bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitotic chromosomes are compacted laterally by KIF4 and condensin and axially by topoisomerase IIα
Authors: Samejima Kumiko , Samejima Itaru , Vagnarelli Paola , Ogawa Hiromi , Vargiu Giulia , Kelly David A. , de Lima Alves Flavia , Kerr Alastair , Green Lydia C. , Hudson Damien F. , Ohta Shinya , Cooke Carol A. , Farr Christine J. , Rappsilber Juri , Earnshaw William C.
Published: November 2012

Mitotic chromosome formation involves a relatively minor condensation of the chromatin volume coupled with a dramatic reorganization into the characteristic “X” shape. Here we report results of a detailed morphological analysis, which revealed that chromokinesin KIF4 cooperated in a parallel pathway with condensin complexes to promote the lateral compaction of chromatid arms. In this analysis, KIF4 and condensin were mutually dependent for their dynamic localization on the chromatid axes. Depletion of either caused sister chromatids to expand and compromised the “intrinsic structure” of the chromosomes (defined in an in vitro assay), with loss of condensin showing stronger effects. Simultaneous depletion of KIF4 and condensin caused complete loss of chromosome morphology. In these experiments, topoisomerase IIα contributed to shaping mitotic chromosomes by promoting the shortening of the chromatid axes and apparently acting in opposition to the actions of KIF4 and condensins. These three proteins are major determinants in shaping the characteristic mitotic chromosome morphology.
RAE-1 ligands for the NKG2D receptor are regulated by E2F transcription factors, which control cell cycle entry
Authors: Jung Heiyoun , Hsiung Benjamin , Pestal Kathleen , Procyk Emily , Raulet David H.
Published: November 2012

The NKG2D stimulatory receptor expressed by natural killer cells and T cell subsets recognizes cell surface ligands that are induced on transformed and infected cells and facilitate immune rejection of tumor cells. We demonstrate that expression of retinoic acid early inducible gene 1 (RAE-1) family NKG2D ligands in cancer cell lines and proliferating normal cells is coupled directly to cell cycle regulation. Raet1 genes are directly transcriptionally activated by E2F family transcription factors, which play a central role in regulating cell cycle entry. Induction of RAE-1 occurred in primary cell cultures, embryonic brain cells in vivo, and cells in healing skin wounds and, accordingly, wound healing was delayed in mice lacking NKG2D. Transcriptional activation by E2Fs is likely coordinated with posttranscriptional regulation by other stress responses. These findings suggest that cellular proliferation, as occurs in cancer cells but also other pathological conditions, is a key signal tied to immune reactions mediated by NKG2D-bearing lymphocytes.
Central Line–Associated Bloodstream Infections in Adult Hematology Patients with Febrile Neutropenia An Evaluation of Surveillance Definitions Using Differential Time to Blood Culture Positivity
Authors: Freeman Joshua T. , Elinder-Camburn Anna , McClymont Catherine , Anderson Deverick J. , Bilkey Mary , Williamson Deborah A. , Berkahn Leanne , Roberts Sally A.
Published: November 2012

We used differential time to positivity between central and peripheral blood cultures to evaluate the positive predictive value (PPV) of the National Healthcare Safety Network central line–associated bloodstream infection (CLABSI) surveillance definition among hematology patients with febrile neutropenia. The PPV was 27.7%, which suggests that, when the definition is applied to this population, CLABSI rates will be substantially overestimated.
The Time Spent Cleaning a Hospital Room Does Not Correlate with the Thoroughness of Cleaning
Authors: Rupp Mark E. , Adler Ann , Schellen Margaret , Cassling Kyle , Fitzgerald Teresa , Sholtz Lee , Lyden Elizabeth , Carling Philip
Published: November 2012

Environmental surfaces in hospital rooms often become contaminated with microbes, and evidence has linked the patient care environment to transmission of potential pathogens. Despite attempts at standardization of training and cleaning techniques, there is great variation between housekeepers with regard to room cleaning practices. Environmental cleanliness can be assessed by direct observation, surface cultures, detection of adenosine triphosphate, or use of a fluorescent marking solution. Each monitoring technique has limitations.

We participated in a multicenter study that demonstrated improved cleaning of high-touch surfaces through the use of a fluorescent marking solution and rapid-cycle performance feedback. As part of an earlier study, housekeepers were instructed about the importance of environmental cleanliness and appropriate cleaning of high-touch surfaces, and a room cleaning checklist was introduced. In this study, we sought to examine the relationship between the amount of time that a housekeeper spent cleaning a hospital room and the thoroughness of surface cleaning.
Use of Medicare Claims to Identify US Hospitals with a High Rate of Surgical Site Infection after Hip Arthroplasty
Authors: Calderwood Michael S. , Kleinman Ken , Bratzler Dale W. , Ma Allen , Bruce Christina B. , Kaganov Rebecca E. , Canning Claire , Piatt Richard , Huang Susan S. ,   Centers for Disease Control and Prevention Epicenters Program and the Oklahoma Foundation for Medical Quality
Published: November 2012

Objective.

