bluuebunny/crossref_metadata_2025 huggingface dataset:
Models, phases and cases of patient participation in decision‐making in surgical treatment in Norway: A qualitative study
Authors: Heggland Liv‐Helen , Mikkelsen Aslaug , Hausken Kjell
Published: November 2012

This study improves our understanding of patients' participation in hospital treatment‐decision processes. We explored the degree of patient participation perceived by both patients and healthcare professionals in four phases of the decision process: information dissemination, formulation of options, integration of information, and control within four models of interactions between healthcare professionals and patients: the paternalistic model, the shared model, the informed model, and the non‐paternalistic model. The analysis was based on 18 in‐depth, exploratory interviews with patients and healthcare professionals in six surgical units in Norway. Knowledge about how patients and healthcare professionals interact in the surgical‐decision process is important for developing systems and arenas for patient participation in practice, and for a climate and culture to further support the implementation.
Long‐term non‐flooded mulching cultivation influences rice productivity and soil organic carbon
Authors: Fan M. S. , Lu S. H. , Jiang R. F. , Six J. , Zhang F. S.
Published: November 2012

A field experiment was conducted for 10 years to examine the long‐term effects of non‐flooded mulching cultivation on rice yield and soil organic carbon on Chengdu Plain, south‐west China. Compared with traditional flooded cultivation (TF), non‐flooded plastic film mulching (PM) resulted in a 14% higher average rice (Oryza sativa L.) yield. However, non‐flooded straw mulching (SM) decreased the average rice yield by 11% compared with TF. After 10 years, PM led to similar or higher (SM) soil organic carbon (SOC) and total soil N (TN) in the top 5 cm of the soil profile compared with TF. No differences were found among the three cultivation systems in SOC or total N at 5–12  and 12–24 cm soil depths. Small macroaggregates (0.25–2 mm) were predominant in the top 5 cm of the soil (58–63% of whole soil) across the three cultivation systems. However, the proportion of large macroaggregates (>2 mm) from SM and PM was significantly larger than from TF in the top 5 cm of the soil. Non‐flooded mulching cultivation led to increased C and N contents in large macroaggregates and mean weight diameter of aggregates in the 0–5 cm soil depth. This suggests that non‐flooded mulching cultivation increased soil aggregation concomitant with soil C stabilization within the improved soil structure.
Generic identities and relationships within the brachiopod family Sowerbyellidae
Authors: COCKS L. ROBIN M.
Published: November 2012

Abstract:  Sowerbyellid brachiopods often formed the dominant constituent in various Late Ordovician and Early Silurian benthic assemblages and had a global distribution under a wide range of water depths on the continental shelves. They persisted after then, but much less abundantly, into the Middle Devonian (Eifelian). However, their classification has varied. The terminology used for each of the individual morphological characters is reviewed and standardised, and those characters are discussed in turn as to their suitability for generic discrimination. Some structures previously used, such as canals developed within the ventral valve hinge area, are now found to be developed polyphyletically within both Sowerbyella and Eochonetes. The systematics of all the nominal genera are reviewed, and synonymies are suggested. Zhilgyzambonites is transferred from the Sowerbyellidae to the Hesperomenidae. Brief revised diagnoses are presented for all the genera and subgenera. Because it is enigmatic, the rare genus Dubioleptina from the Wenlock of Bohemia is revised in detail with new photographs and fresh descriptions, as is the more common but comparably controversial Kozlowskites from the Late Ordovician (Katian) of Bohemia and Wales. Both are confirmed as independent genera.
Metallo‐β‐lactamase structure and function
Authors: Palzkill Timothy
Published: November 2012

β‐Lactam antibiotics are the most commonly used antibacterial agents and growing resistance to these drugs is a concern. Metallo‐β‐lactamases are a diverse set of enzymes that catalyze the hydrolysis of a broad range of β‐lactam drugs including carbapenems. This diversity is reflected in the observation that the enzyme mechanisms differ based on whether one or two zincs are bound in the active site that, in turn, is dependent on the subclass of β‐lactamase. The dissemination of the genes encoding these enzymes among Gram‐negative bacteria has made them an important cause of resistance. In addition, there are currently no clinically available inhibitors to block metallo‐β‐lactamase action. This review summarizes the numerous studies that have yielded insights into the structure, function, and mechanism of action of these enzymes.
Bacterial cell‐wall recycling
Authors: Johnson Jarrod W. , Fisher Jed F. , Mobashery Shahriar
Published: November 2012

Many Gram‐negative and Gram‐positive bacteria recycle a significant proportion of the peptidoglycan components of their cell walls during their growth and septation. In many—and quite possibly all—bacteria, the peptidoglycan fragments are recovered and recycled. Although cell‐wall recycling is beneficial for the recovery of resources, it also serves as a mechanism to detect cell‐wall–targeting antibiotics and to regulate resistance mechanisms. In several Gram‐negative pathogens, anhydro‐MurNAc‐peptide cell‐wall fragments regulate AmpC β‐lactamase induction. In some Gram‐positive organisms, short peptides derived from the cell wall regulate the induction of both β‐lactamase and β‐lactam–resistant penicillin‐binding proteins. The involvement of peptidoglycan recycling with resistance regulation suggests that inhibitors of the enzymes involved in the recycling might synergize with cell‐wall–targeted antibiotics. Indeed, such inhibitors improve the potency of β‐lactams in vitro against inducible AmpC β‐lactamase–producing bacteria. We describe the key steps of cell‐wall remodeling and recycling, the regulation of resistance mechanisms by cell‐wall recycling, and recent advances toward the discovery of cell‐wall–recycling inhibitors.
Slow Relaxation Processes in CCTO Detected by Capacitance Versus Voltage Curves
Authors: Luo Xiao Jing , Yang Chang Ping , Song Xue Ping , Tang Shao‐Long , Xiao Hai‐Bo , Bärner Klaus Herrmann Otto
Published: November 2012

