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Four trigonal topology compounds with three diarylamines redox centers and dibenzofulvene as core bridge have been synthesized. Their radical cations exhibit appealing intramolecular electron transfer pathways between three redox centers, depending on their position on the core bridge. By changing such positions (on either 2,7- or 3,6-), and the length of the bridge, the control of the intramolecular electron transfer pathways was achieved through the electron self-exchange route. These processes were investigated by absorption spectroscopy, electron paramagnetic resonance spectroscopy, and (time-dependent) density functional theory calculations. Hole mobility measurements were carried out as well, to correlate the intramolecular electron transfer with the hole-transporting ability for possible applications in optoelectronic devices.

Many applications in plasmonics are related to the coupling between metallic nanoparticles (MNPs) or between an emitter and a MNP. The theoretical analysis of such a coupling is thus of fundamental importance to analyze the plasmonic behavior and to design new systems. While classical methods neglect quantum and spill-out effects, time-dependent density functional theory (TD-DFT) considers all of them and with Kohn-Sham orbitals delocalized over the whole system. Thus, within TD-DFT, no definite separation of the subsystems (the single MNP or the emitter) and their couplings is directly available. This important feature is obtained here using the subsystem formulation of TD-DFT, which has been originally developed in the context of weakly interacting organic molecules. In subsystem TD-DFT, interacting MNPs are treated independently, thus allowing us to compute the plasmon couplings directly from the subsystem TD-DFT transition densities. We show that subsystem TD-DFT, as well as a simplified version of it in which kinetic contributions are neglected, can reproduce the reference TD-DFT calculations for gap distances greater than about 6 Å or even smaller in the case of hybrid plasmonic systems (i.e., molecules interacting with MNPs). We also show that the subsystem TD-DFT can be also used as a tool to analyze the impact of charge-transfer effects.

Background: FOLFIRINOX has shown promising results in locally advanced (LAPA) or borderline resectable (BRPA) pancreatic adenocarcinoma. We report here a cohort of patients treated with this regimen from the AGEO group., Methods: This is a retrospective multicentre study. We included all consecutive patients with non-pre-treated LAPA or BRPA treated with FOLFIRINOX., Results: We included 330 patients (57.9% male, 65.4% <65 years, 96.4% PS <2). Disease was classified as BRPA in 31.1% or LAPA in 68.9%. Objective response rate with FOLFIRINOX was 29.5% and stable disease 51%. Subsequent CRT was performed in 46.4% of patients and 23.9% had curative intent surgery. Resection rates were 42.1% for BRPA and 15.5% for LAPA. Main G3/4 toxicities were fatigue (15%), neutropenia (12%) and neuropathy (G2/3 35%). After a median follow-up of 26.7 months, median OS (mOS) and PFS were 21.4 and 12.4 months, respectively. For patients treated by FOLFIRINOX alone, or FOLFIRINOX followed by CRT, or FOLFIRINOX + /- CRT + surgery, mOS was 16.8 months, 21.8 months and not reached, respectively (p < 0.0001)., Conclusions: FOLFIRINOX for LAPA and BRPA seems to be effective with a manageable toxicity profile. These promising results in "real-life" patients now have to be confirmed in a Phase 3 randomised trial.

Purpose: To evaluate trimodal conservative treatment as an alternative to radical surgery for urothelial muscle-invasive bladder cancer (MIBC)., Patients and Methods: This retrospective study reported the carcinologic and functional results of patients (pts) presenting a cT2/T3 N 0M0 operable MIBC and fit for surgery, treated by a conservative strategy. Treatment consisted of a transurethral resection (TURB) followed by concomitant bi-fractionated split-course radiochemotherapy (RCT) with 5FU-Cisplatine. A control cystoscopy was performed six weeks after the induction RCT (eq45Gy) with systematic biopsies. Patients with complete histologic response achieved RCT protocol. Salvage surgery was proposed to pts with persistent tumor., Results: 313 pts (83% cT2 and 17% cT3) treated between 1988 and 2013 were included, with a median follow-up of 59 months and 67-year mean age. After the induction RCT, the histologic response rate was 83%. After five years, overall, disease-free, and functional bladder-intact survival rates were respectively 69%, 61%, and 69%, significantly better for pts in complete response after induction RCT. Late urinary and digestive toxicities were limited, with respective rates of 4% and 1.5% of grade 3 toxicity., Conclusion: Trimodal strategy with RCT after TURB showed interesting functional and oncologic results and should be considered as an alternative to surgery in well-selected pts.

Given the omnipresence of noncovalent interactions (NCIs), their accurate simulations are of crucial importance across various scientific disciplines. Here we construct accurate models for the description of NCIs by an interpolation along the Møller-Plesset adiabatic connection (MP AC). Our interpolation approximates the correlation energy, by recovering MP2 at small coupling strengths and the correct large-coupling strength expansion of the MP AC, recently shown to be a functional of the Hartree-Fock density. Our models are size consistent for fragments with nondegenerate ground states, have the same cost as double hybrids, and require no dispersion corrections to capture NCIs accurately. These interpolations greatly reduce large MP2 errors for typical π-stacking complexes (e.g., benzene-pyridine dimers) and for the L7 data set. They are also competitive with state-of-the-art dispersion enhanced functionals and can even significantly outperform them for a variety of data sets, such as CT7 and L7.

