Arterial Blood Gases in Normal Subjects at 2240 Meters Above Sea Level: Impact of Age, Gender, and Body Mass Index.

Background: The values of arterial blood gases (ABG) change with altitude above sea level; empirical verification is essential because ventilatory acclimatization varies with ethnicity and a population's adaptation. Objective: The aim of the study was to describe ABG in a healthy population residing at 2,240 meters above sea level, to identify the mean level of alveolar ventilation (PaCO2), and to know whether a progressive increase in PaCO2 occurs with age and the impact of increasing body mass index (BMI). Methods: We conducted a cross-sectional study in a referral center for respiratory diseases in Mexico City. Associations among variables with correlation coefficient and regression models of PaO2, SaO2, and P(A-a)O2 as dependent variables as a function of age, BMI, minute ventilation, or breathing frequency were explored. Results: Two hundred and seventeen healthy subjects were evaluated with a mean age of 40 ± 15 years, mean of the PaO2 was 71 ± 6 mmHg, SaO2 94% ± 1.6%, PaCO2 30.2 ± 3.4 mmHg, HCO3 20 ± 2 mmol/L, BE-2.9 ± 1.9 mmol/L, and the value of pH was 7.43 ± 0.02. In a linear regression, the main results were PaO2 = 77.5-0.16*age (p < 0.0001) and with aging P(A-a)O2 tended to increase 0.12 mmHg/year. PaCO2 in women increased with age by 0.075 mmHg/year (p = 0.0012, PaCO2 =26.3 + 0.075*age). SaO2 and PaO2 decreased significantly in women with higher BMI 0.14% and 0.52 mmHg per kg/m2, (p = 0.004 and 0.002 respectively). Conclusion: Mean PaCO2 was 30.7 mmHg, implying a mean alveolar ventilation of around 30% above that at sea level.

Arterial Blood Gases in Normal Subjects at 2240 Meters Above Sea Level: Impact of Age, Gender, and Body Mass Index

ABSTRACT Background The values of arterial blood gases (ABG) change with altitude above sea level; empirical verification is essential because ventilatory acclimatization varies with ethnicity and a population's adaptation. Objective The aim of the study was to describe ABG in a healthy population residing at 2,240 meters above sea level, to identify the mean level of alveolar ventilation (PaCO2), and to know whether a progressive increase in PaCO2 occurs with age and the impact of increasing body mass index (BMI). Methods We conducted a cross-sectional study in a referral center for respiratory diseases in Mexico City. Associations among variables with correlation coefficient and regression models of PaO2, SaO2, and P(A-a)O2 as dependent variables as a function of age, BMI, minute ventilation, or breathing frequency were explored. Results Two hundred and seventeen healthy subjects were evaluated with a mean age of 40 ± 15 years, mean of the PaO2 was 71 ± 6 mmHg, SaO2 94% ± 1.6%, PaCO2 30.2 ± 3.4 mmHg, HCO3 20 ± 2 mmol/L, BE-2.9 ± 1.9 mmol/L, and the value of pH was 7.43 ± 0.02. In a linear regression, the main results were PaO2 = 77.5-0.16*age (p < 0.0001) and with aging P(A-a)O2 tended to increase 0.12 mmHg/year. PaCO2 in women increased with age by 0.075 mmHg/year (p = 0.0012, PaCO2 =26.3 + 0.075*age). SaO2 and PaO2 decreased significantly in women with higher BMI 0.14% and 0.52 mmHg per kg/m2, (p = 0.004 and 0.002 respectively). Conclusion Mean PaCO2 was 30.7 mmHg, implying a mean alveolar ventilation of around 30% above that at sea level.

Comparing Spirometric Reference Values From Childhood to Old Age Estimated by LMS and Linear Regression Models / Comparación de los valores de referencia espirométrica de la infancia a la vejez estimada mediante el método LMS y modelos de regresión lineal

