bluuebunny/crossref_metadata_2025 huggingface dataset:
The response of ecosystem water‐use efficiency to rising atmospheric CO2 concentrations: sensitivity and large‐scale biogeochemical implications
Authors: Knauer Jürgen , Zaehle Sönke , Reichstein Markus , Medlyn Belinda E. , Forkel Matthias , Hagemann Stefan , Werner Christiane
Published: November 2016

Ecosystem water‐use efficiency (WUE) is an important metric linking the global land carbon and water cycles. Eddy covariance‐based estimates of WUE in temperate/boreal forests have recently been found to show a strong and unexpected increase over the 1992–2010 period, which has been attributed to the effects of rising atmospheric CO2 concentrations on plant physiology.

To test this hypothesis, we forced the observed trend in the process‐based land surface model JSBACH by increasing the sensitivity of stomatal conductance (gs) to atmospheric CO2 concentration. We compared the simulated continental discharge, evapotranspiration (ET), and the seasonal CO2 exchange with observations across the extratropical northern hemisphere.

The increased simulated WUE led to substantial changes in surface hydrology at the continental scale, including a significant decrease in ET and a significant increase in continental runoff, both of which are inconsistent with large‐scale observations. The simulated seasonal amplitude of atmospheric CO2 decreased over time, in contrast to the observed upward trend across ground‐based measurement sites.

Our results provide strong indications that the recent, large‐scale WUE trend is considerably smaller than that estimated for these forest ecosystems. They emphasize the decreasing CO2 sensitivity of WUE with increasing scale, which affects the physiological interpretation of changes in ecosystem WUE.
Changing One's Mind: Self‐Conscious Belief and Rational Endorsement
Authors: Leite Adam
Published: November 2016

Self‐consciously attempting to shape one's beliefs through deliberation and reasoning requires that one stand in a relation to those beliefs that might be signaled by saying that one must inhabit one's beliefs as one's own view. What does this amount to? A broad swath of philosophical thinking about self‐knowledge, norms of belief, self‐consciousness, and related areas assumes that this relation requires one to endorse, or be rationally committed to endorsing, one's beliefs. In fact, however, fully self‐conscious adherence to epistemic norms requires the ability to self‐consciously hold a belief without endorsing that belief as true, as well‐supported by the evidence, or as meeting some other epistemic standard, and there are cases in which no such commitment is rationally required. This ability is necessary if there is to be any such thing as a fully self‐conscious process of changing one's mind.
Potential benefits of mindfulness during pregnancy on maternal autonomic nervous system function and infant development
Authors: Braeken Marijke A.K.A. , Jones Alexander , Otte Renée A. , Nyklíček Ivan , Van den Bergh Bea R.H.
Published: November 2016

Mindfulness is known to decrease psychological distress. Possible benefits in pregnancy have rarely been explored. Our aim was to examine the prospective association of mindfulness with autonomic nervous system function during pregnancy and with later infant social‐emotional development. Pregnant women (N = 156) completed self‐report mindfulness and emotional distress questionnaires, and had their autonomic function assessed in their first and third trimesters, including heart rate (HR), indices of heart rate variability (HRV), preejection period (PEP), and systolic (SBP) and diastolic blood pressure (DBP). The social‐emotional development of 109 infants was assessed at 4 months of age. More mindful pregnant women had less prenatal and postnatal emotional distress (p < .001) and higher cardiac parasympathetic activity: root mean square of successive differences (RMSSD: p = .03) and high‐frequency (HF) HRV (p = .02). Between the first and third trimesters, women's overall HR increased (p < .001), and HRV (RMSSD, HF HRV, and low‐frequency (LF) HRV: p < .001) and PEP decreased (p < .001). In more mindful mothers, parasympathetic activity decreased less (RMSSD: p = .01; HF HRV: p = .03) and sympathetic activity (inversely related to PEP) increased less (PEP: p = .02) between trimesters. Their offspring displayed less negative social‐emotional behavior (p = .03) compared to offspring of less mindful mothers. Mindfulness in pregnancy was associated with ANS changes likely to be adaptive and with better social‐emotional offspring development. Interventions to increase mindfulness during pregnancy might improve maternal and offspring health, but randomized trials are needed to demonstrate this.
Poststroke QEEG informs early prognostication of cognitive impairment
Authors: Schleiger Emma , Wong Andrew , Read Stephen , Rowland Tennille , Finnigan Simon
Published: November 2016

Cognitive impairment is a common consequence of stroke, but remains difficult to predict. We investigate the ability of early QEEG assessment to inform such prediction, using binary logistic regression. Thirty‐five patients (12 female, ages 18–87) suffering middle cerebral artery, ischemic stroke were studied. Resting‐state EEG was recorded 48–239 h after symptom onset. Relative power for delta, theta, alpha, and beta bands, delta:alpha ratio, and peak alpha frequency were analyzed. Montreal Cognitive Assessment (MoCA) was administered, where possible, on day of EEG and at median 99 days (range 69–138) poststroke. Eight patients could not complete the baseline MoCA, and four the follow‐up MoCA, for varying reasons (most commonly, stroke symptoms). Fifteen patients (48%) had cognitive impairment (MoCA score ≤25) at follow‐up. One QEEG index was able to correctly predict presence/absence of cognitive impairment in 24/31 patients (77.4%), whereas predischarge MoCA did so in 23 patients. This index, relative theta frequency (4–7.5 Hz) power, was computed from only three posterior electrodes over the stroke‐affected hemisphere. Its predictive accuracy (three electrodes) was higher than that of any “global” QEEG measure (averaged over 19 electrodes). These results may signify association between poststroke alpha slowing and cognitive impairment, which may be mediated by attentional (dys)function, which warrants further investigation. Pending further studies, QEEG measure(s)—from a few electrodes—could inform early prognostication of poststroke cognitive outcomes (and clinical decisions), particularly when cognitive function cannot be adequately assessed (due to symptoms, language, or other issues) or when assessment is equivocal.
Evaluation of different fragment sizes and cryoprotectants for cryopreservation of feline testicular tissues
Authors: Macente BI , Toniollo GH , Apparicio M , Mansano CFM , Thomé HE , Canella CL , Tozato MEG , Gutierrez RR
Published: November 2016

