bluuebunny/crossref_metadata_2025 huggingface dataset:
Crestal Bone Loss Around Adjacent Dental Implants Restored with Splinted and Nonsplinted Fixed Restorations: A Systematic Literature Review
Authors: Al Amri Mohammad D. , Kellesarian Sergio Varela
Published: November 2016

Purpose

The aim of this systematic review was to compare the crestal bone loss around splinted and nonsplinted adjacent implants.

Materials and Methods

To address the focused question, “Is crestal bone loss around adjacent implants different with splinted from that with nonsplinted restorations?,” indexed databases were searched from 1965 up to and including May 2016 using various combinations of the following keywords: “implant,” “splinted,” “nonsplinted,” “unsplinted,” “connected,” “unconnected,” “nonconnected,” and “bone loss.” Letters to the editor, commentaries, historic reviews, case reports, case series, animal studies, and studies on full‐arch rehabilitation were excluded.

Results

Six studies were included with titanium implants ranging from 114 to 1187 implants. All studies had nonsplinted and splinted restorations that ranged from 20 to 234 restorations and from 60 to 970 restorations, respectively. In all the studies, the follow‐up period after the restoration placement ranged between 1 and 22 years, with a mean follow‐up ranging between 3 and 10.18 ± 3.18 years. In all studies, the mean crestal bone loss for implants restored with nonsplinted restorations ranged between 0.30 ± 0.65 and 1.3 ± 0.2 mm, whereas the mean crestal bone loss for implants restored with splinted restorations ranged between 0.50 ± 0.8 and 1.22 ± 0.95 mm.

Conclusion

Within the limitations of this review it is concluded that adjacent implants restored with splinted and nonsplinted fixed restorations did not exhibit a difference in crestal bone loss. The evidence from this systematic review suggests further investigation.
Poetry and Fin de Siècle Socialism
Authors: Harris Kirsten
Published: November 2016

Poetry was a major cultural genre of the so‐called ‘socialist revival’ in late 19th‐century Britain. Poems were sung at meetings and Labour Church services, published in socialist newspapers and periodicals, and gathered together in collections and anthologies. Socialist activists took to verse to make social, political and ideological interventions, and looked back through the literature of the 19th century to construct a democratic canon of verse which seemed to have the ‘Socialist passion for man,’ as one socialist commentator described it, at its heart. In a mixed socialist movement, engaged in heated internal debate over its aims and strategies, discussions about the nature and purpose of socialist poetry fed into wider discussions about the nature and purpose of fin de siècle socialism itself. There has been a burgeoning of scholarly interest in this field in the early 21st century, and this article explores this small but growing body of work, suggesting directions for future research.
Activism and Popular Constitutionalism in Contemporary Vietnam
Authors: Son Bui , Nicholson Pip
Published: November 2016

Based on Chinese constitutional analysis, political science, and law and society studies, we argue that work extending the application of popular constitutionalism to authoritarian states applies in Vietnam, as popular constitutionalism targets sites relevant to constitutional reform. We contend that popular constitutionalism located in authoritarian states requires three factors: a tradition of activism, space for reformist and pragmatic dialogue targeting constitutional change, and the political need for legitimacy. This article analyses activism in Vietnam, focusing on the lodging of Petition 72 with the Constitutional Amendment Drafting Commission in 2013, and the resulting responses. We conclude that this activism was pivotal in advocating for new constitutional norms, evidencing popular constitutionalism in Vietnam. The long history of Vietnamese scholar activism, the relative space for governance debates, and the political need for legitimacy made this possible. We also note that popular constitutionalism faces constraints in authoritarian states, which may shape its trajectory.
Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host
Authors: Palomares‐Rius Juan E. , Archidona‐Yuste Antonio , Cantalapiedra‐Navarrete Carolina , Prieto Pilar , Castillo Pablo
Published: November 2016

Bacterial endosymbionts have been detected in some groups of plant‐parasitic nematodes, but few cases have been reported compared to other groups in the phylum Nematoda, such as animal‐parasitic or free‐living nematodes. This study was performed on a wide variety of plant‐parasitic nematode families and species from different host plants and nematode populations. A total of 124 nematode populations (previously identified morphologically and molecularly) were screened for the presence of potential bacterial endosymbionts using the partial 16S rRNA gene and fluorescence in situ hybridization (FISH) and confocal microscopy. Potential bacterial endosymbionts were only detected in nematode species belonging to the genus Xiphinema and specifically in the X. americanum group. Fifty‐seven partial 16S rRNA sequences were obtained from bacterial endosymbionts in this study. One group of sequences was closely related to the genus ‘Candidatus Xiphinematobacter’ (19 bacterial endosymbiont sequences were associated with seven nematode host species, including two that have already been described and three unknown bacterial endosymbionts). The second bacterial endosymbiont group (38 bacterial endosymbiont sequences associated with six nematode species) was related to the family Burkholderiaceae, which includes fungal and soil–plant bacterial endosymbionts. These endosymbionts were reported for the first time in the phylum Nematoda. Our findings suggest that there is a highly specific symbiotic relationship between nematode host and bacterial endosymbionts. Overall, these results were corroborated by a phylogeny of nematode host and bacterial endosymbionts that suggested that there was a high degree of phylogenetic congruence and long‐term evolutionary persistence between hosts and endosymbionts.
Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants
Authors: Perrella Giorgio , Kaiserli Eirini
Published: November 2016

