this article, we present a new approach in solving the problem of selecting proper and excellent cider yeast. Eight different yeast strains commonly used in the cider industry were selected for this experiment. Different ciders were fermented by the yeasts. Sensory evaluation was conducted first. Then, aroma components were identified by the headspace‐solid phase microextraction–gas chromatography–mass spectrometry. Their contents were determined using quantitative standards with known amounts of target components and 2‐octanol as internal standards. A model of fuzzy comprehensive evaluation was established and used to assess and rank the cider‐making attributes of all eight yeast strains. Saccharomyces cerevisiae F14 was selected out of the eight yeasts for the best cider. The results suggest that the method described in this article is more accurate and objective than conventional methods.
‘Marking’ the white terrain in indigenous health research: literature review
Authors: Martin‐McDonald Kristine , McCarthy Alexandra
Published: September 2009

Title.  ‘Marking’ the white terrain in indigenous health research: literature review

Aim.  This paper is a report of a literature review of the concept of whiteness in relation to research partnerships with indigenous Australian healthcare professionals, participants and community members.

Background.  As researchers, we were confronted with the visibility of our whiteness and the oppressive, discriminating history on our indigenous partners wrought by the colour of our skin. This personal discord began an intensely provocative, reflective journey accompanied by a search of the literature on ‘whiteness’.

Methods.  The EBSCOhost, InfoTrac, Blackwell Synergy, ScienceDirect, SAGE Full‐Text Collections and CINAHL databases were searched in 2004. The primary keywords were ‘whiteness’, ‘white studies’ and ‘white privilege’. Secondary keywords: ‘culture’, ‘race’, ‘racism’, ‘indigenous’, ‘indigenous communities’, ‘race relations’ and ‘colonialism’. No date restrictions were imposed, but most of the literature dated from the 1990s.

Findings.  Exposure to the literature on ‘whiteness’ and the experience of working with indigenous Australians challenged us to recognize and address the privilege and power historically and contemporaneously conferred on us as white women. Largely invisible to white people is the structural advantage conferred by the ‘white’ standpoint and the set of ‘unmarked’ cultural practices that are usually set as the default positioning.

Conclusion.  To achieve useful research outcomes that influence the well‐being of indigenous populations necessitates that non‐indigenous researchers and healthcare providers stringently examine their own racial and social positioning. Without doing this we, consciously or otherwise, uphold white hegemony and racialist inequality.
Why relatives do not donate organs for transplants: ‘sacrifice’ or ‘gift of life’?
Authors: Sque Magi , Long Tracy , Payne Sheila , Allardyce Diana
Published: September 2009

Title.  Why relatives do not donate organs for transplants: ‘sacrifice’ or ‘gift of life’?

Aim.  This paper is a report of a study to explore the reasons family members declined organ donation from a deceased relative.

Background.  In the United Kingdom family members’ consent is usually sought before organ donation from their deceased relative can proceed. Knowledge of the concerns that may influence families’ decision‐making could be helpful to nurses supporting bereaved family members.

Method.  A convenience sample of 26 family members, who declined donation of their deceased relatives’ (n = 23) organs, were recruited via three media campaigns in large conurbations and from four intensive care units in the United Kingdom. Data were collected in 2005 using interviews.

Findings.  Donation decisions depended on a number of converging factors in a particular situation and not necessarily on the views of relatives about donation, or the reported wishes of the deceased in life, except if the person had stated that they did not wish to be an organ donor. Therefore, reported pro‐donation views held by the family, or the deceased in life, did not guarantee donation. Protecting the dead body, which related to keeping the body whole and intact was the most frequently‐recurring theme, being reported in 15 interviews.

Conclusion.  Families’ wishes to protect the dead body may stimulate tension between the notions of ‘gift of life’ as supported by transplant policy and ‘sacrifice’ of the body, which must be made if organ donation is to proceed. This could account for the decision of participants to decline donation even if their deceased relative previously held positive views about organ donation.
The role of personality and self‐efficacy in the selection and retention of successful nursing students: a longitudinal study
Authors: McLaughlin Katrina , Moutray Marianne , Muldoon Orla T.
Published: September 2009

Title.  The role of personality and self‐efficacy in the selection and retention of successful nursing students: a longitudinal study

Aim.  This paper is a report of a study to examine the role of personality and self‐efficacy in predicting academic performance and attrition in nursing students.