Contents

This study aimed to evaluate tissue damage of feline testicles sectioned in two different sizes (0.3 or 0.5 cm3) and submitted to different cryoprotectants (propanediol or glycerol). Testicles obtained from 12 domestic cats were sectioned in 0.3 and 0.5 cm3sized pieces and immediately evaluated byTBARSand semi‐quantitatively by histomorphology. The remaining fragments were placed in cryotubes with 1 ml Egg yolk Tris EquexSTMextender containing 3% glycerol or 3% propanediol and cryopreserved by fast‐freezing technique. Frozen‐thawed fragments were also evaluated byTBARSand histomorphology. Statistical analysis was performed using one‐wayANOVAwith Student–Newmann–Keuls post hoc test, withp < .05. Fresh and cryopreserved tissues generally exhibited a similar morphology concerning detachment of cells from the basement membrane and observation of nucleoli, with a great proportion scored as 0 (no alteration). When present, alterations were slight and the morphology was considered to be good (most classified in scores 1). Pyknosis was the main anomaly observed as score 2 in 54.6% and 58.4% of 0.3‐cm3fragments cryopreserved in propanediol and glycerol, respectively (16.7% scored 2 in fresh tissue). InTBARSevaluation, 0.5‐cm3fragments cryopreserved in glycerol produced less free radical compared to the 0.3 cm3cryopreserved in glycerol or propanediol. Our results showed that glycerol was more efficient than propanediol to cryopreserve 0.5‐cm3fragments; this might be attributed to the fact that glycerol molecular weight is larger than propanediol and so its perfusion in the testicular tissue is slower.
Responsiveness of intraovarian dog follicles in vitro to epidermal growth factor and vascular endothelial growth factor depends on ovarian donor age
Authors: Thongkittidilok C , Wildt DE , Songsasen N
Published: November 2016

Contents

We investigated the influence of epidermal growth factor (EGF) and vascular endothelial growth factor (VEGF) on in vitro follicle development within ovarian cortices recovered from pre‐pubertal (≤6 months) versus peri‐pubertal dogs (≥10 months). Ovarian cortices were cultured for 3 or 7 days in EGF (0 or 10 ng/ml) and VEGF (0, 0.1 or 1 ng/ml) and subjected to histological and apoptosis analyses. Fresh cortices from the same dogs served as “non‐cultured controls” (NCC) and were evaluated similarly. The response of ovarian follicles to growth factors differed between pre‐pubertal versus peri‐pubertal tissues. For pre‐pubertal dogs, percentage of structurally normal follicles in cortices cultured for 3 days in low VEGF (0.1 ng/ml) and EGF alone was comparable to that of the NCC. Follicle density declined in all cultured groups even after 3 days. Primary follicle diameter in all cortices cultured for 7 days, except in low VEGF, was smaller than that of the NCC, and percentage apoptotic follicles sharply increased in all treatment groups compared to the NCC. For peri‐pubertal donors, percentages of structurally normal follicles decreased in all culture treatments at 3 and 7 days of incubation compared to the NCC. However, more normal follicles were found in cortices cultured in low VEGF and the two VEGF and EGF combinations than in the absence of growth factors or with EGF alone. Culture reduced the density of developing follicles, but follicle diameter was similar to that of the NCC. TUNEL analysis revealed that high‐VEGF (1 ng/ml) treatment protected follicles against apoptosis, with the proportion of apoptotic follicles at Day 7 being comparable to that of the NCC. The findings demonstrate that the response of ovarian cortices to growth factor supplementation varied between pre‐pubertal versus peri‐pubertal donors.
Unclassifiable interstitial lung diseases: Clinical characteristics and survival
Authors: Hyldgaard Charlotte , Bendstrup Elisabeth , Wells Athol U. , Hilberg Ole
Published: November 2016

ABSTRACT

Background and objective

Unclassifiable disease in chronic interstitial lung disease (ILD) is a common and challenging problem but has been insufficiently studied. The 2013 update of the international multidisciplinary classification of the idiopathic interstitial pneumonias presented a classification based on observed disease behaviour with the purpose of providing guidance to clinicians in the management of these patients. The aim of this study was to apply the new disease behaviour classification (DBC) and the previously validated ILD‐gender age physiology (GAP) score to a cohort of unclassifiable ILD patients and to assess the prognostic value of these two composite approaches.

Methods

Unclassifiable ILD patients were identified from the population‐based ILD registry at Aarhus University Hospital, Denmark, that includes all ILD patients diagnosed at the department from 2003 to 2009. The DBC was assessed retrospectively based on clinical presentation and diagnostic examinations at presentation and short‐term follow‐up.

