A topological view of the replicon.

The replication of circular DNA faces topological obstacles that need to be overcome to allow the complete duplication and separation of newly replicated molecules. Small bacterial plasmids provide a perfect model system to study the interplay between DNA helicases, polymerases, topoisomerases and the overall architecture of partially replicated molecules. Recent studies have shown that partially replicated circular molecules have an amazing ability to form various types of structures (supercoils, precatenanes, knots and catenanes) that help to accommodate the dynamic interplay between duplex unwinding at the replication fork and DNA unlinking by topoisomerases.

Hospital outbreak of methicillin-resistant Staphylococcus aureus caused by a new, possibly hyperepidemic variant from a previously sporadic strain.

Objective: To describe an ongoing outbreak that tripled the annual detection of methicillin-resistant Staphylococcus aureus (MRSA) carriage in a tertiary care hospital. Methods: Active surveillance of MRSA is performed since 20 years in our hospital. Our protocol includes screening of patients transferred from high-incidence health-care institutions or countries, roommates of new MRSA cases, and wards where _2 patients acquired MRSA during the same week. Contact precautions are used for known carriers. PFGE was used for molecular typing until 2004, and was then replaced by Double-Locus Sequence Typing (DLST). Results: A median yearly incidence of 173 new carriers of MRSA was observed from 2002 to 2007. Since September 2008, an increasing number of new cases were observed, mainly as successive clusters limited to distinct wards, reaching a total of 398 until October 2009. The yearly incidence of new cases rose to 275 in 2008 and 613 in 2009. 60% of the cases were due to one strain: DLST 4−4, ST 228, SCCmecI. The incidence of new cases due to the previously predominant strains remained unchanged. The epidemic strain corresponded to a new variant of a clone responsible for a previous outbreak in 2001, and only sporadically isolated (mean of 20 cases/year) since then. A case- control study documented a significant association between acquisition of the epidemic strain and a stay in intensive and intermediary care units, a highest number of internal transfers, but did not identify a point source of transmission. Infection control practices and antibiotic policy had remained unchanged for several years. Compliance with handhygiene as monitored yearly was on the rise. Screening of 313 healthcare workers only found one carrier of the epidemic strain lately in the outbreak. Additional infection control measures were enforced, including screening at ICU admission and discharge with PCR-based rapid test, routine screening for all patients leaving epidemic wards, introduction of PCR-based rapid test for contact tracing, additional working forces for environmental disinfection, and hospital-wide education of healthcare workers. However, the outbreak was still ongoing after 5 months. Conclusions: Factors linked to the dissemination of this new variant in our institution remain undetermined. This unresolved outbreak suggests that this new variant acquired hyperepidemic properties, which calls for further investigations.

Oikeuslähteet ja yleiset opit

Ylänimeke: Oikeudenaloja

Hepatic-specific lipin-1 deficiency exacerbates experimental alcohol-induced steatohepatitis in mice.

Lipin-1 regulates lipid metabolism by way of its function as an enzyme in the triglyceride synthesis pathway and as a transcriptional coregulatory protein and is highly up-regulated in alcoholic fatty liver disease. In the present study, using a liver-specific lipin-1-deficient (lipin-1LKO) mouse model, we aimed to investigate the functional role of lipin-1 in the development of alcoholic steatohepatitis and explore the underlying mechanisms. Alcoholic liver injury was achieved by pair feeding wild-type and lipin-1LKO mice with modified Lieber-DeCarli ethanol-containing low-fat diets for 4 weeks. Surprisingly, chronically ethanol-fed lipin-1LKO mice showed markedly greater hepatic triglyceride and cholesterol accumulation, and augmented elevation of serum liver enzymes accompanied by increased hepatic proinflammatory cytokine expression. Our studies further revealed that hepatic removal of lipin-1 in mice augmented ethanol-induced impairment of hepatic fatty acid oxidation and lipoprotein production, likely by way of deactivation of peroxisome proliferator-activated receptor γ coactivator-1alpha, a prominent transcriptional regulator of lipid metabolism. Conclusions: Liver-specific lipin-1 deficiency in mice exacerbates the development and progression of experimental alcohol-induced steatohepatitis. Pharmacological or nutritional modulation of hepatic lipin-1 may be beneficial for the prevention or treatment of human alcoholic fatty liver disease. (Hepatology 2013; 58:1953-1963).

