Identification and characterisation of ncRNAs in dormant bacteria

Recent years have led to increasing interest and appreciation of the possible importance of single cell heterogeneity in various biological processes. One of the examples of phenotypic heterogeneity in bacterial populations is antibiotic tolerant persister cells. Such an antibiotic tolerance phenotype is of considerable clinical relevance since dormant bacteria can re-establish infections rapidly after the antibiotic treatment has been terminated. Up to now mechanisms for establishing the persistence phenomenon in bacteria have remained largely enigmatic. Persisters are cells considered to be in a dormant state with down regulated gene expression. Only recently small regulatory RNAs (sRNAs) have been appreciated as important regulators of gene expression in response to environmental stimuli and several theoretical studies have suggested a possible involvement of sRNAs in the mechanisms of regulated heterogeneity in bacteria. We have experimentally addressed this potential link between sRNAs and persistence/dormancy in E. coli as an example of heterogeneity. Beside classical sRNAs we are focusing also on sRNAs directly associating with and possibly regulating the ribosome, the central enzyme of gene expression. The persister and dormant cell specific sRNA profile is studied by the comparative analysis of sRNA profile changes of the whole bacterial population after antibiotic killing. From RNA-Seq data ~ 25 000 potentially stable RNA fragments were identified and initial analysis predicted ~300 of them to be dormant/persister cell specific. After further evaluation the most prominent dormant/persister cell specific sRNAs are functionally characterized and their potential role in the persistence/dormancy will be evaluated by applying genetic, molecular and biochemical tools. The potential results of this project will provide a better understanding on the molecular mechanism of bacterial persistence/dormancy and on the role of ribosome-bound sRNA molecules in fine-tuning gene expression.

Identification and characterisation of ncRNAs in dormant bacteria

Recent years have led to increasing interest and appreciation of the possible importance of single cell heterogeneity in various biological processes. One of the examples of phenotypic heterogeneity in bacterial populations is antibiotic tolerant persister cells. Such an antibiotic tolerance phenotype is of considerable clinical relevance since dormant bacteria can re-establish infections rapidly after the antibiotic treatment has been terminated. Up to now mechanisms for establishing the persistence phenomenon in bacteria have remained largely enigmatic. Persisters are cells considered to be in a dormant state with down regulated gene expression. Only recently small regulatory RNAs (sRNAs) have been appreciated as important regulators of gene expression in response to environmental stimuli and several theoretical studies have suggested a possible involvement of sRNAs in the mechanisms of regulated heterogeneity in bacteria. We have experimentally addressed this potential link between sRNAs and persistence/dormancy in E. coli as an example of heterogeneity. Beside classical sRNAs we are focusing also on sRNAs directly associating with and possibly regulating the ribosome, the central enzyme of gene expression. The persister and dormant cell specific sRNA profile is studied by the comparative analysis of sRNA profile changes of the whole bacterial population after antibiotic killing. From RNA-Seq data ~ 25 000 potentially stable RNA fragments were identified and initial analysis predicted ~300 of them to be dormant/persister cell specific. After further evaluation the most prominent dormant/persister cell specific sRNAs are functionally characterized and their potential role in the persistence/dormancy will be evaluated by applying genetic, molecular and biochemical tools. The potential results of this project will provide a better understanding on the molecular mechanism of bacterial persistence/dormancy and on the role of ribosome-bound sRNA molecules in fine-tuning gene expression.