Background.  Despite a considerable amount of research investigating attrition in nursing students and new nurses, concerns remain. This particular issue highlights the need for a more effective selection process whereby those selected are more likely to complete their preregistration programme successfully, and remain employed as Registered Nurses.

Method.  A longitudinal design was adopted. A questionnaire, which included measures of personality and occupational and academic self‐efficacy, was administered to 384 students early in the first year of the study. At the end of the programme, final marks and attrition rates were obtained from university records for a total of 350 students. The data were collected from 1999 to 2002.

Findings.  Individuals who scored higher on a psychoticism scale were more likely to withdraw from the programme. Occupational self‐efficacy was revealed to be a statistically significant predictor of final mark obtained, in that those with higher self‐efficacy beliefs were more likely to achieve better final marks. Extraversion was also shown to negatively predict academic performance in that those with higher extraversion scores were more likely to achieve lower marks.

Conclusion.  More research is needed to explore the attributes of successful nursing students and the potential contribution of psychological profiling to a more effective selection process.
Teamwork: a concept analysis
Authors: Xyrichis Andreas , Ream Emma
Published: September 2009

Title. Teamwork: a concept analysis

Aim. This paper is a report of an analysis of the concept of teamwork.

Background. Teamwork is seen as an important facilitator in delivering quality healthcare services internationally. However, research studies of teamwork in health care are criticized for lacking a basic conceptual understanding of what this concept represents. A universal definition for healthcare settings and professionals is missing from published literature.

Method. Walker and Avant’s approach was used to guide this concept analysis. Literature searches used bibliographic databases (Medline, CINAHL, Web of Science, Proquest CSA), internet search engines (GoogleScholar), and hand searches. Literature published between 1976 and 2006 was reviewed but only material in English was included.

Findings. Based on the analysis undertaken, teamwork is proposed as a dynamic process involving two or more healthcare professionals with complementary backgrounds and skills, sharing common health goals and exercising concerted physical and mental effort in assessing, planning, or evaluating patient care. This is accomplished through interdependent collaboration, open communication and shared decision‐making, and generates value‐added patient, organizational and staff outcomes.

Conclusion. Praising the value of teamwork without a common understanding of what this concept represents endangers both research into this way of working and its effective utilization in practice. The proposed definition helps reconcile discrepancies between how this concept is understood by nurses and doctors, as well as allied health professionals. A common understanding can facilitate communication in educational, research and clinical settings and is imperative for improving clarity and validity of future research.
The spatial legacy of introduction:Celastrus orbiculatusin the southern Appalachians, USA
Authors: Albright Thomas P. , Anderson Dean P. , Keuler Nicholas S. , Pearson Scott M. , Turner Monica G.
Published: September 2009

1. A variety of abiotic, biotic, human and historic variables related to environmental suitability and propagule pressure determine the distribution of invasive plants in a landscape. Understanding the role of these variables for invasive species is challenging because environmental variables are often correlated, many invaders have broad ecological niches, and invasive distributions are often highly dynamic.

2. We examined the role of environmental variables at multiple spatial scales on the distribution of an invasive vineCelastrus orbiculatus(Celastraceae) in the southern Appalachians, USA. Using existing and newly collected occurrence data, we constructed spatial generalized linear mixed models ofC. orbiculatusoccurrence in the whole region as well as the areas nearest (established zone) and farthest (pioneer zone) from the purported introduction locus.

3. For the entire study region, distance from the introduction locus and terrain slope were negatively related to the probability of occurrence ofC. orbiculatus. The model was highly discriminatory, with an area under the receiver‐operating characteristic curve of 0·91.

4. Distance from introduction locus and slope were also important in the models for the pioneer and established zones respectively.

5. The pioneer zone model also indicated a negative relationship with elevation and the established zone model indicated a positive relationship with local topographic position, but these models were less discriminatory.