Background: Microbes are present in almost every environment on Earth, even in those with extreme environmental conditions such as Antarctica, where rocks may represent the main refuge for life. Lithobiontic communities are composed of microorganisms capable of colonizing rocks and, as it is a not so well studied bacterial community, they may represent a very interesting source of diversity and functional traits with potential for biotechnological applications. In this work we analyzed the ability of Antarctic lithobiontic bacterium to synthesize cadmium sulfide quantum dots (CdS QDs) and their potential application in solar cells., Results: A basaltic andesite rock sample was collected from Fildes Peninsula, King George Island, Antarctica, and processed in order to isolate lithobiontic bacterial strains. Out of the 11 selected isolates, strain UYP1, identified as Pedobacter, was chosen for further characterization and analysis due to its high cadmium tolerance. A protocol for the biosynthesis of CdS QDs was developed and optimized for this strain. After 20 and 80 min of synthesis, yellow-green and orange-red fluorescent emissions were observed under UV light, respectively. QDs were characterized through spectroscopic techniques, dynamic light scattering analysis, high-resolution transmission electron microscopy and energy dispersive x-ray spectroscopy. Nanostructures of 3.07 nm, composed of 51.1% cadmium and 48.9% sulfide were obtained and further used as photosensitizer material in solar cells. These solar cells were able to conduct electrons and displayed an open circuit voltage of 162 mV, a short circuit current density of 0.0110 mA cm -2 , and had an efficiency of conversion up to 0.0016%, which is comparable with data previously reported for solar cells sensitized with biologically produced quantum dots., Conclusions: We report a cheap, rapid and eco-friendly protocol for the production of CdS QDs by an Antarctic lithobiontic bacterium, Pedobacter, a genus that was not previously reported as a quantum dot producer. The application of the biosynthesized QDs as sensitizer material in solar cells was validated.

New concepts of medical consultations are currently disrupting the practice of medicine. The use of standardized questionnaires, or patient-reported outcome (PRO and ePRO) has already significantly changed the relationship between the physician and the patient. Telemedicine, or even automatic conversational agents, such as chatbots, are also providing more convenient access to care and medical information for many patients. These tools have a major impact in oncology, precisely because of the rising chronicity of the diseases the radiation oncologists treat. In this article, we provide a detailed analysis of these new concepts., (Copyright © 2020 Société française de radiothérapie oncologique (SFRO). Published by Elsevier Masson SAS. All rights reserved.)

Objective: This study assessed outcomes of inoperable endometrial cancer (IEC) patients treated with definitive external beam radiation therapy (EBRT) followed by a 3D image-guided brachytherapy boost., Methods: All consecutive patients treated with EBRT followed by 3D image-guided brachytherapy for IEC were retrospectively included. EBRT delivered a dose of 45Gy. Then, patients had an uterovaginal brachytherapy guided by 3D imaging. Clinical target volume (CTV BT ) included the whole uterus and the initial disease extent. Gross tumour volume (GTV res ) included the residual disease at time of brachytherapy., Results: Twenty-seven patients were identified. Causes of inoperability were comorbidities (37%) or tumour loco regional extent (63%). Including EBRT and brachytherapy, the median D 90 (minimal dose delivered to 90% of the volume) was 60.7 Gy EQD2 (IQR = 56.4-64.2) for the CTV BT , and was 73.6 Gy EQD2 (IQR = 64.1-83.7) for the GTV res . The median overall treatment time was 50 days (IQR = 46-54). The mean follow-up was 36.5 months (SD = 30.2). The cumulative incidence of local, pelvic and distant failures was 19% (n = 5), 7% (n = 2) and 26% (n = 7), respectively. Five-year overall survival was 63% (95% CI = 43-91). Late urinary and gastro intestinal toxicities ≥ grade 2 were reported in four (15%) and two patients (7%) respectively. No vaginal toxicity ≥ grade 2 was reported., Conclusions: EBRT followed by intracavitary brachytherapy seems to be an effective option for IEC. The implementation of 3D concepts at time of brachytherapy may contribute to high local control probability and low toxicity profile. Large scale retrospective or prospective data are needed to confirm these early data., Competing Interests: Declaration of competing interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020. Published by Elsevier Inc.)

Second-order Møller-Plesset perturbation theory (MP2) approximates the exact Hartree-Fock (HF) adiabatic connection (AC) curve by a straight line. Thus, by using the deviation of the exact curve from the linear behavior, we construct an indicator for the accuracy of MP2. We then use an interpolation along the HF AC to transform the exact form of our indicator into a highly practical MP2 accuracy predictor (MAP) that comes at a negligible additional computational cost. We show that this indicator is already applicable to systems that dissociate into fragments with a nondegenerate ground state, and we illustrate its usefulness by applying it to the S22 and S66 datasets.