Identification and characterisation of ncRNAs in dormant bacteria

Recent years have led to increasing interest and appreciation of the possible importance of single cell heterogeneity in various biological processes. One of the examples of phenotypic heterogeneity in bacterial populations is antibiotic tolerant persister cells. Such an antibiotic tolerance phenotype is of considerable clinical relevance since dormant bacteria can re-establish infections rapidly after the antibiotic treatment has been terminated. Up to now mechanisms for establishing the persistence phenomenon in bacteria have remained largely enigmatic. Persisters are cells considered to be in a dormant state with down regulated gene expression. Only recently small regulatory RNAs (sRNAs) have been appreciated as important regulators of gene expression in response to environmental stimuli and several theoretical studies have suggested a possible involvement of sRNAs in the mechanisms of regulated heterogeneity in bacteria. We have experimentally addressed this potential link between sRNAs and persistence/dormancy in E. coli as an example of heterogeneity. Beside classical sRNAs we are focusing also on sRNAs directly associating with and possibly regulating the ribosome, the central enzyme of gene expression. The persister and dormant cell specific sRNA profile is studied by the comparative analysis of sRNA profile changes of the whole bacterial population after antibiotic killing. From RNA-Seq data ~ 25 000 potentially stable RNA fragments were identified and initial analysis predicted ~300 of them to be dormant/persister cell specific. After further evaluation the most prominent dormant/persister cell specific sRNAs are functionally characterized and their potential role in the persistence/dormancy will be evaluated by applying genetic, molecular and biochemical tools. The potential results of this project will provide a better understanding on the molecular mechanism of bacterial persistence/dormancy and on the role of ribosome-bound sRNA molecules in fine-tuning gene expression.

Completeness of Follow-Up Determines Validity of Study Findings: Results of a Prospective Repeated Measures Cohort Study.

BACKGROUND Current reporting guidelines do not call for standardised declaration of follow-up completeness, although study validity depends on the representativeness of measured outcomes. The Follow-Up Index (FUI) describes follow-up completeness at a given study end date as ratio between the investigated and the potential follow-up period. The association between FUI and the accuracy of survival-estimates was investigated. METHODS FUI and Kaplan-Meier estimates were calculated twice for 1207 consecutive patients undergoing aortic repair during an 11-year period: in a scenario A the population's clinical routine follow-up data (available from a prospective registry) was analysed conventionally. For the control scenario B, an independent survey was completed at the predefined study end. To determine the relation between FUI and the accuracy of study findings, discrepancies between scenarios regarding FUI, follow-up duration and cumulative survival-estimates were evaluated using multivariate analyses. RESULTS Scenario A noted 89 deaths (7.4%) during a mean considered follow-up of 30±28months. Scenario B, although analysing the same study period, detected 304 deaths (25.2%, P<0.001) as it scrutinized the complete follow-up period (49±32months). FUI (0.57±0.35 versus 1.00±0, P<0.001) and cumulative survival estimates (78.7% versus 50.7%, P<0.001) differed significantly between scenarios, suggesting that incomplete follow-up information led to underestimation of mortality. Degree of follow-up completeness (i.e. FUI-quartiles and FUI-intervals) correlated directly with accuracy of study findings: underestimation of long-term mortality increased almost linearly by 30% with every 0.1 drop in FUI (adjusted HR 1.30; 95%-CI 1.24;1.36, P<0.001). CONCLUSION Follow-up completeness is a pre-requisite for reliable outcome assessment and should be declared systematically. FUI represents a simple measure suited as reporting standard. Evidence lacking such information must be challenged as potentially flawed by selection bias.

Assessment of the nonoperated root after apical surgery of the other root in mandibular molars: a 5-year follow-up study

INTRODUCTION If a surgical approach is chosen to treat a multirooted tooth affected by persistent periapical pathosis, usually only the affected roots are operated on. The present study assessed the periapical status of the nonoperated root 5 years after apical surgery of the other root in mandibular molars. METHODS Patients treated with apical surgery of mandibular molars with a follow-up of 5 years were selected. Patient-related and clinical parameters (sex, age, smoking, symptoms, and signs of infection) before surgery were recorded. Preoperative intraoral periapical radiographs and radiographs 5 years after surgery were examined. The following data were collected: tooth, operated root, type and quality of the coronal restoration, marginal bone level, length and homogeneity of the root canal filling, presence of a post/screw, periapical index (PAI) of each root, and radiographic healing of the operated root. The presence of apical pathosis of the nonoperated root was analyzed statistically in relation to the recorded variables. RESULTS Thirty-seven patients fulfilled the inclusion criteria. Signs of periapical pathosis in the nonoperated root 5 years after surgery (PAI ≥ 3) could be observed in only 3 cases (8.1%). Therefore, statistical analysis in relation to the variables was not possible. The PAI of the nonoperated root before surgery had a weak correlation with signs of apical pathosis 5 years after surgery. CONCLUSIONS Nonoperated roots rarely developed signs of new apical pathosis 5 years after apical surgery of the other root in mandibular molars. It appears reasonable to resect and fill only roots with a radiographically evident periapical lesion.