To assess the ability of Medicare claims to identify US hospitals with high rates of surgical site infection (SSI) after hip arthroplasty.

Design.

Retrospective cohort study.

Setting.

Acute care US hospitals.

Participants.

Fee-for-service Medicare patients 65 years of age and older who underwent hip arthroplasty in US hospitals from 2005 through 2007.

Methods.

Hospital rankings were derived from claims codes suggestive of SSI, adjusted for age, sex, and comorbidities, while using generalized linear mixed models to account for hospital volume. Medical records were obtained for validation of infection on a random sample of patients from hospitals ranked in the best and worst deciles of performance. We then calculated the risk-adjusted odds of developing a chart-confirmed SSI after hip arthroplasty in hospitals ranked by claims into worst- versus best-performing deciles.

Results.

Among 524,892 eligible Medicare patients who underwent hip arthroplasty at 3,296 US hospitals, a patient who underwent surgery in a hospital ranked in the worst-performing decile based on claims-based evidence of SSI had 2.9-fold higher odds of developing a chart-confirmed SSI relative to a patient with the same age, sex, and comorbidities in a hospital ranked in the best-performing decile (95% confidence interval, 2.2-3.7).

Conclusions.

Medicare claims successfully distinguished between hospitals with high and low SSI rates following hip arthroplasty. These claims can identify potential outlier hospitals that merit further evaluation. This strategy can also be used to validate the completeness of public reporting of SSI.
Effect of growth temperature on the epitaxy strain relaxation and the
tilt of In
x
Al1−x

As graded layer grown by solid-source molecular beam epitaxy
Authors: Loke Wan Khai , Tan Kian Hua , Wicaksono Satrio , Yoon Soon Fatt , Owen Man Hon Samuel , Yeo Yee-Chia
Published: November 2012

In this study, we investigate the effect of the molecular beam epitaxial growth
temperature on the epilayer tilt and the strain relaxation in the InAlAs
M-buffer layer when the In composition is varied linearly from 6 to 57%
followed by an inverse grading to 52% where InAlAs is lattice-matched to
InP. The samples grown at 420 and 500 °C have final epilayer tilts of
0.66–0.68° about the

axis towards

, whereas the sample grown at 370 °C has a smaller
tilt of 0.15° about the

axis but towards [1 1 0]. Cross-sectional
transmission electron microscopy micrographs showed that the sample grown at
420 °C has the lowest dislocation density
(6 × 106 cm−2) compared
with those grown at 370 and 500 °C. The inversely graded layer in all
samples was shown to be effective in reducing the strain that was accumulated
during the forward graded layer. This resulted in close to fully relaxed
epilayers (92–99%), which are necessary for the prevention of
further occurrence of dislocation nucleation (an important criterion for
subsequent device structure growth).
Repetitive switching behaviour of a memristor for passive crossbar applications
Authors: Yan Z B , Zhu X C , Liu M , Jiang X M , Jiang X F , Liu J-M
Published: November 2012

The evolution of resistance switching behaviour of an Ag/DyMnO3/Ag/DyMnO3/Pt memristor structure under repetitive voltage sweeping is investigated. It is observed that the current–voltage (I–V) characteristic evolves from simple bipolar switching behaviour to a complicated switching sequence, which is applicable in passive crossbar arrays. It is suggested that the filament morphology can be modulated by accumulation and release of the Joule heating and Ag ions/atoms residing inside the DyMnO3 layer during continuous switching. The filament growth/dissolution near the upper surface of the middle Ag layer plays a key role in the consequent I–V characteristics.
Unusual behaviour of current–voltage relations in an unbalanced grid-assisted magnetron sputtering system
Authors: Sagás J C , Duarte D A , Fontana L C
Published: November 2012

Current–voltage relations were measured in an unbalanced grid-assisted magnetron sputtering system at different inter-electrode distances and magnetic field configurations. The intensity and configuration of the magnetic field were adjusted through an electromagnetic coil placed at the magnetron centre. This scheme allows observation of the current–voltage relations under conditions of weak and strong plasma confinement. Surprisingly, for some inter-electrode distances, a decreasing discharge current with increased magnetic field was observed. This unusual behaviour in grid-assisted magnetron discharges can be useful for a better understanding of abnormal glow discharges assisted by a magnetic field.
Cooperative effect of electronic and nuclear stopping on ion irradiation damage in silica
Authors: Backman M , Djurabekova F , Pakarinen O H , Nordlund K , Zhang Y , Toulemonde M , Weber W J
Published: November 2012