We have performed a systematic and broad study of the performance of the ab initio OEP2-sc functional for spin-polarized systems, including the computation of ionization potentials and atomization and reaction energies of closed- and open-shell molecules. The results have revealed that, in line with other second-order methods, OEP2-sc can provide accurate results, being competitive to the orbital-optimized MP2 method. Moreover, the analysis of total and relative energies has shown that, unlike the case of double-hybrid functionals, this relatively good performance is not based on an error cancellation effect.

Stereotactic radiotherapy represents a fundamental change in the practice of radiotherapy of lung cancers. Despite the great heterogeneity of sites, techniques, and doses, most studies found a high local control rate, around 70 to 90% at 2 years, and reduced toxicity, around 5% of grade 3 at 2 years. Stereotactic radiotherapy can be realized either by a dedicated accelerator (CyberKnife ® ) or by a conventional accelerator associated with specific systems. The two modalities deliver a very precise irradiation whose very good results published to date are similar. Some technical characteristics specific to each type of linear accelerator could guide the choice according to the target volume treated., (Copyright © 2019 Société française de radiothérapie oncologique (SFRO). Published by Elsevier Masson SAS. All rights reserved.)

Stereotactic radiotherapy of oligometastases, mono- or hypofractionated, represents a fundamental change in the practice of the specialty as it was developed for a century. Despite the great heterogeneity of sites, techniques, and doses, most studies found a high local control rate, around 70 to 90% at 2 years, and reduced toxicity, around 5% of grade 3 at 2 years. Four main phase II and III trials are underway in France. Future research concerns the association of stereotactic radiotherapy with immunotherapy or different conventional chemotherapy protocols, the identification of the best clinical presentations, and optimization of fractionation and biological dose for poor prognosis localizations., (Copyright © 2019 Société française de radiothérapie oncologique (SFRO). Published by Elsevier Masson SAS. All rights reserved.)

When localized, the reference treatment of urothelial, muscle-invasive bladder tumours relies on radical cystectomy with reconstruction by enterocystoplasty if possible or Bricker bypass. Trimodal therapy combining transurethral resection of the tumour followed by concomitant chemotherapy may be considered as a therapeutic alternative to radical cystectomy in well-selected patients with unifocal tumours, stage T2, non-diverticular location, without in situ carcinoma or hydronephrosis and with macroscopically complete transurethral resection. The functional prognosis of the bladder and quality of life should be discussed with the patient as well as the need for salvage surgery for persistent tumour at a 45-Gy dose level, the latter being a highly unfavourable prognosis factor. On the other hand, this trimodal treatment is the reference in case of surgical contraindication. This article details the methods and results of the main series available in the literature in terms of local control, survival, bladder preservation rates and complications, as well as study prospects., (Copyright © 2019 Société française de radiothérapie oncologique (SFRO). Published by Elsevier Masson SAS. All rights reserved.)

We assess several generalized gradient approximations (GGAs) and Laplacian-level meta-GGAs (LL-MGGA) kinetic energy (KE) functionals for orbital-free density functional theory calculations of bulk metals and semiconductors, considering equilibrium distances, bulk moduli, total and kinetic energies, and the electron densities. We also considered the effects of the pseudopotentials, the vacancy formation energies, and the bond lengths of molecular dimers. We found that LL-MGGA KE functionals are distinctively superior to GGA functionals, showing the importance of the Laplacian of the density in the functional construction. We extended the recently developed Pauli-Gaussian second-order and Laplacian (PGSL) functional ( J. Phys. Chem. Lett. 2018 , 9 , 4385 , DOI: 10.1021/acs.jpclett.8b01926 ) including high-order corrections, achieving higher transferability and accuracy than conventional nonlocal functionals based on the Lindhard response function.

Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. UYCP14C appears to be a novel species of the plant growth-promoting Paraburkholderia genus., (Copyright © 2019 Langleib et al.)

Fluorescent light modulation by small electric potentials has gained huge interest in the past few years. This phenomenon, called electrofluorochromism, is of the utmost importance for applications in optoelectronic devices. Huge efforts are being addressed to developing electrofluorochromic systems with improved performances. One of the most critical issue is their low cyclability, which hampers their widespread use. It mostly depends on the intrinsic reversibility of the electroactive/fluorophore molecular system and on device architecture. Here we show a novel fluorene-based mixed-valence electrofluorochromic system that allows direct electrofluorochromic switching and exhibits incomparable electrochemical reversibility and device cyclability of more than 10 000 cycles.

Heme may represent a major iron-source for bacteria. In the symbiotic nitrogen-fixing bacterium Ensifer meliloti 1021, iron acquisition from heme depends on the outer-membrane heme-receptor ShmR. Expression of shmR gene is repressed by iron in a RirA dependent manner while under iron-limitation its expression requires the small protein HmuP. In this work, we identified highly conserved nucleotide motifs present upstream the shmR gene. These motifs are widely distributed among Alpha and Beta Proteobacteria, and correlate with the presence of HmuP coding sequences in bacterial genomes. According to data presented in this work, we named these new motifs as HmuP-responsive elements (HPREs). In the analyzed genomes, the HPREs were always present upstream of genes encoding putative heme-receptors. Moreover, in those Alpha and Beta Proteobacteria where transcriptional start sites for shmR homologs are known, HPREs were located in the 5'UTR region. In this work we show that in E. meliloti 1021, HPREs are involved in HmuP-dependent shmR expression. Moreover, we show that changes in sequence composition of the HPREs correlate with changes in a predicted RNA secondary structure element and affect shmR gene expression.