Results

Unclassifiable ILD was diagnosed in 24% of the cohort (105 of 431). Survival in unclassifiable ILD was intermediate between idiopathic pulmonary fibrosis (IPF) and non‐IPF controls (idiopathic non‐specific interstitial pneumonia (NSIP), hypersensitivity pneumonitis and connective tissue disease‐associated ILD). The DBC and the ILD‐GAP index were strong individual predictors of outcome in a dichotomized regression model (hazard ratio (HR): 6.3 (95% CI: 1.8–21.2) for the DBC and HR: 6.7 (95% CI: 2.2–20.0) for ILD‐GAP). Both approaches remained significant in a common regression model (HR: 4.5 (95% CI: 1.3–15.7) for the DBC and HR: 5.1 (95% CI: 1.3–15.7) for ILD‐GAP).

Conclusion

The DBC approach showed strong prognostic value in unclassifiable ILD. The DBC and the ILD‐GAP were complementary predictors of outcome in unclassifiable ILD.
The dynamics of dining out in the 21st century: Insights from organizational theory
Authors: DeSoucey Michaela , Demetry Daphne
Published: November 2016

The world of restaurants—as organizations as well as indicators of social status and cultural tastes—has, thus far in the 21st century, become especially dynamic in the United States and elsewhere. Social scientists have begun to engage seriously with issues concerning germane shifts in the culinary profession and the emergence of new forms of cooking and dining out. For sociologists interested in consumption, organizations, and creative work, this offers a number of timely topics, such as restaurants' financing strategies and ownership models, the institutionalization of new culinary trends, the expanding roles of chefs, and the labor practices of upmarket restaurants. This article synthesizes recent scholarship on the modern culinary field in the United States, specifically examining three interrelated themes: tensions between concurrent demands for creativity and financial returns, new ways of catering to consumer desires for authenticity, and issues of inequality in professional kitchens. It concludes by discussing several issues facing the future of dining out, as forecast by field leaders themselves, which offer further opportunities for burgeoning sociological and organizational inquiry.
Race and critical tourism studies: An analytical literature review
Authors: Jamerson W. Trevor
Published: November 2016

This analytical literature review focuses on critical tourism studies and its intersections with racial analyses. The tourism industry has long relied on desires to experience a sense of Otherness to generate economic growth, which makes race a valuable heuristic site to consider ways culture and economy are intertwined in the global marketplace. Two theories of race—Omi and Winant's () racial formation and Goldberg's () racial neoliberalism—are offered as avenues through that scholars might better investigate intersections of race and tourism. Race is commodified in tourism through orienting the concept around loci of value, and different types of tourism feature more racial prominence than others. Critical tourism scholars may benefit from an increased racial awareness in their work towards providing a counternarrative to strictly business‐based tourism research. Meanwhile, race scholars might benefit from an increased understanding of ways racial difference operates within tourism, as it is a major site of negotiations of Otherness. Although racial themes are more prevalent in some types of tourism than others, the two theories provided together force us to consider ways that tourism studies might further racialize its critical inquiries.
Substance use and decision‐making in adolescent best friendship dyads: The role of popularity
Authors: de Water Erik , Burk William J. , Cillessen Antonius H. N. , Scheres Anouk
Published: November 2016

In adolescent best friendship dyads, we examined: (a) similarity in substance use and decision‐making; (b) associations between participants' decision‐making and their own and best friend's substance use, (c) the influence of relative popularity within the dyad on these associations. Participants (n = 172; 12–18 years) named their best friend, completed popularity ratings, and a substance use questionnaire. Computer tasks were administered to assess risk‐taking and immediate reward preferences. Reciprocated same‐sex best friendship dyads (n = 49) were distinguished on their popularity, and we controlled for age differences between dyads in the analyses. Best friends were similar in substance use and risk‐taking preferences. More popular friends' risk‐taking preferences were positively associated with alcohol use of less popular friends. These findings underscore best friendship similarity in risky behaviors, and the influence of popular friends.
Epidemiology of infections following haploidentical peripheral blood hematopoietic cell transplantation
Authors: Slade Michael , Goldsmith Scott , Romee Rizwan , DiPersio John F. , Dubberke Erik R. , Westervelt Peter , Uy Geoffrey L. , Lawrence Steven J.
Published: November 2016

Background

The use of T‐cell replete haploidentical hematopoietic cell transplant (haplo‐HCT) has increased substantially since the introduction of post‐transplant cyclophosphamide (PTCy) regimens. Limited data exist concerning infectious complications of haplo‐HCT utilizing mobilized peripheral blood (PB) hematopoietic cells.

Methods

This retrospective cohort study included all adult patients at our institution undergoing PB haplo‐HCT with PTCy between June 2009 and June 2015. Infections were microbiologically confirmed. Invasive fungal infections (IFI) classified as “proven” or “probable” by standard definitions were included.

Results

In total, 104 patients were identified. Median follow‐up was 218 days (range: 6–1576). A total of 322 episodes of infection were recorded. Eighty‐nine percent of patients experienced at least one infection. Median time to first infection was 22 days. Patients experiencing at least one bacterial, viral, and IFI were 62%, 72%, and 6%, respectively. The majority (69%) of bacterial infections were caused by enteric organisms. Seven cases of Staphylococcus aureus infection were recorded, with one bacteremia case. Cytomegalovirus (CMV) viremia occurred in 54/71 (76%) at‐risk patients at a median time of 24 days. Sixteen (15%) patients developed CMV disease. Nineteen percent (20/104) of patients developed BK polyomavirus‐associated cystitis. Six (6%) patients experienced a total of seven IFI. Infection was the primary cause of death for 12% (6/51) of patients and was a secondary cause for 41%.