Radiation damage by ions is conventionally believed to be produced either by displacement cascades or electronic energy deposition acting separately. There is, however, a range of ion energies where both processes are significant and can contribute to irradiation damage. The combination of two computational methods, namely binary collision approximation and molecular dynamics, the latter with input from the inelastic thermal spike model, makes it possible to examine the simultaneous contribution of both energy deposition mechanisms on the structural damage in the irradiated structure. We study the effect in amorphous SiO2 irradiated by Au ions with energies ranging between 0.6 and 76.5 MeV. We find that in the intermediate energy regime, the local heating due to electronic excitations gives a significant contribution to the displacement cascade damage.
Investigations on irreversible- and reversible-type gas sensing for ZnO and Mg0.5Zn0.5Fe2O4 chemi-resistive sensors
Authors: Mukherjee K , Gaur A P S , Majumder S B
Published: November 2012

Semiconducting metal oxides are attractive material candidates for combustible gas sensors. Little or marginal base resistance drift of these metal oxide sensors is desirable during repeated response and recovery cycles. However, due to the partial recovery, often a significant drift in base resistance is observed. The gas sensing is termed irreversible when there is a partial recovery of base resistance, whereas for reversible sensing the base resistance is fully recovered. For reducing gas (hydrogen and carbon monoxide) sensing we have reported reversible and irreversible resistance transients for magnesium zinc ferrite and zinc oxide sensing elements, respectively. For a wide range of gas concentrations and operating temperatures, the response transients for these sensing elements are modelled using the Langmuir–Hinshelwood reaction mechanism. It is revealed that for irreversible-type sensing, the response time is reduced with the increase in test gas concentration. On the other hand, for reversible-type sensing, the response time is found to be independent of the gas concentration. Based on the estimation of pore size, pore size distribution and specific surface area of the calcined powder together with the analyses of the surface morphology of the sensing elements we have argued that due to the porous morphology of the magnesium zinc ferrite sensing element the oxidized product can easily desorb from the sensor during recovery. Therefore, irrespective of the test gas concentration, the base resistance of the magnesium zinc ferrite sensor recovers fully during the recovery process.
Decreased incidence of severe ovarian hyperstimulation syndrome in high risk in-vitro fertilization patients receiving intravenous albumin: a prospective study
Authors: Shalev E. , Giladi Y. , Matilsky M. , Ben-Ami M.
Published: November 2012

The administration of human serum albumin has been reported to prevent severe ovarian hyperstimulation syndrome (OHSS) in patients considered at risk of developing OHSS while undergoing ovarian stimulation protocols for in-vitro fertilization (IVF). This prospective, randomized study investigated the effectiveness of a single dose of human serum albumin (20 g) administered i.v. immediately after oocyte retrieval. Women enrolled in the IVF programme were treated with the long gonadotrophin-releasing hormone agonist, triptorelin, and an individually-adjusted human menopausal gonadotrophin protocol. The criteria for inclusion in the study were young age, nonobesity, oestradiol concentration >9200 pmol/l on the day of human chorionic gonadotrophin administration and >20 follicles >14 mm diameter as observed by transvaginal sonography. The treatment group (n = 22) received albumin while the control group (n = 18) did not. Patients were followed-up using ultrasound every 3 days. There was a significantly higher number of severe OHSS cases in the control group (n = 4) than in the treatment group (n = 0) (P = 0.035). Where the data base was restricted to patients with an oestradiol concentration >15 000 pmol/l, the difference between control and treatment groups was highly significant (P = 0.008). These findings support the use of i.v. albumin in preventing severe OHSS during IVF treatment.
Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007–2010
Authors: Onyango Clayton O. , Njeru Regina , Kazungu Sidi , Achilla Rachel , Bulimo Wallace , Welch Stephen R. , Cane Patricia A. , Gunson Rory N. , Hammitt Laura L. , Scott J. Anthony G. , Berkley James A. , Nokes D. James
Published: November 2012

Background

 Influenza data gaps in sub-Saharan Africa include incidence, case fatality, seasonal patterns, and associations with prevalent disorders.

Methods

 Nasopharyngeal samples from children aged <12 years who were admitted to Kilifi District Hospital during 2007–2010 with severe or very severe pneumonia and resided in the local demographic surveillance system were screened for influenza A, B, and C viruses by molecular methods. Outpatient children provided comparative data.

Results

 Of 2002 admissions, influenza A virus infection was diagnosed in 3.5% (71), influenza B virus infection, in 0.9% (19); and influenza C virus infection, in 0.8% (11 of 1404 tested). Four patients with influenza died. Among outpatients, 13 of 331 (3.9%) with acute respiratory infection and 1 of 196 without acute respiratory infection were influenza positive. The annual incidence of severe or very severe pneumonia, of influenza (any type), and of influenza A, was 1321, 60, and 43 cases per 100 000 <5 years of age, respectively. Peak occurrence was in quarters 3–4 each year, and approximately 50% of cases involved infants: temporal association with bacteremia was absent. Hypoxia was more frequent among pneumonia cases involving influenza (odds ratio, 1.78; 95% confidence interval, 1.04–1.96). Influenza A virus subtypes were seasonal H3N2 (57%), seasonal H1N1 (12%), and 2009 pandemic H1N1 (7%).