Background: Proper reference values for lung function testing are essential for achieving adequate interpretations. The LMS procedure (lambda, mu, sigma) permits continuous analyses of entire populations avoiding gaps in the transition between childhood and adulthood. It also allows more precise calculations of average values, dispersion, and 5th percentiles, which are usually considered the lower limit of normality. The objective of this study was to compare our results fitted with the LMS method with standard multiple linear regression, and with those from international Global Lung Function Initiative (GLI) equations.Methods: Data from 9835 healthy residents of the metropolitan area of Mexico City aged 8–80 years were compiled from several studies: EMPECE, PLATINO, adult Mexican workers and two unpublished studies. The LMS procedure and multiple linear regression models were fit to obtain reference equations using R software.Results: Residuals from the LMS models had a median closer to zero, and smaller dispersion than those from the linear model, but differences although statistically significant were very small and of questionable practical relevance. For example, for females and ln(FEV1), median residual was −0.001 with p25 of −0.08 and p75 of 0.08 for LMS, compared with 0.004 (−0.08, 0.09) [p<0.05] for the linear model. Average spirometric values for a given height for our population, were higher than those predicted by the GLI study.Conclusion: Continuous reference equations for the Mexican population calculated using the LMS technique showed slightly better fit than linear regression models. (AU)

Contexto general: Unos valores de referencia apropiados para las pruebas de la función pulmonar son esenciales para realizar unas interpretaciones adecuadas. El método LMS (lambda, mu, sigma) permite realizar análisis continuos de poblaciones enteras evitando brechas en la transición entre la infancia y la edad adulta. También permite cálculos más precisos de valores medios, dispersiones y percentiles 5, que generalmente se consideran el límite inferior de la normalidad. El objetivo de este estudio fue comparar nuestros resultados ajustados con el método LMS con la regresión lineal múltiple estándar y con los de las ecuaciones internacionales de la Iniciativa Global de Función Pulmonar (GLI).Métodos: Se recopilaron datos de 9.835 residentes sanos del área metropolitana de la Ciudad de México con edades comprendidas entre 8 y 80 años a partir de varios estudios: EMPECE, PLATINO, trabajadores adultos mexicanos y 2 estudios no publicados. El método LMS y los modelos de regresión lineal múltiple se ajustaron para obtener ecuaciones de referencia utilizando el software R.Resultados:Los residuos de los modelos LMS tuvieron una mediana más cercana a cero y una dispersión menor que las del modelo lineal, pero las diferencias, aunque estadísticamente significativas, fueron muy pequeñas y de una relevancia práctica cuestionable. Por ejemplo, para las mujeres y el ln(FEV1), la mediana residual fue de −0,001 con p25 de −0,08 y p75 de 0,08 para LMS, en comparación con 0,004 (−0,08, 0,09) (p<0,05) para el modelo lineal. Los valores espirométricos medios para una altura dada para nuestra población fueron más altos que los pronosticados por el estudio GLI.Conclusión: Las ecuaciones de referencia continua para la población mexicana calculadas usando la técnica LMS mostraron un ajuste ligeramente mejor que los modelos de regresión lineal. (AU)

Comparing Spirometric Reference Values From Childhood to Old Age Estimated by LMS and Linear Regression Models.

BACKGROUND: Proper reference values for lung function testing are essential for achieving adequate interpretations. The LMS procedure (lambda, mu, sigma) permits continuous analyses of entire populations avoiding gaps in the transition between childhood and adulthood. It also allows more precise calculations of average values, dispersion, and 5th percentiles, which are usually considered the lower limit of normality. The objective of this study was to compare our results fitted with the LMS method with standard multiple linear regression, and with those from international Global Lung Function Initiative (GLI) equations. METHODS: Data from 9835 healthy residents of the metropolitan area of Mexico City aged 8-80 years were compiled from several studies: EMPECE, PLATINO, adult Mexican workers and two unpublished studies. The LMS procedure and multiple linear regression models were fit to obtain reference equations using R software. RESULTS: Residuals from the LMS models had a median closer to zero, and smaller dispersion than those from the linear model, but differences although statistically significant were very small and of questionable practical relevance. For example, for females and ln(FEV1), median residual was -0.001 with p25 of -0.08 and p75 of 0.08 for LMS, compared with 0.004 (-0.08, 0.09) [p<0.05] for the linear model. Average spirometric values for a given height for our population, were higher than those predicted by the GLI study. CONCLUSION: Continuous reference equations for the Mexican population calculated using the LMS technique showed slightly better fit than linear regression models.