The temperature and frequency dependence of capacitance versus voltage (C–V) curves was investigated for ceramic CaCu3Ti4O12 samples sintered in atmospheres of vacuum, air and oxygen, respectively. A drastic capacitance rise at higher dc voltages and low ac frequencies was observed for all these CaCu3Ti4O12CCTO samples, and it is especially strong for the sample sintered in vacuum, which has not been found previously. The shape as well as the asymmetry of the C–V curves suggest that the dielectric behavior is related to charged trap states. It also indicates that a slow relaxation process, which is strongly correlated with the re‐positioning of oxygen vacancies related trap charges, takes place in CCTO. The main trap charge relaxation process is thought to occur between the boundaries perpendicular and parallel to the external electric field, and the anisotropy of the defect dipoles provide the possibilities for trap charge repositioning which maybe the reason of the huge dielectric constant.
Helium Solubility in SON68 Nuclear Waste Glass
Authors: Fares Toby , Peuget Sylvain , Chamssedine Fadel , Sauvage Thierry , Bouty Olivier , Broudic Véronique , Deschanels Xavier , Maugeri Emilio , Bes René , Jégou Christophe
Published: November 2012

Helium behavior in a sodium borosilicate glass (SON68) dedicated to the immobilization of high‐level nuclear waste is examined. Two experimental approaches on nonradioactive glass specimens are implemented: pressurized helium infusion experiments and 3He ion implantation experiments. The temperature variation of helium solubility in SON68 glass was determined and analyzed with the harmonic oscillator model to determine values of the energy of interaction E(0) at the host sites (about −4000 J/mol), the vibration frequency (about 1.7 × 1011 s−1), and the density of solubility sites (2.2 × 1021 sites cm−3). The implantation experiments show that a nondiffusive transport phenomenon (i.e., athermal diffusion) is involved in the material when the helium concentration exceeds 2.3 × 1021 He cm−3, and thus probably as soon as it exceeds the density of solubility sites accessible to helium in the glass. We propose that this transport mechanism could be associated with the relaxation of the stress gradient induced by the implanted helium profile, which is favored by the glass damage. Microstructural characterization by TEM and ESEM of glass specimens implanted with high helium concentrations showed a homogeneous microstructure free of bubbles, pores, or cracking at a scale of 10 nm.
Effect of Seed Addition on SnO2‐Based Varistors for Low Voltage Application
Authors: Cilense Mario , Ramirez Miguel Angel , Foschini Cesar Renato , Leite Daniela Russo , Simões Alexandre Zirpoli , Bassi Welson , Longo Elson , Varela José Arana
Published: November 2012

The effect of seed addition on the microstructure and non‐ohmic properties of the SnO2 + 1%CoO + 0.05%Nb2O5 ceramic‐based system was analyzed. Two classes of seeds were prepared: 99% SnO2 + 1%CuO and 99% SnO2 + 1%CoO (mol%); both classes were added to the ceramic‐based system in the amount of 1%, 5%, and 10%. The two systems containing 1% of seeds resulted in a larger grain size and a lower breakdown voltage. The addition of 1% copper seeds produces a breakdown voltage (Vb) of ~ 37 V and a leakage current (fic) of 29 μA. On the other hand, the addition of 1% cobalt seeds produced a breakdown voltage of 57 V and a leakage current of 70 μA. Both systems are of great technological interest for low voltage varistor applications, by means of appropriate strategies to reduce the leakage current. Using larger amounts of seeds was not effective since the values of breakdown voltage in both cases are close to a system without seeds. To our knowledge, there are no reports in the literature regarding the use of seeds in the SnO2 system for low voltage applications. A potential barrier model which illustrates the formation of oxygen species (O′2(ads), O′ads, and O″ads) at the expense of clusters near the interface between grains is proposed.
Preparation of NaA Zeolite Membranes Using Poly(Ethyleneimine) as Buffer Layer, and Study of Their Permeation Behavior
Authors: Dey Kartick P. , Kundu Debtosh , Chatterjee Minati , Naskar Milan K.
Published: November 2012