Conclusion

In PB haplo‐HCT patients, a high incidence of CMV viremia and disease was observed. Infections with enteric bacteria were common. Fungal and staphylococcal infections were uncommon. Further studies are needed to compare infectious complications in haplo‐HCT with other transplant modalities.
Liminal geopolitics: the subjectivity and spatiality of diplomacy at the margins
Authors: McConnell Fiona
Published: November 2016

This paper argues that the lens of liminality has the potential to enrich scholarship in critical geopolitics by offering a nuanced approach to the geographies and ambivalence of political subjectivity. In the context of a perceived proliferation of ‘new’ actors the paper turns critical attention to what happens at the threshold between the categories of state and non‐state, official and unofficial diplomacy. It asks what such a perspective on diplomacy might mean for understandings of who is, and who should be, a legitimate actor in international politics by turning to the notion of liminality as developed in cultural anthropology. This is a concept that surprisingly has been overlooked in political geography and this paper asks how geographers might engage more productively with it, particularly in light of emergent critical international relations research on liminality as a paradigm for understanding stability and change in institutionalised orders. Empirically, the paper focuses on the articulation of liminal political subjectivities and spatialities through the lens of the Unrepresented Nations and Peoples Organization (UNPO), a coalition of almost 50 stateless nations, indigenous communities and national minorities that currently are denied a place at international diplomatic forums. Drawing on this case study, the paper examines three areas of geopolitical enquiry that the notion of liminality opens up. First is the spatiality of diplomacy in terms of the out‐of‐placeness of liminal actors and the construction of transformative spaces of quasi‐official diplomacy. Second are particular qualities of political subjectivity, including the blurring of boundaries between diplomacy and activism, and the notion of geopolitical shapeshifters. Finally, attention turns to the notion ofcommunitasto draw out the politics of belonging, recognition and legitimacy. The paper concludes by suggesting that the idea of ambivalence that underpins liminality is a useful provocation to take creativity and aspiration seriously in geopolitics.
Maternal red blood cell alloantibodies identified in blood samples obtained from Iranian pregnant women: the first population study in Iran
Authors: Shahverdi Ehsan , Moghaddam Mostafa , Gorzin Fateme
Published: November 2016

BACKGROUND

The objective was to determine the frequency of occurrence of alloantibodies among pregnant women in Iran.

STUDY DESIGN AND METHODS

This was a prospective cross‐sectional study, which was carried out in the immunohematology reference laboratory of the Iranian Blood Transfusion Organization in Tehran, Iran, in 2008 to 2015. Screening and identification of red blood cell (RBC) alloantibodies was done on the sera of 7340 pregnant females using the standard tube method and gel column agglutination technique.

RESULTS

Alloantibodies were identified in the serum of 332 of the 7340 (4.5%) pregnant women. A total of 410 antibodies were detected in 332 positive maternal serum samples with no previous history of blood transfusion. Anti‐D was the most common antibody accounting for 70.5% of all the antibodies formed in D– women. The incidence of specific alloimmunization other than Rh group was 14.4%.

CONCLUSION

We concluded that the alloimmunization rate was high in comparison with wide pattern in previous studies. In Iran, like other developing countries, alloimmunization screening tests are performed only to detect anti‐D in pregnant D– women. This high rate of alloimmunization, quite possibly, is due to the fact that the majority of blood samples came from pregnant women known to have previous obstetric problems. However, we suggest that RBC antibody screening tests should be extended to all D+ women.
High COX‐2 expression in canine mast cell tumours is associated with proliferation, angiogenesis and decreased overall survival
Authors: Gregório H. , Raposo T. , Queiroga F. L. , Pires I. , Pena L. , Prada J.
Published: November 2016

COX‐2 overexpression is associated with several hallmarks of carcinogenesis such as proliferation, angiogenesis, invasion and metastasis. Fifty cases of canine mast cell tumours (MCT) were retrospectively evaluated and submitted to immunohistochemistry for COX‐2, CD31, Ki‐67, MAC‐387 and CD3. Furthermore its relationship with clinicopathological variables and overall survival (OS) was analysed. COX‐2 intensity (P = 0.016), but not COX‐2 extension nor score was associated with decreased OS and higher grades of malignancy according to Patnaik (P = 0.002) and Kiupel (P < 0.001) grading systems. Cox‐2 intensity was also associated with higher Ki‐67 scores (P = 0.009), higher mitotic index (P = 0.022) and higher microvascularization density (P = 0.045). No association was observed for COX‐2 intensity and CD3‐T lymphocyte (P = 0.377) and macrophage infiltration (P = 0.261) by MAC‐387 immunollabelling, suggesting an active role of COX‐2 in MCT oncogenesis mainly through proliferation and angiogenesis stimulation making it a potentially clinical relevant prognosis marker and therapeutic target.
Proof of concept of the preventive efficacy of high‐dose recombinant mono‐allergen immunotherapy in atopic dogs sensitized to the Dermatophagoides farinae allergen Der f 2
Authors: Olivry Thierry , Paps Judy S. , Dunston Stanley M.
Published: November 2016

Background

Allergen immunotherapy is currently the only intervention proposed to specifically prevent clinical flares after allergen challenges. The low molecular weight Der f 2 (Df2) is a major allergen in Japanese dogs sensitized to Dermatophagoides farinae house dust mites.