We have studied the correlation potentials produced by various adiabatic connection models (ACMs) for several atoms and molecules. The results have been compared to accurate reference potentials (coupled cluster and quantum Monte Carlo results) as well as to state-of-the-art ab initio DFT approaches. We have found that all the ACMs yield correlation potentials that exhibit a correct behavior, quite resembling scaled second-order Görling-Levy (GL2) potentials and including most of the physically meaningful features of the accurate reference data. The behavior and contribution of the strong-interaction limit potentials have also been investigated and discussed.

We show that the leading term in the strong-interaction limit of the adiabatic connection that has as weak-interaction expansion the Møller-Plesset perturbation theory can be fully determined from a functional of the Hartree-Fock density. We analyze this functional and highlight similarities and differences with the strong-interaction limit of the density-fixed adiabatic connection case of Kohn-Sham density functional theory.

This study was designed to investigate the cytotoxicity and haemotoxicity of the Western barred (zebra) spitting cobra ( Naja nigricincta nigricincta ) venom to help explain atypical and inconsistent reports on syndromes by Namibian physicians treating victims of human ophidian accidents. Freeze-dried venom milked from adult zebra snakes was dissolved in phosphate buffered saline (PBS) for use in this study. Haemorrhagic and necrotic activity of venom were studied in New Zealand albino rabbits. Oedema-forming activity was investigated in 10-day-old Cobb500 broiler chicks. Procoagulant and thrombolytic activity was investigated in adult Kalahari red goat blood in vitro . The rabbit skin minimum hemorrhagic dose (MHD) for N. n. nigricincta was 9.8 μ g. The minimum necrotizing dose (MND) for N. n. nigricincta venom was 12.2 μ g. The N. n. nigricincta venom showed linear dose-dependent procoagulant activity on goat blood (p<0.05). Likewise, N. n. nigricincta venom showed linear dose-dependent thrombolytic activity on goat blood (p<0.05, n = 6). Subplantar injection of N. n. nigricincta venom (25 μ g, 50 μ g, 75 μ g, and 100 μ g) into chick paw resulted in peak oedema of 35.5%, 38.5%, 42.9%, and 47.5%, respectively, two hours after injection. Paw oedema subsided within five hours to a mean volume ranging from 5% (25 μ g venom) to 17.6% (100 μ g venom). In conclusion, though N. n. nigricincta belongs to the genus Elapidae , the current study has shown its venom to possess potent hemorrhagic, necrotic (cytotoxic), and paradoxically, both procoagulant and thrombolytic activity. The authors propose further work to fractionate, isolate, and elucidate the structure of the various N. n. nigricincta venom toxins as a prelude to the development of an antivenom.

Kinetic energy (KE) approximations are key elements in orbital-free density functional theory. To date, the use of nonlocal functionals, possibly employing system-dependent parameters, has been considered mandatory in order to obtain satisfactory accuracy for different solid-state systems, whereas semilocal approximations are generally regarded as unfit to this aim. Here, we show that, instead, properly constructed semilocal approximations, the Pauli-Gaussian (PG) KE functionals, especially at the Laplacian level of theory, can indeed achieve similar accuracy as nonlocal functionals and can be accurate for both metals and semiconductors, without the need for system-dependent parameters.

Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero&#95;2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero&#95;1277, and an inner membrane ferrous iron permease, coded by Hsero&#95;2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero&#95;1277 and Hsero&#95;3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero&#95;2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero&#95;2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.

Approximate exchange-correlation functionals built by modeling in a nonlinear way the adiabatic connection (AC) integrand of density functional theory have many attractive features, being virtually parameter-free and satisfying different exact properties, but they also have a fundamental flaw: they violate the size-consistency condition, crucial to evaluate interaction energies of molecular systems. We show that size consistency in the AC-based functionals can be restored in a very simple way at no extra computational cost. Results on a large set of benchmark molecular interaction energies show that functionals based on the interaction strength interpolation approximations are significantly more accurate than second-order perturbation theory.

The performance of functionals based on the idea of interpolating between the weak- and the strong-interaction limits the global adiabatic-connection integrand is carefully studied for the challenging case of noble-metal clusters. Different interpolation formulas are considered and various features of this approach are analyzed. It is found that these functionals, when used as a correlation correction to Hartree-Fock, are quite robust for the description of atomization energies, while performing less well for ionization potentials. Future directions that can be envisaged from this study and a previous one on main group chemistry are discussed.