6. Synthesis and applications. Distance from introduction locus was the most powerful variable examined, suggesting an enduring legacy of introduction for the current distribution ofC. orbiculatus.The varying results in the three zones highlight the importance of accounting for both introduction history and uneven propagule pressure in studies of observed invasive species distributions. The observed relationships with distance and elevation suggest that land managers should prepare forC. orbiculatusto expand its distribution in the region over time and with a warming climate.
SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage
Authors: Úbeda Carles , Maiques Elisa , Barry Peter , Matthews Avery , Tormo María Ángeles , Lasa Íñigo , Novick Richard P. , Penadés José R.
Published: September 2009

The SaPIs are chromosomal islands in staphylococci and other Gram‐positive bacteria that carry genes for superantigens, virulence factors, resistance and certain metabolic functions. They have intimate relationships with certain temperate phages involving phage‐induced excision, replication and efficient packaging in special small‐headed infective phage‐like particles, resulting in very high transfer frequencies. They generally contain 18–22 ORFs. We have systematically inactivated each of these ORFs and determined their functional groupings. In other reports, we have shown that five are involved in excision/integration, replication and packaging. In this report, we summarize the mutational analysis and focus on two key ORFs involved in regulation of the SaPI excision–replication–packaging cycle vis‐à‐vis phage induction. These two genes are divergently transcribed and define the major transcriptional organization of the SaPI genome. One of them, stl, encodes a master repressor, possibly analogous to the standard cI phage repressor. Mutational inactivation of this gene results in SaPI excision and replication in the absence of any inducing phage. This replicated SaPI DNA is not packaged; however, since the capsid components are provided by the helper phage. We have not yet ascertained any specific function for the second putative regulatory gene, though it is highly conserved among the SaPIs.
Activation of the Cpx regulon destabilizes the F plasmid transfer activator, TraJ, via the HslVU protease in Escherichia coli
Authors: Lau‐Wong Isabella C. , Locke Troy , Ellison Michael J. , Raivio Tracy L. , Frost Laura S.
Published: September 2009

The Escherichia coli CpxAR two‐component signal transduction system senses and responds to extracytoplasmic stress. The cpxA101* allele was previously found to reduce F plasmid conjugation by post‐transcriptional inactivation of the positive activator TraJ. Microarray analysis revealed upregulation of the protease–chaperone pair, HslVU, which was shown to degrade TraJ in an E. coli C600 cpxA101* background. Double mutants of cpxA101* and hslV or hslU restored TraJ and F conjugation to wild‐type levels. The constitutive overexpression of nlpE, an outer membrane lipoprotein that induces the Cpx stress response, also led to HslVU‐mediated degradation of TraJ and repression of F transfer. However, Cpx‐mediated TraJ degradation appears to be growth phase‐dependent, as induction of nlpE in mid‐log phase cells did not appreciably alter TraJ levels. Further, His6‐TraJ was sensitive to HslVU degradation in vitro only when it was purified from cells overexpressing nlpE. Thus, TraJ appears to become resistant to HslVU during normal growth, with this resistance mapping to the F transfer region. Extracytoplasmic stress prevents this modification of TraJ, leaving it susceptible to HslVU. Thus, the CpxAR stress response indirectly controls the synthesis of the F mating apparatus, a complex transenvelope type IV secretion system, by degrading TraJ.
Small mobile sequences in bacteria display diverse structure/function motifs
Authors: Delihas Nicholas
Published: September 2009

Small repeat sequences in bacterial genomes, which represent non‐autonomous mobile elements, have close similarities to archaeon and eukaryotic miniature inverted repeat transposable elements. These repeat elements are found in both intergenic and intragenic chromosomal regions, and contain an array of diverse motifs. These can include DNA sequences containing an integration host factor binding site and a proposed DNA methyltransferase recognition site, transcribed RNA secondary structural motifs, which are involved in mRNA regulation, and translated open reading frames found fused to other open reading frames. Some bacterial mobile element fusions are in evolutionarily conserved protein and RNA genes. Others might represent or lead to creation of new protein genes. Here we review the remarkable properties of these small bacterial mobile elements in the context of possible beneficial roles resulting from random insertions into the genome.
DivS, a novel SOS‐inducible cell‐division suppressor in Corynebacterium glutamicum
Authors: Ogino Hidetaka , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki
Published: September 2009