Objectives

Pilot, blinded, placebo‐controlled experiment testing the efficacy of subcutaneous immunotherapy (SCIT) with high doses of recombinant Df2 conjugated to the maltotriose pullulan (rDf2‐P).

Methods

Eight Maltese beagle atopic dogs were sensitized to rDf2 then randomized to SCIT with rDf2‐P (six dogs) or placebo (two). The immunotherapy consisted of six weekly injections of increasing doses (0.1–10.0 μg) of rDf2‐P followed by four monthly injections of 10 μg of this allergen. Epicutaneous rDf2 challenges, rDf2‐specific IgE serology and intradermal reactivity, as well as serum cytokine level measurements, were performed throughout the study.

Results

Subcutaneous injections of placebo did not alter the cutaneous reactivity after rDf2 challenge, while that of the dogs treated with rDf2‐P SCIT disappeared in five of six dogs (83%) and was reduced in one of six (17%). During SCIT maintenance, skin lesion scores were significantly lower in dogs receiving SCIT compared to those treated with placebo. This clinical improvement was accompanied by a concurrent, yet not significant, decrease in rDf2‐specific IgE serology and immediate intradermal reactivity. Cytokine serum levels were inconclusive. There were no adverse events seen with rDf2‐P SCIT.

Conclusions and clinical importance

The new mono‐allergen SCIT appears safe and effective for reducing skin lesions after allergen challenges; it deserves further testing in dogs with spontaneous atopic dermatitis.
Decentralized Formation Control Based on Adaptive Super Twisting
Authors: Hernández-Alemán Rubén , Salas-Peña Oscar , De León-Morales Jesús
Published: November 2016

In this paper, a decentralized formation control based on adaptive super-twisting algorithm (ASTA) is designed for a group of unicycle mobile robots. According to this approach, movements of robots are driven through a sequence of formation patterns. This control scheme increases robustness against unknown dynamics and disturbances, whose bounds are not required to be known. Furthermore, a high-order differentiator is designed to estimate unmeasurable signals, in order to implement the proposed controller. Finally, simulation results illustrate the effectiveness of the proposed control scheme.
Continuum and Kinetic Simulations of Heat Transfer Trough Rarefied Gas in Annular and Planar Geometries in the Slip Regime
Authors: Hadj-Nacer Mustafa , Maharjan Dilesh , Ho Minh-Tuan , Stefanov Stefan K. , Graur Irina , Greiner Miles
Published: November 2016

Steady-state heat transfer through a rarefied gas confined between parallel plates or coaxial cylinders, whose surfaces are maintained at different temperatures, is investigated using the nonlinear Shakhov (S) model kinetic equation and Direct Simulation Monte Carlo (DSMC) technique in the slip regime. The profiles of heat flux and temperature are reported for different values of gas rarefaction parameter δ, ratios of hotter to cooler surface temperatures T, and inner to outer radii ratio R. The results of S-model kinetic equation and DSMC technique are compared to the numerical and analytical solutions of the Fourier equation subjected to the Lin and Willis temperature-jump boundary condition. The analytical expressions are derived for temperature and heat flux for both geometries with hotter and colder surfaces having different values of the thermal accommodation coefficient. The results of the comparison between the kinetic and continuum approaches showed that the Lin and Willis temperature-jump model accurately predicts heat flux and temperature profiles for small temperature ratio T=1.1 and large radius ratios R≥0.5; however, for large temperature ratio, a pronounced disagreement is observed.
A novel mutation, cog, which results in production of a new porin protein (OmpG) of Escherichia coli K-12
Authors: Misra R , Benson S A
Published: November 2016

A mutant of Escherichia coli K-12 which produces a new outer membrane protein, OmpG, was isolated and genetically and biochemically characterized. The presence of OmpG allows growth on maltodextrins in the absence of the LamB maltoporin. The data obtained from in vivo growth and uptake experiments suggested that the presence of the OmpG protein results in an increase in outer membrane permeability for small hydrophilic compounds. In light of these findings, we suggest that OmpG is a porinlike protein. The mutation which results in the expression of OmpG has been termed cog (for control of OmpG) and mapped to 29 min on the E. coli chromosome. Diploid analysis shows that the mutant cog-192 allele is recessive for both the Dex+ and OmpG+ phenotypes. We propose that the cog mutation destroys a negative regulatory function and therefore derepresses ompG expression.
Excision of an 11-kilobase-pair DNA element from within the nifD gene in anabaena variabilis heterocysts
Authors: Brusca J S , Hale M A , Carrasco C D , Golden J W
Published: November 2016

The 3' region of the Anabaena variabilis nifD gene contains an 11-kilobase-pair element which is excised from the chromosome during heterocyst differentiation. We have sequenced the recombination sites which border the element in vegetative cells and the rearranged heterocyst sequences. In vegetative cells, the element was flanked by 11-base-pair direct repeats which were identical to the repeats present at the ends of the nifD element in Anabaena sp. strain PCC 7120 (Anabaena strain 7120). Although Anabaena strain 7120 and A. variabilis are quite distinct in many ways, the overall sequence similarity between the two strains for the regions sequenced was 96%. Like the Anabaena strain 7120 element, the A. variabilis element was excised in heterocysts to produce a functional nifD gene and a free circularized element which was neither amplified nor degraded. The Anabaena strain 7120 xisA gene is located at the nifK-proximal end of the nifD element and is required for excision of the element in heterocysts. The A. variabilis element also contained an xisA gene which could complement a defective Anabaena strain 7120 xisA gene. A. variabilis did not contain the equivalent of the Anabaena strain 7120 fdxN 55-kilobase-pair element.
Implication of nifA in regulation of genes located on a Rhizobium meliloti cryptic plasmid that affect nodulation efficiency
Authors: Sanjuan J , Olivares J
Published: November 2016