We have developed a simplified coupled cluster (SCC) methodology, using the basic idea of scaled MP2 methods. The scheme has been applied to the coupled cluster double equations and implemented in three different non-iterative variants. This new method (especially the SCCD[3] variant, which utilizes a spin-resolved formalism) has been found to be very efficient and to yield an accurate approximation of the reference CCD results for both total and interaction energies of different atoms and molecules. Furthermore, we demonstrate that the equations determining the scaling coefficients for the SCCD[3] approach can generate non-empirical SCS-MP2 scaling coefficients which are in good agreement with previous theoretical investigations.

Using the semiclassical neutral atom theory, we developed a modified fourth-order kinetic energy (KE) gradient expansion (GE4m) that keeps unchanged all the linear-response terms of the uniform electron gas and gives a significant improvement with respect to the known semilocal functionals for both large atoms and jellium surfaces. On the other hand, GE4m is not accurate for light atoms; thus, we modified the GE4m coefficients making them dependent on a novel ingredient, the reduced Hartree potential, recently introduced in the Journal of Chemical Physics 2016, 145, 084110, in the context of exchange functionals. The resulting KE gradient expansion functional, named uGE4m, belongs to the novel class of u-meta-generalized-gradient-approximations (uMGGA) whose members depend on the conventional ingredients (i.e., the reduced gradient and Laplacian of the density) as well as on the reduced Hartree potential. To test uGE4m, we defined an appropriate benchmark (including total KE and KE differences for atoms, molecules and jellium clusters) for gradient expansion functionals, that is, including only those systems which are mainly described by a slowly varying density regime. While most of the GGA and meta-GGA KE functionals (we tested 18 of them) are accurate for some properties and inaccurate for others, uGE4m shows a consistently good performance for all the properties considered. This represents a qualitative boost in the KE functional development and highlights the importance of the reduced Hartree potential for the construction of next-generation KE functionals.

Herein we present organic mixed-valence compounds with an innovative H-shape design, where four redox centres are bridged "vertically" via a dibenzofulvene backbone and "horizontally" via a bis-(dibenzofulvene)-thiophene bridge. These compounds are easily oxidized to stable highly charged radical species which show intense intervalence charge transfer transitions in the near infrared region. Interestingly, depending on the position of the arylamine substituents on the bridge, both vertical and horizontal electron transfer pathways can be optically induced.

In this work we found that the bfr gene of the rhizobial species Ensifer meliloti , encoding a bacterioferritin iron storage protein, is involved in iron homeostasis and the oxidative stress response. This gene is located downstream of and overlapping the smc03787 open reading frame (ORF). No well-predicted RirA or Irr boxes were found in the region immediately upstream of the bfr gene although two presumptive RirA boxes and one presumptive Irr box were present in the putative promoter of smc03787 We demonstrate that bfr gene expression is enhanced under iron-sufficient conditions and that Irr and RirA modulate this expression. The pattern of bfr gene expression as well as the response to Irr and RirA is inversely correlated to that of smc03787 Moreover, our results suggest that the small RNA SmelC759 participates in RirA- and Irr-mediated regulation of bfr expression and that additional unknown factors are involved in iron-dependent regulation. IMPORTANCE E. meliloti belongs to the Alphaproteobacteria , a group of bacteria that includes several species able to associate with eukaryotic hosts, from mammals to plants, in a symbiotic or pathogenic manner. Regulation of iron homeostasis in this group of bacteria differs from that found in the well-studied Gammaproteobacteria In this work we analyzed the effect of rirA and irr mutations on bfr gene expression. We demonstrate the effect of an irr mutation on iron homeostasis in this bacterial genus. Moreover, results obtained indicate a complex regulatory circuit where multiple regulators, including RirA, Irr, the small RNA SmelC759, and still unknown factors, act in concert to balance bfr gene expression., (Copyright © 2017 American Society for Microbiology.)

Electromechanical coupling through piezoelectric polymer chains allows the emission of organic molecules in active nanowires to be tuned. This effect is evidenced by highly bendable arrays of counter-ion dye-doped nanowires made of a poly(vinylidenefluoride) copolymer. A reversible redshift of the dye emission is found upon the application of dynamic stress during highly accurate bending experiments. By density functional theory calculations it is found that these photophysical properties are associated with mechanical stresses applied to electrostatically interacting molecular systems, namely to counterion-mediated states that involve light-emitting molecules as well as charged regions of piezoelectric polymer chains. These systems are an electrostatic class of supramolecular functional stress-sensitive units, which might impart new functionalities in hybrid molecular nanosystems and anisotropic nanostructures for sensing devices and soft robotics., (© 2017 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The development of semilocal models for the kinetic energy density (KED) is an important topic in density functional theory (DFT). This is especially true for subsystem DFT, where these models are necessary to construct the required non-additive embedding contributions. In particular, these models can also be efficiently employed to replace the exact KED in meta-Generalized Gradient Approximation (meta-GGA) exchange-correlation functionals allowing to extend the subsystem DFT applicability to the meta-GGA level of theory. Here, we present a two-dimensional scan of semilocal KED models as linear functionals of the reduced gradient and of the reduced Laplacian, for atoms and weakly bound molecular systems. We find that several models can perform well but in any case the Laplacian contribution is extremely important to model the local features of the KED. Indeed a simple model constructed as the sum of Thomas-Fermi KED and 1/6 of the Laplacian of the density yields the best accuracy for atoms and weakly bound molecular systems. These KED models are tested within subsystem DFT with various meta-GGA exchange-correlation functionals for non-bonded systems, showing a good accuracy of the method.