Zeolite NaA membranes were prepared hydrothermally by secondary crystallization process at different temperatures (55°C–75°C) on porous α‐alumina‐based support tubes (inner side) precoated with poly(ethyleneimine) (PEI) buffer layer and NaA seed particles. The NaA seed crystals synthesized at 65°C/2 h in the size range 100–200 nm having BET surface area of 71.57 m2g−1 were used for secondary crystallization of the membranes. The secondary crystallization at 65°C for (4 + 4) h (double‐stage) showed highly dense NaA grains in the microstructure of the membrane with a thickness of 5 μm. It rendered the permeance values of 50.6 × 10−8, 2.47 × 10−8, and 0.55 × 10−8 molm−2s−1Pa−1 for H2, N2, and CO2, respectively, with their permselectivity of 20.48 (H2/N2), 92 (H2/CO2), and 4.49 (N2/CO2). A tentative mechanism was illustrated for the interaction of PEI with the support substrate and NaA seed crystals.
Structural Evolving Sequence and Porous Ba6Zr2Nb8O30 Ferroelectric Ceramics with Ultrahigh Breakdown Field and Zero Strain
Authors: Zhang Shan‐Tao , Yuan Guoliang , Chen Jun , Gu Zheng‐Bin , Yang Bin , Yin Jiang , Cao Wenwu
Published: November 2012

Microstructural evolving sequence of relaxor ferroelectric Ba6Zr2Nb8O30 (BZN) ceramics has been investigated and discussed. Porous BZN, which has an irregular grain network with pores, can be obtained within a narrow sintering window (sintering temperature of ~1250°C and dwelling time of ~5 h in our experiments). X‐ray diffraction‐based structure refinements determine the atomic positions and confirm that the porous ceramics has tetragonal tungsten bronze structure with P4bm space group symmetry. It is found that the most porous ceramic has the lowest dielectric constant, highest electric field breakdown strength, and nearly zero macroscopic electric field‐induced strain. These features can be related to the porous microstructures by comparing with the denser counterparts and can be well understood by using brick‐wall model. Our results may provide useful information for the understanding of microstructure evolving sequence of BZN during sintering and the structural effects on electric properties of ceramics. Our work may also provide a reliable way for developing porous ferroelectric ceramics with special properties.
Synthesis of Nanofiber‐like Mesoporous γ‐Al2O3 toward Its Adsorption Efficiency for Congo Red
Authors: Ghosh Sourav , Dey Kartick P. , Naskar Milan K.
Published: November 2012

Nanofiber‐like mesoporous γ‐Al2O3 was synthesized using freshly prepared boehmite sol in the presence of triblock copolymer, P123 following evaporation‐induced self‐assembly (EISA) process followed by calcinations at 400°C–1000°C. The samples were characterized by thermogravimetry (TG), differential thermal analysis (DTA), X‐ray diffraction (XRD), N2 adsorption–desorption, and transmission electron microscopy (TEM). The adsorption efficiency of the samples with Congo red (CR) was studied by UV–vis spectroscopy. XRD results showed boehmite phase in the as‐prepared sample while γ‐Al2O3 phase obtained at 400°C was stable up to 900°C, a little transformation of θ‐Al2O3 resulted at 1000°C. The Brunauer‐Emmett‐Teller surface area of the 400°C‐treated sample was found to be 175.5 m2g−1. The TEM micrograph showed nanofiber‐like morphology of γ‐Al2O3. The 400°C‐treated sample showed about 100% CR adsorption within 60 min.
Elaboration, Structure, and Luminescence of Eu3+‐Doped BaLuF5‐Based Transparent Glass‐Ceramics
Authors: Liu XueYun , Wei YunLe , Wei RongFei , Yang JingWen , Guo Hai
Published: November 2012

Novel Eu3+‐doped transparent oxyfluoride glass‐ceramics containing BaLuF5 nanocrystals were successfully fabricated by melt‐quenching technique for the first time. Analyses of XRD patterns prove that the new precipitated glass‐ceramics are crystallized in cubic BaLuF5 based on isostructural BaGdF5. Intense red emissions observed in glass ceramics are attributed to the enrichment of Eu3+ ions into BaLuF5 nanocrystals. Besides, obvious stark splitting emissions, low forced electric dipole 5D0→7F2 transition, and long decay lifetimes of Eu3+ ions also evidence the partition of Eu3+ ions into BaLuF5 nanocrystals with low phonon energy. Such transparent material may find applications in photonics.
Electrical Conduction and Dielectric Properties of the Rb‐doped CaCu3Ti4O12
Authors: Yang Zhi , Zhang Yue , Lu Zhihong , Zhang Kun , Xiong Rui , Shi Jing
Published: November 2012

Ca1−xRbxCu3Ti4O12 (x = 0, 0.03, and 0.05) ceramics were synthesized by the sol‐gel method. Their microstructure and electrical properties were investigated. In the Rb‐doped samples, the Cu‐rich and Ti‐poor grain‐boundary layers are formed, and electrical properties are also changed by doping: With the increase in doping concentration, the grain resistivity and the grain‐boundary Schottky potential barrier are changed, the grain‐boundary resistivity is enhanced, and the low‐frequency dielectric constants and loss are reduced. These results were discussed in terms of the internal barrier layer capacitor (IBLC) mechanism, particularly focusing on the electrical properties in grains and the cationic nonstoichiometry at grain boundaries.
Effects of Pueraria mirifica and miroestrol on the antioxidation-related enzymes in ovariectomized mice
Authors: Chatuphonprasert Waranya , Udomsuk Latiporn , Monthakantirat Orawan , Churikhit Yaowared , Putalun Waraporn , Jarukamjorn Kanokwan
Published: November 2012

Objectives

The influences of Pueraria candollei var. mirifica (PM), a Thai medicinal plant with long tradition of medicinal consumption among menopausal women for rejuvenation and estrogen hormone replacement, on oxidative status in ovariectomized (OVX) mice were determined.