We examined the contribution of a cryptic plasmid, pRmeGR4b, to the nodulation of Medicago sativa by strain GR4 of Rhizobium meliloti. A 905-base-pair PstI DNA fragment in pRmeGR4b was found to hybridize DNA of the R. meliloti fixA promoter region as a probe. Sequence analysis of the PstI fragment showed a 206-base-pair region displaying high homology with the DNA upstream of the RNA start points of the P1 and P2 symbiotic promoters. Putative nif promoter consensus sequences were conserved in this DNA segment. Expression of DNA downstream of the nif promoterlike sequence, monitored by beta-galactosidase activity of different lacZ fusions, was demonstrated to depend on a functional nifA gene, both in microaerobically free-living cells and in nodules. Individual transposon Tn3-HoHo1 insertions in this DNA region caused a reduced nodulation competitiveness. This new symbiotic region, occupying approximately 5 kilobases of pRmeGR4b DNA, was called nfe (nodule formation efficiency).
Dual control of the Bradyrhizobium japonicum symbiotic nitrogen fixation regulatory operon fixR nifA: analysis of cis- and trans-acting elements
Authors: Thöny B , Anthamatten D , Hennecke H
Published: November 2016

Aerobic expression of the fixR nifA operon in Bradyrhizobium japonicum was shown to depend on a cis-acting, promoter-upstream DNA sequence located between the -24/-12 promoter and position -86 relative to the transcription start site. An adenine at position -66 was essential for maximal expression. A chromosomal deletion of the upstream activator sequence (UAS) led to a symbiotically defective phenotype which was typical of nifA mutants. B. japonicum crude extracts contained a protein that bound to the UAS. By using chromosomally integrated fixR-lacZ fusions, the level of expression of the fixR nifA operon was found to be fivefold higher under reduced oxygen tension than under aerobiosis. This increase was due to autoactivation by the NifA protein and was partly independent of the UAS. Based on these data, we propose a model for the regulation of nitrogen fixation genes in B. japonicum that involves dual positive control of the fixR nifA operon. At high oxygen concentrations, the operon is expressed at a moderate level, subject to activation by the binding of a trans-acting factor to the UAS. Under such conditions, the nifA gene product is known to be inactive. At very low oxygen concentrations--a condition favorable to NifA activity--the NifA protein is the trans-acting factor which (i) enhances the level of fixR nifA expression (and hence its own synthesis) and (ii) activates other nif and fix genes.
Separation of the SOS-dependent and SOS-independent components of alkylating-agent mutagenesis
Authors: Couto L B , Chaudhuri I , Donahue B A , Demple B , Essigmann J M
Published: November 2016

Escherichia coli plasmids containing the rpsL+ gene (Strs phenotype) as the target for mutation were treated in vitro with N-methyl-N-nitrosourea. Following fixation of mutations in E. coli MM294A cells (recA+ Strs), an unselected population of mutant and wild-type plasmids was isolated and transferred into a second host, E. coli 6451 (recA Strr). Strains carrying plasmid-encoded forward mutations were then selected as Strr isolates, while rpsL+ plasmids conferred the dominant Strs phenotype in the second host. Mutation induction and reduced survival of N-methyl-N-nitrosourea-treated plasmids were shown to be dose dependent. Because this system permitted analysis and manipulation of the levels of certain methylated bases produced in vitro by N-methyl-N-nitrosourea, it afforded the opportunity to assess directly the relative roles of these bases and of SOS functions in mutagenesis. The methylated plasmid DNA gave a mutation frequency of 6 X 10(-5) (a 40-fold increase over background) in physiologically normal cells. When the same methylated plasmid was repaired in vitro by using purified O6-methylguanine DNA methyltransferase (to correct O6-methylguanine and O4-methylthymine), no mutations were detected above background levels. In contrast, when the methylated plasmid DNA was introduced into host cells induced by UV light for the SOS functions, rpsL mutagenesis was enhanced eightfold over the level seen without SOS induction. This enhancement of mutagenesis by SOS was unaffected by prior treatment of the DNA with O6-methylguanine DNA methyltransferase. These results demonstrate a predominant mutagenic role for alkylation lesions other than O6-methylguanine or O4-methylthymine when SOS functions are induced. The mutation spectrum of N-methyl-N-nitrosourea under conditions of induced SOS functions revealed a majority of mutagenic events at A . T base pairs.
Identification of multiple repressor recognition sites in the hut system of Pseudomonas putida
Authors: Hu L , Allison S L , Phillips A T
Published: November 2016