We present the draft genome of Cupriavidus UYMMa02A, a rhizobium strain isolated from root nodules of Mimosa magentea The assembly has approximately 8.1 million bp with an average G+C of 64.1%. Symbiotic and metal-resistance genes were identified. The study of this genome will contribute to the understanding of rhizobial evolution., (Copyright © 2016 Iriarte et al.)

The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle., Importance: A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria., (Copyright © 2016 Rosconi et al.)

We have tested the original interaction-strength-interpolation (ISI) exchange-correlation functional for main group chemistry. The ISI functional is based on an interpolation between the weak and strong coupling limits and includes exact-exchange as well as the Görling-Levy second-order energy. We have analyzed in detail the basis-set dependence of the ISI functional, its dependence on the ground-state orbitals, and the influence of the size-consistency problem. We show and explain some of the expected limitations of the ISI functional (i.e., for atomization energies) but also unexpected results, such as the good performance for the interaction energy of dispersion-bonded complexes when the ISI correlation is used as a correction to Hartree-Fock.

Crude glycerol obtained as a by-product of biodiesel production is a reliable feedstock with the potential to be converted into reduced chemicals with high yields. It has been previously shown that ethanol is the primary product of glycerol fermentation by Escherichia coli. However, few efforts were made to enhance this conversion by means of the expression of heterologous genes with the potential to improve glycerol transport or metabolism. In this study, a fosmid-based metagenomic library constructed from an anaerobic reactor purge sludge was screened for genetic elements that promote the use and fermentation of crude glycerol by E. coli. One clone was selected based on its improved growth rate on this feedstock. The corresponding fosmid, named G1, was fully sequenced (41 kbp long) and the gene responsible for the observed phenotype was pinpointed by in vitro insertion mutagenesis. Ethanol production from both pure and crude glycerol was evaluated using the parental G1 clone harboring the ethanologenic plasmid pLOI297 or the industrial strain LY180 complemented with G1. In mineral salts media containing 50 % (v/v) pure glycerol, ethanol concentrations increased two-fold on average when G1 was present in the cells reaching up to 20 g/L after 24 h fermentation. Similar fermentation experiments were done using crude instead of pure glycerol. With an initial OD620 of 8.0, final ethanol concentrations after 24 h were much higher reaching 67 and 75 g/L with LY180 cells carrying the control fosmid or the G1 fosmid, respectively. This translates into a specific ethanol production rate of 0.39 g h(-1) OD(-1) L(-1).

Herbaspirillum seropedicae Z67 is a diazotrophic endophyte able to colonize the interior of many economically relevant crops such as rice, wheat, corn and sorghum. Under iron-deficient conditions, this organism secretes serobactins, a suite of lipopetide siderophores. The role of siderophores in the interaction between endophytes and their plant hosts are not well understood. In this work, we aimed to determine the importance of serobactins-mediated iron acquisition systems in the interaction of H. seropedicae with rice plants. First we provide evidence, by using a combination of genome analysis, proteomic and genetic studies, that the Hsero&#95;2345 gene encodes a TonB-dependent receptor involved in iron-serobactin complex internalization when iron bioavailability is low. Our results show that survival of the Hsero&#95;2345 mutant inside rice plants was not significantly different from that of the wild-type strain. However, when plants were co-inoculated at equal ratios with the wild-type strain and with a double mutant defective in serobactins synthesis and internalization, recovery of mutant was significantly impaired after 8 days post-inoculation. These results demonstrate that serobactins-mediated iron acquisition contributes to competitive fitness of H. seropedicae inside host plants., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)

We introduce a novel non-local ingredient for the construction of exchange density functionals: the reduced Hartree parameter, which is invariant under the uniform scaling of the density and represents the exact exchange enhancement factor for one- and two-electron systems. The reduced Hartree parameter is used together with the conventional meta-generalized gradient approximation (meta-GGA) semilocal ingredients (i.e., the electron density, its gradient, and the kinetic energy density) to construct a new generation exchange functional, termed u-meta-GGA. This u-meta-GGA functional is exact for the exchange of any one- and two-electron systems, is size-consistent and non-empirical, satisfies the uniform density scaling relation, and recovers the modified gradient expansion derived from the semiclassical atom theory. For atoms, ions, jellium spheres, and molecules, it shows a good accuracy, being often better than meta-GGA exchange functionals. Our construction validates the use of the reduced Hartree ingredient in exchange-correlation functional development, opening the way to an additional rung in the Jacob's ladder classification of non-empirical density functionals.