DNA damage‐induced SOS response elicits the induction of cell‐division suppressor as well as DNA repair genes. In Gram‐positive bacteria, cell‐division suppressor genes, so far characterized from Bacillus subtilis (yneA) and Mycobacterium tuberculosis (rv2719c), share limited homology, but are both located in the vicinity of lexA on their respective genomes. Using this proximity to lexA, Corynebacterium glutamicum R divS (cgR1759) was identified as an SOS‐inducible cell‐division suppressor in this study. The amino acid sequence of DivS showed no homology to that of YneA and Rv2719c. divS expression was markedly induced by DNA‐damaging mitomycin C treatment in wild‐type cells, but not in its ΔrecA mutant cells, which are unable to induce the SOS response. Wild‐type C. glutamicum R cells exposed to DNA‐damaging mitomycin C exhibited elongated morphology that, using green fluorescent protein–FtsZ fusion protein, was attributed to defects in FtsZ ring assembly. Cells defective in FtsZ ring assembly were subsequently incapable of septum wall synthesis. In the presence of mitomycin C, divS mutant cells did not exhibit this elongated morphology, whereas cells overexpressing divS were elongated and abnormally branched.
The membrane‐integrated transcriptional activator CadC of Escherichia coli senses lysine indirectly via the interaction with the lysine permease LysP
Authors: Tetsch Larissa , Koller Christiane , Haneburger Ina , Jung Kirsten
Published: September 2009

In an acidic (pH 5.8) and lysine‐rich environment Escherichia coli induces expression of the cadBA operon which encodes CadA, catalysing the decarboxylation of lysine to cadaverine, and CadB, the lysine/cadaverine antiporter. cadBA expression is dependent on CadC, a membrane‐integrated transcriptional activator which belongs to the ToxR‐like protein family and directly binds to the DNA in the cadBA promoter region. Here we describe that CadC senses the extracellular lysine not directly but indirectly requiring the interplay with the lysine permease LysP. Biochemical analyses of isolated CadC or the periplasmic domain of CadC (CadC188–512) revealed an unexpectedly low affinity for lysine, making it unlikely that CadC is a direct sensor for this substrate. Moreover, CadC hybrid proteins, in which the transmembrane domain or single amino acids were replaced, supported lysine‐independent cadBA expression but retained a pH‐dependent regulation. These CadC mutants were resistant to the effect of an overproduction of LysP, which represses cadBA expression in wild‐type cells. Our results suggest a model according to which CadC is inactivated by an interaction with LysP at a low external lysine concentration. When lysine is abundantly available, the interaction between LysP and CadC is released, and CadC becomes susceptible to activation by low pH.
ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor σE in Escherichia coli by both direct and indirect mechanisms
Authors: Costanzo Alessandra , Nicoloff Herve , Barchinger Sarah E. , Banta Amy B. , Gourse Richard L. , Ades Sarah E.
Published: September 2009

One of the major signalling pathways responsible for intercompartmental communication between the cell envelope and cytoplasm in Escherichia coli is mediated by the alternative sigma factor, σE. σE has been studied primarily for its role in response to the misfolding of outer membrane porins. This response is essentially reactionary; cells are stressed, porin folding is disrupted, and the response is activated. σE can also be activated following starvation for a variety of nutrients by the alarmone ppGpp. This response is proactive, as σE is activated in the absence of any obvious damage to the cell envelope sensed by the stress signalling pathway. Here we examine the mechanism of regulation of σE by ppGpp. ppGpp has been proposed to activate at least two alternative sigma factors, σN and σS, indirectly by altering the competition for core RNA polymerase between the alternative sigma factors and the housekeeping sigma factor, σ70. In vivo experiments with σE are consistent with this model. However, ppGpp and its cofactor DksA can also activate transcription by EσEin vitro, suggesting that the effects of ppGpp on σE activity are both direct and indirect.
Single amino acid substitutions in either YhjD or MsbA confer viability to 3‐deoxy‐d‐manno‐oct‐2‐ulosonic acid‐depleted Escherichia coli
Authors: Mamat Uwe , Meredith Timothy C. , Aggarwal Parag , Kühl Annika , Kirchhoff Paul , Lindner Buko , Hanuszkiewicz Anna , Sun Jennifer , Holst Otto , Woodard Ronald W.
Published: September 2009