Conclusions

 The burden of influenza was small during 2007–2010 in this pediatric hospital in Kenya. Influenza A virus subtype H3N2 predominated, and 2009 pandemic influenza A virus subtype H1N1 had little impact.
Is there another player in the game of Rubisco regulation?
Authors: Keys Alfred J. , Major Lain , Parry Martin A.J.
Published: November 2012

Leaves of French bean plants, whether collected in the dark or in the light, contained a tight-binding inhibitor of ribulose 1,5-bisphosphate carboxylase/ oxygenase (Rubisco). Wheat leaves contained such an inhibitor only in the light. The inhibitor in wheat leaves was not 2-carboxy-D-arabinitol 1-phosphate (CA1P) and not xylulose 1,5-bisphosphate. It was stable in acid conditions, but was destroyed during low pressure anion exchange chromatography and in alkaline conditions, especially during concentration of solutions. Although the kinetics of inhibition suggested tight-binding, the inhibitor did not survive attempts at purification by binding it to purified Rubisco followed by denaturation of the protein. The retention time of the inhibitory component on HPLC anion-exchange columns suggested that the substance was a sugar bisphosphate. Reduction with tritiated sodium borohydride and dephosphorylation produced radioactive sugar alcohols identified by TLC as ribitol and arabinitol. The small amounts of this inhibitor detected do not suggest a major physiological role, but instability during extraction may be obscuring its true importance.
Manipulating photosynthetic metabolism to improve crops: an inversion of ends and means
Authors: Walker David A.
Published: November 2012

The manipulation of photosynthetic carbon metabolism to bring about crop improvement or increased crop productivity is discussed against the background of population increase and an increasing tendency to favour investigations perceived to be of immediate practical advantage rather than supporting research of a more fundamental nature. The feasibility of improving productivity at a rate capable of matching the current daily increase in population of approximately 350 000 is considered and thought is given to the consequences of achieving that goal. Some environmental and intrinsic factors which are known to constrain photosynthesis are examined and it is proposed that, whereas there is no reasonable possibility of increasing quantum efficiency, there are many aspects of photosynthesis which are worthy of investigation in their own right and that these, if subjected to further investigation of a fundamental nature, could result in improvements in ‘efficiency’ in the wider sense of the word. It is concluded, nevertheless, that the greatest limitation on global agriculture is not water, temperature, pests or disease, but the cost and availability of fossil fuels, and that this fact should be kept uppermost when defining priorities in the light of future scenarios in which fossil fuel reserves are bound to dwindle more and more quickly during a period of massive population increase.
Engineering Rubisco to change its catalytic properties
Authors: Bainbridge Graeme , Madgwick Pippa , Parmar Saroj , Mitchell Rowan , Paul Matthew , Pitts Jim , Keys Alfred J. , Parry Martin A.J.
Published: November 2012

The initial steps of carbon assimilation and photorespiration are catalysed by ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39). Natural variation in the kinetic properties of the enzyme suggest that it is possible to alter the enzyme to favour the carboxylation activity relative to oxygenation. Mutagenesis in vitro of the gene encoding the large subunit of the enzyme from Anacystis nidulans has been used to modify catalytic properties. Residues at the C-terminal end of loop 6 of the β/α barrel structure of the large subunit influence specificity towards the gaseous substrates, CO2 and O2. None of the residues altered by mutagenesis appear to interact directly with the transition state analogue and their effect on the reaction of the enediolate intermediate with the gaseous substrates and stabilization of the resulting transition state intermediates by lysine 334 must be indirect. Interactions with other parts of the enzyme must also be important in determining substrate specificity. Backbone carbonyl groups close to lysine 334 interact with lysine 128; mutation of lysine 128 to residues of less positive polarity reduces enzyme activity and favours oxygenation relative to carboxylation. The likely effects on assimilation rates of altering the kinetic properties of Rubisco have been modelled. A leaf with cyanobacterial Rubisco may out-perform a higher plant Rubisco at elevated CO2 and cool temperatures.
Effects of light and atmospheric carbon dioxide enrichment on photosynthesis and carbon partitioning in the leaves of tomato (Lycopersicon esculentum L.) plants over-expressing sucrose phosphate synthase
Authors: Galtier Nathalie , Foyer Christine H. , Murchie Erik , Aired Rhu , Quick Paul , Voelker Toni A. , Thépenier Catherine , Lascève Gerard , Betsche Thomas
Published: November 2012