Follow-up care of young childhood cancer survivors: attendance and parental involvement.

PURPOSE Despite recommendations, only a proportion of long-term childhood cancer survivors attend follow-up care. We aimed to (1) describe the follow-up attendance of young survivors aged 11-17 years; (2) describe the parental involvement in follow-up, and (3) investigate predictors of follow-up attendance and parental involvement. METHODS As part of the Swiss Childhood Cancer Survivor Study, a follow-up questionnaire was sent to parents of childhood cancer survivors aged 11-17 years. We assessed follow-up attendance of the child, parents' involvement in follow-up, illness perception (Brief IPQ), and sociodemographic data. Clinical data was available from the Swiss Childhood Cancer Registry. RESULTS Of 309 eligible parents, 189 responded (67 %; mean time since diagnosis 11.3 years, range 6.8-17.2) and 75 % (n = 141) reported that their child still attended follow-up. Of these, 83 % (n = 117) reported ≥1 visit per year and 17 % (n = 23) reported <1 visit every year. Most survivors saw pediatric oncologists (n = 111; 79 % of 141), followed by endocrinologists (n = 24, 17 %) and general practitioners (n = 22, 16 %). Most parents (92 %) reported being involved in follow-up (n = 130). In multivariable and Cox regression analyses, longer time since diagnosis (p = 0.025) and lower perceived treatment control (assessed by IPQ4: how much parents thought follow-up can help with late effects; p = 0.009) were associated with non-attendance. Parents' overall information needs was significantly associated with parental involvement in the multivariable model (p = 0.041). CONCLUSION Educating survivors and their parents on the importance and effectiveness of follow-up care might increase attendance in the longer term.

Cosmic-ray exposure ages of pallasites

We analyzed cosmogenic nuclides in metal and/or silicate (primarily olivine) separated from the main-group pallasites Admire, Ahumada, Albin, Brahin, Brenham, Esquel, Finmarken, Glorieta Mountain, Huckitta, Imilac, Krasnojarsk, Marjalahti, Molong, Seymchan, South Bend, Springwater, and Thiel Mountains and from Eagle Station. The metal separates contained an olivine fraction which although small, <1 wt% in most cases, nonetheless contributes significantly to the budgets of some nuclides (e.g., up to 35% for Ne-21 and Al-26). A correction for olivine is therefore essential and was made using model calculations and/or empirical relations for the production rates of cosmogenic nuclides in iron meteoroids and/or measured elemental concentrations. Cosmic-ray exposure (CRE) ages for the metal phases of the main-group pallasites range from 7 to 180 Ma, but many of the ages cluster around a central peak near 100 Ma. These CRE ages suggest that the parent body of the main-group pallasites underwent a major break-up that produced most of the meteorites analyzed. The CRE age distribution for the pallasites overlaps only a small fraction of the distribution for the IIIAB iron meteorites. Most pallasites and IIIAB irons originated in different collisions, probably on different parent bodies; a few IIIABs and pallasites may have come out of the same collision but a firm conclusion requires further study. CRE ages calculated from noble gas and radionuclide data of the metal fraction are higher on average than the Ne-21 exposure ages obtained for the olivine samples. As the metal and olivine fractions were taken in most cases from different specimens, the depth-dependency of the production rate ratio Be-10/Ne-21 in metal, not accounted for in our calculations, may explain the difference.

Are Some Indian Bank Too Large? A Examination of Size Efficiency in Indian Banking

In this paper we use data from the years 1997 through 2003 to evaluate the size efficiency of Indian banks. Following Maindiratta (1990) we consider a bank to be too large if breaking it up into a number of smaller units would result in a larger output bundle than what could be produced from the same input by a single bank. When this is the case, the bank is not size efficient. Our analysis shows that many of the banks are, in deed, too large in various years. We also find that often a bank is operating in the region of diminishing returns to scale but is not a candidate for break up.

Federally regulated institutional review boards: The aspects of a "model" IRB---Is the current system in need of a tune up or complete overhaul?

