A conserved loop in polynucleotide phosphorylase (PNPase) essential for both RNA and ADP/phosphate binding

Polynucleotide phosphorylase (PNPase) reversibly catalyzes RNA phosphorolysis and polymerization of nucleoside diphosphates. Its homotrimeric structure forms a central channel where RNA is accommodated. Each protomer core is formed by two paralogous RNase PH domains: PNPase1, whose function is largely unknown, hosts a conserved FFRR loop interacting with RNA, whereas PNPase2 bears the putative catalytic site, ∼20 Å away from the FFRR loop. To date, little is known regarding PNPase catalytic mechanism. We analyzed the kinetic properties of two Escherichia coli PNPase mutants in the FFRR loop (R79A and R80A), which exhibited a dramatic increase in Km for ADP/Pi binding, but not for poly(A), suggesting that the two residues may be essential for binding ADP and Pi. However, both mutants were severely impaired in shifting RNA electrophoretic mobility, implying that the two arginines contribute also to RNA binding. Additional interactions between RNA and other PNPase domains (such as KH and S1) may preserve the enzymatic activity in R79A and R80A mutants. Inspection of enzyme structure showed that PNPase has evolved a long-range acting hydrogen bonding network that connects the FFRR loop with the catalytic site via the F380 residue. This hypothesis was supported by mutation analysis. Phylogenetic analysis of PNPase domains and RNase PH suggests that such network is a unique feature of PNPase1 domain, which coevolved with the paralogous PNPase2 domain.

Towards [NiFe]-hydrogenase biomimetic models that couple H2 binding with functionally relevant intramolecular electron transfers: a quantum chemical study

[FeFe]- and [NiFe]-hydrogenases are dihydrogen-evolving metalloenzymes that share striking structural and functional similarities, despite being phylogenetically unrelated. Most notably, they are able to combine substrate binding and redox functionalities, which has important bearings on their efficiency. Model complexes of [FeFe]-hydrogenases that are able to couple H2 binding with a substrate-dependent intramolecular electron transfer promoting dihydrogen activation were recently shown to reproduce the complex redox chemistry of the all-iron enzyme. Notably, coupling of H2 binding and intramolecular redox events was proposed to have a key role also in [NiFe]-hydrogenases, but this feature is not reproduced in currently available nickel-iron biomimetic compounds. In the present study, we exploit dedicated density functional theory approaches to show that H2 binding and activation on a NiFe core can be favored by the installment of conveniently substituted isocyanoferrocenes, thanks to their ability to undergo intramolecular reduction upon substrate binding. Our results support the concept that a unified view on hydrogenase chemistry is a key element to direct future efforts in the modeling of microbial H2 metabolism.

Prevalence of hospital-associated infections can be decreased effectively in developing countries

BACKGROUND

Hospital-acquired infections (HAI) are an important public health problem worldwide. Little information is available from African countries, but published data show that the burden of HAI is greater in Africa than in developed countries. In 2002, the World Health Organization (WHO) published guidelines for preventing HAI.

AIM

To evaluate the impact of a hospital infection control programme on the prevalence of HAI among patients in a large Ugandan hospital.

METHODS

A one-day cross-sectional prevalence survey and a ward procedure survey were performed in Lacor Hospital in March 2010 using standardized questionnaires. All patients admitted to hospital not less than two days before the survey were eligible to participate in the prevalence survey. Modified WHO criteria for HAI were used. The ward procedure survey examined the procedures to prevent HAI. Several hospital infection control measures were subsequently implemented, in accordance with WHO infection control guidelines, starting in October 2010. The prevalence survey and ward procedure survey were repeated in October 2011.

FINDINGS

The prevalence of HAI was 34% in 2010 and 17% in 2011. The prevalence of infected patients reduced from 28% to 14%. The prevalence of HAI was lower in all age groups and for all types of HAI except urinary tract infections following the implementation of infection control activities.

CONCLUSION

This study showed that HAI is an important problem in this large African hospital, and that the prevalence of HAI can be reduced effectively following the adoption of basic infection control procedures.