Light is a powerful stimulus regulating many aspects of plant development and phenotypic plasticity. Plants sense light through the action of specialized photoreceptor protein families that absorb different wavelengths and intensities of light. Recent discoveries in the area of photobiology have uncovered photoreversible changes in nuclear organization correlated with transcriptional regulation patterns that lead to de‐etiolation and photoacclimation. Novel signalling components bridging photoreceptor activation with chromatin remodelling and regulation of gene expression have been discovered. Moreover, coregulated gene loci have been shown to relocate to the nuclear periphery in response to light. The study of photoinduced changes in nuclear architecture is a flourishing area leading to major discoveries that will allow us to better understand how highly conserved mechanisms underlying genomic reprogramming are triggered by environmental and endogenous stimuli. This review aims to discuss fundamental and innovative reports demonstrating how light triggers changes in chromatin and nuclear architecture during photomorphogenesis.
Aggradational lobe fringes: The influence of subtle intrabasinal seabed topography on sediment gravity flow processes and lobe stacking patterns
Authors: Spychala Yvonne T. , Hodgson David M. , Stevenson Christopher J. , Flint Stephen S.
Published: November 2016

Seabed topography is ubiquitous across basin‐floor environments, and influences sediment gravity flows and sediment dispersal patterns. The impact of steep (several degrees) confining slopes on sedimentary facies and depositional architecture has been widely documented. However, the influence of gentle (fraction of a degree) confining slopes is less well‐documented, largely due to outcrop limitations. Here, exceptional outcrop and research borehole data from Unit A of the Permian Laingsburg Formation, South Africa, provide the means to examine the influence of subtle lateral confinement on flow behaviour and lobe stacking patterns. The dataset describes the detailed architecture of subunits A.1 to A.6, a succession of stacked lobe complexes, over a palinspastically restored 22 km across‐strike transect. Facies distributions, stacking patterns, thickness and palaeoflow trends indicate the presence of a south‐east facing low angle (fraction of a degree) lateral intrabasinal slope. Interaction between stratified turbidity currents with a thin basal sand‐prone part and a thick mud‐prone part and the confining slope results in facies transition from thick‐bedded sandstones to thin‐bedded heterolithic lobe fringe‐type deposits. Slope angle dictates the distance over which the facies transition occurs (hundreds of metres to kilometres). These deposits are stacked vertically over tens of metres in successive lobe complexes to form an aggradational succession of lobe fringes. Extensive slides and debrites are present at the base of lobe complexes, and are associated with steeper restored slope gradients. The persistent facies transition across multiple lobe complexes, and the mass flow deposits, suggests that the intrabasinal slope was dynamic and was never healed by deposition during Unit A times. This study demonstrates the significant influence that even subtle basin‐floor topography has on flow behaviour and depositional architecture of submarine lobe complexes. In addition, we present a new aggradational lobe fringe facies associations and recognition criteria for subtle confinement in less well‐exposed and subsurface basin fills.
Exact Goodness‐of‐Fit Testing for the Ising Model
Authors: Martín del Campo Abraham , Cepeda Sarah , Uhler Caroline
Published: November 2016

The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness of fit. Here, we propose various test statistics and an exact goodness‐of‐fit test for the finite‐lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness‐of‐fit testing using a Monte Carlo approach. However, finding a Markov basis is often computationally intractable. Thus, we develop a Monte Carlo method for exact goodness‐of‐fit testing for the Ising model that avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.
Congenital cutaneous melanoma in a dog
Authors: Meyrer Bruna , Bianchi Simone Passos , Pavarini Saulo Petinatti , Gerardi Daniel Guimarães
Published: November 2016

Background

Melanocytic tumours are derived from melanocytes and are common in older dogs with dark pigmented skin. Primary congenital cutaneous melanoma has been described in domestic mammals although there are no reports in the dog.

Hypothesis/objective

We describe a case of canine congenital cutaneous melanoma with rapid progression to metastasis and death.

Animal

A male, mixed breed dog was born with a circular ulcerated lesion near the left ear. By 12 days of age the lesion had grown significantly, with multiple soft, round nodules located at the outer base of the ear.

Methods and results

Histopathological examination showed the proliferation of round and elongated neoplastic cells with eosinophilic cytoplasm that occasionally contained granules of melanin. Immunohistochemical analysis was positive for melan A, S‐100 protein, neuron‐specific enolase (NSE) and vimentin, confirming the diagnosis of melanoma. The tumour progressed rapidly and at six months the dog died suddenly. Postmortem examination revealed pulmonary, cardiac and lymph node metastases.

Conclusions and clinical importance

To the best of the authors' knowledge, this is the first report of a primary congenital melanoma in the dog. The neoplastic condition showed malignant behaviour and high metastatic potential.
Bypass Flow Resistance in Prismatic Gas-Cooled Nuclear Reactors
Authors: McEligot Donald M. , Johnson Richard W.
Published: November 2016