Institutional Review Boards (IRBs) are the primary gatekeepers for the protection of ethical standards of federally regulated research on human subjects in this country. This paper focuses on what general, broad measures that may be instituted or enhanced to exemplify a "model IRB". This is done by examining the current regulatory standards of federally regulated IRBs, not private or commercial boards, and how many of those standards have been found either inadequate or not generally understood or followed. The analysis includes suggestions on how to bring about changes in order to make the IRB process more efficient, less subject to litigation, and create standardized educational protocols for members. The paper also considers how to include better oversight for multi-center research, increased centralization of IRBs, utilization of Data Safety Monitoring Boards when necessary, payment for research protocol review, voluntary accreditation, and the institution of evaluation/quality assurance programs. ^ This is a policy study utilizing secondary analysis of publicly available data. Therefore, the research for this paper focuses on scholarly medical/legal journals, web information from the Department of Health and Human Services, Federal Drug Administration, and the Office of the Inspector General, Accreditation Programs, law review articles, and current regulations applicable to the relevant portions of the paper. ^ Two issues are found to be consistently cited by the literature as major concerns. One is a need for basic, standardized educational requirements across all IRBs and its members, and secondly, much stricter and more informed management of continuing research. There is no federally regulated formal education system currently in place for IRB members, except for certain NIH-based trials. Also, IRBs are not keeping up with research once a study has begun, and although regulated to do so, it does not appear to be a great priority. This is the area most in danger of increased litigation. Other issues such as voluntary accreditation and outcomes evaluation are slowing gaining steam as the processes are becoming more available and more sought after, such as JCAHO accrediting of hospitals. ^ Adopting the principles discussed in this paper should promote better use of a local IRBs time, money, and expertise for protecting the vulnerable population in their care. Without further improvements to the system, there is concern that private and commercial IRBs will attempt to create a monopoly on much of the clinical research in the future as they are not as heavily regulated and can therefore offer companies quicker and more convenient reviews. IRBs need to consider the advantages of charging for their unique and important services as a cost of doing business. More importantly, there must be a minimum standard of education for all IRB members in the area of the ethical standards of human research and a greater emphasis placed on the follow-up of ongoing research as this is the most critical time for study participants and may soon lead to the largest area for litigation. Additionally, there should be a centralized IRB for multi-site trials or a study website with important information affecting the trial in real time. There needs to be development of standards and metrics to assess the performance of the IRBs for quality assurance and outcome evaluations. The boards should not be content to run the business of human subjects' research without determining how well that function is actually being carried out. It is important that federally regulated IRBs provide excellence in human research and promote those values most important to the public at large.^

Metabolic syndrome and cardiovascular mortality among participants of the hypertension detection and follow-up program

Metabolic Syndrome (MetS) is a clustering of cardiovascular (CV) risk factors that includes obesity, dyslipidemia, hyperglycemia, and elevated blood pressure. Applying the criteria for MetS can serve as a clinically feasible tool for identifying patients at high risk for CV morbidity and mortality, particularly those who do not fall into traditional risk categories. The objective of this study was to examine the association between MetS and CV mortality among 10,940 American hypertensive adults, ages 30-69 years, participating in a large randomized controlled trial of hypertension treatment (HDFP 1973-1983). MetS was defined as the presence of hypertension and at least two of the following risk factors: obesity, dyslipidemia, or hyperglycemia. Of the 10,763 individuals with sufficient data available for analysis, 33.2% met criteria for MetS at baseline. The baseline prevalence of MetS was significantly higher among women (46%) than men (22%) and among non-blacks (37%) versus blacks (30%). All-cause and CV mortality was assessed for 10,763 individuals. Over a median follow-up of 7.8 years, 1,425 deaths were observed. Approximately 53% of these deaths were attributed to CV causes. Compared to individuals without MetS at baseline, those with MetS had higher rates of all-cause mortality (14.5% v. 12.6%) and CV mortality (8.2% versus 6.4%). The unadjusted risk of CV mortality among those with MetS was 1.31 (95% confidence interval [CI], 1.12-1.52) times that for those without MetS at baseline. After multiple adjustment for traditional risk factors of age, race, gender, history of cardiovascular disease (CVD), and smoking status, individuals with MetS, compared to those without MetS, were 1.42 (95% CI, 1.20-1.67) times more likely to die of CV causes. Of the individual components of MetS, hyperglycemia/diabetes conferred the strongest risk of CV mortality (OR 1.73; 95% CI, 1.39-2.15). Results of the present study suggest MetS defined as the presence of hypertension and 2 additional cardiometabolic risk factors (obesity, dyslipidemia, or hyperglycemia/diabetes) can be used with some success to predict CV mortality in middle-aged hypertensive adults. Ongoing and future prospective studies are vital to examine the association between MetS and cardiovascular morbidity and mortality in select high-risk subpopulations, and to continue evaluating the public health impact of aggressive, targeted screening, prevention, and treatment efforts to prevent future cardiovascular disability and death.^