Methods

The crude extract of PM and its active phytoestrogen, miroestrol (MR), were given to OVX mice. The effect of them on antioxidation enzymes and glutathione (GSH) levels in livers and uteri were examined in OVX mice and compared with the synthetic estradiol hormone.

Key findings

Ovariectomy significantly decreased total GSH content, reduced GSH content, and the ratio of GSH to oxidized glutathione (GSSG) in both the livers and the uteri of mice. Moreover, an ovariectomy reduced the activities of glutathione peroxidase (GPx), superoxide dismutase (SOD), and catalase (CAT). The crude extract of PM as well as MR significantly increased levels of GSH, levels of reduced GSH, and the ratio of GSH/GSSG in both the livers and the uteri, while estradiol did not. In addition, the potential of PM and MR to return the activities of GPx, SOD, and CAT to normal levels was noted.

Conclusions

These observations support using PM and MR as promising alternative medicine candidates for hormone replacement therapy of estradiol because of their ability to improve GSH levels and the activities of antioxidative enzymes, especially in OVX mice.
Increasing sleep duration to lower beat‐to‐beat blood pressure: a pilot study
Authors: Haack Monika , Serrador Jorge , Cohen Daniel , Simpson Norah , Meier‐Ewert Hans , Mullington Janet M.
Published: November 2012

Strong evidence has accumulated over the last several years, showing that low sleep quantity and/or quality plays an important role in the elevation of blood pressure. We hypothesized that increasing sleep duration serves as an effective behavioral strategy to reduce blood pressure in prehypertension or type 1 hypertension. Twenty‐two participants with prehypertension or stage 1 hypertension, and habitual sleep durations of 7 h or less, participated in a 6‐week intervention study. Subjects were randomized to a sleep extension group (48 ± 12 years, N = 13) aiming to increase bedtime by 1 h daily over a 6‐week intervention period, or to a sleep maintenance group (47 ± 12 years, N = 9) aiming to maintain habitual bedtimes. Both groups received sleep hygiene instructions. Beat‐to‐beat blood pressure was monitored over 24 h, and 24‐h urine and a fasting blood sample were collected pre‐ and post‐intervention. Subjects in the sleep extension group increased their actigraphy‐assessed daily sleep duration by 35 ± 9 min, while subjects in the sleep maintenance condition increased slightly by 4 ± 9 min (P = 0.03 for group effect). Systolic and diastolic beat‐to‐beat blood pressure averaged across the 24‐h recording period significantly decreased from pre‐ to post‐intervention visit in the sleep extension group by 14 ± 3 and 8 ± 3 mmHg, respectively (P < 0.05). Though the reduction of 7 ± 5 and 3 ± 4 mmHg in the sleep maintenance group was not significant, it did not differ from the blood pressure reduction in the sleep extension group (P = 0.15 for interaction effect). These changes were not paralleled by pre‐ to post‐intervention changes in inflammatory or sympatho‐adrenal markers, nor by changes in caloric intake. While these preliminary findings have to be interpreted with caution due to the small sample size, they encourage future investigations to test whether behavioral interventions designed to increase sleep duration serve as an effective strategy in the treatment of hypertension.
New Evidence on the Impact of Legal Status on Immigrant Labor Market Performance: The Spanish Case
Authors: Amuedo‐Dorantes Catalina , Malo Miguel A. , Muñoz‐Bullón Fernando
Published: November 2012

Using a recent and rich Spanish data set on immigrants, we examine the impact of legal status on two measures of labor market performance: the likelihood of being employed and earnings. The Spanish case is of special interest given the rapid increase in immigration over the past 15 years and the large number of amnesties granted during the 1990s and 2000s. We find that a 10 per cent increase in the share of legal immigrants would raise the overall employment likelihood of immigrants by 4 percentage points and their earnings by 3.3 per cent. The results, which prove robust to alternative sample specifications, confirm the well‐known importance of being legal for the economic assimilation of immigrants.
Candiduria in haematologic malignancy patients without a urinary catheter: nothing more than a frailty marker?
Authors: Georgiadou Sarah P. , Tarrand Jeffrey , Sipsas Nikolaos V. , Kontoyiannis Dimitrios P.
Published: November 2012

There is scarcity of data regarding significance of candiduria in patients with haematologic malignancies and its association with invasive candidiasis. To that end, we retrospectively evaluated all hospitalised, non‐intensive care unit patients with haematologic malignancies and candiduria during a 10‐year period (2001–2011). To decrease the possibility of bladder colonisation and sample contamination, we excluded all patients with candiduria who had urinary catheters and those with concomitant bacteriuria. Twenty‐four such patients (21 females) were identified, with median age at diagnosis 62 years (range, 20–82 years). Acute leukaemia was the most common underlying disease (54%); 62% of these cases were not in remission. Twenty‐nine percent of the patients had diabetes mellitus and 25% were neutropenic. The most common isolated Candida species was Candida glabrata (37%), followed by C. albicans (29%). Only 8% of them had urinary tract infection symptoms. However, 88% received systemic antifungals. Candidemia and crude mortality rates at 4 weeks were low (4% and 12% respectively). Isolated candiduria in patients with haematologic malignancies has risk factors similar to those in other hospitalised patients, and it does not seem to be a strong predictor of subsequent invasive candidiasis.
Association genetics of chemical wood properties in black poplar (Populus nigra)
Authors: Guerra Fernando P. , Wegrzyn Jill L. , Sykes Robert , Davis Mark F. , Stanton Brian J. , Neale David B.
Published: November 2012

Black poplar (Populus nigra) is a potential feedstock for cellulosic ethanol production, although breeding for this specific end use is required. Our goal was to identify associations between single nucleotide polymorphism (SNP) markers within candidate genes encoding cellulose and lignin biosynthetic enzymes, with chemical wood property phenotypic traits, toward the aim of developing genomics‐based breeding technologies for bioethanol production.