Photosynthetic carbon assimilation, carbon partitioning and foliar carbon budgets were measured in the leaves of transformed tomato plants expressing a maize sucrose-phosphate synthase (SPS) gene in addition to the native enzyme, and in untransformed controls. The maize SPS gene was expressed under control of either the promoter of the small subunit of ribulose 1,5-bisphosphate carboxylase (rbcS promoter; lines 2, 9 and 18) or the 35S promoter from cauliflower mosaic virus (CaMV promoter; line 13). The rate of sucrose synthesis was increased relative to that of starch and sucrose/starch ratios were higher throughout the photoperiod in the leaves of all plants expressing high SPS activity. The leaf carbon budget over the day/night cycle in air at low irradiance (180μmol photon m−2 s−1) was similar in all plants. Net photosynthesis measured in air and at elevated CO2 (800–1500 μl l−1) on whole plants grown in air at 400μmol m−2 s−1 irradiance was significantly increased in the high SPS expressors compared to the untransformed controls and was highest where SPS activity was greatest. At high CO2 the stimulation of photosynthesis was more pronounced. We conclude that SPS activity is a major point of control of photosynthesis particularly under saturating light and CO2.
The isolation and characterization of mutants of the C4 photosynthetic pathway
Authors: Dever L.V. , Blackwell R.D. , Fullwood N.J. , Lacuesta M. , Leegood R.C. , Onek L.A. , Pearson M. , Lea P.J.
Published: November 2012

Three novel classes of the C4 plant Amaranthus edulis are described. (1) A mutant that contains less than 10% of the normal activity and protein of phosphoenol-pyruvate carboxylase. (2) A mutant that is deficient in NAD-malic enzyme activity, but contains the normal two subunits of the enzyme protein. (3) Four mutant plants that accumulate high concentrations of glycine following exposure to air. A common characteristic of all the mutant plants is that they grow poorly in air and exhibit very low rates of photosynthetic CO2 assimilation.

The characteristics of the mutant lines are discussed with reference to our current knowledge of the regulation of the C4 photosynthesis pathway. The possibility that C4 plants undergo photorespiratory nitrogen and carbon metabolism when grown in air is considered in detail.
Functioning of the tonoplast in vacuolar C-storage and remobilization in crassulacean acid metabolism
Authors: Lüttge Ulrich , Fischer-Schliebs Elke , Ratajczak Rafael , Kramer Detlef , Berndt Ekkehart , Kluge Manfred
Published: November 2012

Nocturnal fixation of CO2 and storage of carbon in the form of malic acid in vacuoles of photosynthetically active cells are key processes of crassulacean acid metabolism (CAM). A prerequisite for malate transport into the vacuole is the concerted action of primary-active H+ -pumps, i.e. the tonoplast V0V1-H+-ATPase and H+ -PPiase, and a secondary-active carboxylate transporter. During the transition from C3-photosynthesis to CAM the H+ -ATPase of the C3/CAM-inter-mediate plant Mesembryanthemum crystallinum undergoes particular structural changes indicating an adaptation of the enzyme to the requirements for an increased capacity of tonoplast transport systems. The role of the H+-PPiase in energization of carbon transport in CAM remains unclear. While in Kalanchoë blossfeldiana cv. Tom Thumb, where CAM is induced by shortening of daylength, there is a higher expression of the H+-PPiase in the CAM state as compared to the C3-state, the enzyme disappears in M. crystallinum when CAM is induced by salt stress. However, the H+-PPiase could also be involved in the regulation of the H+-ATPase as shown by the PPistimulated ATP-dependent H+-transport activity found in K. daigremontiana and K. blossfeldiana cv. Tom Thumb. Although the tonoplast carboxylate transporter has not yet been identified, the kinetic parameters of the enzyme were characterized after partial purification and functional reconstitution into proteo-liposomes. While the influx of malate into the vacuole is mediated by the co-operation of different enzymes, the regulation of the passive efflux of malic acid from the tonoplast during the day may depend on biophysical membrane properties, i.e. the degree of order of the vacuolar membrane, which seems to be modulated by Ca2+.
The regulation and control of photorespiration
Authors: Leegood Richard C. , Lea Peter J. , Adcock Michael D. , Häusler Rainer E.
Published: November 2012

The photorespiratory pathway is described, together with the mutants which have been isolated for this metabolic pathway. Some of the key regulatory properties of the photorespiratory cycle are reviewed together with the regulatory interactions that might occur between photorespiration and other processes, such as the Benson-Calvin cycle and anaplerotic carbon flow into organic acids. These are discussed in relation to recent studies of the regulation and control of photorespiratory carbon and nitrogen metabolism in photorespiratory mutants, including possible mechanisms for the control of photosynthetic and photorespiratory carbon and nitrogen metabolism and of the activation state of ribulose-1,5-bisphosphate carboxylase/oxygenase in heterozygous barley mutants with reduced activities of glutamine synthetase or glutamate synthase.
Decarboxylation of primary and end products of photosynthesis at different oxygen concentrations
Authors: Pärnik Tiit , Keerberg Olav
Published: November 2012