The hutC gene in Pseudomonas putida encodes a repressor protein that negatively regulates the expression of all hut genes. We have overexpressed this cloned hutC gene in Escherichia coli to identify P. putida hut regions that could specifically bind the repressor. Ten restriction fragments, some of which were partially overlapping and spanned the coding portions of the P. putida hut region, were labeled and tested for their ability to recognize repressor in a filter binding assay. This procedure identified three binding sites, thus supporting previous indications that there were multiple operons. A 1.0-kilobase-pair SalI restriction fragment contained the operator region for the hutUHIG operon, whereas a 1.9-kilobase-pair SmaI fragment contained the hutF operator. A 2.9-kilobase-pair XhoI segment appeared to contain the third operator, corresponding to a separate and perhaps little used control region for hutG expression only. The addition of urocanate, the normal inducer, caused dissociation of all operator-repressor complexes, whereas N-formylglutamate, capable of specifically inducing expression of the hutG gene, inhibited binding only of repressor to fragments containing that gene. Formylglutamate did not affect the action of urocanate on the repressor-hutUHIG operator complex, indicating that it binds to a site separate from urocanate on the repressor. DNA footprinting and gel retardation analyses were used to locate more precisely the operator for the hutUHIG operon. A roughly 40-base-pair portion was identified which contained a 16-base-pair region of dyad symmetry located near the transcription initiation site for this operon.
A novel sigma factor is involved in expression of the rpoH gene of Escherichia coli
Authors: Wang Q P , Kaguni J M
Published: November 2016

The Escherichia coli rpoH gene encoding sigma 32, which is involved in the heat shock response, is transcribed from as many as four promoters. We have isolated a novel sigma factor of about 24 kilodaltons that allows core RNA polymerase to transcribe preferentially from one of these promoters, rpoH3p. This promoter is known to be regulated by DnaA protein. The sigma 24 factor was isolated from a preparation of RNA polymerase by electroelution from sodium dodecyl sulfate-polyacrylamide gels followed by renaturation. Expression of heat shock proteins is induced by treatments which include those that induce the stringent response. Under such conditions, decreased transcription from rpoH3p and no increase in transcription from other rpoH promoters were observed. This result suggests that induction of heat shock proteins by the stringent response is not mediated by increased transcription of the rpoH gene.
Actively replicating nucleoids influence positioning of division sites in Escherichia coli filaments forming cells lacking DNA
Authors: Mulder E , Woldringh C L
Published: November 2016

The positioning of constrictions in Escherichia coli filaments pinching off anucleate cells was analyzed by fluorescence microscopy of dnaX(Ts), dnaX(Ts) sfiA, dnaA46(Ts), gyrA(Am) supF(Ts), and gyrB(Ts) mutants. In filaments with actively replicating nucleoids, constrictions were positioned close to the nucleoid, whereas in nonreplicating filaments, positioning of constrictions within the anucleate region was nearly random. We conclude that constriction positioning depends in an unknown way on nucleoid replication activity.
Lysis of Escherichia coli by the bacteriophage phi X174 E protein: inhibition of lysis by heat shock proteins
Authors: Young K D , Anderson R J , Hafner R J
Published: November 2016

Lysis of Escherichia coli by the cloned E protein of bacteriophage phi X174 was more rapid than expected when bacteria were shifted from 30 to 42 degrees C at the time of E induction. Since such treatment also induces the heat shock response, we investigated the effect of heat shock proteins on lysis. An rpoH mutant was more sensitive to lysis by E, but a secondary suppressor mutation restored lysis resistance to parental levels, which suggests that the sigma 32 subunit itself did not directly increase lysis resistance. At 30 degrees C, mutants in five heat shock genes (dnaK, dnaJ, groEL, groES, and grpE) were more sensitive to lysis than were their wild-type parents. The magnitude of lysis sensitivity varied with mutation and strain background, with dnaK, dnaJ, and groES mutants consistently exhibiting the greatest sensitivities. Extended protection against lysis occurred when overproduction of heat shock proteins was induced artificially in cells that contained a plasmid with the rpoH+ gene under control of the tac promoter. This protective effect was completely abolished by mutations in dnaK, dnaJ, or groES but not by grpE or groEL mutations. Altered membrane behavior probably explains the contradiction whereby an actual temperature shift sensitized cells to lysis, but production of heat shock proteins exhibited protective effects. The results demonstrate that E-induced lysis can be divided into two distinct operations which may now be studied separately. They also emphasize a role for heat shock proteins under non-heat-shock conditions and suggest cautious interpretation of lysis phenomena in systems where E protein production is under control of a temperature-sensitive repressor.
Construction of TnphoA gene fusions in Rhodobacter sphaeroides: isolation and characterization of a respiratory mutant unable to utilize dimethyl sulfoxide as a terminal electron acceptor during anaerobic growth in the dark on glucose
Authors: Moore M D , Kaplan S
Published: November 2016

We have constructed a suicide vector, pU1800, containing the transposable element TnphoA (Tn5 IS50L::phoA), for the purpose of producing protein fusions in vivo between the Escherichia coli alkaline phosphatase (APase) and proteins of the facultative photoheterotroph, Rhodobacter sphaeroides. We introduced TnphoA into the genome of R. sphaeroides at a coupled conjugation-transposition frequency of approximately 1 x 10(-6). Fusions giving rise to APase expression, as judged by blue-colony pigmentation when exconjugants were plated on growth medium containing the chromogenic indicator 5-bromo-4-chloro-3-indolyl phosphate, were observed in about 1% of the exconjugants. Numerous, distinguishable mutant phenotypes have been generated by this method, including those which lack the ability to use dimethyl sulfoxide as a terminal electron acceptor during anaerobic respiration, as well as those which are photosynthetically incompetent or altered in pigment synthesis, and others that express resistance to chlorate. The growth and spectral characteristics of several of these mutants, as well as the localization and quantitation of subcellular APase activity under different physiological conditions, have been examined. The presence of TnphoA in the host genome has been confirmed for each mutant analyzed, and specifically tagged DNA fragments containing TnphoA have been identified and localized; cosmids containing R. sphaeroides genomic DNA capable of complementing individual mutants have also been isolated. The usefulness of this approach in studying gene activity in R. sphaeroides is discussed.
Role of Na+ cycle in cell volume regulation of Mycoplasma gallisepticum
Authors: Shirvan M H , Schuldiner S , Rottem S
Published: November 2016