Pyrolysis molecular beam mass spectrometry was used to determine contents of five‐ and six‐carbon sugars, lignin, and syringyl : guaiacyl ratio. The association population included 599 clones from 17 half‐sib families, which were successfully genotyped using 433 SNPs from 39 candidate genes. Statistical analyses were performed to estimate genetic parameters, linkage disequilibrium (LD), and single marker and haplotype‐based associations.

A moderate to high heritability was observed for all traits. The LD, across all candidate genes, showed a rapid decay with physical distance. Analysis of single marker–phenotype associations identified six significant marker–trait pairs, whereas nearly 280 haplotypes were associated with phenotypic traits, in both an individual and multiple trait‐specific manner.

The rapid decay of LD within candidate genes in this population and the genetic associations identified suggest a close relationship between the associated SNPs and the causative polymorphisms underlying the genetic variation of lignocellulosic traits in black poplar.
An Arabidopsis reticulon and the atlastin homologue RHD3‐like2 act together in shaping the tubular endoplasmic reticulum
Authors: Lee Hannah , Sparkes Imogen , Gattolin Stefano , Dzimitrowicz Natasha , Roberts Lynne M. , Hawes Chris , Frigerio Lorenzo
Published: November 2012

The endoplasmic reticulum (ER) is a network of membrane sheets and tubules connected via three‐way junctions. A family of proteins, the reticulons, are responsible for shaping the tubular ER. Reticulons interact with other tubule‐forming proteins (Dp1 and Yop1p) and the GTPase atlastin. The Arabidopsis homologue of Dp1/Yop1p is HVA22.

We show here that a seed‐specific isoform of HVA22 labels the ER in tobacco (Nicotiana tabacum) cells but its overexpression does not alter ER morphology. The closest plant homologue of atlastin is RHD3. We show that RHD3‐like 2 (RL2), the seed‐specific isoform of RHD3, locates to the ER without affecting its shape or Golgi mobility. Expression of RL2‐bearing mutations within its GTPase domain induces the formation of large ER strands, suggesting that a functional GTPase domain is important for the formation of three‐way junctions.

Coexpression of the reticulon RTNLB13 with RL2 resulted in a dramatic alteration of the ER network. This alteration did not depend on an active GTPase domain but required a functional reticulon, as no effect on ER morphology was seen when RL2 was coexpressed with a nonfunctional RTNLB13. RL2 and its GTPase mutants coimmunoprecipitate with RTNLB13.

These results indicate that RL2 and RTNLB13 act together in modulating ER morphology.
Effects of plant age on disease development and virulence of Clavibacter michiganensis subsp. michiganensis on tomato
Authors: Sharabani G. , Shtienberg D. , Borenstein M. , Shulhani R. , Lofthouse M. , Sofer M. , Chalupowicz L. , Barel V. , Manulis‐Sasson S.
Published: November 2012

The effect of plant age at the time of inoculation on the severity of bacterial wilt and canker disease caused by Clavibacter michiganensis subsp. michiganensis (Cmm) was examined in six greenhouse experiments. The period during which inoculations led to wilt and death of tomato plants was defined. This period, designated ‘window of vulnerability’, ranged from transplanting to the 17‐ to 18‐leaf stage. Plants inoculated after this period expressed disease symptoms but did not wilt or die. No significant changes in disease incidence were observed when leaves of different ages were inoculated. Yield accumulation was significantly reduced in plants inoculated within the window of vulnerability compared with those inoculated after this period. Expression of virulence genes, viz. celA, encoding a secreted cellulase, and the serine protease‐encoding pat‐1, chpC and ppaA, was induced during the early stages after inoculation in plants inoculated within the window of vulnerability. Differences in Cmm population between plants inoculated within and outside of this period were insignificant after the first week post‐inoculation, indicating that differences in disease severity, yield loss and expression of virulence determinants are not correlated with Cmm population level. Results suggest that implementation of precautionary measures during the window of vulnerability to avoid secondary spread of Cmm will have a season‐long effect on plant mortality and may minimize, or even prevent, yield losses.
Integrative taxonomy and conservation of cryptic beetles in the Mediterranean region (Hydrophilidae)
Authors: Arribas Paula , Andújar Carmelo , Sánchez‐Fernández David , Abellán Pedro , Millán Andrés
Published: November 2012

Arribas, P., Andújar, C., Sánchez‐Fernández, D., Abellán, P. & Millán, A. (2012). Integrative taxonomy and conservation of cryptic beetles in the Mediterranean region (Hydrophilidae). —Zoologica Scripta, 00, 000–000.