A radiogasometric method for the determination of the rates of intracellular decarboxylation of primary and end products of steady-state photosynthesis in the light has been worked out. On the basis of oxygen dependence of the CO2 evolution, two types of decarboxylation, oxygenase (photorespiration) and oxidase (dark respiration), have been distinguished. Oxygenase decarboxylation is linearly dependent on O2 concentration in the range from 0 to 210 mmol mol−1, which is characteristic of the oxygenation of RuBP, the ratelimiting reaction of the glycolate cycle. Oxidase decarboxylation is saturated at relatively low O2 concentration (of about 15 mmol mol−1), similar to the oxidative reactions associated with glycolysis and the Krebs cycle. In the C3 plants (tobacco, wheat, barley) we have studied, primary products were decarb-oxylated predominantly via the oxygenase mechanism; the oxidase component was 3–15% of the total rate of the decarboxylation of primary photosynthates in the light. The oxygenase mechanism was also involved in the decarboxylation of end products of photosynthesis. The rate of this component exceeded by 3 to 5 times the rate of oxidase decarboxylation of end products in the light. It has been suggested that compounds derived from the degradation of end products of photosynthesis are incorporated into the reductive pentose phosphate cycle and, via the cycle, into the glycolate cycle where they are decarboxylated. In this way, four components of plant leaf respiration in the light may be distinguished according to the substrates and mechanisms of decarboxylation. In the dark, only one of them, oxidase decarboxylation of end products, is functioning. The rate of this component has been shown to be partially suppressed by light.
Development of PCR Primers to Identify Fusarium oxysporum f. sp. fragariae
Authors: Suga H. , Hirayama Y. , Morishima M. , Suzuki T. , Kageyama K. , Hyakumachi M.
Published: November 2012

Fusarium oxysporum f. sp. fragariae is a fungal pathogen causing Fusarium wilt on strawberry. Polymerase chain reaction (PCR) primers that can discriminate F. oxysporum f. sp. fragariae from nonpathogenic F. oxysporum would greatly assist pathogen identification. In order to develop a molecular diagnostic tool for this pathogen, transposable elements in the pathogen were characterized and used for designing a specific set of PCR primers. Portions of the transposable elements Fot3, Han, Hop, Hornet1, and Skippy were detected in all 33 strains of F. oxysporum f. sp. fragariae tested by PCR, whereas Foxy was detected in 32 strains and Impala sequences were detected in 30 strains. Two types of sequences were detected for Hop, two types for Impala, and three types for Skippy. The genomic region between Han and Skippy was amplified by an inter-retrotransposon amplified polymorphism technique, and PCR primers (FofraF and FofraR) to specifically identify F. oxysporum f. sp. fragariae were designed from this region. The developed PCR primers discriminated F. oxysporum f. sp. fragariae strains from nonpathogenic F. oxysporum strains and five other formae speciales. Conidia of F. oxysporum f. sp. fragariae could be detected in brown lowland-type soil by PCR using the primers. After preculturing the soil sample on FoG2 medium, 1 × 102 conidia/g of soil could be detected; without preculturing, 1 × 103 conidia/g of soil were detected.
Epigenetic inheritance mediated by histone lysine methylation: maintaining transcriptional states without the precise restoration of marks?
Authors: Huang Chang , Xu Mo , Zhu Bing
Published: November 2012

‘Epigenetics’ has been defined as the study of ‘mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence’. Chromatin modifications are major carriers of epigenetic information that both reflect and affect the transcriptional states of underlying genes. Several histone modifications are key players that are responsible for classical epigenetic phenomena. However, the mechanisms by which cells pass their histone modifications to daughter cells through mitotic division remain to be unveiled. Here, we review recent progress in the field and conclude that epigenetic modifications are not precisely maintained at a near-mononucleosome level of precision. We also suggest that transcription repression may be maintained by a buffer system that can tolerate a certain degree of fluctuation in repressive histone modification levels. This buffer system protects the repressed genes from potential improper derepression triggered by chromatin modification-level fluctuation resulting from cellular events, such as the cell-cycle-dependent dilution of the chromatin modifications and local responses to environmental cues.
Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?
Authors: Sharif Jafar , Shinkai Yoichi , Koseki Haruhiko
Published: November 2012

Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.
Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier
Authors: Watanabe Akira , Yamada Yasuhiro , Yamanaka Shinya
Published: November 2012

The differentiation and reprogramming of cells are accompanied by drastic changes in the epigenetic profiles of cells. Waddington's classical model clearly describes how differentiating cells acquire their cell identity as the developmental potential of an individual cell population declines towards the terminally differentiated state. The recent discovery of induced pluripotent stem cells as well as of somatic cell nuclear transfer provided evidence that the process of differentiation can be reversed. The identity of somatic cells is strictly protected by an epigenetic barrier, and these cells acquire pluripotency by breaking the epigenetic barrier by reprogramming factors such as Oct3/4, Sox2, Klf4, Myc and LIN28. This review covers the current understanding of the spatio-temporal regulation of epigenetics in pluripotent and differentiated cells, and discusses how cells determine their identity and overcome the epigenetic barrier during the reprogramming process.
Metabolic Engineering of Tomato Fruit Organic Acid Content Guided by Biochemical Analysis of an Introgression Line
Authors: Morgan Megan J. , Osorio Sonia , Gehl Bernadette , Baxter Charles J. , Kruger Nicholas J. , Ratcliffe R. George , Fernie Alisdair R. , Sweetlove Lee J.
Published: November 2012

