Search for Low-Molecular-Weight Biomarkers in Plant Tissues and Seeds Using Metabolomics: Tools, Strategies, and Applications

This chapter summarises the metabolomic strategies currently in force used in plant science and describes the methods used. The metabolite profiling and fingerprinting of plant tissues through MS- and/or NMR-based approaches and the subsequent identification of biomarkers is detailed. Strategies for the microisolation and de novo identification of unknown biomarkers are also discussed. The various approaches are illustrated by a metabolomic study of the maize response to herbivory. A review of recent metabolomic studies performed on seed and crop plant tissues involving various analytical strategies is provided.

Determinants of Weight Evolution Among HIV-Positive Patients Initiating Antiretroviral Treatment in Low-Resource Settings.

BACKGROUND In resource-limited settings, clinical parameters, including body weight changes, are used to monitor clinical response. Therefore, we studied body weight changes in patients on antiretroviral treatment (ART) in different regions of the world. METHODS Data were extracted from the "International Epidemiologic Databases to Evaluate AIDS," a network of ART programmes that prospectively collects routine clinical data. Adults on ART from the Southern, East, West, and Central African and the Asia-Pacific regions were selected from the database if baseline data on body weight, gender, ART regimen, and CD4 count were available. Body weight change over the first 2 years and the probability of body weight loss in the second year were modeled using linear mixed models and logistic regression, respectively. RESULTS Data from 205,571 patients were analyzed. Mean adjusted body weight change in the first 12 months was higher in patients started on tenofovir and/or efavirenz; in patients from Central, West, and East Africa, in men, and in patients with a poorer clinical status. In the second year of ART, it was greater in patients initiated on tenofovir and/or nevirapine, and for patients not on stavudine, in women, in Southern Africa and in patients with a better clinical status at initiation. Stavudine in the initial regimen was associated with a lower mean adjusted body weight change and with weight loss in the second treatment year. CONCLUSIONS Different ART regimens have different effects on body weight change. Body weight loss after 1 year of treatment in patients on stavudine might be associated with lipoatrophy.

Age-specific and sex-specific weight gain norms to monitor antiretroviral therapy in children in low-income and middle-income countries.

BACKGROUND Viral load and CD4% are often not available in resource-limited settings for monitoring children's responses to antiretroviral therapy (ART). We aimed to construct normative curves for weight gain at 6, 12, 18, and 24 months following initiation of ART in children, and to assess the association between poor weight gain and subsequent responses to ART. DESIGN Analysis of data from HIV-infected children younger than 10 years old from African and Asian clinics participating in the International epidemiologic Databases to Evaluate AIDS. METHODS The generalized additive model for location, scale, and shape was used to construct normative percentile curves for weight gain at 6, 12, 18, and 24 months following ART initiation. Cox proportional models were used to assess the association between lower percentiles (< 50th) of weight gain distribution at the different time points and subsequent death, virological suppression, and virological failure. RESULTS Among 7173 children from five regions of the world, 45% were underweight at baseline. Weight gain below the 50th percentile at 6, 12, 18, and 24 months of ART was associated with increased risk of death, independent of baseline characteristics. Poor weight gain was not associated with increased hazards of virological suppression or virological failure. CONCLUSION Monitoring weight gain on ART using age-specific and sex-specific normative curves specifically developed for HIV-infected children on ART is a simple, rapid, sustainable tool that can aid in the identification of children who are at increased risk of death in the first year of ART.

Less invasive ventilation in extremely low birth weight infants from 1997 to 2011: survey versus evidence.

UNLABELLED Evidence for target values of arterial oxygen saturation (SaO2), CO2, and pH has changed substantially over the last 20 years. A representative survey concerning treatment strategies in extremely low-birth-weight infants (ELBW) was sent to all German neonatal intensive care units (NICUs) treating ELBW infants in 1997. A follow-up survey was conducted in 2011 and sent to all NICUs in Germany, Austria, and Switzerland. During the observation period, NICUs targeting SaO2 of 80, 85, and 90 % have increased, while units aiming for 94 and 96 % decreased (all p < 0.001). Similarly, NICUs aiming for pH 7.25 or lower increased, while 7.35 or higher decreased (both p < 0.001). Furthermore, more units targeted a CO2 of 50 mmHg (7.3 kPa) or higher (p < 0.001), while fewer targeted 40 or 35 mmHg (p < 0.001). Non-invasive ventilation (NIV) was used in 80.2 % of NICUs in 2011. The most frequently used ventilation modes were synchronized intermittent mandatory ventilation (SIMV) (67.5 %) and intermittent positive pressure ventilation (IPPV) (59.7 %) in 1997 and SIMV (77.2 %) and synchronized intermittent positive pressure ventilation (SIPPV) (26.8 %) in 2011. NICUs reporting frequent or always use of IPPV decreased to 11.0 % (p < 0.001). SIMV (77.2 %) and SIPPV (26.8 %) did not change from 1997 to 2011, while high-frequency oscillation (HFO) increased from 9.1 to 19.7 % (p = 0.018). Differences between countries, level of care, and size of the NICU were minimal. CONCLUSIONS Target values for SaO2 decreased, while CO2 and pH increased significantly during the observation period. Current values largely reflect available evidence at time of the surveys. WHAT IS KNOWN • Evidence concerning target values of oxygen saturation, CO 2 , and pH in extremely low-birth-weight infants has grown substantially. • It is not known to which extent this knowledge is transferred into clinical practice and if treatment strategies have changed. WHAT IS NEW • Target values for oxygen saturation in ELBW infants decreased between 1997 and 2011 while target values for CO 2 and pH increased. • Similar treatment strategies existed in different countries, hospitals of different size, or university versus nonuniversity hospitals in 2011.