Because biodiversity inventory forms the basis for the effective conservation of species and habitats, there is an imperative need to discover and describe new species. A significant part of presently unknown biodiversity is constituted by cryptic species complexes, where traditional taxonomy usually fails due to a lack of clear taxonomic characters in the external structures of specimens. Integrative taxonomy offers a powerful tool to shed light on this part of encrypted biodiversity, combining multiple operational criteria in an evolutionary context in order to delineate species boundaries. The present study used an integrative approach to explore the species boundaries in a water beetle complex (Enochrus falcarius species complex) inhabiting saline streams, a rare and threatened habitat across the Mediterranean region. First, hypotheses about the candidate species on the basis of phylogenetic analyses and biogeographical information were proposed. Second, lineage divergence was evaluated between candidate species using (i) molecular cluster delimitation, (ii) morphometry (both linear body morphometrics and pronotum outlines) and (iii) ecological niche similarity estimates. We found divergence between candidate species on the basis of molecular, biogeographical and niche information, and consequently, four species were delimited within the E. falcarius complex (i.e. Enochrus jesusarribasi sp. n., Enochrus blazquezae sp. n., Enochrus risii sp. n. and Enochrus falcarius), despite the fact that they showed high morphological similarity. Enochrus falcarius, as previously considered, had not been proposed to be of conservational concern, because until now, it had been regarded as a single broadly distributed species in the Mediterranean region. However, the four entities here delimited within this species complex displayed characteristics that categorised them as vulnerable taxa. Hence, these results show how applying integrative taxonomy approaches and rapid vulnerability assessments to lineages from threatened habitats with the potential to comprise cryptic diversity could become a fundamental tool for biodiversity conservation, driving the discovery of cryptic species and consequently the modification of previous, inadequately evaluated vulnerability categorisations.
The COMPASS Subunit Spp1 Links Histone Methylation to Initiation of Meiotic Recombination
Authors: Acquaviva Laurent , Székvölgyi Lóránt , Dichtl Bernhard , Dichtl Beatriz Solange , Saint André Christophe de La Roche , Nicolas Alain , Géli Vincent
Published: November 2012

Repair and Recombination

In most sexually reproducing organisms, the haploid gametes are produced by meiosis, a specialized cell-division during which recombination between the parental chromosomes ensures proper chromosome segregation. Double-strand breaks (DSB) generated in the DNA drive this recombination and are linked to recombination hotspots in the chromatin where histone H3 is methylated on lysine residue 4 (H3K4me) by the Set1C/COMPASS enzyme complex.

Acquaviva
et al.

(p.
215
, published online 15 November) show that the Mer2/Mei4/Rec114 complex of the DSB generating machinery is linked to the Set1C/COMPASS enzyme complex through the Spp1 subunit, which contains a PHD-finger capable of binding to H3K4me. The Spp1 subunit recruits the Mer2 protein to sites where recombination will occur, probably by binding to both the H3K4me-marked chromatin and other factors.
Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders
Authors: O’Roak Brian J. , Vives Laura , Fu Wenqing , Egertson Jarrett D. , Stanaway Ian B. , Phelps Ian G. , Carvill Gemma , Kumar Akash , Lee Choli , Ankenman Katy , Munson Jeff , Hiatt Joseph B. , Turner Emily H. , Levy Roie , O’Day Diana R. , Krumm Niklas , Coe Bradley P. , Martin Beth K. , Borenstein Elhanan , Nickerson Deborah A. , Mefford Heather C. , Doherty Dan , Akey Joshua M. , Bernier Raphael , Eichler Evan E. , Shendure Jay
Published: November 2012

Autism Genes, Again and Again

Despite recent advances in sequencing technologies and their lowered costs—effective, highly sensitive, and specific sequencing of multiple genes of interest from large cohorts remains expensive.

O'Roak
et al.

(p.
1619
; published online 15 November) modified molecular inversion probe methods for target-specific capture and sequencing to resequence candidate genes in thousands of patients. The technique was applied to 44 candidate genes to identify de novo mutations in a large cohort of individuals with and without autism spectrum disorder. The analysis revealed several de novo mutations in genes that together contribute to 1% of sporadic autism spectrum disorders, supporting the notion that multiple genes underlie autism-spectrum disorders.
Optomechanical Dark Mode
Authors: Dong Chunhua , Fiore Victor , Kuzyk Mark C. , Wang Hailin
Published: November 2012

Inducing a Quiet Space

The interaction between light and matter forms the foundation of many applications in communication and sensing, as well as provides insights into fundamental quantum-level processes. Optical coupling of a mechanical system can be used to study these processes. However, because the mechanical oscillator is unavoidably coupled to its environment, thermal noise can spoil the sensitivity of the optomechanical coupling.

Dong
et al.