The Escherichia coli K‐12 strain KPM22, defective in synthesis of 3‐deoxy‐d‐manno‐oct‐2‐ulosonic acid (Kdo), is viable with an outer membrane (OM) composed predominantly of lipid IVA, a precursor of lipopolysaccharide (LPS) biosynthesis that lacks any glycosylation. To sustain viability, the presence of a second‐site suppressor was proposed for transport of lipid IVA from the inner membrane (IM), thus relieving toxic side‐effects of lipid IVA accumulation and providing sufficient amounts of LPS precursors to support OM biogenesis. We now report the identification of an arginine to cysteine substitution at position 134 of the conserved IM protein YhjD in KPM22 that acts as a compensatory suppressor mutation of the lethal ΔKdo phenotype. Further, the yhjD400 suppressor allele renders the LPS transporter MsbA dispensable for lipid IVA transmembrane trafficking. The independent derivation of a series of non‐conditional KPM22‐like mutants from the Kdo‐dependent parent strain TCM15 revealed a second class of suppressor mutations localized to MsbA. Proline to serine substitutions at either residue 18 or 50 of MsbA relieved the Kdo growth dependence observed in the isogenic wild‐type strain. The possible impact of these suppressor mutations on structure and function are discussed by means of a computationally derived threading model of MsbA.
Deletion of the archaeal histone in Methanosarcina mazei Gö1 results in reduced growth and genomic transcription
Authors: Weidenbach Katrin , Glöer Jens , Ehlers Claudia , Sandman Kathleen , Reeve John N. , Schmitz Ruth A.
Published: September 2009

HMm is the only archaeal histone in Methanosarcina mazei Göl and recombinant HMm, synthesized by expression of MM1825 in Escherichia coli, has been purified and confirmed to have the DNA binding and compaction properties characteristic of an archaeal histone. Insertion of a puromycin resistance conferring cassette (pac) into MM1825 was not lethal but resulted in mutants (M. mazei MM1825::pac) that have impaired ability to grow on methanol and trimethylamine. Loss of HMm also resulted in increased sensitivity to UV light and decreased transcript levels for ∼25% of all M. mazei genes. For most genes, the transcript decrease was 3‐ to 10‐fold, but transcripts of MM483 (small heat‐shock protein), MM1688 (trimethylamine:corrinoid methyl transferase) and MM3195 (transcription regulator), were reduced 100‐, 100‐ and 25‐fold, respectively, in M. mazei MM1825::pac cells. Transcripts of only five adjacent genes that appear to constitute an aromatic amino acid biosynthetic operon were elevated in M. mazei MM1825::pac cells. Complementary synthesis of HMm from a plasmid transformed into M. mazei MM1825::pac restored wild‐type growth and transcript levels.
Compensation for the loss of the conserved membrane targeting sequence of FtsA provides new insights into its function
Authors: Shiomi Daisuke , Margolin William
Published: September 2009