Simulación con paciente estandarizado y simuladores de baja fidelidad (PESiBaF) como primer acercamiento a un paciente en estudiantes de primer año de la carrera de médico cirujano / Standardised patient simulation and low fidelity simulators (PESiBaF) as a first approach to a patient in first year students of the medicine degree

En la actualidad, la medicina incorpora diferentes recursos y estrategias para mejorar la educación que brinda a los estudiantes, entre ellas las actividades de aprendizaje por simulación. La simulación trae consigo varios beneficios, pero para ello es necesario saber implementarla y contar con los recursos necesarios, y además, tener claros los objetivos de aprendizaje que se plantearán en esta y valorar qué tan útil resulta para el participante. Retomando lo anterior, se realizó un estudio descriptivo en el que participaron estudiantes de primer año de la licenciatura de médico cirujano de la Facultad de Medicina de la UNAM, quienes, a través de la simulación, tuvieron un acercamiento introductorio a la importancia de la relación médico-paciente y aprendieron la técnica de exploración ginecológica en una actividad dividida en 3 fases, utilizando pacientes estandarizados y simuladores de baja fidelidad. Al término de la actividad, esta fue evaluada por los participantes mediante una lista de cotejo clasificada en 4rubros para conocer su perspectiva, que ayudará a mejorar la calidad de la simulación planteada y a saber si el estudiante considera que ha adquirido habilidades propias del médico

Medicine currently incorporates different resources and strategies to improve the education it provides to students, including simulation-based activities. Simulation brings several benefits, but for this it is necessary to know how to implement it and have the necessary resources, as well as having clear learning objectives that will be raised in it and assess how useful it is for the participant. With this objective, a descriptive study was conducted in which first year medical students of the UNAM's Faculty of Medicine participated. Using the simulation, they had an introductory approach to the importance of the doctor-patient relationship, and learned the technique of gynaecological examination in an activity that was divided into 3 phases, using standardised patients and low fidelity simulation models. At the end, this was evaluated by the participants through a checklist classified into 4areas in order to determine their perspective. This would help improve the quality of the simulation and to determine if the students consider that they have acquired their doctor skills

Shorter corridors can be used for the six-minute walk test in subjects with chronic lung diseases.

BACKGROUND: The main limitation of the six-minute walk test (6-MWT) is that not all pulmonary function testing facilities have an indoor flat, 30-m-long corridor. Therefore, this study aimed 1) to evaluate the correlation and agreement of the distances walked in 30-m- vs. 15-m-long corridors by subjects with chronic lung diseases (CLD group) and 2) to compare the levels of oxygen saturation (nSpO2), blood pressure (BP), heart rate recovery at minute one post-exercise (HRR1), and Borg scale scores for dyspnea and fatigue between the two distances walked. METHODS: A prospective, cross-sectional study was conducted at the National Institute of Respiratory Diseases in Mexico City. Subjects with chronic lung diseases and healthy adults were invited to participate. The distance of the 6-MWT was randomly assigned based on whether the first test was in the 15-m or 30-m corridor. RESULTS: Ninety individuals were included; the correlation in meters walked between the two corridors was r = 0.96 in CLD; the 95% limits of agreement for the 6-MWT ranged from -73 to +37 m. Most subjects walked further in the 30-m corridor (82%); however, the percent predicted values for the CLD group were 3.5% lower for the 15-m corridor than the 30-m corridor. Only 10.5% of the subjects with CLD would have been falsely classified as having a normal 6-MWT (false negative). No significant differences in the nSpO2, Borg scale, BP or HRR1 were found between the two 6-MWT corridor lengths. CONCLUSION: The 6-MWT can be performed using a 15-m corridor in subjects with CLD, and the results for the distance walked, HRR1, nSpO2, and Borg scale scores are similar to between the 15-m and 30-m corridors.

Inspiratory Capacity and Vital Capacity of Healthy Subjects 9-81 Years of Age at Moderate-High Altitude.

BACKGROUND: Measurements of inspiratory capacity (IC) and vital capacity (VC) are used to recognize dynamic hyperinflation, but appropriate reference values are required to achieve accurate clinical interpretations. Altitude above sea level is a potential determining factor for lung volumes, including IC and VC. OBJECTIVE: To describe IC and VC for healthy people who live in Mexico City at an altitude of 2,240 m above sea level. METHODS: Healthy subjects ages 9-81 y completed slow spirometry by following 2005 American Thoracic Society/European Respiratory Society standards. Once associations were explored, linear regression models were constructed and values were compared with those from previously published equations. RESULTS: A total of 441 healthy subjects (55.1% women) participated. The mean age was 32 y (minimum age, 9 y; maximum age, 81 y). IC and VC measurements were associated with sex, age, height, and weight. An accelerated increase in IC and VC was evident from 9 to 20 y of age, followed by a gradual decrease in both sexes. In general, IC was higher in our population than predicted by previously published reference equations. CONCLUSIONS: IC in healthy people at 2,240 m above sea level was higher than that of previous reports about European and Latin-American subjects of the same height, sex, and age who were at sea level. The present study provided robust reference values for persons who lived at a moderate altitude.