(p.
1609
, published online 15 November) exploit the ability to form a mechanical “dark state” that can effectively isolate the mechanical system from thermal-induced noise. The formation of such a noise-free zone may provide a simpler route to probe quantum optomechanical systems that circumvents the need to cool the oscillator to its quantum limit where all thermal motion is frozen out.
C/EBP Transcription Factors Mediate Epicardial Activation During Heart Development and Injury
Authors: Huang Guo N. , Thatcher Jeffrey E. , McAnally John , Kong Yongli , Qi Xiaoxia , Tan Wei , DiMaio J. Michael , Amatruda James F. , Gerard Robert D. , Hill Joseph A. , Bassel-Duby Rhonda , Olson Eric N.
Published: November 2012

Enhancing Heart Function

The epicardium, a protective layer of tissue surrounding the mammalian heart, plays a critical role during embryogenesis because it supplies growth factors and multipotent progenitor cells essential for heart development. In adults, the epicardium is dormant but it becomes reactivated when the heart is injured, a response that leads to re-expression of developmental genes. Studying mouse models,

Huang
et al.

(p.
1599
, published online 15 November; see the Perspective by

Rosenzweig

) found that the C/EBP transcription factors activated the epicardium during development and injury. Blockade of C/EBP signaling in the epicardium of injured (ischemic) hearts reduced inflammation and improved heart function, a finding that could ultimately lead to new strategies for the repair of heart damage.
Mycobacteriophage Ms6 LysA: a Peptidoglycan Amidase and a Useful Analytical Tool
Authors: Mahapatra Sebabrata , Piechota Charles , Gil Filipa , Ma Yufang , Huang Hairong , Scherman Michael S. , Jones Victoria , Pavelka Martin S. , Moniz-Pereira Jose , Pimentel Madalena , McNeil Michael R. , Crick Dean C.
Published: November 2012

Since the peptidoglycan isolated from
Mycobacterium
spp. is refractory to commercially available murolytic enzymes, possibly due to the presence of various modifications found on this peptidoglycan, the utility of a mycobacteriophage-derived murolytic enzyme was assessed for an analysis of peptidoglycan from mycobacteria. We cloned, expressed, and purified the
lysA
gene product, a protein with homology to known peptidoglycan-degrading amidases, from bacteriophage Ms6. The recombinant protein was shown to cleave the bond between
l
-Ala and
d
-muramic acid of muramyl pentapeptide and to release up to 70% of the diaminopimelic acid present in the isolated mycobacterial cell wall. In contrast to lysozyme, which, in culture, inhibits the growth of both
Mycobacterium smegmatis
and
Mycobacterium tuberculosis
, LysA had no effect on the growth of either species. However, the enzyme is useful for solubilizing the peptide chains of isolated mycobacterial peptidoglycan for analysis. The data indicate that the stem peptides from
M. smegmatis
are heavily amidated, containing few free carboxylic acids, regardless of the cross-linking status.
Use of Flow Cytometry for Rapid, Quantitative Detection of Poliovirus-Infected Cells via TAT Peptide-Delivered Molecular Beacons
Authors: Sivaraman Divya , Yeh Hsiao-Yun , Mulchandani Ashok , Yates Marylynn V. , Chen Wilfred
Published: November 2012

Rapid and efficient detection of viral infection is crucial for the prevention of disease spread during an outbreak and for timely clinical management. In this paper, the utility of Tat peptide-modified molecular beacons (MBs) as a rapid diagnostic tool for the detection of virus-infected cells was demonstrated. The rapid intracellular delivery mediated by the Tat peptide enabled the detection of infected cells within 30 s, reaching saturation in signal in 30 min. This rapid detection scheme was coupled with flow cytometry (FC), resulting in an automated, high-throughput method for the identification of virus-infected cells. Because of the 2-order-of-magnitude difference in fluorescence intensity between infected and uninfected cells, as few as 1% infected cells could be detected. Because of its speed and sensitivity, this approach may be adapted for the practical diagnosis of multiple viral infections.
Contribution of Nitrate Assimilation to the Fitness of Pseudomonas syringae pv. syringae B728a on Plants
Authors: Parangan-Smith Audrey , Lindow Steven
Published: November 2012

The ability of
Pseudomonas syringae
pv. syringae to use nitrate as a nitrogen source in culture and on leaves was assessed. Substantial amounts of leaf surface nitrate were detected directly and by use of a bioreporter of nitrate on bean plants grown with a variety of nitrogen sources. While a nitrate reductase mutant,
P. syringae
Δ
nasB
, exhibited greatly reduced growth in culture with nitrate as the sole nitrogen source, it exhibited population sizes similar to those of the wild-type strain on leaves. However, the growth of the Δ
nasB
mutant was much less than that of the wild-type strain when cultured in bean leaf washings supplemented with glucose, suggesting that
P. syringae
experiences primarily carbon-limited and only secondarily nitrogen-limited growth on bean leaves. Only a small proportion of the cells of a green fluorescent protein (GFP)-based
P. syringae
nitrate reductase bioreporter, LK2(pOTNas4), exhibited fluorescence on leaves. This suggests that only a subset of cells experience high nitrate levels or that nitrate assimilation is repressed by the presence of ammonium or other nitrogenous compounds in many leaf locations. While only a subpopulation of
P. syringae
consumes nitrate at a given time on the leaves, the ability of those cells to consume this resource would be strongly beneficial to those cells, especially in environments in which nitrate is the most abundant form of nitrogen.
Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations
Authors: Lamendella Regina , Li Kent C. , Oerther Daniel , Santo Domingo Jorge W.
Published: November 2012

