Temporal Proteomic Analysis of BK Polyomavirus Infection Reveals Virus-Induced G2 Arrest and Highly Effective Evasion of Innate Immune Sensing.

BK polyomavirus (BKPyV) is a small DNA virus that establishes a life-long persistent infection in the urinary tract of most people. BKPyV is known to cause severe morbidity in renal transplant recipients and can lead to graft rejection. The simple 5.2-kbp double-stranded DNA (dsDNA) genome expresses just seven known proteins; thus, it relies heavily on the host machinery to replicate. How the host proteome changes over the course of infection is key to understanding this host-virus interplay. Here, for the first time quantitative temporal viromics has been used to quantify global changes in >9,000 host proteins in two types of primary human epithelial cells throughout 72 h of BKPyV infection. These data demonstrate the importance of cell cycle progression and pseudo-G2 arrest in effective BKPyV replication, along with a surprising lack of an innate immune response throughout the whole virus replication cycle. BKPyV thus evades pathogen recognition to prevent activation of innate immune responses in a sophisticated manner.IMPORTANCE BK polyomavirus can cause serious problems in immune-suppressed patients, in particular, kidney transplant recipients who can develop polyomavirus-associated kidney disease. In this work, we have used advanced proteomics techniques to determine the changes to protein expression caused by infection of two independent primary cell types of the human urinary tract (kidney and bladder) throughout the replication cycle of this virus. Our findings have uncovered new details of a specific form of cell cycle arrest caused by this virus, and, importantly, we have identified that this virus has a remarkable ability to evade detection by host cell defense systems. In addition, our data provide an important resource for the future study of kidney epithelial cells and their infection by urinary tract pathogens.Isaac Newton Trust (part funding of ISSF award to C.M.C.

Traffic-Related Air Pollution and All-Cause Mortality during Tuberculosis Treatment in California.

BackgroundAmbient air pollution and tuberculosis (TB) have an impact on public health worldwide, yet associations between the two remain uncertain.ObjectiveWe determined the impact of residential traffic on mortality during treatment of active TB.MethodsFrom 2000-2012, we enrolled 32,875 patients in California with active TB and followed them throughout treatment. We obtained patient data from the California Tuberculosis Registry and calculated traffic volumes and traffic densities in 100- to 400-m radius buffers around residential addresses. We used Cox models to determine mortality hazard ratios, controlling for demographic, socioeconomic, and clinical potential confounders. We categorized traffic exposures as quintiles and determined trends using Wald tests.ResultsParticipants contributed 22,576 person-years at risk. There were 2,305 deaths during treatment for a crude mortality rate of 1,021 deaths per 10,000 person-years. Traffic volumes and traffic densities in all buffers around patient residences were associated with increased mortality during TB treatment, although the findings were not statistically significant in all buffers. As the buffer size decreased, fifth-quintile mortality hazards increased, and trends across quintiles of traffic exposure became more statistically significant. Increasing quintiles of nearest-road traffic volumes in the 100-m buffer were associated with 3%, 14%, 19%, and 28% increased risk of death during TB treatment [first quintile, referent; second quintile hazard ratio (HR)=1.03 [95% confidence interval (CI): 0.86, 1.25]; third quintile HR=1.14 (95% CI: 0.95, 1.37); fourth quintile HR=1.19 (95% CI: 0.99, 1.43); fifth quintile HR=1.28 (95% CI: 1.07, 1.53), respectively; p-trend=0.002].ConclusionsResidential proximity to road traffic volumes and traffic density were associated with increased all-cause mortality in patients undergoing treatment for active tuberculosis even after adjusting for multiple demographic, socioeconomic, and clinical factors, suggesting that TB patients are susceptible to the adverse health effects of traffic-related air pollution. https://doi.org/10.1289/EHP1699

Bi-directional modulation of AMPA receptor unitary conductance by synaptic activity