Diffusing Capacity of the Lung for Carbon Monoxide in Mexican/Latino Children. Quality Control and Reference Values.

RATIONALE: Single-breath diffusing capacity of the lung for carbon monoxide (DlCOsb) values are used to evaluate gas exchange; however, the quality of maneuvers performed by children has not been evaluated, and reference values for young people living at moderate altitudes are not well established. OBJECTIVES: Our objectives were 1) to determine whether DlCOsb maneuvers performed by a pediatric population would meet 2017 European Respiratory Society/American Thoracic Society (ERS/ATS) quality control standards; and 2) to report normal DlCOsb values for Mexican/Latino children and adolescents living at moderate altitudes. METHODS: This study involved healthy young people 4-20 years of age from the metropolitan area of Mexico City (2,240 m above sea level) who were recruited in schools from July 2014 to August 2017. DlCOsb testing was performed according to the 2005 ATS/ERS standards, and the quality control of each maneuver was analyzed according to the 2017 ERS/ATS standards. We constructed models for DlCOsb with linear and quadratic terms for weight, height, and age as independent variables using shrinkage statistics, variance inflation factors, the Akaike information criterion, and R2 to compare the results of different models. RESULTS: Results were obtained for 420 individuals (53% boys) with a mean age of 11.7 ± 4.5 standard deviation (SD) years; 47% of maneuvers from children age 4-6 years were grade A (13% grade B), and 90% of those in children older than 13 years were grade A or B. Forty-six percent of the subjects had a DlCOsb repeatability of <1 ml/min/mm Hg. The mean DlCOsb was higher for boys than for girls (32.4 ± 13.6 [SD] vs. 24.1 ± 7.5 ml/min/mm Hg, respectively). The reference equation for boys was DlCOsb = exp(1.63469 + [0.03251 × age] + [0.00846 × height] + [0.00304 × weight]), R2 = 0.87; for girls, the best equation was DlCOsb = exp(1.56516 + [0.0193 × age] + [0.00893 × height] + [0.00273 × weight]), R2 = 0.75. The single-breath transfer coefficient of the lung for carbon monoxide remained constant with age and height, with a lower limit of normal of 6.5 ml/min/mm Hg/L in boys and 5.4 ml/min/mm Hg/L in girls. Measured DlCOsb was higher than predicted by other authors (P < 0.001 by paired t test). CONCLUSIONS: Individuals 4-20 years of age can complete high-quality DlCOsb tests. Children and adolescents living at 2,240 m have higher DlCOsb values than those living at sea level. Reference equations for DlCOsb obtained at sea level are poor predictors of the values measured at moderate altitude.

Maximum Voluntary Ventilation in a Population Residing at 2,240 Meters Above Sea Level.

BACKGROUND: Measured maximum voluntary ventilation (MVV) correlates with maximum ventilatory capacity during exercise. As a shortcut, MVV is often estimated by multiplying measured FEV1 times 35 or 40, but this index varies with altitude due to reduced air density. The objective was to describe MVV in healthy individuals residing at 2,240 m above sea level and compare it with the reference values customarily employed. METHODS: We recruited a convenience sample of respiratory-healthy, non-obese volunteers >10 y of age who had resided for >2 y in Mexico City. All participants performed forced spirometry and MVV according to current standards. Multiple regression models were fitted, including age, height, and measured FEV1, separately for males and females to obtain reference values. The impact of lower air density on MVV at this elevation was estimated from the reported increase in peak flow in relation to altitude. RESULTS: We studied 381 individuals (210 females [55.1%]) age 10-80 y with a mean MVV of 145.6 ± 48 L/min. Both FEV1 × 35 and FEV1 × 40 underestimated the MVV observed: in males by approximately 26% and in females by approximately 10%. MVV for our population approached FEV1 × 45 (98 ± 15.6% of real MVV). Multiple regression models including height, weight, and measured FEV1 explained 70% of residual variability once sex was taken into account. CONCLUSIONS: At an altitude of 2,240 m, MVV is about 45 times the measured FEV1, and it can be estimated for other altitudes. The best predicting equations for MVV were calculated separately for females and males and included the following predictors: age, age2, and measured FEV1. The study found that reference values for MVV from studies conducted at sea level are inaccurate at this altitude.

