Ultra-high-resolution paleoenvironmental records via direct laser-based analysis of lipid biomarkers in sediment core samples

Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single submillimeter-sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional liquid chromatography/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (∼4-y temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the ∼200-y de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and environmental factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments.Microbial lipids in aquatic sediments reflect phylogeny, environmental conditions, and biogeochemistry of the water column in which they were produced. After sedimentation and because of the persistence of lipid structures in the sedimentary record, the information archived in these lipids remains available on geological time scales. Retrieval of this information from sediments and rocks has increasingly contributed to our understanding of past environments, microbial communities, and biogeochemical processes (e.g., refs. 1–5). Merged with the concept of molecular stratigraphy (2, 6), i.e., the analysis of selected biomarkers in solvent extracts of sediment samples in a stratigraphic framework, unique information can be gleaned regarding the temporal changes of past ecological and environmental conditions in aquatic systems. Because of analytical requirements, the temporal resolution is typically limited by centimeter-scale-sized samples, which, dependent on the depositional setting, tend to integrate time periods of decades to millennia, even in high-sedimentation settings such as the Santa Barbara Basin (e.g., refs. 4, 7, 8). In consequence, our knowledge of the temporal changes of the environmental and ecological history recorded by lipid biomarkers is rather coarse and based on long-term averages of their distributions in the sedimentary record.In this study we seek to extend this approach to ultra-high-resolution molecular stratigraphy. We focused on archaeal glycerol dialkyl glycerol tetraethers (GDGTs), which are produced by planktonic archaeal communities and are ubiquitous and persistent components in marine sediments (e.g., refs. 9, 10) with widely recognized potential for paleoenvironmental studies. The number of cycloalkyl rings in GDGTs (Fig. S1) appears highly sensitive to ecological and environmental factors such as phylogeny (ref. 5 and references therein), temperature (ref. 11 and references therein), or pH (12, 13). This sensitivity of GDGT composition to environmental and ecological factors has driven the development of multiple molecular proxies. Adaptation to temperature has been demonstrated in thermophilic cultures of archaea (e.g., ref. 14) and serves as concept for the reconstruction of paleo sea surface temperatures (SST) in sediments using the TEX₈₆ (tetraether index of 86 carbon atoms) (3), which is based on fossil lipids of planktonic archaea. This proxy has been used to characterize oscillations of SST in different geological episodes (e.g., refs. 8, 15, 16). Complications could arise from additional GDGT sources, e.g., allochthonous inputs of GDGT-bearing soils, lateral transport, in situ production, and/or recycling by sedimentary archaea (cf. refs. 5, 17). Relative GDGT distributions required for proxy calculations are obtained by HPLC atmospheric pressure chemical ionization mass spectrometry (HPLC/APCI-MS) of solvent extracts from gram-sized sediment samples (18, 19).To enhance temporal resolution of GDGT-based proxies, we explored the utility of laser desorption ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (LDI FTICR-MS). In LDI, the impact of a pulsed laser beam on the sample leads to desorption, vaporization and ionization of the analytes, forming a cloud of charged molecules. An additional matrix is frequently applied to facilitate the generation of ions (matrix assisted laser desorption ionization [MALDI]). A complete understanding of underlying ionization mechanisms has not been achieved yet (20). LDI or MALDI are best known in the field of proteins or peptides and have also been successfully used in lipid research (21). The fact that LDI analysis can generate ions directly from the sample placed on a sample holder without time-consuming wet-chemical pretreatment while producing mass spectra from submillimeter-sized spots (as small as 10 µm) makes this technique particularly attractive for molecular stratigraphy. LDI may allow direct analysis of nanogram-sized samples on the surface of cut, intact sediment cores at ultra-high spatial resolution, equivalent to temporal resolution on the order of months to decades.We aimed to develop a technique that takes advantage of both the exquisite sensitivity and unequivocal molecular information of ultra-high-resolution mass spectrometry by FTICR-MS and the high spatial resolution of LDI within an intact and unaltered sedimentological context. The key steps of validation and implementation included (Fig. S2) (i) the detection of archaeal GDGTs, (ii) verification of results obtained by LDI FTICR-MS by parallel analysis using established HPLC/APCI-MS methods, and (iii) the examination of the first continuous high-resolution GDGT profile from a sediment core section of the eastern Mediterranean sapropel S1, which was deposited under anoxic conditions during the Holocene climatic optimum (HCO; refs. 22, 23). The data thus may provide an unprecedented view of the dynamic variations of both SST and ecological and environmental factors during sapropel formation.     