H2 binding and splitting on a new-generation [FeFe]-hydrogenase model featuring a redox-active decamethylferrocenyl phosphine ligand: a theoretical investigation

[FeFe]-hydrogenases are dihydrogen-evolving metalloenzymes that are able to combine substrate binding and redox functionalities, a feature that has important bearing on their efficiency. New-generation bioinspired systems such as Fe(2)[(SCH(2))(2)NBn](CO)(3)(Cp*Fe(C(5)Me(4)CH(2)PEt(2)))(dppv) were shown to mimic H(2) oxidation and splitting processes performed by the [FeFe]-hydrogenase/ferredoxin system, and key mechanistic aspects of such reaction are theoretically investigated in the present contribution. We found that H(2) binding and heterolytic cleavage take place concomitantly on DFT models of the synthetic catalyst, due to a substrate-dependent intramolecular redox process that promotes dihydrogen activation. Therefore, formation of an iron-dihydrogen complex as a reaction intermediate is excluded in the biomimetic system, at variance with the case of the enzyme. H(2) uptake at the synthetic system also requires an energetically disfavored isomerization of the amine group acting as a base during splitting. A possible strategy to stabilize the conformation competent for H(2) binding is proposed, along with an analysis of the reactivity of a triiron complex in which di(thiomethyl)amine--the chelating group naturally occurring in [FeFe]-hydrogenases--substitutes the benzyl-containing dithiolate ligand.

Bilistick: a low-cost point-of-care system to measure total plasma bilirubin

BACKGROUND

Severe neonatal hyperbilirubinemia, with consequent encephalopathy, remains a common cause of morbidity and death in many regions of the world. Poor access to clinical laboratory resources and screening programs to measure plasma bilirubin levels is a major contributor to delayed treatment in developing countries, and the cost of existing point-of-care screening instruments precludes their dissemination.

OBJECTIVES

We are evaluating the accuracy of a low-cost, minimally invasive point-of-care system (Bilistick) requiring a 25-µl blood sample that could be used in low-resource environments to evaluate patients with neonatal jaundice.

METHODS

We compared plasma bilirubin levels in divided blood samples by clinical laboratories and by Bilistick at two medical centers serving term and near-term newborns from ethnically different populations.

RESULTS

118 neonates with bilirubin levels ranging from 24.8 to 501.0 µmol/l were analyzed. The mean bilirubin concentration (±SD) was 215.6 ± 85.5 µmol/l for Bilistick and 226.1 ± 86.4 µmol/l by laboratory determination. Pearson's correlation coefficient between all paired results was 0.961, and the Bland-Altman analysis showed a mean difference of 10.3 µmol/l with a 95% interval of agreement of -38.0 to 58.7 µmol/l.

CONCLUSION

Bilistick is a minimally invasive method for measuring total bilirubin concentration over a wide range of values and should provide an affordable and accurate system for pre-discharge and follow-up screening of jaundiced infants, particularly in low-resource environments.

Radiotherapy and hepatocellular carcinoma: update and review of the literature

Historically radiotherapy has always played a limited role for the treatment of HCC due to the low tolerance of the liver and the subsequent risk of radiation induced liver disease (RILD). Technologist advancements in radiation planning and treatment delivery such as Stereotactic Body Radiotherapy (SBRT) combined with Image Guided Radiotherapy (IGRT) has allowed us to further increase tumor dose while maximally sparing the surrounding not involved liver. Furthermore, together with the growing knowledge of radiobiological models in liver disease, several mono-institutional retrospective and prospective series are reporting very encouraging results. Therefore, radiotherapy might play a significant role for the treatment of unresectable HCC, alone or combined with other locoregional treatment such as transarterial chemoembolisation (TACE). The rationale for studying this technique is really strong and it should be tested in well designed prospective randomized clinical trials.

Understanding the distinctive elastic constants in an oxadiazole bent-core nematic liquid crystal

The splay and bend elastic constants of the bent-core oxadiazole material [C5-Ph-ODBP-Ph-OC12] have been investigated as a function of temperature across the nematic phase. The bend constant K(33) is found to take values of ~3.0 pN and to be almost temperature independent, whereas, the splay constant K(11) increases monotonically from ~3.5 pN close to the isotropic phase transition to values of ~9 pN deep in the nematic phase. No pretransitional divergence is observed in either K(11) or K(33) at temperatures approaching the underlying phase. This behavior of the elastic constants is distinct from that observed in rodlike liquid crystal systems but appears to share characteristics with the few other bent-core nematic systems studied to date. We discuss the interdependence of the elastic constants, the birefringence, and the order parameter to allow a comparison of the observed behavior with theory. We show that calculations of the elastic constants via molecular-field theory and atomistic modeling are in excellent qualitative as well as good quantitative (within 2 pN) agreement with the measurements across the temperature range, offering a deeper understanding of the elasticity in bent-core nematic materials than has been, hitherto, available.