Validating Reference Equations for Impulse Oscillometry in Healthy Mexican Children.

BACKGROUND: The impulse oscillometry system (IOS) measures the impedance (Z) of the respiratory system, but proper interpretation of its results requires adequate reference values. The objectives of this work were: (1) to validate the reference equations for the IOS published previously by our group and (2) to compare the adjustment of new available reference equations for the IOS from different countries in a sample of healthy children. METHODS: Subjects were healthy 4-15-y-old children from the metropolitan area of Mexico City, who performed an IOS test. The functional IOS parameters obtained were compared with the predicted values from 12 reference equations determined in studies of different ethnic groups. The validation methods applied were: analysis of the differences between measured and predicted values for each reference equation; correlation and concordance coefficients; adjustment by Z-score values; percentage of predicted value; and the percentage of patients below the lower limit of normality or above the upper limit of normality. RESULTS: Of the 224 participants, 117 (52.3%) were girls, and the mean age was 8.6 ± 2.3 y. The equations that showed the best adjustment for the different parameters were those from the studies by Nowowiejska et al (2008) and Gochicoa et al (2015). The equations proposed by Frei et al (2005), Hellinckx et al (1998), Kalhoff et al (2011), Klug and Bisgaard (1998), de Assumpção et al (2016), and Dencker et al (2006) overestimated the airway resistance of the children in our sample, whereas the equation of Amra et al (2008) underestimated it. In the analysis of the lower and upper limits of normality, Gochicoa et al equation was the closest, since 5% of subjects were below or above percentiles 5 and 95, respectively. The study found that, in general, all of the equations showed greater error at the extremes of the age distribution. CONCLUSIONS: Because of the robust adjustment of the present study reference equations for the IOS, it can be recommended for both clinical and research purposes in our population. The differential adjustment of other equations underlines the need to obtain local reference values.

Changes in liver proteins of rats fed standard and high-fat and sucrose diets induced by fish omega-3 PUFAs and their combination with grape polyphenols according to quantitative proteomics.

This study considered the physiological modulation of liver proteins due to the supplementation with fish oils under two dietary backgrounds: standard or high in fat and sucrose (HFHS), and their combination with grape polyphenols. By using a quantitative proteomics approach, we showed that the capacity of the supplements for regulating proteins depended on the diet; namely, 10 different proteins changed into standard diets, while 45 changed into the HFHS diets and only scarcely proteins were found altered in common. However, in both contexts, fish oils were the main regulatory force, although the addition of polyphenols was able to modulate some fish oils' effects. Moreover, we demonstrated the ability of fish oils and their combination with grape polyphenols in improving biochemical parameters and reducing lipogenesis and glycolysis enzymes, enhancing fatty acid beta-oxidation and insulin signaling and ameliorating endoplasmic reticulum stress and protein oxidation when they are included in an unhealthy diet.

Long-Term Stability of a Portable Carbon Monoxide Single-Breath Diffusing Capacity Instrument.

BACKGROUND: The 2005 American Thoracic Society/European Respiratory Society guidelines for single-breath diffusing capacity of the lung for carbon monoxide (DLCO) recommend a weekly biological control test and/or DLCO simulator to detect instrument error drift. Very little has been published regarding the results of such a quality assurance program. Our aim was to analyze the long-term stability of a portable DLCO instrument. METHODS: We used a new EasyOne Pro system and checked its accuracy using a DLCO simulator with 2 reference gases (concentration A: carbon monoxide [CO] = 0.1% and helium = 6.52%; concentration B: CO = 0.08% and helium = 7.21%) during the first 3 y of use in our large clinical laboratory. To detect instrument drift, a healthy woman (MSC), age 43 y old at baseline, tested herself every week during this period of time. RESULTS: More than 6,000 spirometry and 5,000 DLCO maneuvers were done using this instrument for patients during these 3 y. There were no failures in the daily volume and flow checks or the CO and helium calibration checks performed automatically by the instrument. The differences between the simulator DLCO and the measured DLCO were -0.91 ± 1.33 mL/min/mm Hg and -0.61 ± 1.45 mL/min/mm Hg for concentration A and concentration B, respectively. The results of the 110 biological control tests were: mean 30.8 ± 1.7 mL/min/mm Hg (95% CI 30.5-31.1), coefficient of variation of 5.4% in DLCO, and repeatability of 2.5 mL/min/mm Hg. Only 4 measurements were outside ±3 mL/min/mm Hg (3.6%). Her mean alveolar volume was 4.2 ± 0.25 L with coefficient of variation of 6.2%; her inspired volume was 3.05 ± 0.14 L, and coefficient of variation = 4.5%. CONCLUSIONS: Measurements of DLCO were stable over the 3-y period without any need for manual recalibration of the instrument. The biological control was as good as the DLCO simulator to evaluate this kind of device in a long-term laboratory quality control program.