The low molecular weight (LMW) isoforms of cyclin E provide a novel mechanism of cell cycle deregulation

Cyclin E, in complex with cyclin dependent kinase 2 (CDK2), is a positive regulator of G1 to S phase progression of the cell cycle. Deregulation of G1/S phase transition occurs in the majority of tumors. Cyclin E is overexpressed and post-translationally generates low molecular weight (LMW) isoforms in breast cancer, but not normal cells. Such alteration of cyclin E is linked to poor prognosis. Therefore, we hypothesized that the LMW isoforms of cyclin E provide a novel mechanism of cell cycle de-regulation in cancer cells. Insect cell expression system was used to explore the biochemical properties of the cyclin E isoforms. Non-tumorigenic (76NE6) and tumorigenic (T47D) mammary epithelial cells transfected with the cyclin E isoforms and breast tumor tissue endogenously expressing the LMW isoforms were used to study the biologic consequences of the LMW isoforms of cyclin E. All model systems studied show that the LMW forms (compared to full-length cyclin E) have increased kinase activity when partnered with CDK2. Increases in the percentage of cells in S phase and colony formation were also observed after overexpression of LMW compared to full-length cyclin E. The LMW isoforms of cyclin E utilize several mechanisms to attain their hyper-activity. They bind CDK2 more efficiently, and are resistant to inhibition by cyclin dependent kinase inhibitors (CKIs) as compared to full-length cyclin E. In addition, the LMW isoforms sequester the CKIs from full-length cyclin E abrogating the overall negative regulation of cyclin E. Despite their correlation with adverse biological consequences, the direct role of the LMW isoforms of cyclin E in mediating tumorigenesis remained unanswered. Subsequent to LMW cyclin E expression in 76NE6 cells, they lose their ability to enter quiescence and exhibit genomic instability, both characteristic of a tumor cell phenotype. Furthermore, injection of 76NE6 cells overexpressing each of the cyclin E isoforms into the mammary fat pad of nude mice revealed that the LMW isoforms of cyclin E yield tumors, whereas the full-length cyclin E does not. In conclusion, the LMW isoforms of cyclin E utilize several mechanisms to acquire a hyperactive phenotype that results in deregulation of the cell cycle and initiates the tumorigenic process in otherwise non-transformed mammary epithelial cells. ^

Vitamin A supplementation in very low birth weight infants

PURPOSE: In United States, the percentage of Extremely Low Birth Weight (ELBW) born for year 2006 was 0.8% (approximately 32,000 babies) & Very Low Birth Weight (VLBW) 1.48% (1). ELBW babies account for nearly half (49%) of the infant mortality for United States. Very Low birth weight infants are at a significant risk for high mortality and morbidity due to their multi system involvement and predisposition to lung prematurity and impaired immune function. One of the common causes cited is Vitamin A deficiency (2, 3).The purpose of this study is to look at published literature on Vitamin A supplementation in very low birth weight (VLBW) infants. ^ RESEARCH DESIGN: Systematic review of literature of published articles meeting the pre-defined criteria. ^ PROCEDURE: Studies included in this review were those which looked at very low birth weight infants defined as birth weight<1500gms. All experimental studies were reviewed. Studies looking at the effect of Vitamin A supplementation in comparison with a placebo or by itself in varying dosing regimens as an intervention were reviewed. Vitamin A deficiency and its manifestations were of interest. We used key words such as "very low birth weight", "mortality", "Vitamin A", "retinol" and "supplementation" in our search. ^ RISKS & POTENTIAL BENEFITS: We do not see any potential risks associated with this study. The potential benefit is recommendation for future studies based on the review of literature available currently. ^ IMPORTANCE OF KNOWLEDGE THAT MAY REASONABLY BE EXPECTED TO RESULT: The systematic review of literature of all experimental studies in VLBW infants showed uniform correlation of parenteral Vitamin A dosing and high plasma concentrations achieved. The recommended dosage for use is 5000 IU 3 times/week given intramuscularly for 4 weeks to prevent CLD. Higher doses have not shown benefit, with a potential for toxicity, while lower doses are inadequate. There is no role of use of Vitamin A in closure of patent ductus arteriosus & reducing mortality. However, it is important to state that the number of studies done so far is limited with small sample sizes. There is a need in the future for experimental studies to ascertain the role of Vitamin A to improve outcomes in VLBW. Atleast, one more RCT should be conducted using the dosage recommended above to make this a standard practice.^