Diurnal inhibition of NMDA-EPSCs at rat hippocampal mossy fibre synapses through orexin-2 receptors.

Diurnal release of the orexin neuropeptides orexin-A (Ox-A, hypocretin-1) and orexin-B (Ox-B, hypocretin-2) stabilises arousal, regulates energy homeostasis and contributes to cognition and learning. However, whether cellular correlates of brain plasticity are regulated through orexins, and whether they do so in a time-of-day-dependent manner, has never been assessed. Immunohistochemically we found sparse but widespread innervation of hippocampal subfields through Ox-A- and Ox-B-containing fibres in young adult rats. The actions of Ox-A were studied on NMDA receptor (NMDAR)-mediated excitatory synaptic transmission in acute hippocampal slices prepared around the trough (Zeitgeber time (ZT) 4-8, corresponding to 4-8 h into the resting phase) and peak (ZT 23) of intracerebroventricular orexin levels. At ZT 4-8, exogenous Ox-A (100 nm in bath) inhibited NMDA receptor-mediated excitatory postsynaptic currents (NMDA-EPSCs) at mossy fibre (MF)-CA3 (to 55.6 ± 6.8% of control, P = 0.0003) and at Schaffer collateral-CA1 synapses (70.8 ± 6.3%, P = 0.013), whereas it remained ineffective at non-MF excitatory synapses in CA3. Ox-A actions were mediated postsynaptically and blocked by the orexin-2 receptor (OX2R) antagonist JNJ10397049 (1 μm), but not by orexin-1 receptor inhibition (SB334867, 1 μm) or by adrenergic and cholinergic antagonists. At ZT 23, inhibitory effects of exogenous Ox-A were absent (97.6 ± 2.9%, P = 0.42), but reinstated (87.2 ± 3.3%, P = 0.002) when endogenous orexin signalling was attenuated for 5 h through i.p. injections of almorexant (100 mg kg(-1)), a dual orexin receptor antagonist. In conclusion, endogenous orexins modulate hippocampal NMDAR function in a time-of-day-dependent manner, suggesting that they may influence cellular plasticity and consequent variations in memory performance across the sleep-wake cycle.

Highway Work Zone Capacity Estimation Using Field Data from Kansas, TPF-5(081), 2015

Although extensive research has been conducted on urban freeway capacity estimation methods, minimal research has been carried out for rural highway sections, especially sections within work zones. This study attempted to fill that void for rural highways in Kansas, by estimating capacity of rural highway work zones in Kansas. Six work zone locations were selected for data collection and further analysis. An average of six days’ worth of field data was collected, from mid-October 2013 to late November 2013, at each of these work zone sites. Two capacity estimation methods were utilized, including the Maximum Observed 15-minute Flow Rate Method and the Platooning Method divided into 15-minute intervals. The Maximum Observed 15-minute Flow Rate Method provided an average capacity of 1469 passenger cars per hour per lane (pcphpl) with a standard deviation of 141 pcphpl, while the Platooning Method provided a maximum average capacity of 1195 pcphpl and a standard deviation of 28 pcphpl. Based on observed data and analysis carried out in this study, the suggested maximum capacity can be considered as 1500 pcphpl when designing work zones for rural highways in Kansas. This proposed standard value of rural highway work zone capacity could be utilized by engineers and planners so that they can effectively mitigate congestion at or near work zones that would have otherwise occurred due to construction/maintenance.

Understanding diffusion MR imaging techniques: from scalar diffusion-weighted imaging to diffusion tensor imaging and beyond.

The complex structural organization of the white matter of the brain can be depicted in vivo in great detail with advanced diffusion magnetic resonance (MR) imaging schemes. Diffusion MR imaging techniques are increasingly varied, from the simplest and most commonly used technique-the mapping of apparent diffusion coefficient values-to the more complex, such as diffusion tensor imaging, q-ball imaging, diffusion spectrum imaging, and tractography. The type of structural information obtained differs according to the technique used. To fully understand how diffusion MR imaging works, it is helpful to be familiar with the physical principles of water diffusion in the brain and the conceptual basis of each imaging technique. Knowledge of the technique-specific requirements with regard to hardware and acquisition time, as well as the advantages, limitations, and potential interpretation pitfalls of each technique, is especially useful.

The IBO germination quantitative trait locus encodes a phosphatase 2C-related variant with a nonsynonymous amino acid change that interferes with abscisic acid signaling.