The bacterial actin homologue FtsA has a conserved C‐terminal membrane targeting sequence (MTS). Deletion or point mutations in the MTS, such as W408E, were shown previously to inactivate FtsA function and inhibit cell division. Because FtsA binds to the tubulin‐like FtsZ protein that forms the Z ring, it is thought that the MTS of FtsA is required, along with the transmembrane protein ZipA, to assemble the Z ring and anchor it to the cytoplasmic membrane. Here, we show that despite its reduced membrane binding, FtsA‐W408E could localize to the Z ring and recruit the late cell division protein FtsI, but was defective in self‐interaction and recruitment of FtsN, another late cell division protein. These defects could be suppressed by a mutation that stimulates membrane association of FtsA‐W408E, or by expressing a tandem FtsA‐W408E. Remarkably, the FtsA MTS could be completely replaced with the transmembrane domain of MalF and remain functional for cell division. We propose that FtsA function in cell division depends on additive effects of membrane binding and self‐interaction, and that the specific requirement of an amphipathic helix for tethering FtsA to the membrane can be bypassed.
Common CCR 5 Polymorphism in Stroke The CCR 5 Δ32 Polymorphism Differentiates Cardioembolism from Other Aetiologies of Ischaemic Cerebrovascular Diseases
Authors: Nikolaos K. , Ioanna M. , Vasilios K. , Jan H. , Konstantinos K.
Published: September 2009

Inflammation is involved in the development of atherosclerosis. The CC chemokine receptor 5 (CCR5) initiates chemotaxis and modulates the inflammation secondary to atherosclerosis and related vascular diseases. The CCR5 Δ32 polymorphism influences the expression of CCR5 on the cell surface. The purpose of this study was to examine the effect of the Δ32 polymorphism in ischaemic cerebrovascular disease (ICVD). The CCR5 Δ32 polymorphism was genotyped in 1462 individuals: 562 ischaemic stroke (IS), 97 transient ischaemic attack (TIA) and in 803 healthy controls. All 659 ICVD patients were categorized according to the Trial of Org 10172 in Acute Stroke Treatment aetiological classification. The investigated subtypes were large artery atherosclerosis (LAA), cardioembolism (CE), small artery occlusion (SAO) and cryptogenic disease (CRYPT). Genotyping was performed with the TaqMan polymerase chain reaction. The Δ32 allele was less frequent in CE patients compared with LAA (OR, 0.4; 95% CI, 0.24–0.79; P = 0.008), SAO (OR, 0.5; 95% CI, 0.29–0.84; P = 0.01), CRYPT (OR, 0.5; 95% CI, 0.28–0.82; P = 0.008) and controls (OR, 0.5; 95% CI, 0.36–0.82; P = 0.002). Multiple logistic regression analysis showed that the Δ32 allele is associated with a lower risk for cardioembolic ICVD (OR 0.5; 95% CI, 0.28–0.75; P = 0.002) when compared with ICVD of other causes. The Δ32 polymorphism of CCR5 may differentiate cardioembolism from the remaining causes of ICVD.
New Alternative Vaccine Component Against Mycobacterium Tuberculosis– Heat Shock Protein 16.3 or its T‐Cell Epitope
Authors: Shi C. , Zhang H. , Zhang T. , Wang X. , Bai B. , Zhao Y. , Zhang C. , Xu Z.
Published: September 2009

Heat shock protein 16.3 (Hsp16.3) of Mycobacterium tuberculosis (MTB) containing T‐cell and B‐cell epitopes not only plays an important role in the survival of MTB against macrophages, but also has great potential to be used to develop new TB vaccines. In order to study whether Hsp16.3 can be replaced with its T‐cell epitope for producing a vaccine against TB, we expressed and purified Hsp16.3 protein of MTB H37Rv strain and confirmed by immunoblotting. The immune responses and protection against the H37Rv induced by Hsp16.3 protein were compared with its T‐cell epitope synthetic peptide in mice. The results showed that both Hsp16.3 and its synthetic peptide induced significantly stronger specific antibodies than the classical TB vaccine–BCG (bacillus Calmette‐Guérin). Compared with BCG, the stimulation index in the splenolymphocyte proliferation of both recombinant protein and its synthetic peptide were remarkably enhanced, but the levels of IFN‐γ release were lower. Dramatic reduction in the numbers of MTB colony forming units (CFU) in the spleens and lungs was observed in the mice immunized with Hsp16.3 or its synthetic peptide. The protection provided by Hsp16.3 or its synthetic peptide in the lungs was equivalent to that provided by BCG. Both Hsp16.3 and its T‐cell epitope are effective components and Hsp16.3 can be replaced with its T‐cell epitope while developing the vaccine against TB, without requiring the complicated procedure of expressing and purifying Hsp16.3.