Available computational fluid dynamics (CFD) predictions of pressure distributions in the vertical bypass flow between blocks in a prismatic gas-cooled reactor (GCR) have been analyzed to deduce apparent friction factors and loss coefficients for nuclear engineering systems and network codes. Calculations were performed for vertical gap spacings “s” of 2, 6, and 10 mm — representing 1, 3, and 5 mm in a GCR design, horizontal gaps between the blocks of 2 mm and two flow rates, giving a range of vertical gap Reynolds numbers ReDh of about 40–5300. The present focus is on the examination of the flow in the vertical gaps. Horizontal gaps are treated in CFD calculations but their flows are not examined. Laminar predictions of the fully developed friction factor ffd were about 3–10% lower than the classical infinitely wide channel. In the entry region, the local apparent friction factor was slightly higher than the classic idealized case, but the hydraulic entry length Lhy was approximately the same. The per cent reduction in flow resistance was greater than the per cent increase in flow area at the vertical corners of the blocks. The standard k–ϵ turbulence model was employed for flows expected to be turbulent. Its predictions of ffd and flow resistance were significantly higher than direct numerical simulations (DNS) for the classic case; the value of Lhy was about 30 gap spacings. Initial quantitative information for entry coefficients and loss coefficients for the expansion–contraction junctions between blocks is also presented. The present study demonstrates how CFD predictions can be employed to provide integral quantities needed in systems and network codes.
Failure Theory/Failure Criteria for Fiber Composite Laminates
Authors: Christensen Richard M. , Lonkar Kuldeep
Published: November 2016

Failure criteria are derived for the case of a quasi-isotropic laminate and for the more general case of orthotropic laminates. The former requires two calibrating failure properties obtained directly from laminate testing and the latter requires five standard experimental measurements for its calibration. Then the quasi-isotropic failure theory is taken much further, also admitting full calibration by only the two composites tow failure properties, the associated unidirectional tensile, and compressive strengths. The theoretically predicted failure envelope for the quasi-isotropic laminate is favorably compared with some comprehensive testing data. As a related matter, the general failure criteria for unidirectional fiber composites are also reviewed.
Evaluation of a Numerical Analysis Model for the Transient Response of Nuclear Steam Generator Secondary Side to a Sudden Steam Line Break
Authors: Chull Jo Jong , Ki Min Bok , Jun Jeong Jae
Published: November 2016

This paper presents an evaluation of the applicability of a numerical analysis model to the transient thermal-hydraulic response of steam generator (SG) secondary side to blowdown following a steam line break (SLB) at a pressurized water reactor (PWR). To do this, the numerical analysis model was applied to simulate the same blowdown situation as in an available experiment which was conducted for a simplified SG blowdown model, and the numerical results were compared with the measurements. As a result, both are in reasonably good agreement with each other. Consequently, the present numerical analysis model is evaluated to have the applicability for numerical simulations of the transient phase change heat transfer and flow situations in PWR SGs during blowdown following a SLB.
Turbulence Characteristics of Flow Under Combined Wave–Current Motion
Authors: Singh Santosh Kumar , Debnath Koustuv
Published: November 2016

This paper describes an experimental study carried out in a laboratory flume with a smooth surface to investigate the effect of a surface wave on unidirectional current. The measured velocity data were analyzed within the framework of the phase averaging for combined wave–current flow and verified by velocity equations based on the phase-averaged Prandtl momentum-transfer theory. The results highlight the changes induced on the mean velocity profile, turbulence intensity, and Reynolds shear stress in a plane of symmetry due to the superposition of surface waves of different frequencies. Modifications in the mean velocities, the turbulence intensities, and the Reynolds shear stresses with respect to the current-only flow are explored. As the frequency of the surface waves in unidirectional current changes, the results show variations in the mean flow and in the turbulence statistics that may affect the local sediment mobility in the coastal region.
Disilane addition versus silane-hydrogen flow rate effect on the PECVD of silicon thin films
Authors: Dimitrakellis Panagiotis , Amanatides Eleftherios , Mataras Dimitrios , Kalampounias Angelos G. , Spiliopoulos Nikolaos , Lahootun Vanina , Coeuret François , Madec Alain
Published: November 2016

The effect of small disilane addition to the silane/hydrogen mixture and of the total silane/hydrogen flow rate on the silicon thin film growth rate and crystallinity were investigated. The study was performed by using simplified gas phase chemistry model along with plasma diagnostics such as electrical and deposition rate measurements. The results showed that even small disilane addition induces an increase in the electron density, silane electron-induced dissociation rate, and film growth rate. The increase in the total flow rate caused a linear increase in the film growth rate despite the negligible effect on the discharge microscopic parameters. Similar deposition rates and crystallinities were achieved with both disilane addition and increase in the flow rate, but the deposition efficiency was much higher in the case of disilane addition. The simplified gas phase chemistry model indicated an increase in the silyl production rate either with the disilane addition or the increase in the flow rate. Almost the same silyl production rates were calculated for both parameters, but for the disilane addition case, this was achieved with much less silicon containing molecules in the gas feed. Finally, the increase in the silyl production rate combined to the almost constant hydrogen atoms production, and consumption rate is estimated as the main reason for the drop in the crystallinity with the increase in disilane fraction in the mixture or the total flow rate.
Complete Genome Sequence of the Avian-Pathogenic Escherichia coli Strain APEC O18
Authors: Nicholson Bryon A. , Wannemuehler Yvonne M. , Logue Catherine M. , Li Ganwu , Nolan Lisa K.
Published: November 2016

Avian-pathogenic
Escherichia coli
(APEC) is the causative agent of colibacillosis, a disease that affects all facets of poultry production worldwide, resulting in multimillion dollar losses annually. Here, we report the genome sequence of an APEC O18 sequence type 95 (ST95) strain associated with disease in a chicken.
Draft Genome Sequence of Strain LSUCC0135, an Early Diverging Member of the Order
Methylophilales
in the Phylum
Betaproteobacteria
Authors: Lanclos V. Celeste , Henson Michael W. , Pitre David M. , Thrash J. Cameron
Published: November 2016