SIRPα-Antibody Fusion Proteins Selectively Bind and Eliminate Dual Antigen-Expressing Tumor Cells.

PURPOSE: CD47 is highly expressed on a variety of tumor cells. The interaction of CD47 with signal regulatory protein alpha (SIRPα), a protein on phagocytic cells, transmits a "don't eat me" signal that negatively regulates phagocytosis. CD47-SIRPα antagonists enable phagocytosis by disrupting the inhibitory signal and can synergize with Fc-mediated pro-phagocytic signals for potent elimination of tumor cells. A potential limitation of therapeutic CD47-SIRPα antagonists is that expression of CD47 on normal cells may create sites of toxicity or an "antigen sink." To overcome these limitations and address selective tumor targeting, we developed SIRPabodies to improve the therapeutic benefits of CD47-SIRPα blockade specifically toward tumor. EXPERIMENTAL DESIGN: SIRPabodies were generated by grafting the wild-type SIRPα either to the N-terminus or to the C-terminus of the heavy chain of rituximab. Selective tumor binding was tested using CFSE-labeled human primary CLL cells in the presence of 20-fold excess of human RBCs. NSG mice were transplanted with Raji-luciferase cells and were assigned to controls versus SIRPabody treatment. Cynomolgus nonhuman primates were administered a single intravenous infusion of SIRPabody at 3, 10, or 30 mg/kg. RESULTS: SIRPabodies selectively bound to dual antigen-expressing tumor cells in the presence of a large antigen sink. SIRPabody reduced tumor burden and extended survival in mouse xenograft lymphoma models. SIRPabody caused no significant toxicity in nonhuman primates. CONCLUSIONS: These findings establish SIRPabodies as a promising approach to deliver the therapeutic benefit of CD47-SIRPα blockade specifically toward tumor cells. SIRPabodies may be applied to additional cancer types by grafting SIRPα onto other tumor-specific therapeutic antibodies. Clin Cancer Res; 22(20); 5109-19. ©2016 AACR.

A bispecific antibody targeting CD47 and CD20 selectively binds and eliminates dual antigen expressing lymphoma cells.

Agents that block the anti-phagocytic signal CD47 can synergize with pro-phagocytic anti-tumor antigen antibodies to potently eliminate tumors. While CD47 is overexpressed on cancer cells, its expression in many normal tissues may create an 'antigen sink' that could minimize the therapeutic efficacy of CD47 blocking agents. Here, we report development of bispecific antibodies (BsAbs) that co-target CD47 and CD20, a therapeutic target for non-Hodgkin lymphoma (NHL), that have reduced affinity for CD47 relative to the parental antibody, but retain strong binding to CD20. These characteristics facilitate selective binding of BsAbs to tumor cells, leading to phagocytosis. Treatment of human NHL-engrafted mice with BsAbs reduced lymphoma burden and extended survival while recapitulating the synergistic efficacy of anti-CD47 and anti-CD20 combination therapy. These findings serve as proof of principle for BsAb targeting of CD47 with tumor-associated antigens as a viable strategy to induce selective phagocytosis of tumor cells and recapitulate the synergy of combination antibody therapy. This approach may be broadly applied to cancer to add a CD47 blocking component to existing antibody therapies.

Identification of Toxoplasma gondii antigens associated with different types of infection by serum antibody profiling.

