Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity.

Cyanobacterial carboxysomes encapsulate carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Genetic deletion of the major structural proteins encoded within the ccm operon in Synechococcus sp. PCC 7002 (ΔccmKLMN) disrupts carboxysome formation and significantly affects cellular physiology. Here we employed both metabolite pool size analysis and isotopically nonstationary metabolic flux analysis (INST-MFA) to examine metabolic regulation in cells lacking carboxysomes. Under high CO2 environments (1%), the ΔccmKLMN mutant could recover growth and had a similar central flux distribution as the control strain, with the exceptions of moderately decreased photosynthesis and elevated biomass protein content and photorespiration activity. Metabolite analyses indicated that the ΔccmKLMN strain had significantly larger pool sizes of pyruvate (>18 folds), UDPG (uridine diphosphate glucose), and aspartate as well as higher levels of secreted organic acids (e.g., malate and succinate). These results suggest that the ΔccmKLMN mutant is able to largely maintain a fluxome similar to the control strain by changing in intracellular metabolite concentrations and metabolite overflows under optimal growth conditions. When CO2 was insufficient (0.2%), provision of acetate moderately promoted mutant growth. Interestingly, the removal of microcompartments may loosen the flux network and promote RuBisCO side-reactions, facilitating redirection of central metabolites to competing pathways (i.e., pyruvate to heterologous lactate production). This study provides important insights into metabolic regulation via enzyme compartmentation and cyanobacterial compensatory responses.

Measurement and modeling of CO2 solubility in natural and synthetic formation brines for CO2 sequestration.

CO2 solubility data in the natural formation brine, synthetic formation brine, and synthetic NaCl+CaCl2 brine were collected at the pressures from 100 to 200 bar, temperatures from 323 to 423 K. Experimental results demonstrate that the CO2 solubility in the synthetic formation brines can be reliably represented by that in the synthetic NaCl+CaCl2 brines. We extended our previously developed model (PSUCO2) to calculate CO2 solubility in aqueous mixed-salt solution by using the additivity rule of the Setschenow coefficients of the individual ions (Na(+), Ca(2+), Mg(2+), K(+), Cl(-), and SO4(2-)). Comparisons with previously published models against the experimental data reveal a clear improvement of the proposed PSUCO2 model. Additionally, the path of the maximum gradient of the CO2 solubility contours divides the P-T diagram into two distinct regions: in Region I, the CO2 solubility in the aqueous phase decreases monotonically in response to increased temperature; in region II, the behavior of the CO2 solubility is the opposite of that in Region I as the temperature increases.

Life history and bionomics of Glycobius speciosus (Coleoptera: Cerambycidae: Cerambycinae: Clytini).

Glycobius speciosus (Say) was studied in New York State to elucidate poorly known aspects of its biology. Head capsule size from excavated larvae coupled with gallery lengths measured at the time of excavation was used to characterize larval development. Partial life tables indicated nearly 20% of G. speciosus survive to adulthood. Larvae experienced 30% of their mortality during early development, 27% during mid-larval development, and 43% during late larval development. Predation by hairy woodpeckers, Dryobates villosus (Linnaeus) (Piciformes: Picidae), the only unambiguous source of mortality, accounted for 43% mortality in naturally infested trees located and followed 2004-2009, and 74% late instar mortality. One parasitoid, Dolichomitus irritator (Fabricius) (Hymenoptera: Ichneumonidae), was recovered from a single larva. Beetles emerged between 316 accumulated DD (base 10 °C) and 648 DD. Males emerged prior to, or simultaneously with, females and lived longer. Female fecundity averaged 41.3 ± 6 eggs. Larval eclosion occurred 7-10 days after oviposition. Non-functional ovipositors observed in 16% of females represented an appreciable reproductive loss. In 77% of infested trees 1 oviposition site was located and in 70% of oviposition sites examined only 1 or 2 larvae successfully eclosed, penetrated the bark to the phloem-xylem interface, and began feeding. Beetles preferred southern and eastern aspects for oviposition which occurred preferentially on the lower bole (<20 cm). Male beetles had longer and wider antennae than females, pronotal pits containing gland pores, and a straight to concave posterior margin of the terminal sternite compared to the more rounded margin of females.