The mechanism for the extrusion of Na+ from Mycoplasma gallisepticum cells was examined. Na+ efflux from cells was studied by diluting 22Na+-loaded cells into an isoosmotic NaCl solution and measuring the residual 22Na+ in the cells. Uphill 22Na+ efflux was found to be glucose dependent and linear with time over a 60-s period and showed almost the same rate in the pH range of 6.5 to 8.0. 22Na+ efflux was markedly inhibited by dicyclohexylcarbodiimide (DCCD, 10 microM), but not by the proton-conducting ionophores SF6847 (0.5 microM) or carbonyl cyanide m-chlorophenylhydrazone (CCCP, 10 microM) over the entire pH range tested. An ammonium diffusion potential and a pH gradient were created by diluting intact cells or sealed membrane vesicles of M. gallisepticum loaded with NH4Cl into a choline chloride solution. The imposed H+ gradient (inside acid) was not affected by the addition of either NaCl or KCl to the medium. Dissipation of the proton motive force by CCCP had no effect on the growth of M. gallisepticum in the pH range of 7.2 to 7.8 in an Na+-rich medium. Additionally, energized M. gallisepticum cells were stable in an isoosmotic NaCl solution, even in the presence of proton conductors, whereas nonenergized cells tended to swell and lyse. These results show that in M. gallisepticum Na+ movement was neither driven nor inhibited by the collapse of the electrochemical gradient of H+, suggesting that in this organism Na+ is extruded by an electrogenic primary Na+ pump rather than by an Na+-H+ exchange system energized by the proton motive force.
Volume regulation in Mycoplasma gallisepticum: evidence that Na+ is extruded via a primary Na+ pump
Authors: Shirvan M H , Schuldiner S , Rottem S
Published: November 2016

The primary extrusion of Na+ from Mycoplasma gallisepticum cells was demonstrated by showing that when Na+-loaded cells were incubated with both glucose (10 mM) and the uncoupler SF6847 (0.4 microM), rapid acidification of the cell interior occurred, resulting in the quenching of acridine orange fluorescence. No acidification was obtained with Na+-depleted cells or with cells loaded with either KCl, RbCl, LiCl, or CsCl. Acidification was inhibited by dicyclohexylcarbodiimide (50 microM) and diethylstilbesterol (50 microM), but not by vanadate (100 microM). By collapsing delta chi with tetraphenylphosphonium (200 microM) or KCl (25 mM), the fluorescence was dequenched. The results are consistent with a delta chi-driven uncoupler-dependent proton gradient generated by an electrogenic ion pump specific for Na+. The ATPase activity of M. gallisepticum membranes was found to be Mg2+ dependent over the entire pH range tested (5.5 to 9.5). Na+ (greater than 10 mM) caused a threefold increase in the ATPase activity at pH 8.5, but had only a small effect at pH 5.5. In an Na+-free medium, the enzyme exhibited a pH optimum of 7.0 to 7.5, with a specific activity of 30 +/- 5 mumol of phosphate released per h per mg of membrane protein. In the presence of Na+, the optimum pH was between 8.5 and 9.0, with a specific activity of 52 +/- 6 mumol. The Na+-stimulated ATPase activity at pH 8.5 was much more stable to prolonged storage than the Na+-independent activity. Further evidence that two distinct ATPases exist was obtained by showing that M. gallisepticum membranes possess a 52-kilodalton (kDa) protein that reacts with antibodies raised against the beta-subunit of Escherichia coli ATPase as well as a 68-kDa protein that reacts with the anti-yeast plasma membrane ATPases antibodies. It is postulated that the Na+ -stimulated ATPases functions as the electrogenic Na+ pump.
Gene transfer system for Rhodopseudomonas viridis
Authors: Lang F S , Oesterhelt D
Published: November 2016

A gene transfer system for Rhodopseudomonas viridis was established which uses conjugation with Escherichia coli S17-I as the donor and mobilizable plasmids as vectors. Initially, plasmids of the incompatibility group P1 (pRK290 and pRK404) were used. The more effective shuttle vectors between E. coli and R. viridis, pKV1 and pKVS1, were derived from plasmid pBR322 and showed the highest conjugation frequency (10(-2] thus far demonstrated in purple bacteria. It was also demonstrated that Rhizobium meliloti can be used as a donor for conjugation with R. viridis. From a genomic cosmid library of R. viridis constructed in the vector pHC79, clones that coded for subunits H (puh operon), L, M and cytochrome c (puf operon) of the photosynthetic reaction center were isolated and characterized. For linkage of the two operons on the genome, cosmids that overlapped with the operon-carrying clones were identified. The relative positions of the two operons could not be determined, but the operons must be more than 100 kilobase pairs apart. Thus, the genomic organization of the reaction center in R. viridis is different from that of Rhodobacter capsulatus, for which a distance of about 39 kilobase pairs was determined. From a spontaneous mutant of R. viridis that is resistant to the herbicide terbutryn, the puf operon was cloned in pKVS1 and transferred by conjugation into R. viridis wild-type cells. The resulting exconjugants were resistant to the herbicide, which demonstrated that the puf operon on pKVS1 constructions was functionally expressed in R. viridis.