Acquisition of acute toxoplasmosis during the first trimester of pregnancy can have catastrophic consequences for the foetus. Diagnosis is routinely based on the detection of maternal Toxoplasma gondii--antibodies using whole parasite extracts as detection antigen. While such assays are sensitive, they show no specificity for the stage of infection. We hypothesized diagnosis might be improved using recombinant antigens for detection, particularly if antibodies to certain antigen(s) were associated with early or late stages of infection. To address this, protein microarrays comprising 1513 T. gondii exon products were probed with well-characterized sera from seronegative ('N') controls, and acute ('A'), chronic/IgM-persisting ('C/M') and chronic ('C') toxoplasmosis cases from Turkey. Three reactive exon products recognized preferentially in A infections, and three recognized preferentially in C/M infections, were expressed in Escherichia coli and tested for discrimination in IgG ELISAs. The best discriminators were exon 1 of TGME49_086450 (GRA5) which detected C/M infections with 70.6% sensitivity and 81.8% specificity, and exon 6 of TGME49_095700 (ubiquitin transferase domain-containing protein) which detected A infections with 84.8% sensitivity and 82.4% specificity. Overall, the data support a recombinant protein approach for the development of improved serodiagnostic tests for toxoplasmosis.

Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.

Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.

Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.

The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate using derivatized nano-particles, and subsequent identification by mass spectrometry. Candidate genes encoding these proteins were cloned and expressed in Escherichia coli, and the recombinant proteins were purified and characterized biochemically and their biochemical parameters compared with the native ones. These proteins include a guanosine triphosphate (GTP) cyclohydrolase (HP0959), an ATPase (HP1079), an adenosine deaminase (HP0267), a phosphodiesterase (HP1042), an aminopeptidase (HP1037), and new substrates were characterized for a peptidoglycan deacetylase (HP0310). Generally, characterized enzymes were active at acidic to neutral pH (4.0-7.5) with temperature optima ranging from 35 to 55°C, although some exhibited outstanding characteristics.

Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.

Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.

O-GlcNAc modification of the coat protein of the potyvirus Plum pox virus enhances viral infection.

O-GlcNAcylation is a dynamic protein modification which has been studied mainly in metazoans. We reported previously that an Arabidopsis thaliana O-GlcNAc transferase modifies at least two threonine residues of the Plum pox virus (PPV) capsid protein (CP). Now, six additional residues were shown to be involved in O-GlcNAc modification of PPV CP. CP O-GlcNAcylation was abolished in the PPV CP7-T/A mutant, in which seven threonines were mutated. PPV CP7-T/A infected Nicotiana clevelandii, Nicotiana benthamiana, and Prunus persica without noticeable defects. However, defects in infection of A. thaliana were readily apparent. In mixed infections of wild-type arabidopsis, the CP7-T/A mutant was outcompeted by wild-type virus. These results indicate that CP O-GlcNAcylation has a major role in the infection process. O-GlcNAc modification may have a role in virion assembly and/or stability as the CP of PPV CP7-T/A was more sensitive to protease digestion than that of the wild-type virus.

Inhibition of Sox2 Expression in the Adult Neural Stem Cell Niche In Vivo by Monocationic-based siRNA Delivery.

RNA interference (RNAi) is a major tool for basic and applied investigations. However, obtaining RNAi data that have physiological significance requires investigation of regulations and therapeutic strategies in appropriate in vivo settings. To examine in vivo gene regulation and protein function in the adult neural stem cell (NSC) niche, we optimized a new non-viral vector for delivery of siRNA into the subventricular zone (SVZ). This brain region contains the neural stem and progenitor cells populations that express the stem cell marker, SOX2. Temporally and spatially controlled Sox2 knockdown was achieved using the monocationic lipid vector, IC10. siRNA/IC10 complexes were stable over time and smaller (<40 nm) than jetSi complexes (≈400 nm). Immunocytochemistry showed that siRNA/IC10 complexes efficiently target both the progenitor and stem cell populations in the adult SVZ. Injection of the complexes into the lateral brain ventricle resulted in specific knockdown of Sox2 in the SVZ. Furthermore, IC10-mediated transient in vivo knockdown of Sox2-modulated expression of several genes implicated in NSC maintenance. Taken together, these data show that IC10 cationic lipid formulation can efficiently vectorize siRNA in a specific area of the adult mouse brain, achieving spatially and temporally defined loss of function.Molecular Therapy-Nucleic Acids (2013) 2, e89; doi:10.1038/mtna.2013.8; published online 23 April 2013.