We present the draft genome of
Methylophilales
sp. strain LSUCC0135, isolated using high-throughput dilution-to-extinction culturing methods from the coast of Freshwater City, Louisiana, USA. The genome indicates metabolic flexibility for differing oxygen concentrations and electron donors.
Genome Sequence of
Pandoraea
sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil
Authors: Kumar Madan , Gazara Rajesh Kumar , Verma Sandhya , Kumar Manish , Verma Praveen Kumar , Thakur Indu Shekhar
Published: November 2016

We report here the genome sequence of
Pandoraea
sp. ISTKB, a betaproteobacterium isolated from rhizospheric soil in the backwaters of Alappuzha, Kerala, India. The strain is alkalotolerant and grows on medium containing lignin as a sole carbon source. Genes and pathways related to lignin degradation were complemented by genomic analysis.
Draft Genome Sequence of
Piscirickettsia litoralis
, Isolated from Seawater
Authors: Wan Xuehua , Lee Alex J. , Hou Shaobin , Ushijima Blake , Nguyen Yen P. , Thawley Jessica A. , Donachie Stuart P.
Published: November 2016

One species of
Piscirickettsia
, a pathogen of salmonid fish, has been described. The genome sequence of a putative second and free-living species may provide insights into the evolution of pathogenicity in the genus.
Oxygen regulation of ribulose 1,5-bisphosphate carboxylase activity in Rhodospirillum rubrum
Authors: Cook L S , Tabita F R
Published: November 2016

The carboxylase activity of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBPC/O) decreased when an anaerobic culture of Rhodospirillum rubrum was exposed to atmospheric levels of oxygen. From 70 to 80% of the activity was lost within 12 to 24 h. Inactivation was apparent when the enzyme was assayed in situ (in whole cells) and when activity was measured in dialyzed crude extracts. The quantity of enzyme protein, as estimated from sodium dodecyl sulfate-polyacrylamide gels or as quantified immunologically, did not decrease within 24 h of exposure to air. Following extended exposure to aerobic conditions (48 to 72 h), degradation of enzyme occurred. These results indicate that the inactivation of RuBPC/O in R. rubrum may be due to an alteration or modification of the preformed enzyme, followed by eventual degradation of the inactive enzyme. When shifted back to anaerobic conditions (under an argon atmosphere), the RuBPC/O activity increased rapidly. This increase appeared to be due to de novo synthesis of enzyme. The increase in activity was not observed when the culture was maintained in the dark or in the absence of a suitable carbon source. Thus, the oxygen-mediated inactivation of RuBPC/O appeared to be due to some form of irreversible modification. The cloned R. rubrum RuBPC/O gene, expressed in Escherichia coli, yielded functional enzyme that was not affected by oxygen, indicating that inactivation in R. rubrum is mediated by a gene product(s) not found in E. coli.
Molecular analysis of a pathogenicity locus in Pseudomonas syringae pv. syringae
Authors: Mukhopadhyay P , Williams J , Mills D
Published: November 2016

One of the chromosomal regions of Pseudomonas syringae pv. syringae encoding pathogenicity factors had been mapped into a 3.9-kilobase-pair fragment in previous studies. Promoter probe analysis indicated the existence of a promoter near one end of the fragment. DNA sequencing of this fragment revealed the existence of a consensus promoter sequence in the region of the promoter activity and two open reading frames (ORFs) downstream. These ORFs, ORF1 and ORF2, encoded putative polypeptides of 40 and 83 kilodaltons, respectively. All ORF1::Tn5 as well as ORF2::Tn5 mutant strains were nonpathogenic on susceptible host bean plants and were unable to elicit hypersensitive reactions on nonhost tobacco plants. The deduced amino acid sequence of the 83-kilodalton polypeptide contained features characteristic of known integral membrane proteins. Fusion of the lacZ gene to ORF2 led to the expression of a hybrid protein inducible in Escherichia coli. The functions of the putative proteins encoded by ORF1 and ORF2 are unknown at present.
Genes encoding core components of the phycobilisome in the cyanobacterium Calothrix sp. strain PCC 7601: occurrence of a multigene family
Authors: Houmard J , Capuano V , Coursin T , Tandeau de Marsac N
Published: November 2016

The phycobilisome is the major light-harvesting complex of cyanobacteria. It is composed of a central core from which six rods radiate. Allphycocyanin, an alpha beta oligomer (alpha AP and beta AP), is the main component of the core which also contains three other phycobiliproteins (alpha APB, beta 18.3, and L92CM) and a small linker polypeptide (L7.8C). By heterologous DNA hybridization, two EcoRI DNA fragments of 3.5 and 3.7 kilobases have been cloned from the chromatically adapting cyanobacterium Calothrix sp. strain PCC 7601. Nucleotide sequence determination has allowed the identification of five apc genes: apcA1 (alpha AP1), apcA2 (alpha AP2), apcB1 (beta AP1), apcC (L7.8C), and apcE (L92CM). Four of these genes are adjacent on the chromosome and form the apcEA1B1C gene cluster. In contrast, no genes have been found close to the apcA2 gene which is carried by the 3.5-kilobase EcoRI fragment. Transcriptional analysis and 5'-end-mapping experiments were performed. The results obtained demonstrate that the apcEA1B1C gene cluster forms an operon from which segmented transcripts originate, whereas the apcA2 gene behaves as a monocistronic unit. Qualitatively, the same transcripts were identified regardless of the light wavelengths received during cell growth. The deduced amino acid sequences of the apc gene products are very similar to their known homologs of either cyanobacterial or eucaryotic origin. It was interesting, however, that in the apcA1 and apcA2 genes, whose products correspond to alpha-type allophycocyanin subunits, nucleotide sequences were more conserved (67%) than were the deduced amino acid sequences (59%).
Mutations that affect production of branched RNA-linked msDNA in Myxococcus xanthus
Authors: Dhundale A , Furuichi T , Inouye M , Inouye S
Published: November 2016