The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study.

Untargeted lipidomics allows analysis of a broader range of lipids than targeted methods and permits discovery of unknown compounds. Previous ring trials have evaluated the reproducibility of targeted lipidomics methods, but inter-laboratory comparison of compound identification and unknown feature detection in untargeted lipidomics has not been attempted. To address this gap, five laboratories analyzed a set of mammalian tissue and biofluid reference samples using both their own untargeted lipidomics procedures and a common chromatographic and data analysis method. While both methods yielded informative data, the common method improved chromatographic reproducibility and resulted in detection of more shared features between labs. Spectral search against the LipidBlast in silico library enabled identification of over 2,000 unique lipids. Further examination of LC-MS/MS and ion mobility data, aided by hybrid search and spectral networking analysis, revealed spectral and chromatographic patterns useful for classification of unknown features, a subset of which were highly reproducible between labs. Overall, our method offers enhanced compound identification performance compared to targeted lipidomics, demonstrates the potential of harmonized methods to improve inter-site reproducibility for quantitation and feature alignment, and can serve as a reference to aid future annotation of untargeted lipidomics data.

Reduced mortality: the unexpected impact of a telephone-based care management intervention for older adults in managed care.

OBJECTIVE: This analysis evaluated mortality over 24 months for Medicare managed care members who participated in the Care Advocate Program (CA Program) designed to link those with high health care utilization to home- and community-based services. DATA SOURCE: Secondary data from the CA Program, part of the California HealthCare Foundation's Elders in Managed Care Initiative. STUDY DESIGN: Randomized-control trial in which participants (N=781) were randomly assigned to intent-to-treat (ITT) and control groups. ITT group received telephonic social care management and 12 months of follow-up. Various multivariate analyses were used to evaluate mortality risk throughout multiple study periods controlling for sociodemographic characteristics, health status, and health care utilization. POPULATION STUDIED: Older adults (65+) enrolled in a Medicare managed care plan who had high health care utilization in the previous year. PRINCIPAL FINDINGS: ITT group had a significantly lower odds of mortality throughout the study (OR=0.55; p=.005) and during the care management intervention (OR=0.45; p=.006), whereas differential risk in the postintervention period was not statistically significant. Other significant predictors of mortality were age, gender, three chronic conditions (cancer, heart disease, and kidney disease), and emergency room utilization. CONCLUSIONS: Findings suggest that the care advocate model of social care management affected mortality while the program was in progress, but not after completion of the intervention phase. Key model elements accounted for the findings, which include individualized targeting, assessment, and monitoring; consumer choice, control, and participant self-management; and bridging medical and social service delivery systems through direct linkages and communication.

Monitoring populations of saddled prominent (Lepidoptera: Notodontidae) with pheromone-baited traps.

Field trials with three types of pheromone traps were performed in eight northern hardwood stands in northern New York state to develop a population-monitoring tool for the saddled prominent, Heterocampa guttivitta (Walker) (Lepidoptera: Notodontidae). Lure specificity and the relationship between pheromone trap catch and subsequent egg density were examined. A study of moth emergence in relation to temperature was designed to determine whether moth activity throughout the flight season can be predicted using a growing degree-day (DD) model. Pherocon 1C wing traps were significantly more effective than the green Unitrap bucket style. Catch was not affected by position when traps were > or =20 m from an opening (road), and lures were specific to saddled prominent. Lure specificity was examined using green Multipher bucket traps, which effectively attracted and held moths. In the first year of the study, number of viable eggs per 10 leaf clusters was significantly correlated (r2 = 0.59) with average moth catch/trap in pheromone-baited Pherocon traps. When differences in stand density (basal area) and relative abundance of sugar maple (percentage of total stems per hectare), the principle host, were accounted for, the multiple regression model also was significant and r2 = 0. 83. Neither model, however, was significant the second year. Using a base temperature of 5.5 degrees C and on-site temperature data, the peak of moth flight occurred at 316 +/- 8 DD and end of flight occurred at 533 +/- 9 DD.