One important property of Kohn-Sham (KS) density functional theory is the exact equality of the energy of the highest occupied KS orbital (HOMO) with the negative ionization potential of the system. This exact feature is out of reach for standard density-dependent semilocal functionals. Conversely, accurate results can be obtained using orbital-dependent functionals in the optimized effective potential (OEP) approach. In this article, we investigate the performance, in this context, of some advanced OEP methods, with special emphasis on the recently proposed scaled-opposite-spin OEP functional. Moreover, we analyze the impact of the so-called HOMO condition on the final quality of the HOMO energy. Results are compared to reference data obtained at the CCSD(T) level of theory. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

In this work, we investigate the optical and structural properties of the well-known triplet emitter bis(4',6'-difluorophenylpyridinato)-iridium(III) picolinate (FIrpic), showing that its ability to pack in two different ordered crystal structures promotes attractive photophysical properties that are useful for solid-state lighting applications. This approach allows the detrimental effects of the nonradiative pathways on the luminescence performance in highly concentrated organic active materials to be weakened. The remarkable electro-optical behavior of sky-blue phosphorescent organic light-emitting diodes incorporating crystal domains of FIrpic, dispersed into an appropriate matrix as an active layer, has also been reported as well as the X-ray diffraction, nuclear magnetic resonance, electro-ionization mass spectrometry, and scanning electron microscopy analyses of the crystalline samples. We consider this result as a crucial starting point for further research aimed at the use of a crystal triplet emitter in optoelectronic devices to overcome the long-standing issue of luminescence self-quenching.

Unlabelled: The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found., Importance: With the aim of exploring the diversity of rhizobia associated with native Mimosa species, symbionts were isolated from root nodules on five Mimosa species that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genus Mimosa, Brazil and Mexico, where it is mainly associated with Burkholderia and Rhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genus Cupriavidus Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic species C. taiwanensis, but instead they were related to other Cupriavidus species such as C. necator and C. pinatubonensis These data suggest the existence of a higher diversity within beta-rhizobial Cupriavidus than was previously suspected, and that Mimosa spp. from Sierra del Abra de Zabaleta, may be natural reservoirs for novel rhizobia., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Three new metal-free organic dyes with the [1]benzothieno[3,2-b]benzothiophene (BTBT) π-bridge, having the structure donor-π-acceptor (D-π-A) and labeled as 19, 20 and 21, have been designed and synthesized for application in dye-sensitized solar cells (DSSC). Once the design of the π-acceptor block was fixed, containing the BTBT as the π-bridge and the cyanoacrylic group as the electron acceptor and anchoring unit, we selected three donor units with different electron-donor capacity, in order to assemble new chromophores with high molar extinction coefficients (ε), whose absorption features well reflect the good performance of the final DSSC devices. Starting with the 19 dye, which shows a molar extinction coefficient ε of over 14,000 M(-1) cm(-1) and takes into account the absorption maximun at the longer wavelength, the substitution of the BFT donor unit with the BFA yields a great enhancement of absorptivity (molar extinction coefficient ε > 42,000 M(-1) cm(-1)), until reaching the higher value (ε > 69,000 M(-1) cm(-1)) with the BFPhz donor unit. The good general photovoltaic performances obtained with the three dyes highlight the suitable properties of electron-transport of the BTBT as the π-bridge in organic chromophore for DSSC, making this very cheap and easy to synthesize molecule particularly attractive for efficient and low-cost photovoltaic devices.

Ensifer meliloti is a nitrogen-fixing symbiont of the alfalfa legume able to use heme as an iron source. The transport mechanism involved in heme acquisition in E. meliloti has been identified and characterized, but the fate of heme once inside the cell is not known. In silico analysis of E. meliloti 1021 genome revealed no canonical heme oxygenases although two genes encoding putative heme degrading enzymes, smc01518 and hmuS, were identified. SMc01518 is similar to HmuQ of Bradyrhizobium japonicum, which is weakly homologous to the Staphylococcus aureus IsdG heme-degrading monooxygenase, whereas HmuS is homolog to Pseudomonas aeruginosa PhuS, a protein reported as a heme chaperone and as a heme degrading enzyme. Recombinant HmuQ and HmuS were able to bind hemin with a 1:1 stoichiometry and displayed a Kd value of 5 and 4 µM, respectively. HmuS degrades heme in vitro to the biliverdin isomers IX-β and IX-δ in an equimolar ratio. The HmuQ recombinant protein degrades heme to biliverdin IX-δ only. Additionally, in this work we demonstrate that humS and hmuQ gene expression is regulated by iron and heme in a RirA dependent manner and that both proteins are involved in heme metabolism in E. meliloti in vivo.