Low-molecular-weight hydrocarbons in sediments at DSDP Sites 89-585 and 89-586

C2-C8 hydrocarbon concentrations (about 35 compounds identified, including saturated, aromatic, and olefinic compounds) from 38 shipboard sealed, deep-frozen core samples of Deep Sea Drilling Project Sites 585 (East Mariana Basin) and 586 (Ontong-Java Plateau) were determined by a gas stripping-thermovaporization method. Total concentrations, which represent the hydrocarbons dissolved in the pore water and adsorbed on the mineral surfaces of the sediment, vary from 20 to 630 ng/g of rock at Site 585 (sub-bottom depth range 332-868 m). Likewise, organic-carbon normalized yields range from 3*10**4 to 9*10**5 ng/g Corg, indicating that the organic matter is still in the initial, diagenetic evolutionary stage. The highest value (based on both rock weight and organic carbon) is measured in an extremely organic-carbon-poor sample of Lithologic Subunit VB (Core 585-30). In this unit (504-550 m) several samples with elevated organic-carbon contents and favorable kerogen quality including two thin "black-shale" layers deposited at the Cenomanian/Turonian boundary (not sampled for this study) were encountered. We conclude from a detailed comparison of light hydrocarbon compositions that the Core 585-30 sample is enriched in hydrocarbons of the C2-C8 molecular range, particularly in gas compounds, which probably migrated from nearby black-shale source layers. C2-C8 hydrocarbon yields in Site 586 samples (sub-bottom depth range 27-298 m) did not exceed 118 ng/g of dry sediment weight (average 56 ng/g), indicating the immaturity of these samples.

Low-molecular-weight hydrocarbon concentrations, organic carbon contents, and Rock-Eval pyrolysis hydrogen indices at DSDP Holes 75-530A and 75-532

A series of C2-C8 hydrocarbons (including saturated, aromatic, and olefinic compounds) from deep-frozen core samples taken during DSDP Leg 75 (Holes 530A and 532) were analyzed by a combined hydrogen-stripping/thermovaporization method. Concentrations representing both hydrocarbons dissolved in the pore water and adsorbed on the mineral surfaces vary in Hole 530A from about 10 to 15,000 ng/g of dry sediment weight depending on the lithology (organic-carbon-lean calcareous oozes versus "black shales"). Likewise, the organic-carbon-normalized C2-C8 hydrocarbon concentrations vary from 3,500 to 93,100 ng/g Corg, reflecting drastic differences in the hydrogen contents and hence the hydrocarbon potential of the kerogens. The highest concentrations measured of nearly 10**5 ng/g Corg are about two orders of magnitude below those usually encountered in Type-II kerogen-bearing source beds in the main phase of petroleum generation. Therefore, it was concluded that Hole 530A sediments, even at 1100 m depth, are in an early stage of evolution. The corresponding data from Hole 532 indicated lower amounts (3,000-9,000 ng/g Corg), which is in accordance with the shallow burial depth and immaturity of these Pliocene/late Miocene sediments. Significant changes in the light hydrocarbon composition with depth were attributed either to changes in kerogen type or to maturity related effects. Redistribution pheonomena, possibly the result of diffusion, were recognized only sporadically in Hole 530A, where several organic-carbon lean samples were enriched by migrated gaseous hydrocarbons. The core samples from Hole 530A were found to be severely contaminated by large quantities of acetone, which is routinely used as a solvent during sampling procedures on board Glomar Challenger.

Low-molecular-weight hydrocarbons in sediments of Broken Ridge and Ninetyeast Ridge

Core samples taken during Leg 121 drilling aboard the JOIDES Resolution in the central Indian Ocean were analyzed for their low-molecular-weight hydrocarbon contents. Forty-three samples from the Broken Ridge and 39 samples from the Ninetyeast Ridge drill sites, deep-frozen on board immediately after recovery, were studied by a dynamic headspace technique (hydrogen-stripping/thermovaporization). Light hydrocarbons (saturated and olefinic) with two to four carbon atoms, and toluene as a selected aromatic compound, were identified. Total C2-C4 saturated hydrocarbon yields vary considerably from virtually zero in a Paleogene calcareous ooze from Hole 757B to nearly 600 nanogram/gram of dry-weight sediment (parts per billion) in a Cretaceous claystone from Hole 758A. An increase of light-hydrocarbon yields with depth, and hence with sediment temperature, was observed from Hole 758A samples down to a depth of about 500 meters below seafloor. Despite extreme data scatter due to lithological changes over this depth interval, this increased yield indicates the onset of temperature-controlled hydrocarbon formation reactions. Toluene contents are also extremely variable (generally between 10 and 100 ppb) and reach more than 300 ppb in two samples of tuffaceous lithology (Sections 121-755A-17R-4 and 121-758A-48R-4). As for the saturated hydrocarbons, there was also an increase of toluene yields with increasing depth in Hole 758A.