BACKGROUND: Knowledge of how synapses alter their efficiency of communication is central to the understanding of learning and memory. The most extensively studied forms of synaptic plasticity are long-term potentiation (LTP) and its counterpart long-term depression (LTD) of AMPA receptor-mediated synaptic transmission. In the CA1 region of the hippocampus, it has been shown that LTP often involves a rapid increase in the unitary conductance of AMPA receptor channels. However, LTP can also occur in the absence of any alteration in AMPA receptor unitary conductance. In the present study we have used whole-cell dendritic recording, failures analysis and non-stationary fluctuation analysis to investigate the mechanism of depotentiation of LTP. RESULTS: We find that when LTP involves an increase in unitary conductance, subsequent depotentiation invariably involves the return of unitary conductance to pre-LTP values. In contrast, when LTP does not involve a change in unitary conductance then depotentiation also occurs in the absence of any change in unitary conductance, indicating a reduction in the number of activated receptors as the most likely mechanism. CONCLUSIONS: These data show that unitary conductance can be bi-directionally modified by synaptic activity. Furthermore, there are at least two distinct mechanisms to restore synaptic strength from a potentiated state, which depend upon the mechanism of the previous potentiation

Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations

Understanding and control of structures and rates involved in protein-ligand binding are es- sential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot di- rectly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25−109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescales using simulations of an all-atom MD model, with high accuracy and pre- cision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissoci- ation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.Funding is acknowledged by European Commission (ERC StG “pcCells” to F.N.), Deutsche Forschungsgemeinschaft (SFB 1114/C3, SFB 740/D7, and TRR 186/A12 to F.N. and SFB 1114/A4 to F.N. and T.W.). J.C. is a Wellcome Trust Senior Research Fellow (WT 095195MA). J.S. is a Marie Sklodowska-Curie Internationally outgoing fellow. M.D.C. is supported by a Biotechnology and Biological Sciences Research Council (BBSRC) studentship

A robotic system for steel bridge maintenance: Research challenges and system design

This paper presents the research on and development of a robotic system for stripping paint and rust from steel bridges, with the ultimate objective of preventing human exposure to hazardous and dangerous debris (containing rust, paint particles, lead and/or asbestos), relieving human workers from labor intensive tasks and reducing costs associated with bridge maintenance. The robot system design, the key research challenges and enabling technologies and system development are discussed in detail. Research results obtained so far and discussions on some key issues are also presented

Methods to estimate acclimatization to urban heat island effects on heat- and cold-related mortality

Background: Investigators have examined whether heat mortality risk is increased in neighborhoods subject to the urban heat island (UHI) effect but have not identified degrees of difference in susceptibility to heat and cold between cool and hot areas, which we call acclimatization to the UHI. Objectives: We developed methods to examine and quantify the degree of acclimatization to heat- and cold-related mortality in relation to UHI anomalies and applied these methods to London, UK. Methods: Case–crossover analyses were undertaken on 1993–2006 mortality data from London UHI decile groups defined by anomalies from the London average of modeled air temperature at a 1-km grid resolution. We estimated how UHI anomalies modified excess mortality on cold and hot days for London overall and displaced a fixed-shape temperature-mortality function (“shifted spline” model). We also compared the observed associations with those expected under no or full acclimatization to the UHI. Results: The relative risk of death on hot versus normal days differed very little across UHI decile groups. A 1°C UHI anomaly multiplied the risk of heat death by 1.004 (95% CI: 0.950, 1.061) (interaction rate ratio) compared with the expected value of 1.070 (1.057, 1.082) if there were no acclimatization. The corresponding UHI interaction for cold was 1.020 (0.979, 1.063) versus 1.030 (1.026, 1.034) (actual versus expected under no acclimatization, respectively). Fitted splines for heat shifted little across UHI decile groups, again suggesting acclimatization. For cold, the splines shifted somewhat in the direction of no acclimatization, but did not exclude acclimatization. Conclusions: We have proposed two analytical methods for estimating the degree of acclimatization to the heat- and cold-related mortality burdens associated with UHIs. The results for London suggest relatively complete acclimatization to the UHI effect on summer heat–related mortality, but less clear evidence for cold–related mortality

Enhanced cosmic-ray flux toward zeta Persei inferred from laboratory study of H3+ - e- recombination rate

The H3+ molecular ion plays a fundamental role in interstellar chemistry, as it initiates a network of chemical reactions that produce many interstellar molecules. In dense clouds, the H3+ abundance is understood using a simple chemical model, from which observations of H3+ yield valuable estimates of cloud path length, density, and temperature. On the other hand, observations of diffuse clouds have suggested that H3+ is considerably more abundant than expected from the chemical models. However, diffuse cloud models have been hampered by the uncertain values of three key parameters: the rate of H3+ destruction by electrons, the electron fraction, and the cosmic-ray ionisation rate. Here we report a direct experimental measurement of the H3+ destruction rate under nearly interstellar conditions. We also report the observation of H3+ in a diffuse cloud (towards zeta Persei) where the electron fraction is already known. Taken together, these results allow us to derive the value of the third uncertain model parameter: we find that the cosmic-ray ionisation rate in this sightline is forty times faster than previously assumed. If such a high cosmic-ray flux is indeed ubiquitous in diffuse clouds, the discrepancy between chemical models and the previous observations of H3+ can be resolved.Comment: 6 pages, Nature, in pres