With the aim of improving current ethanologenic Escherichia coli strains, we screened a metagenomic library from bovine ruminal fluid for cellulolytic enzymes. We isolated one fosmid, termed Csd4, which was able to confer to E. coli the ability to grow on complex cellulosic material as the sole carbon source such as avicel, carboxymethyl cellulose, filter paper, pretreated sugarcane bagasse, and xylan. Glucanolytic activity obtained from E. coli transformed with Csd4 was maximal at 24 h of incubation and was inhibited when glucose or xylose were present in the media. The 34,406-bp DNA fragment of Csd4 was completely sequenced, and a putative endoglucanase, a xylosidase/arabinosidase, and a laccase gene were identified. Comparison analysis revealed that Csd4 derived from an organism closely related to Prevotella ruminicola, but no homologies were found with any of the genomes already sequenced. Csd4 was introduced into the ethanologenic E. coli MS04 strain and ethanol production from CMC, avicel, sugarcane bagasse, or filter paper was observed. Exogenously expressed β-glucosidase had a positie effect on cell growth in agreement with the fact that no putative β-glucosidase was found in Csd4. Ethanol production from sugarcane bagasse was improved threefold by Csd4 after saccharification by commercial Trichoderma reesei cellulases underlining the ability of Csd4 to act as a saccharification enhancer to reduce the enzymatic load and time required for cellulose deconstruction.

Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.

A metagenomic fosmid library from bovine rumen was used to identify clones with lipolytic activity. One positive clone was isolated. The gene responsible for the observed phenotype was identified by in vitro transposon mutagenesis and sequencing and was named est10. The 367 amino acids sequence harbors a signal peptide, the conserved secondary structure arrangement of alpha/beta hydrolases, and a GHSQG pentapeptide which is characteristic of esterases and lipases. Homology based 3D-modelling confirmed the conserved spatial orientation of the serine in a nucleophilic elbow. By sequence comparison, Est10 is related to hydrolases that are grouped into the non-specific Pfam family DUF3089 and to other characterized esterases that were recently classified into the new family XV of lipolytic enzymes. Est10 was heterologously expressed in Escherichia coli as a His-tagged fusion protein, purified and biochemically characterized. Est10 showed maximum activity towards C4 aliphatic chains and undetectable activity towards C10 and longer chains which prompted its classification as an esterase. However, it was able to efficiently catalyze the hydrolysis of aryl esters such as methyl phenylacetate and phenyl acetate. The optimum pH of this enzyme is 9.0, which is uncommon for esterases, and it exhibits an optimal temperature at 40 °C. The activity of Est10 was inhibited by metal ions, detergents, chelating agents and additives. We have characterized an alkaline esterase produced by a still unidentified bacterium belonging to a recently proposed new family of esterases.

Three fluorenone-derived two-photon fluorescent probes (TK) targeting the lysosomes (TK-Lyso) and mitochondria (TK-Mito1 and TK-Mito2) were synthesized by introducing different diphenylamine moieties into the fluorenone core. The TK dyes showed high biocompatibility and long-term retention, low cytotoxicity, large Stokes shift and good fluorescence quantum yield. The results of the present work disclose a class of organic dyes with potential wide applications as specific and efficient probes for lysosomes and mitochondria in the study of various biological processes.

We analyze the methodology and the performance of subsystem density functional theory (DFT) with meta-generalized gradient approximation (meta-GGA) exchange-correlation functionals for non-bonded molecular systems. Meta-GGA functionals depend on the Kohn-Sham kinetic energy density (KED), which is not known as an explicit functional of the density. Therefore, they cannot be directly applied in subsystem DFT calculations. We propose a Laplacian-level approximation to the KED which overcomes this limitation and provides a simple and accurate way to apply meta-GGA exchange-correlation functionals in subsystem DFT calculations. The so obtained density and energy errors, with respect to the corresponding supermolecular calculations, are comparable with conventional approaches, depending almost exclusively on the approximations in the non-additive kinetic embedding term. An embedding energy error decomposition explains the accuracy of our method.

Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. The 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Colloidal quantum dots (QDs) stand among the most attractive light-harvesting materials to be exploited for solution-processed optoelectronic applications. To this aim, quantitative replacement of the bulky electrically insulating ligands at the QD surface coming from the synthetic procedure is mandatory. Here we present a conceptually novel approach to design light-harvesting nanomaterials demonstrating that QD surface modification with suitable short conjugated organic molecules permits us to drastically enhance light absorption of QDs, while preserving good long-term colloidal stability. Indeed, rational design of the pendant and anchoring moieties, which constitute the replacing ligand framework leads to a broadband increase of the optical absorbance larger than 300% for colloidal PbS QDs also at high energies (>3.1 eV), which could not be predicted by using formalisms derived from effective medium theory. We attribute such a drastic absorbance increase to ground-state ligand/QD orbital mixing, as inferred by density functional theory calculations; in addition, our findings suggest that the optical band gap reduction commonly observed for PbS QD solids treated with thiol-terminating ligands can be prevalently ascribed to 3p orbitals localized on anchoring sulfur atoms, which mix with the highest occupied states of the QDs. More broadly, we provide evidence that organic ligands and inorganic cores are inherently electronically coupled materials thus yielding peculiar chemical species (the colloidal QDs themselves), which display arising (opto)electronic properties that cannot be merely described as the sum of those of the ligand and core components.

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 2011, 106, 186406] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetic and structural testing, including thermochemistry and geometry, transition metal complexes, noncovalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semiempirical dispersion corrections are also provided.