A deletion mutation of the gene (msd-msr) for the branched RNA-linked msDNA of Myxococcus xanthus was constructed by replacing the chromosomal 0.7-kilobase (kb) SmaI-XhoI fragment encompassing msd-msr with a 1.4-kb fragment carrying a gene for kanamycin resistance. It was found that this deletion strain (delta msSX) could not produce msDNA, although it still contained another species of msDNA, mrDNA (msDNA, reduced size). No apparent differences between delta msSX and the wild-type strain were observed in terms of cell growth, morphogenesis, fruiting-body formation, or motility. Both a deletion mutation at the region 100 base pairs upstream of msd and an insertion mutation at a site 500 base pairs upstream of msd showed a significant reduction of msDNA production, indicating that there is a cis- or trans-acting positive element in this region. When the 3.5-kb BamHI fragment carrying msd-msr from Stigmatella aurantiaca was inserted into the M. xanthus chromosome, the S. aurantiaca msDNA was found to be produced in M. xanthus.
Effects of potassium ions on proton motive force in Rhodobacter sphaeroides
Authors: Abee T , Hellingwerf K J , Konings W N
Published: November 2016

The proton motive force (PMF) was determined in Rhodobacter sphaeroides under anaerobic conditions in the dark and under aerobic-dark and anaerobic-light conditions. Anaerobically in the dark in potassium phosphate buffer, the PMF at pH 6 was -20 mV and was composed of an electrical potential (delta psi) only. At pH 7.9 the PMF was composed of a high delta psi of -98 mV and was partially compensated by a reversed pH gradient (delta pH) of +37 mV. ATPase inhibitors did not affect the delta psi, which was most likely the result of a K+ diffusion potential. Under energized conditions in the presence of K+ the delta psi depolarized due to electrogenic K+ uptake. This led to the generation of a delta pH (inside alkaline) in the external pH range of 6 to 8. This delta pH was dependent on the K+ concentration and was maximal at external K+ concentrations larger than 1.2 mM. In energized cells in 50 mM KPi buffer containing 5 mM MgSO4, a delta pH (inside alkaline) was present at external pHs from pH 6 to 8. As a result the overall magnitude of the PMF at various external pHs remained constant at -130 mV, which was significantly higher than the PMF under anaerobic-dark conditions. In the absence of K+, in 50 mM NaPi buffer containing 5 mM MgSO4, no depolarization of the delta psi was found and the PMF was composed of a large delta psi and a small delta pH. The delta pH became even reversed (inside acidic) at alkaline pHs (pH>7.3), resulting in a lowering of the PMF. These results demonstrate that in R. sphaeroides K+ uptake is essential for the generation of a delta pH and plays a central role in the regulation of the internal pH.
Physical and functional analyses of the syrA and syrB genes involved in syringomycin production by Pseudomonas syringae pv. syringae
Authors: Xu G W , Gross D C
Published: November 2016

The syrA and syrB genes involved in syringomycin production in Pseudomonas syringae pv. syringae B301D were identified from an EcoRI-pLAFR3 cosmid library and then physically and functionally analyzed in relation to plant pathogenicity. Homologous recombination of the genes required for syringomycin production from cosmids pGX183 (syrA) and pGX56 (syrB), respectively, introduced into nontoxigenic (Tox-) Tn5 mutants W4S2545 and W4S770 resulted in the concomitant restoration of toxin production and full virulence. The disease indices of the Tox+ strains obtained by recombination of the cloned, homologous DNA into the corresponding Tn5 mutant were essentially equivalent to that of strain B301D-R and significantly higher than those of W4S2545 and W4S770. A 12-kilobase (kb) EcoRI fragment from pGX183 was subcloned (i.e., pGX15) and found to contain the sequences necessary for syringomycin production. A map of pGX15 prepared by a combination of restriction endonuclease digestions and Tn5 mutagenesis showed that the syrA sequence was 2.3 to 2.8 kb. Marker exchange of syrA::Tn5 from pGX15 into B301D-R yielded nonpathogenic phenotypes, indicating that syrA is a regulatory gene since it is necessary for both syringomycin production and pathogenicity. The 4.9-kb EcoRI fragment from pGX56 was subcloned (i.e., pGX4) and shown to carry the syrB sequence which was 2.4 to 3.3 kb. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of protein extracts from B301D-R associated five proteins, ranging from approximately 130,000 to approximately 470,000 in molecular weight, with syringomycin production. The syrA and syrB genes were required for the formation of proteins SR4 (approximately 350,000) and SR5 (approximately 130,000), which are believed to be components of the syringomycin synthetase complex.
Effect of DNA sequence and structure on nuclease activity of the DexA protein of bacteriophage T4
Authors: Gruber H , Kern G , Gauss P , Gold L
Published: November 2016