Primary central nervous system lymphomas: Indian experience, and review of literature

Primary central nervous system lymphomas (PCNSLs) are a rare form of non-Hodgkin\u2032s lymphoma which arise within and remain confined primarily to the central nervous system (CNS). They generally account for 1-2% of all primary brain tumors and are reported to be on the rise due to the Acquired Immune Deficiency Syndrome (AIDS) epidemic. Aims and Objectives: To study the clinicopathological and immunophenotypic characteristics of PCNSLs and look for any differences in PCNSLs reported in India from those in other countries. Materials and Methods : All cases of PCNSLs between January 1998 and December 2006 were reviewed. Presence of lymphadenopathy, organomegaly and bone marrow study was done to exclude the possibility of secondary involvement by lymphoma. The diagnosis was confirmed by histopathology with Hematoxylin and Eosin and reticulin stains. Immunohistochemistry (IHC) with leucocyte common antigen (LCA), CD 20 and CD 3 was performed on available blocks. The immune status was evaluated by clinical examination and human immunodeficiency virus (HIV) serology (since 1996). Results : In a 19-year study period, there were 56 patients of PCNSLs, accounting for 1.07% of all intracranial neoplasms. The patients ranged from 10-75 years of age with a median age of 42 years. Barring one patient who was HIV positive, all the others were immunocompetent. All cases were diffuse large cell lymphomas on histopathology. IHC with LCA and CD 20 revealed positivity in 100% and 86.4% cases respectively. There was a single case of CD 3 positive T-cell lymphoma. In the present study, PCNSLs occurred in young immunocompetent patients and majority were diffuse large B cell lymphomas

Primary central nervous system lymphomas: Indian experience, and review of literature

Primary central nervous system lymphomas (PCNSLs) are a rare form of non-Hodgkin\u2032s lymphoma which arise within and remain confined primarily to the central nervous system (CNS). They generally account for 1-2% of all primary brain tumors and are reported to be on the rise due to the Acquired Immune Deficiency Syndrome (AIDS) epidemic. Aims and Objectives: To study the clinicopathological and immunophenotypic characteristics of PCNSLs and look for any differences in PCNSLs reported in India from those in other countries. Materials and Methods : All cases of PCNSLs between January 1998 and December 2006 were reviewed. Presence of lymphadenopathy, organomegaly and bone marrow study was done to exclude the possibility of secondary involvement by lymphoma. The diagnosis was confirmed by histopathology with Hematoxylin and Eosin and reticulin stains. Immunohistochemistry (IHC) with leucocyte common antigen (LCA), CD 20 and CD 3 was performed on available blocks. The immune status was evaluated by clinical examination and human immunodeficiency virus (HIV) serology (since 1996). Results : In a 19-year study period, there were 56 patients of PCNSLs, accounting for 1.07% of all intracranial neoplasms. The patients ranged from 10-75 years of age with a median age of 42 years. Barring one patient who was HIV positive, all the others were immunocompetent. All cases were diffuse large cell lymphomas on histopathology. IHC with LCA and CD 20 revealed positivity in 100% and 86.4% cases respectively. There was a single case of CD 3 positive T-cell lymphoma. In the present study, PCNSLs occurred in young immunocompetent patients and majority were diffuse large B cell lymphomas

Interactions between downslope flows and a developing cold-air pool

A numerical model has been used to characterize the development of a region of enhanced cooling in an alpine valley with a width of order (Formula presented.) km, under decoupled stable conditions. The region of enhanced cooling develops largely as a region of relatively dry air which partitions the valley atmosphere dynamics into two volumes, with airflow partially trapped within the valley by a developing elevated inversion. Complex interactions between the region of enhanced cooling and the downslope flows are quantified. The cooling within the region of enhanced cooling and the elevated inversion is almost equally partitioned between radiative and dynamic effects. By the end of the simulation, the different valley atmospheric regions approach a state of thermal equilibrium with one another, though this cannot be said of the valley atmosphere and its external environment.Peer reviewe