Interaction with plant transcription factors can mediate nuclear import of phytochrome B

Phytochromes (phy) are red/far-red-absorbing photoreceptors that regulate the adaption of plant growth and development to changes in ambient light conditions. The nuclear transport of the phytochromes upon light activation is regarded as a key step in phytochrome signaling. Although nuclear import of phyA is regulated by the transport facilitators far red elongated hypocotyl 1 (FHY1) and fhy1-like, an intrinsic nuclear localization signal was proposed to be involved in the nuclear accumulation of phyB. We recently showed that nuclear import of phytochromes can be analyzed in a cell-free system consisting of isolated nuclei of the unicellular green algae Acetabularia acetabulum. We now show that this system is also versatile to elucidate the mechanism of the nuclear transport of phyB. We tested the nuclear transport characteristics of full-length phyB as well as N- and C-terminal phyB fragments in vitro and showed that the nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). In vivo measurements of phyB nuclear accumulation in the absence of PIF1, -3, -4, and -5 indicate that these PIFs are the major transport facilitators during the first hours of deetiolation. Under prolonged irradiations additional factors might be responsible for phyB nuclear transport in the plant.     

Preparation of unnatural N-to-N and C-to-C protein fusions

Standard genetic approaches allow the production of protein composites by fusion of polypeptides in head-to-tail fashion. Some applications would benefit from constructions that are genetically impossible, such as the site-specific linkage of proteins via their N or C termini, when a remaining free terminus is required for biological activity. We developed a method for the production of N-to-N and C-to-C dimers, with full retention of the biological activity of both fusion partners and without inflicting chemical damage on the proteins to be joined. We use sortase A to install on the N or C terminus of proteins of interest the requisite modifications to execute a strain-promoted copper-free cycloaddition and show that the ensuing ligation proceeds efficiently. Applied here to protein-protein fusions, the method reported can be extended to connecting proteins with any entity of interest.     

Usefulness of Doppler Echocardiographic Left Ventricular Diastolic Function and Peak Exercise Oxygen Consumption to Predict Cardiovascular Outcomes in Patients With Systolic Heart Failure (from HF-ACTION)

Heart Failure: A Controlled Trial Investigating Outcomes of Exercise Training (HF-ACTION) was a multicenter, randomized controlled trial designed to examine the safety and efficacy of aerobic exercise training versus usual care in 2,331 patients with systolic heart failure (HF). In HF-ACTION patients with rest transthoracic echocardiographic measurements, the predictive value of 8 Doppler echocardiographic measurements-left ventricular (LV) diastolic dimension, mass, systolic (ejection fraction) and diastolic (mitral valve peak early diastolic/peak late diastolic [E/A] ratio, peak mitral valve early diastolic velocity/tissue Doppler peak early diastolic myocardial velocity [E/E'] ratio, and deceleration time) function, left atrial dimension, and mitral regurgitation severity-was examined for a primary end point of all-cause death or hospitalization and a secondary end point of cardiovascular disease death or HF hospitalization. Also compared was the prognostic value of echocardiographic variables versus peak oxygen consumption (Vo(2)). Mitral valve E/A and E/E' ratios were more powerful independent predictors of clinical end points than the LV ejection fraction but less powerful than peak Vo(2). In multivariate analyses for predicting the primary end point, adding E/A ratio to a basic demographic and clinical model increased the C-index from 0.61 to 0.62, compared with 0.64 after adding peak Vo(2). For the secondary end point, 6 echocardiographic variables, but not the LV ejection fraction or left atrial dimension, provided independent predictive power over the basic model. The addition of E/E' or E/A to the basic model increased the C-index from 0.70 to 0.72 and 0.73, respectively (all p values <0.0001). Simultaneously adding E/A ratio and peak Vo(2) to the basic model increased the C-index to 0.75 (p <0.0005). No echocardiographic variable was significantly related to the change from baseline to 3 months in exercise peak Vo(2). In conclusion, the addition of echocardiographic LV diastolic function variables improves the prognostic value of a basic demographic and clinical model for cardiovascular disease outcomes.     