The bacteriophage T4 dexA gene product is required during infection of Escherichia coli strains carrying a mutation in the optA gene. We purified the DexA protein from cells which overproduced the protein. The protein was assayed for nuclease activity on synthetic di- and oligonucleotide substrates of known sequence and secondary structure. Sequence and structure significantly affected nuclease activity. The properties of the enzyme may explain the requirement for the DexA protein during infection of optA mutant hosts.
Role of cell wall in Saccharomyces cerevisiae mutants resistant to Hg2+
Authors: Ono B , Ohue H , Ishihara F
Published: November 2016

Hg2+-resistant mutants were isolated from Saccharomyces cerevisiae. Although they were very much like the parental strains in terms of colony-forming ability, they grew faster than the parental strains in the presence of sublethal doses of Hg2+. The Hg2+-resistant mutations were dominant. They were centromere linked and were divided into two groups by means of recombination; one of the mutations, designated HGR1-1, was mapped on chromosome IV because of its linkage to the TRP1 locus. The Hg2+-resistant mutants took up Hg2+ as much as, or slightly more than, the parental strains did. The mutants and parental strains retained only about 5 and 15%, respectively, of the cell-associated Hg2+ after removal of the cell wall; therefore, the mutants had less spheroplast-associated Hg2+ than did the parental strains. These results indicate that the cell wall plays an important role in protection against Hg2+ by acting as an adsorption filter and that the mutations described confer Hg2+ resistance by increasing the Hg2+-binding capacity of the cell wall.
A protein antigen of Mycobacterium leprae is related to a family of small heat shock proteins
Authors: Nerland A H , Mustafa A S , Sweetser D , Godal T , Young R A
Published: November 2016

The gene encoding an immunologically important 18-kilodalton protein antigen of Mycobacterium leprae has been sequenced, and the amino acid sequence of the antigen has been deduced. The 18-kilodalton antigen is strikingly similar in size and sequence to a family of eucaryotic heat shock proteins.
Nucleotide sequence of the Bacillus subtilis phoR gene
Authors: Seki T , Yoshikawa H , Takahashi H , Saito H
Published: November 2016

The nucleotide sequence of phoR, the positive and negative regulatory gene for alkaline phosphatase and phosphodiesterase formation in Bacillus subtilis, was determined. The sequence data predicted an open reading frame of 1,740 base pairs (579 amino acids) which overlaps the 5 base pairs of the preceding phoP coding sequence. The deduced amino acid sequence was significantly homologous with that of the Escherichia coli phoR gene product, which is the sensory element for the pho regulon.
A single base pair change in proline biosynthesis genes causes osmotic stress tolerance
Authors: Dandekar A M , Uratsu S L
Published: November 2016

A single base pair change has been found in a site corresponding to a regulatory region of the first enzyme in the proline biosynthetic pathway. This change alters feedback inhibition and is responsible for the synthesis of high levels of proline that enable Escherichia coli to withstand osmotic stress.
Nucleotide sequence of an Rts1 fragment causing temperature-dependent instability
Authors: Tanaka M , Okawa N , Mori K , Suyama Y , Kaji A
Published: November 2016

Rts1 is a multiphenotypic drug resistance plasmid which is eliminated from host bacteria at 42 degrees C but not at 32 degrees C. This phenotype has been called temperature-dependent instability (Tdi). We determined the nucleotide sequence of the Rts1 DNA b' segment which causes this phenotype. Within this 786-base-pair segment, several open reading frames (ORFs) were found, including one which encodes a protein with a molecular weight of 16,000. A protein approximately corresponding to this protein is expressed in Escherichia coli minicells harboring plasmids containing the b' segment. In addition, we found the chi sequence at 112 bases proximal to this ORF. Temperature-dependent elimination due to this segment was not observed in the RecA strain of E. coli, but the RecB protein was not required for expression of this phenotype. We constructed various deletion derivatives and found that three portions, the region containing the chi (nucleotides 1 to 24), ORF (nucleotides 25 to 546), and tail (nucleotides 631 to 786) sequences are necessary for Tdi activity. Site-directed mutagenesis studies indicated that ORF I is required for Tdi expression.
Characterization of the Azorhizobium sesbaniae ORS571 genomic locus encoding NADPH-glutamate synthase
Authors: Donald R G , Lapointe J , Ludwig R A
Published: November 2016

Sixteen independent Azorhizobium sesbaniae ORS571 vector insertion (Vi) mutants defective in ammonium assimilation (Asm-) were selected; genomic DNA sequences flanking the insertion endpoints were cloned directly. Resulting recombinant plasmids were used to identify, by hybridization, corresponding wild-type DNA sequences from an A. sesbaniae lambda EMBL3 genomic library (lambda Asm phages). All 16 Asm- Vi mutants physically mapped to a single genomic locus. Plasmid subclones of recombinant phage lambda Asm152 were able to complement both Escherichia coli gltB and A. sesbaniae Asm- Vi mutants; NADPH-glutamate synthase activity was detected in all such strains complemented to Asm+. Heterologous and homologous complementations required both A. sesbaniae gltA+ and (inferred) gltB+ genes. Eleven A. sesbaniae Asm- Vi mutants mapped to a 4-kilobase-pair (kbp) DNA region that exhibited homology with Bacillus subtilis gltA+. In E. coli maxicell labeling experiments, this 4-kbp DNA region encoded a 165-kilodalton polypeptide that was inferred to be the product of the A. sesbaniae gltA+ gene (glutaminase NADPH-dependent L-glutamate synthase subunit). Site-directed Tn5-lacZ mutagenesis of a glt plasmid subclone identified a region that bisected this locus into (at least) two cistrons. Because the remaining five A. sesbaniae Asm- mutants mapped to a 1.5-kbp region adjacent to gltA+, these mutants probably define a single gltB+ gene (glutamate dehydrogenase NADPH-dependent L-glutamate synthase subunit); this region did not exhibit homology with the B. subtilis gltB+ gene.
First committed step of lipid A biosynthesis in Escherichia coli: sequence of the lpxA gene
Authors: Coleman J , Raetz C R
Published: November 2016