Natural genetic variation is crucial for adaptability of plants to different environments. Seed dormancy prevents precocious germination in unsuitable conditions and is an adaptation to a major macro-environmental parameter, the seasonal variation in temperature and day length. Here we report the isolation of IBO, a quantitative trait locus (QTL) that governs c. 30% of germination rate variance in an Arabidopsis recombinant inbred line (RIL) population derived from the parental accessions Eilenburg-0 (Eil-0) and Loch Ness-0 (Lc-0). IBO encodes an uncharacterized phosphatase 2C-related protein, but neither the Eil-0 nor the Lc-0 variant, which differ in a single amino acid, have any appreciable phosphatase activity in in vitro assays. However, we found that the amino acid change in the Lc-0 variant of the IBO protein confers reduced germination rate. Moreover, unlike the Eil-0 variant of the protein, the Lc-0 variant can interfere with the activity of the phosphatase 2C ABSCISIC ACID INSENSITIVE 1 in vitro. This suggests that the Lc-0 variant possibly interferes with abscisic acid signaling, a notion that is supported by physiological assays. Thus, we isolated an example of a QTL allele with a nonsynonymous amino acid change that might mediate local adaptation of seed germination timing.

Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease.

The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for antiviral intervention but also a key player in the persistence and pathogenesis of HCV. It cleaves and thereby inactivates two crucial adaptor proteins in viral RNA sensing and innate immunity, mitochondrial antiviral signaling protein (MAVS) and TRIF, a phosphatase involved in growth factor signaling, T-cell protein tyrosine phosphatase (TC-PTP), and the E3 ubiquitin ligase component UV-damaged DNA-binding protein 1 (DDB1). Here we explored quantitative proteomics to identify novel cellular substrates of the NS3-4A protease. Cell lines inducibly expressing the NS3-4A protease were analyzed by stable isotopic labeling using amino acids in cell culture (SILAC) coupled with protein separation and mass spectrometry. This approach identified the membrane-associated peroxidase GPx8 as a bona fide cellular substrate of the HCV NS3-4A protease. Cleavage by NS3-4A occurs at Cys 11, removing the cytosolic tip of GPx8, and was observed in different experimental systems as well as in liver biopsies from patients with chronic HCV. Overexpression and RNA silencing studies revealed that GPx8 is involved in viral particle production but not in HCV entry or RNA replication. Conclusion: We provide proof-of-concept for the use of quantitative proteomics to identify cellular substrates of a viral protease and describe GPx8 as a novel proviral host factor targeted by the HCV NS3-4A protease. (Hepatology 2014;59:423-433).

Neonatal herpes simplex virus infections in Switzerland: results of a 6-year national prospective surveillance study.

A large variation in neonatal herpes incidence is observed in USA and Europe. Better knowledge of neonatal herpes epidemiology is important to inform local prevention strategies. Between 2002 and 2008, the Swiss Paediatric Surveillance Unit reported prospectively proven neonatal herpes simplex virus infections. During the study period seven cases were declared, for an incidence of 1.6/100,000 (95% CI 0.64-3.28/100,000) live births. This is one of the lowest incidences of neonatal herpes reported.

Real-time, in vivo intracellular recordings of caterpillar-induced depolarization waves in sieve elements using aphid electrodes.

Plants propagate electrical signals in response to artificial wounding. However, little is known about the electrophysiological responses of the phloem to wounding, and whether natural damaging stimuli induce propagating electrical signals in this tissue. Here, we used living aphids and the direct current (DC) version of the electrical penetration graph (EPG) to detect changes in the membrane potential of Arabidopsis sieve elements (SEs) during caterpillar wounding. Feeding wounds in the lamina induced fast depolarization waves in the affected leaf, rising to maximum amplitude (c. 60 mV) within 2 s. Major damage to the midvein induced fast and slow depolarization waves in unwounded neighbor leaves, but only slow depolarization waves in non-neighbor leaves. The slow depolarization waves rose to maximum amplitude (c. 30 mV) within 14 s. Expression of a jasmonate-responsive gene was detected in leaves in which SEs displayed fast depolarization waves. No electrical signals were detected in SEs of unwounded neighbor leaves of plants with suppressed expression of GLR3.3 and GLR3.6. EPG applied as a novel approach to plant electrophysiology allows cell-specific, robust, real-time monitoring of early electrophysiological responses in plant cells to damage, and is potentially applicable to a broad range of plant-herbivore interactions.