Multi-century record of anthropogenic impacts on an urbanized mesotidal estuary: Salem Sound, MA.

Salem, MA, located north of Boston, has a rich, well-documented history dating back to settlement in 1626 CE, but the associated anthropogenic impacts on Salem Sound are poorly constrained. This project utilized dated sediment cores from the sound to assess the proxy record of anthropogenic alterations to the system and compared the proxy records to the known history. Proxies included bulk stable isotopes of organic matter, magnetic susceptibility, and trace metal concentrations. Our data reveal clear changes in organic matter composition and concentration associated with land use changes and twentieth century sewage disposal practices. Further, metals data correspond with local industrial activity, particularly the historic tanning industry in Peabody, MA. Although conservation practices of past decades have improved the state of Salem Sound, the stratigraphic record demonstrates that the environment is still affected by anthropogenic influences, and has not attained conditions consistent with pre-anthropogenic baseline. The approach and results of this study are applicable to coastal embayments that are being assessed for remediation, especially those with scant historic or monitoring data.

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.

Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.

Reductions in costly healthcare service utilization: findings from the Care Advocate Program.

OBJECTIVES: To determine whether a telephone care-management intervention for high-risk Medicare health maintenance organization (HMO) health plan enrollees can reduce costly medical service utilization. DESIGN: Randomized, controlled trial measuring healthcare services utilization over three 12-month periods (pre-, during, and postintervention). SETTING: Two social service organizations partnered with a Medicare HMO and four contracted medical groups in southern California. PARTICIPANTS: Eight hundred twenty-three patients aged 65 and older; eligibility was determined using an algorithm to target older adults with high use of insured healthcare services. INTERVENTION: After assessment, members in the intervention group were offered mutually agreed upon referrals to home- and community-based services (HCBS), medical groups, or Medicare HMO health plan and followed monthly for 1 year. MEASUREMENTS: Insured medical service utilization was measured across three 12-month periods. Acceptance and utilization of Care Advocate (CA) referrals were measured during the 12-month intervention period. RESULTS: CA intervention members were significantly more likely than controls to use primary care physician services (odds ratio (OR)=2.05, P<.001), and number of hospital admissions (OR=0.43, P<.01) and hospital days (OR=0.39, P<.05) were significantly more stable for CA group members than for controls. CONCLUSION: Results suggest that a modest intervention linking older adults to HCBS may have important cost-saving implications for HMOs serving community-dwelling older adults with high healthcare service utilization. Future studies, using a national sample, should verify the role of telephone care management in reducing the use of costly medical services.

Aging with cardiopulmonary disease: the rehab perspective.

Cardiac disease is a leading cause of disability. This article reviews the epidemiology, pathophysiology, and risk factors for coronary heart disease. We explore the latest research in risk stratification, exercise training, and screening for cardiac rehabilitation in the elderly patient. The rehabilitation specialist will see how this select population differs in their medical and rehabilitative needs.

Partnering managed care and community-based services for frail elders: the care advocate program.

OBJECTIVES: To describe a demonstration program that uses master's-level care managers (care advocates) to link Medicare managed care enrollees to home- and community-based services, testing whether referrals to noninsured services can reduce service usage and increase member satisfaction and retention. DESIGN: Using an algorithm designed to target frail, high-cost users of Medicare insured healthcare services, the program partners PacifiCare's Secure Horizons and four of its medical groups with two social service organizations. SETTING: Three care advocates located in two community-based social services agencies using telephone interviews to interact with targeted elders living in the community. PARTICIPANTS: Three hundred ninety PacifiCare members aged 69 to 96 receiving care from four PacifiCare-contracted medical groups. INTERVENTION: The 12-month intervention provides telephone assessment, links to eight types of home- and community-based services, and monthly follow-up contacts. MEASUREMENTS: Sociodemographic characteristics of intervention participants, types of service referrals, and acceptance rates. RESULTS: Lessons learned included the importance of building a shared vision among partners, building on existing relationships between members and providers, and building trust without face-to-face interactions. CONCLUSION: The program builds on current insured case management services and offers a practical bridge to community-based services.