Lewis acid trapping of an elusive copper-tosylnitrene intermediate using scandium triflate

High-valent copper-nitrene intermediates have long been proposed to play a role in copper-catalyzed aziridination and amination reactions. However, such intermediates have eluded detection for decades, preventing the unambiguous assignments of mechanisms. Moreover, the electronic structure of the proposed copper-nitrene intermediates has also been controversially discussed in the literature. These mechanistic questions and controversy have provided tremendous motivation to probe the accessibility and reactivity of Cu(III)-NR/Cu(II)N(•)R species. In this paper, we report a breakthrough in this field that was achieved by trapping a transient copper-tosylnitrene species, 3-Sc, in the presence of scandium triflate. The sufficient stability of 3-Sc at -90 °C enabled its characterization with optical, resonance Raman, NMR, and X-ray absorption near-edge spectroscopies, which helped to establish its electronic structure as Cu(II)N(•)Ts (Ts = tosyl group) and not Cu(III)NTs. 3-Sc can initiate tosylamination of cyclohexane, thereby suggesting Cu(II)N(•)Ts cores as viable reactants in oxidation catalysis.

Diagnostic accuracy of 320-row computed tomography as compared with invasive coronary angiography in unselected, consecutive patients with suspected coronary artery disease

Noninvasive coronary angiography with multislice computed tomography (CT) scanners is feasible with high sensitivity and negative predictive value. The radiation exposure associated with this technique, however, is high and concerns in the widespread use of CT have arisen. We evaluated the diagnostic accuracy of coronary angiography using 320-row CT, which avoids exposure-intensive overscanning and overranging. We prospectively studied 118 unselected consecutive patients with suspected coronary artery disease (CAD) referred for invasive coronary angiography (ICA). All patients had 320-row CT within 1 week of ICA, which, together with quantitative analysis, served as the reference standard. Of the 65 out of 118 patients who were diagnosed as having CAD by ICA, 64 (98 %) were correctly identified at 320-row CT. Noteworthy, 320-row CT correctly detected CAD in 3 patients with atrial fibrillation and ruled out the disease in the other 8 patients. From 151 significant coronary stenoses detected on ICA, 137 (91 %) were correctly identified with 320-row CT. In the per-patient analysis, sensitivity and specificity of 320-row CT were 98 and 91 %, respectively. In the per-vessel analysis, sensitivity and specificity of 320-row CT were 93 and 95 %, respectively. In the per segment analysis, sensitivity and specificity of 320-row CT were 91 and 99 %, respectively. Diameter stenosis determined with the use of CT showed good correlation with ICA (P < 0.001, R = 0.81) without significant underestimation or overestimation (-3.1 ± 24.4 %; P = 0.08). Comparison of CT with ICA revealed a significantly smaller effective radiation dose (3.1 ± 2.3 vs. 6.5 ± 4.2 mSv; P < 0.05) and amount of contrast agent required (99 ± 51 vs. 65 ± 42 ml, P < 0.05) for 320 row CT. The present study in an unselected population including patients with atrial fibrillation demonstrates that 320-row CT may significantly reduce the radiation dose and amount of contrast agent required compared with ICA while maintaining a very high diagnostic accuracy.

BLUF hydrogen network dynamics and UV/Vis spectra: a combined molecular dynamics and quantum chemical study

Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations ("W(in)"/"W(out)"), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in W(in) position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated π → π* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach.

Validation of DN4 as a screening tool for neuropathic pain in painful diabetic polyneuropathy

AIMS

DN4 (Douleur Neuropathique en 4 Questions) is a screening tool for neuropathic pain consisting of interview questions (DN4-interview) and physical tests. It has not formally been validated in diabetes. We evaluated the validity and diagnostic accuracy of DN4 and DN4-interview in identifying neuropathic pain of painful diabetic polyneuropathy.

METHODS

In 158 patients with diabetes, the presence of diabetic polyneuropathy and neuropathic pain was assessed using scoring system for symptoms and signs, quantitative sensory testing, nerve conduction studies, pain history, numerical rating scale, and Short-Form McGill Pain Questionnaire. Painful diabetic polyneuropathy was defined as the presence of diabetic polyneuropathy plus chronic neuropathic pain in the same area as neuropathic deficits. A blinded investigator performed DN4.

RESULTS

The DN4 score was significantly related to all the neurological and electrophysiological measurements and to Short-Form McGill Pain Questionnaire (ρ = 0.58, P < 0.0001). DN4 and DN4-interview scores showed a high diagnostic accuracy for painful diabetic polyneuropathy with areas under the receiver operating characteristic curve of 0.94 and 0.93, respectively. At the cut-off of 4, DN4 displayed sensitivity of 80%, specificity of 92%, positive predictive value (PPV) of 82%, negative predictive value (NPV) of 91%, and likelihood ratio for a positive result (LR(+) ) of 9.6. At the cut-off of 3, DN4-interview showed sensitivity and specificity of 84%, PPV of 71%, NPV of 92%, and LR(+) of 5.3.

CONCLUSIONS

This is the first validation study of DN4 for painful diabetic polyneuropathy, which supports its usefulness as both a screening tool for neuropathic pain in diabetes and a reliable component of the diagnostic work up for painful diabetic polyneuropathy.