Sedimentological and clay mineralogical analysis of ODP sites in the central Fram Strait

This study presents the results of high-resolution sedimentological and clay mineralogical investigations on sediments from ODP Sites 908A and 909AlC located in the central Fram Strait. The objective was to reconstruct the paleoclimate and paleoceanography of the high northern latitudes since the middle Miocene. The sediments are characterised in particular by a distinctive input of ice-rafted material, which most probably occurs since 6 Ma and very likely since 15 Ma. A change in the source area at 1 1.2 Ma is clearly marked by variations within clay mineral composition and increasing accumulation rates. This is interpreted as a result of an increase in water mass exchange through the Fram Strait. A further period of increasing exchange between 4-3 Ma is identified by granulometric investigations and points to a synchronous intensification of deep water production in the North Atlantic during this time interval. A comparison of the components of coarse and clay fraction clearly shows that both are not delivered by the Same transport process. The input of the clay fraction can be related to transport mechanisms through sea ice and glaciers and very likely also through oceanic currents. A reconstruction of source areas for clay minerals is possible only with some restrictions. High smectite contents in middle and late Miocene sediments indicate a background signal produced by soil formation together with sediment input, possibly originating from the Greenland- Scotland Ridge. The applicability of clay mineral distribution as a climate proxy for the high northern latitudes can be confirmed. Based on a comparison of sediments from Site 909C, characterised by the smectite/illite and chlorite ratio, with regional and global climatic records (oxygen isotopes), a middle Miocene cooling phase between 14.8-14.6 Ma can be proposed. A further cooling phase between 10-9 Ma clearly shows similarities in its Progress toward drastic decrease in carbonate sedimentation and preservation in the eastern equatorial Pacific. The modification in sea water and atmosphere chemistry may represent a possible link due to the built-up of equatorial carbonate platforms. Between 4.8-4.6 Ma clay mineral distribution indicates a distinct cooling trend in the Fram Strait region. This is not accompanied by relevant glaciation, which would otherwise be indicated by the coarse fraction. The intensification of glaciation in the northern hemisphere is distinctly documented by a rapid increase of illite and chlorite starting from 3.3 Ma, which corresponds to oxygen isotope data trends from North Atlantic.

Chemical characteristics of coal pebbles and Barzas-type coals

Coal pebbles found in 1994 in the Greham Bell Island (Franz Josef Land Archipelago) are made up of Barzas-type cuticular liptobiolith. The coal belongs to the initial stage of catagenesis and is characterized by high content of cutinite (up to 70%) with very low reflectance (Ro = 0.1%). Maceration products show some tegillate elements of Arthropoda and individual Devonian spores. It is supposed that plant cuticle and Arthropoda exocuticle are present in this coal. Obtained data suggest presence of Paleozoic rocks in the sedimentary sequence, although they are not yet recovered. These data complement available information on distribution of specific Devonian coals and allow to have a new insight into zoogenic material involved in coal formation.