Left ventricular mass and function with reduced-fat or reduced-carbohydrate hypocaloric diets in overweight and obese subjects

In animals, carbohydrate and fat composition during dietary interventions influenced cardiac metabolism, structure, and function. Because reduced-carbohydrate and reduced-fat hypocaloric diets are commonly used in the treatment of obesity, we investigated whether these interventions differentially affect left ventricular mass, cardiac function, and blood pressure. We randomized 170 overweight and obese subjects (body mass index, 32.9±4.4; range, 26.5-45.4 kg/m(2)) to 6-month hypocaloric diets with either reduced carbohydrate intake or reduced fat intake. We obtained cardiac MRI and ambulatory blood pressure recordings over 24 hours before and after 6 months. Ninety subjects completing the intervention period had a full cardiac MRI data set. Subjects lost 7.3±4.0 kg (7.9±3.8%) with reduced-carbohydrate diet and 6.2±4.2 kg (6.7±4.4%) with reduced-fat diet (P<0.001 within each group; P=not significant between interventions). Caloric restriction led to similar significant decreases in left ventricular mass with low-carbohydrate diets (5.4±5.4 g) or low-fat diets (5.2±4.8 g; P<0.001 within each group; P=not significant between interventions). Systolic and diastolic left ventricular function did not change with either diet. The 24-hour systolic blood pressure decreased similarly with both interventions. Body weight change (β=0.33; P=0.02) and percentage of ingested n-3 polyunsaturated fatty acids (β=-0.27; P=0.03) predicted changes in left ventricular mass. In conclusion, weight loss induced by reduced-fat diets or reduced-carbohydrate diets similarly improved left ventricular mass in overweight and obese subjects over a 6-month period. However, n-3 polyunsaturated fatty acid ingestion may have an independent beneficial effect on left ventricular mass.     

Mycobacterium avium ss paratuberculosis-associated Diseases: Piecing the Crohn's Puzzle Together

The relation of Mycobacterium avium ss paratuberculosis (MAP) to Crohn's Disease (CD) and other MAP-associated conditions remains controversial. New data, coupled with the analogous Helicobacter pylori (H. pylori) story, has permitted us to piece together the MAP puzzle and move forward with a more scientific way of treating inflammatory bowel disease, particularly CD. As infection moves centre stage in inflammatory bowel disease, the dated "aberrant reaction" etiology has lost scientific credibility. Now, our growing understanding of MAP-associated diseases demands review and articulation. We focus here on (1) the concept of MAP-associated diseases; (2) causality, Johne Disease, the "aberrant reaction" hypothesis; and (3) responses to published misconceptions questioning MAP as a pathogen in CD.     

Factors associated with external ventricular drain placement accuracy: data from an electronic health record repository

Background

We evaluated external ventricular drain placement for factors associated with placement accuracy. Data were acquired using an electronic health record data requisition tool.

Method

Medical records of all patients who underwent ventriculostomy from 2003 to 2010 were identified and evaluated. Patient demographics, diagnosis, type of guidance and number of catheter passes were searched for and recorded. Post-procedural hemorrhage and/or infection were identified. A grading scale was used to classify accuracy of catheter placements. A multiple logistic regression model was developed to assess features associated with accurate catheter placement.

Results

One hundred nine patients who underwent 111 ventriculostomies from 2003 to 2010 were identified. Patient diagnoses were classified into vascular (63 %), tumor (21 %), trauma (14 %), and cyst (2 %). Procedures were performed freehand in 90 (81 %), with the Ghajar guide in 17 (15 %), and with image guidance in 4 (4 %) patients. Eighty-eight (79 %) catheters were placed in the correct location. Trauma patients were more likely to have catheters misplaced (p?=?0.007) whereas patients in other diagnostic categories were not significantly associated with misplaced catheters. Post-procedural hemorrhage was noted in 2 (1.8 %) patients on post-procedural imaging studies. Five (4.5 %) definite and 6 (5.4 %) suspected infections were identified.

Conclusions

External ventricular drain placement can be performed accurately in most patients. Patients with trauma are more likely to have catheters misplaced. Further development is required to identify and evaluate procedure outcomes using an electronic health record repository.     

Traumatische Karotisdissektion

Traumatic dissection of the carotid artery is an easily overlooked consequence of trauma with notable morbidity and mortality which can be observed in up to 4?% of cases involving multiple trauma. Certain mechanisms and patterns of injury as well as specific symptoms should serve as indicators of a dissection and should therefore result in further diagnostic measures. An early diagnosis is of major relevance. This report describes the case of a 45-year-old victim of a traffic accident who showed symptoms of a dissection which had initially not been diagnosed.