The min 4 region of the Escherichia coli genome contains genes (lpxA and lpxB) that encode proteins involved in lipid A biosynthesis. We have determined the sequence of 1,350 base pairs of DNA upstream of the lpxB gene. This fragment of DNA contains the complete coding sequence for the 28.0-kilodalton lpxA gene product and an upstream open reading frame capable of encoding a 17-kilodalton protein (ORF17). In addition there appears to be an additional open reading frame (ORF?) immediately upstream of ORF17. The initiation codon for lpxA is a GUG codon, and the start codon for ORF17 is apparently a UUG codon. The start and stop codons overlap between ORF? and ORF17, ORF17 and lpxA, and lpxA and lpxB. This overlap is suggestive of translational coupling and argues that the genes are cotranscribed. Crowell et al. (D.N. Crowell, W.S. Reznikoff, and C.R.H. Raetz, J. Bacteriol. 169:5727-5734, 1987) and Tomasiewicz and McHenry (H.G. Tomasiewicz and C.S. McHenry, J. Bacteriol. 169:5735-5744, 1987) have demonstrated that there are three similarly overlapping coding regions downstream of lpxB including dnaE, suggesting the existence of a complex operon of at least seven genes: 5'-ORF?-ORF17-lpxA-lpxB-ORF23-dnaE-ORF37-3 '.
Bacteriophage T4 late transcription from plasmid templates is enhanced by negative supercoiling
Authors: Albright L M , Kassavetis G A , Geiduschek E P
Published: November 2016

Concurrent viral replication is normally required to activate bacteriophage T4 late promoters; replication is thought to provide a template structure which is competent for late transcription. Transcription from plasmid-borne T4 late promoters, however, is independent of replication in vivo and in vitro. In this work, we have shown that, when the late gene 23 promoter is located on a plasmid, its utilization in vivo depends upon the ability of host DNA gyrase to maintain some degree of negative superhelicity. This suggests that an alternative pathway exists for activation of late promoters: DNA which is under sufficient negative torsional stress is already competent for late transcription. We also describe a method for isolating ternary complexes of plasmid DNA, RNA polymerase, and nascent RNA which have initiated transcription in vivo. The topoisomer distribution of such ternary complexes prepared from T4-infected cells showed that, late in infection, transcriptional activity resides primarily in the subset of the plasmid population with the most negatively supercoiled topoisomers. However, the overall transcriptional pattern in these ternary complexes indicated that both vector and T4 sequences are actively transcribed. Much of this transcriptional activity could be independent of gp55, the T4-specific RNA polymerase-binding protein that confers late promoter recognition.
Analysis of the variable endpoints generated by one-ended transposition of Tn21
Authors: Avila P , Grinsted J , de la Cruz F
Published: November 2016

One-ended transposition of Tn21 generates recombinants usually containing a whole copy of the donor replicon plus a short duplication of it (S. Mötsch, R. Schmitt, P. Avila, F. de la Crue, E. Ward, and J. Grinsted, Nucleic Acids Res. 13:3335-3342, 1985). This work shows that recombinants containing less than a whole copy of the donor replicon (hereafter called short recombinants) could also be detected when plasmid donors which contained two selectable genetic markers were used. Short recombinants were produced at the same frequency from TnpR+ donor molecules as from TnpR- donor molecules in a RecA- background. Therefore, they were not resolution products of larger recombinants. This result invalidates a previous hypothesis to explain one-ended transposition, that is, that one-ended transposition arises from the use of secondary ends by the transposition apparatus. On the other hand, it suggests that one-ended transposition of Tn21 occurs via a simple insertion mechanism.
Cloning of the egl gene of Pseudomonas solanacearum and analysis of its role in phytopathogenicity
Authors: Roberts D P , Denny T P , Schell M A
Published: November 2016

The egl gene of Pseudomonas solanacearum was cloned on a cosmid and expressed in Escherichia coli. Restriction endonuclease mapping, transposon mutagenesis, and subclone analysis showed that the egl gene was located on a 2.7-kilobase XhoI-SalI P. solanacearum DNA fragment. Immunoabsorption experiments and sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis showed that the egl gene encodes the 43-kilodalton endoglucanase that is the major excreted endoglucanase of P. solanacearum. In E. coli, the egl gene appeared to be expressed from its own promoter, but its product was restricted to the cytoplasm. The cloned egl gene was mutagenized with Tn5 and used to specifically mutate the chromosomal egl gene of P. solanacearum by site-directed mutagenesis. The resultant mutant was identical to the wild-type strain in production of extracellular polysaccharide and extracellular polygalacturonase as well as several other excreted proteins but produced at least 200-fold less endoglucanase. This mutant strain was significantly less virulent on tomato than the wild-type strain in plant bioassay experiments. Virulence of the endoglucanase-deficient strain was restored to near wild-type levels by complementation in trans with the cloned egl gene, indicating that the egl gene is important but not absolutely required for pathogenesis.
Purification and properties of Escherichia coli dimethyl sulfoxide reductase, an iron-sulfur molybdoenzyme with broad substrate specificity
Authors: Weiner J H , MacIsaac D P , Bishop R E , Bilous P T
Published: November 2016