Several swine-specific microbial source tracking methods are based on PCR assays targeting
Bacteroidales
16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600 bp in length)
Bacteroidales
16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major
Bacteroidales
populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many
Bacteroidales
populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications.
Improved Production of
l
-Threonine in Escherichia coli by Use of a DNA Scaffold System
Authors: Lee Jun Hyoung , Jung Suk-Chae , Bui Le Minh , Kang Kui Hyeon , Song Ji-Joon , Kim Sun Chang
Published: November 2012

Despite numerous approaches for the development of
l
-threonine-producing strains, strain development is still hampered by the intrinsic inefficiency of metabolic reactions caused by simple diffusion and random collisions of enzymes and metabolites. A scaffold system, which can promote the proximity of metabolic enzymes and increase the local concentration of intermediates, was reported to be one of the most promising solutions. Here, we report an improvement in
l
-threonine production in
Escherichia coli
using a DNA scaffold system, in which a zinc finger protein serves as an adapter for the site-specific binding of each enzyme involved in
l
-threonine production to a precisely ordered location on a DNA double helix to increase the proximity of enzymes and the local concentration of metabolites to maximize production. The optimized DNA scaffold system for
l
-threonine production significantly increased the efficiency of the threonine biosynthetic pathway in
E. coli
, substantially reducing the production time for
l
-threonine (by over 50%). In addition, this DNA scaffold system enhanced the growth rate of the host strain by reducing the intracellular concentration of toxic intermediates, such as homoserine. Our DNA scaffold system can be used as a platform technology for the construction and optimization of artificial metabolic pathways as well as for the production of many useful biomaterials.
Contribution of Bacillomycin D in Bacillus amyloliquefaciens SQR9 to Antifungal Activity and Biofilm Formation
Authors: Xu Zhihui , Shao Jiahui , Li Bing , Yan Xin , Shen Qirong , Zhang Ruifu
Published: November 2012

Bacillus amyloliquefaciens
strains are capable of suppressing soilborne pathogens through the secretion of an array of lipopeptides and root colonization, and biofilm formation ability is considered a prerequisite for efficient root colonization. In this study, we report that one of the lipopeptide compounds (bacillomycin D) produced by the rhizosphere strain
Bacillus amyloliquefaciens
SQR9 not only plays a vital role in the antagonistic activity against
Fusarium oxysporum
but also affects the expression of the genes involved in biofilm formation. When the bacillomycin D and fengycin synthesis pathways were individually disrupted, mutant SQR9M1, which was deficient in the production of bacillomycin D, only showed minor antagonistic activity against
F. oxysporum
, but another mutant, SQR9M2, which was deficient in production of fengycin, showed antagonistic activity equivalent to that of the wild-type strain of
B. amyloliquefaciens
SQR9. The results from
in vitro
, root
in situ
, and quantitative reverse transcription-PCR studies demonstrated that bacillomycin D contributes to the establishment of biofilms. Interestingly, the addition of bacillomycin D could significantly increase the expression levels of
kinC
gene, but KinC activation is not triggered by leaking of potassium. These findings suggest that bacillomycin D contributes not only to biocontrol activity but also to biofilm formation in strain
B. amyloliquefaciens
SQR9.
Profiling
In Situ
Microbial Community Structure with an Amplification Microarray
Authors: Chandler Darrell P. , Knickerbocker Christopher , Bryant Lexi , Golova Julia , Wiles Cory , Williams Kenneth H. , Peacock Aaron D. , Long Philip E.
Published: November 2012

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an
in situ
field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO
3
−
) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (
Flexibacter
,
Geobacter
,
Rhodoferax
, and
Shewanella
) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO
3
, but at much lower signal intensities and with a much more rapid decline (to nondetection).
Azoarcus
,
Thaurea
, and
Methylobacterium
were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.
Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids
Authors: Mizuno Carolina Megumi , Rodriguez-Valera Francisco , Garcia-Heredia Inmaculada , Martin-Cuadrado Ana-Belen , Ghai Rohit
Published: November 2012

Cellular metagenomes are primarily used for investigating microbial community structure and function. However, cloned fosmids from such metagenomes capture phage genome fragments that can be used as a source of phage genomes. We show that fosmid cloning from cellular metagenomes and sequencing at a high coverage is a credible alternative to constructing metaviriomes and allows capturing and assembling novel, complete phage genomes. It is likely that phages recovered from cellular metagenomes are those replicating within cells during sample collection and represent “active” phages, naturally amplifying their genomic DNA and increasing chances for cloning. We describe five sets of siphoviral contigs (MEDS1, MEDS2, MEDS3, MEDS4, and MEDS5), obtained by sequencing fosmids from the cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three of these represent complete siphoviral genomes and two represent partial ones. This is the first set of phage genomes assembled directly from cellular metagenomic fosmid libraries. They exhibit low sequence similarities to one another and to known siphoviruses but are remarkably similar in overall genome architecture. We present evidence suggesting they infect picocyanobacteria, likely
Synechococcus
. Four of these sets also define a novel branch in the phylogenetic tree of phage large subunit terminases. Moreover, some of these siphoviral groups are globally distributed and abundant in the oceans, comparable to some known myoviruses and podoviruses. This suggests that, as more siphoviral genomes become available, we will be better able to assess the abundance and influence of this diverse and polyphyletic group in the marine habitat.