Organic acid content is regarded as one of the most important quality traits of fresh tomato (Solanum lycopersicum). However, the complexity of carboxylic acid metabolism and storage means that it is difficult to predict the best way to engineer altered carboxylic acid levels. Here, we used a biochemical analysis of a tomato introgression line with increased levels of fruit citrate and malate at breaker stage to identify a metabolic engineering target that was subsequently tested in transgenic plants. Increased carboxylic acid levels in introgression line 2-5 were not accompanied by changes in the pattern of carbohydrate oxidation by pericarp discs or the catalytic capacity of tricarboxylic acid cycle enzymes measured in isolated mitochondria. However, there was a significant decrease in the maximum catalytic activity of aconitase in total tissue extracts, suggesting that a cytosolic isoform of aconitase was affected. To test the role of cytosolic aconitase in controlling fruit citrate levels, we analyzed fruit of transgenic lines expressing an antisense construct against SlAco3b, one of the two tomato genes encoding aconitase. A green fluorescent protein fusion of SlAco3b was dual targeted to cytosol and mitochondria, while the other aconitase, SlAco3a, was exclusively mitochondrial when transiently expressed in tobacco (Nicotiana tabacum) leaves. Both aconitase transcripts were decreased in fruit from transgenic lines, and aconitase activity was reduced by about 30% in the transgenic lines. Other measured enzymes of carboxylic acid metabolism were not significantly altered. Both citrate and malate levels were increased in ripe fruit of the transgenic plants, and as a consequence, total carboxylic acid content was increased by 50% at maturity.
Entering a Dialogue: Positioning Case Study Findings towards Theory
Authors: Ridder Hans‐Gerd , Hoon Christina , McCandless Baluch Alina
Published: November 2012

Demonstrating a theoretical contribution is seen as a central challenge in case study research; however, the literature provides little guidance on the crucial step of positioning the study's theoretical claims in relationship to prior theory. This paper addresses the question of how to enter into a dialogue with extant theory in theory building case study research in the field of management. We present three ways of positioning to demonstrate a theoretical contribution, illustrating each with examples from recent case studies drawing on the dynamic capabilities approach. By distinguishing between seeking complementarities and dissimilarities in theory building, we add to this discussion and shed light on the benefits of entering a synergistic, antagonistic and pluralistic dialogue for making a significant theoretical contribution. Methodologically, we more fully specify how case study researchers can elaborate upon their theoretical claims in relation to prior theory.
Accelerated pentose utilization by Corynebacterium glutamicum for accelerated production of lysine, glutamate, ornithine and putrescine
Authors: Meiswinkel Tobias M. , Gopinath Vipin , Lindner Steffen N. , Nampoothiri K. Madhavan , Wendisch Volker F.
Published: November 2012

Because of their abundance in hemicellulosic wastes arabinose and xylose are an interesting source of carbon for biotechnological production processes. Previous studies have engineered several Corynebacterium glutamicum strains for the utilization of arabinose and xylose, however, with inefficient xylose utilization capabilities. To improve xylose utilization, different xylose isomerase genes were tested in C. glutamicum. The gene originating from Xanthomonas campestris was shown to have the highest effect, resulting in growth rates of 0.14 h−1, followed by genes from Bacillus subtilis, Mycobacterium smegmatis and Escherichia coli. To further increase xylose utilization different xylulokinase genes were expressed combined with X. campestris xylose isomerase gene. All combinations further increased growth rates of the recombinant strains up to 0.20 h−1 and moreover increased biomass yields. The gene combination of X. campestris xylose isomerase and C. glutamicum xylulokinase was the fastest growing on xylose and compared with the previously described strain solely expressing E. coli xylose isomerase gene delivered a doubled growth rate. Productivity of the amino acids glutamate, lysine and ornithine, as well as the diamine putrescine was increased as well as final titres except for lysine where titres remained unchanged. Also productivity in medium containing rice straw hydrolysate as carbon source was increased.
Primary malignant achromic melanoma of the lung
Authors: Lazarou Ilias , Purek Lesek , Duc Christophe , Licker Marc‐Joseph , Spiliopoulos Anastase , Tschopp Jean‐Marie
Published: November 2012

Currently, less than thirty cases of primary malignant melanoma of the lung have been reported in the literature. Thus, strict criteria for diagnosis have been published and include: malignant melanoma associated with bronchial epithelial changes; a solitary lung tumor; no prior history of skin, mucous membrane, intestinal or ocular melanoma; and absence of any other detectable tumor at the time of diagnosis. In this article we present a case of melanoma of the lung without evidence of extra‐pulmonary disease.
Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging
Authors: Delaney Joe R. , Ahmed Umema , Chou Annie , Sim Sylvia , Carr Daniel , Murakami Christopher J. , Schleit Jennifer , Sutphin George L. , An Elroy H. , Castanza Anthony , Fletcher Marissa , Higgins Sean , Jelic Monika , Klum Shannon , Muller Brian , Peng Zhao J. , Rai Dilreet , Ros Vanessa , Singh Minnie , Wende Helen V. , Kennedy Brian K. , Kaeberlein Matt
Published: November 2012

Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long‐lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long‐lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2‐independent but Gcn4‐dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.
Rural Clinical Experiences for Emergency Medicine Residents: A Curriculum Template
Authors: Wadman Michael C. , Clark Ted R. , Kupas Douglas F. , Macht Marlow , McLaughlin Steve , Mize Terry , Casaletto Jennifer , Muelleman Robert L.
Published: November 2012

Rural emergency departments (EDs) in the United States are less likely to be staffed with emergency medicine (EM) residency–trained and American Board of Emergency Medicine (ABEM)‐certified physicians than urban EDs. Rural EM clinical experiences during residency training have been suggested as a strategy to encourage future rural practice, but past Accreditation Council for Graduate Medical Education (ACGME) Residency Review Committee for Emergency Medicine program requirements and a lack of familiarity with rural rotations in the EM graduate medical education (GME) community have limited their availability. To provide a template for the development and implementation of a rural EM clinical experience, Kern's six‐step approach was followed.
Effect of a Physician Assistant as Triage Liaison Provider on Patient Throughput in an Academic Emergency Department
Authors: Nestler David M. , Fratzke Alesia R. , Church Christopher J. , Scanlan‐Hanson Lori , Sadosty Annie T. , Halasy Michael P. , Finley Janet L. , Boggust Andy , Hess Erik P.
Published: November 2012

Objectives

Overcapacity issues plague emergency departments (EDs). Studies suggest that triage liaison providers (TLPs) may shorten patient length of stay (LOS) and reduce the proportion of patients who leave without being seen (LWBS), but these results are not universal. Previous studies used physicians as TLPs. We evaluated whether a physician assistant (PA), acting as a TLP, would shorten LOS and decrease LWBS rates.

Methods

The authors used an observational cohort controlled before‐and‐after study design with predefined outcome measures, comparing 8 pilot days to 8 control days. The TLP evaluated all Emergency Severity Index (ESI) level 3, 4, and 5 patients, excluding pediatric and behavioral health patients.

Results

A total of 353 patients were included on pilot days and 371 on control days. LOS was shorter on pilot days than control days (median [interquartile range {IQR}] = 229 [168 to 303] minutes vs. 270 [187 to 372] minutes, p < 0.001). Waiting room times were similar between pilot and control days (median [IQR] = 69 [20 to 119] minutes vs. 70 [19 to 137] minutes, p = 0.408), but treatment room times were shorter (median [IQR] = 151 [92 to 223] minutes vs. 187 [110 to 254] minutes, p < 0.001). Finally, a lower proportion of patients LWBS on pilot days (1.4% vs. 9.7%, p < 0.001).

Conclusions

The addition of a PA as a TLP was associated with a 41‐minute decrease in median total LOS and a lower proportion of patients who LWBS. The decrease in total LOS is likely attributable to the addition of the TLP, with patients having shorter duration in treatment rooms on pilot days compared to control days.
The Utility of Early Lactate Testing in Undifferentiated Pediatric Systemic Inflammatory Response Syndrome
Authors: Scott Halden F. , Donoghue Aaron J. , Gaieski David F. , Marchese Ronald F. , Mistry Rakesh D.
Published: November 2012

Objectives

Failure to recognize shock contributes to inadequate early resuscitation in many children with sepsis. Serum lactate levels are used to identify adult patients with septic shock, but physical examination diagnosis alone is recommended in pediatric sepsis. The authors sought to test the utility of lactate testing in pediatric emergency department (ED) patients with systemic inflammatory response syndrome (SIRS). The hypothesis was that early hyperlactatemia (serum lactate ≥ 4.0 mmol/L) would be associated with increased risk of organ dysfunction.

Methods

This was a prospective cohort study of children younger than 19 years with SIRS presenting to a pediatric ED. The primary outcome was organ dysfunction within 24 hours of triage; secondary outcomes included disposition, serious bacterial infection (SBI), treatments, and mortality. Study personnel measured venous lactate level on a point‐of‐care meter, with clinicians blinded to results, and patients received usual care.

Results

A total of 239 subjects were enrolled; 18 had hyperlactatemia. The hyperlactatemia group had a relative risk of 5.5 (95% confidence interval [CI] = 1.9 to 16.0) of developing 24‐hour organ dysfunction. As a test for organ dysfunction, hyperlactatemia had a positive likelihood ratio of 5.0, a sensitivity of 31% (95% CI = 13% to 58%), and specificity of 94% (95% CI = 90% to 96%). Subjects with hyperlactatemia were significantly more likely to receive intravenous (IV) antibiotics and fluid boluses; despite increased therapy, they were at significantly increased risk for intensive care unit (ICU) admission and bacterial infection.

Conclusions

Among undifferentiated children with SIRS, early hyperlactatemia is significantly associated with increased risk of organ dysfunction, resuscitative therapies, and critical illness. The addition of serum lactate testing to the currently recommended clinical assessment may improve early identification of pediatric sepsis requiring resuscitation.