Dimethyl sulfoxide reductase, a terminal electron transfer enzyme, was purified from anaerobically grown Escherichia coli harboring a plasmid which codes for dimethyl sulfoxide reductase. The enzyme was purified to greater than 90% homogeneity from cell envelopes by a three-step purification procedure involving extraction with the detergent Triton X-100, chromatofocusing, and DEAE ion-exchange chromatography. The purified enzyme was composed of three subunits with molecular weights of 82,600, 23,600, and 22,700 as identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The native molecular weight was determined by gel electrophoresis to be 155,000. The purified enzyme contained 7.5 atoms of iron and 0.34 atom of molybdenum per mol of enzyme. The presence of molybdopterin cofactor in dimethyl sulfoxide reductase was identified by reconstitution of cofactor-deficient NADPH nitrate reductase activity from Neurospora crassa nit-I mutant and by UV absorption and fluorescence emission spectra. The enzyme displayed a very broad substrate specificity, reducing various N-oxide and sulfoxide compounds as well as chlorate and hydroxylamine.
Significance of braided trichomes in the cyanobacterium Mastigocladus laminosus
Authors: Hernández-Muñiz W , Stevens S E
Published: November 2016

Loops and braids in filaments of the cyanobacterium Mastigocladus laminosus were observed. Braided filaments were generally in the form of a right-handed helix (87%) but were occasionally observed as left-handed helices (13%). It was demonstrated by time-lapse photomicrography that braids continued to grow as braids and that loops coiled into braids as growth proceeded. Measurements of the distance between grooves in 74 braids yielded an average distance of 13 +/- 3 micron, a result which suggests that braid formation is not random. We propose that the braids arise as a consequence of the helical growth of cells that make up the filaments of M. laminosus.
Molecular cloning and sequencing of the gene encoding the fimbrial subunit protein of Bacteroides gingivalis
Authors: Dickinson D P , Kubiniec M A , Yoshimura F , Genco R J
Published: November 2016

The gene encoding the fimbrial subunit protein of Bacteroides gingivalis 381, fimbrilin, has been cloned and sequenced. The gene was present as a single copy on the bacterial chromosome, and the codon usage in the gene conformed closely to that expected for an abundant protein. The predicted size of the mature protein was 35,924 daltons, and the secretory form may have had a 10-amino-acid, hydrophilic leader sequence similar to the leader sequences of the MePhe fimbriae family. The protein sequence had no marked similarity to known fimbrial sequences, and no homologous sequences could be found in other black-pigmented Bacteroides species, suggesting that fimbrillin represents a class of fimbrial subunit protein of limited distribution.
Intermediates in bacteriophage Mu lysogenization of Escherichia coli him hosts
Authors: Bourret R B , Fox M S
Published: November 2016

Characterization of a putative intermediate in the Mu lysogenization pathway is possible in a variant Escherichia coli himD strain which exhibits greatly diminished lysogen formation. In this strain, most infecting Mu genomes form stable, transcribable, nonreplicating structures. Many of these genomes can be mobilized to form lysogens by a second Mu infection, which can be delayed by at least 100 min. This intermediate structure can be formed in the absence of Mu A or B function. We suggest that the inferred intermediate could be the previously reported protein-linked circular form of the Mu genome. Providing Mu B function from a plasmid enhances Mu lysogenization in this him strain, and the enhancement is much greater when both Mu A and B functions are provided.
Purification and characterization of a bacterial nitrophenol oxygenase which converts ortho-nitrophenol to catechol and nitrite
Authors: Zeyer J , Kocher H P
Published: November 2016

A nitrophenol oxygenase which stoichiometrically converted ortho-nitrophenol (ONP) to catechol and nitrite was isolated from Pseudomonas putida B2 and purified. The substrate specificity of the enzyme was broad and included several halogen- and alkyl-substituted ONPs. The oxygenase consisted of a single polypeptide chain with a molecular weight of 58,000 (determined by gel filtration) or 65,000 (determined on a sodium dodecyl sulfate-polyacrylamide gel). The enzymatic reaction was NADPH dependent, and one molecule of oxygen was consumed per molecule of ONP converted. Enzymatic activity was stimulated by magnesium or manganese ions, whereas the addition of flavin adenine dinucleotide, flavin mononucleotide, or reducing agents had no effect. The apparent Kms for ONP and NADPH were 8 and 140 microM, respectively. 2,4-Dinitrophenol competitively (Ki = 0.5 microM) inhibited ONP turnover. The optimal pH for enzyme stability and activity was in the range of 7.5 to 8.0. At 40 degrees C, the enzyme was totally inactivated within 2 min; however, in the presence of 1 mM ONP, 40% of the activity was recovered, even after 10 min. Enzymatic activity was best preserved at -20 degrees C in the presence of 50% glycerol.