Isotopomer measurement techniques in metabolic flux analysis II: mass spectrometry.

Mass spectrometry (MS) offers a sensitive, reliable, and highly accurate method for measurement of isotopic labeling, which is required for generating comprehensive flux maps using metabolic flux analysis (MFA). We present protocols for assessing isotope labeling in a wide range of biochemical species, including proteinogenic amino acids, free organic and amino acids, sugar phosphates, lipids, starch-glucose, and RNA-ribose. We describe the steps of sample preparation, MS analysis, and data handling required to obtain high-quality isotope labeling measurements that are applicable to MFA. By selecting target analytes that maximize identifiability of the key fluxes of interest, MS measurements of isotope labeling can provide a powerful platform for assessing metabolic fluxes in complex biochemical networks.

Nontraditional families and childhood progress through school: a comment on Rosenfeld.

We reexamine Rosenfeld's (2010) study on the association between child outcomes and same-sex family structure. Using the same data set, we replicate and generalize Rosenfeld's findings and show that the implications of his study are different when using either alternative comparison groups or alternative sample restrictions. Compared with traditional married households, we find that children being raised by same-sex couples are 35 % less likely to make normal progress through school; this difference is statistically significant at the 1 % level.

Equivalent latitude computation using regions of interest (ROI).

This paper introduces a novel algorithm to compute equivalent latitude by applying regions of interest (ROI). The technique is illustrated using code written in Interactive Data Language (IDL). The ROI method is compared with the "piecewise-constant" method, the approach commonly used in atmospheric sciences, using global fields of atmospheric potential vorticity. The ROI method is considerably more accurate and computationally faster than the piecewise-constant method, and it also works well with irregular grids. Both the ROI and piecewise-constant IDL codes for equivalent latitude are included as a useful reference for the research community.

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

BACKGROUND: Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem. RESULTS: Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches. CONCLUSION: Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.

Sequestration of dissolved CO2 in the Oriskany formation.

Experiments were conducted to determine the solubility of CO2 in a natural brine solution of the Oriskany formation under elevated temperature and pressure conditions. These data were collected at temperatures of 22 and 75 degrees C and pressures between 100 and 450 bar. Experimentally determined data were compared with CO2 solubility predictions using a model developed by Duan and Sun (Chem. Geol. 2003, 193, 257-271). Model results compare well with Oriskany brine CO2 solubility data collected experimentally, suggesting that the Duan and Sun model is a reliable tool for estimating solution CO2 capacity in high salinity aquifers in the temperature and pressure range evaluated. The capacity for the Oriskany formation to sequester dissolved CO2 was calculated using results of the solubility models, estimation of the density of CO2 saturated brine, and available geographic information system (GIS) information on the formation depth and thickness. Results indicate that the Oriskany formation can hold approximately 0.36 gigatonnes of dissolved CO2 if the full basin is considered. When only the region where supercritical CO2 can exist (temperatures greaterthan 31 degrees C and pressures greaterthan 74 bar) is considered, the capacity of the Oriskany formation to sequester dissolved CO2 is 0.31 gigatonnes. The capacity estimate considering the potential to sequester free-phase supercritical CO2 if brine were displaced from formation pore space is 8.8 gigatonnes in the Oriskany formation.

Risks and complications of neuraxial anesthesia and the use of anticoagulation in the surgical patient.

Recognition of the risk of thromboembolic phenomena to patients in the postsurgical period has resulted in the practice of administering prophylactic anticoagulant agents to those patients who are at high risk for this complication. Institution of a perioperative anticoagulant or antithrombotic protocol needs to be considered when a regional anesthetic is proposed as part of, or as the total, anesthetic management of the patient. This article reviews current data on the risks involved in the use of neuraxial regional anesthesia in the care of surgical patients in whom prophylactic thromboembolic anticoagulant therapy is planned. Guidelines are established to help the physician minimize the risks of a neuraxial hematoma forming, monitor the patient for this complication, and optimally treat him or her if a hematoma were to occur.