Stable carbon and oxygen isotope record of foraminifera of IODP Site 303-1307

A major tipping point of Earth's history occurred during the mid-Pliocene: the onset of major Northern-Hemisphere Glaciation (NHG) and of pronounced, Quaternary-style cycles of glacial-to-interglacial climates, that contrast with more uniform climates over most of the preceding Cenozoic and continue until today (Zachos et al., 2001, doi:10.1126/science.1059412). The severe deterioration of climate occurred in three steps between 3.2 Ma (warm MIS K3) and 2.7 Ma (glacial MIS G6/4) (Lisiecki and Raymo, 2005, doi:10.1029/2004PA001071). Various models (sensu Driscoll and Haug, 1998, doi:10.1126/science.282.5388.436) and paleoceanographic records (intercalibrated using orbital age control) suggest clear linkages between the onset of NHG and the three steps in the final closure of the Central American Seaways (CAS), deduced from rising salinity differences between Caribbean and the East Pacific. Each closing event led to an enhanced North Atlantic meridional overturning circulation and this strengthened the poleward transport of salt and heat (warmings of +2-3°C) (Bartoli et al., 2005, doi:10.1016/j.epsl.2005.06.020). Also, the closing resulted in a slight rise in the poleward atmospheric moisture transport to northwestern Eurasia (Lunt et al., 2007, doi:10.1007/s00382-007-0265-6), which probably led to an enhanced precipitation and fluvial run-off, lower sea surface salinity (SSS), and an increased sea-ice cover in the Arctic Ocean, hence promoting albedo and the build-up of continental ice sheets. Most important, new evidence shows that the closing of the CAS led to greater steric height of the North Pacific and thus doubled the low-saline Arctic Throughflow from the Bering Strait to the East Greenland Current (EGC). Accordingly, Labrador Sea IODP Site 1307 displays an abrupt but irreversible EGC cooling of 6°C and freshening by ~2 psu from 3.25/3.16-3.00 Ma, right after the first but still reversible attempt of closing the CAS.

Nd, Pb, and Be isotopes of ferromanaganese crusts of the South Pacific

The application of radiogenic isotopes to the study of Cenozoic circulation patterns in the South Pacific Ocean has been hampered by the fact that records from only equatorial Pacific deep water have been available. We present new Pb and Nd isotope time series for two ferromanganese crusts that grew from equatorial Pacific bottom water (D137-01, 'Nova', 7219 m water depth) and southwest Pacific deep water (63KD, 'Tasman', 1700 m water depth). The crusts were dated using 10Be/9Be ratios combined with constant Co-flux dating and yield time series for the past 38 and 23 Myr, respectively. The surface Nd and Pb isotope distributions are consistent with the present-day circulation pattern, and therefore the new records are considered suitable to reconstruct Eocene through Miocene paleoceanography for the South Pacific. The isotope time series of crusts Nova and Tasman suggest that equatorial Pacific deep water and waters from the Southern Ocean supplied the dissolved trace metals to both sites over the past 38 Myr. Changes in the isotopic composition of crust Nova are interpreted to reflect development of the Antarctic Circumpolar Current and changes in Pacific deep water circulation caused by the build up of the East Antarctic Ice Sheet. The Nd isotopic composition of the shallower water site in the southwest Pacific appears to have been more sensitive to circulation changes resulting from closure of the Indonesian seaway.

Chlorophyll a concentration and zooplankton abundance and biomass below melting sea ice in the Amundsen Gulf

Early summer in the Arctic with extensive ice melt and break-up represents a dramatic change for sympagic-pelagic fauna below seasonal sea ice. As part of the International Polar Year-Circumpolar Flaw Lead system study (IPY-CFL), this investigation quantified zooplankton in the meltwater layer below landfast ice and remaining ice fauna below melting ice during June (2008) in Franklin Bay and Darnley Bay, Amundsen Gulf, Canada. The ice was in a state of advanced melt, with fully developed melt ponds. Intense melting resulted in a 0.3- to 0.5-m-thick meltwater layer below the ice, with a strong halocline to the Arctic water below. Zooplankton under the ice, in and below the meltwater layer, was sampled by SCUBA divers. Dense concentrations (max. 1,400 ind./m**3) of Calanus glacialis were associated with the meltwater layer, with dominant copepodid stages CIV and CV and high abundance of nauplii. Less abundant species included Pseudocalanus spp., Oithona similis and C. hyperboreus. The copepods were likely feeding on phytoplankton (0.5-2.3 mg Chl-a/m**3) in the meltwater layer. Ice amphipods were present at low abundance (<10 ind./m**2) and wet biomass (<0.2 g/m**2). Onisimus glacialis and Apherusa glacialis made up 64 and 51% of the total ice faunal abundance in Darnley Bay and Franklin Bay, respectively. During early summer, the autochthonous ice fauna becomes gradually replaced by allochthonous zooplankton, with an abundance boom near the meltwater layer. The ice amphipod bust occurs during late stages of melting and break-up, when their sympagic habitat is diminished then lost.