Informatics and quantitative analysis in biological imaging

Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.     

A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A

The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei, reveals a similarity to Escherichia coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of glutamine-339 of the translation initiation factor eIF4A, abolishing its helicase activity and inhibiting translation. We propose to name BPSL1549 Burkholderia lethal factor 1.     

N-linked glycan profiling of mature human milk by high-performance microfluidic chip liquid chromatography time-of-flight tandem mass spectrometry

N-Linked glycans of skim human milk proteins were determined for three mothers. N-Linked glycans are linked to immune defense, cell growth, and cell-cell adhesion, but their functions in human milk are undetermined. Protein-bound N-linked glycans were released with peptidyl N-glycosidase F (PNGase F), enriched by graphitized carbon chromatography, and analyzed with Chip-TOF MS. To be defined as N-glycans, compounds were required, in all three procedural replicates, to match, within 6 ppm, against a theoretical human N-glycan library and be at least 2-fold higher in abundance in PNGase F-treated than in control samples. Fifty-two N-linked glycan compositions were identified, and 24 were confirmed via tandem mass spectra analysis. Twenty-seven compositions have been found previously in human milk, and 25 are novel compositions. By abundance, 84% of N-glycans were fucosylated and 47% were sialylated. The majority (70%) of total N-glycan abundance was composed of N-glycans found in all three milk samples.     

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems

This study coupled stable isotope probing with phospholipid fatty acid analysis (¹³C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced ¹³C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g⁻¹ soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g⁻¹ soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.     

A clinical study on the effect in horses during medetomidine-isoflurane anaesthesia, of butorphanol constant rate infusion on isoflurane requirements, on cardiopulmonary function and on recovery characteristics

ObjectiveTo test if the addition of butorphanol by constant rate infusion (CRI) to medetomidine–isoflurane anaesthesia reduced isoflurane requirements, and influenced cardiopulmonary function and/or recovery characteristics.Study designProspective blinded randomised clinical trial.Animals61 horses undergoing elective surgery.MethodsHorses were sedated with intravenous (IV) medetomidine (7 μg kg^?1); anaesthesia was induced with IV ketamine (2.2 mg kg^?1) and diazepam (0.02 mg kg^?1) and maintained with isoflurane and a CRI of medetomidine (3.5 μg kg^?1 hour^?1). Group MB (n = 31) received butorphanol CRI (25 μg kg^?1 IV bolus then 25 μg kg^?1 hour^?1); Group M (n = 30) an equal volume of saline. Artificial ventilation maintained end-tidal CO₂ in the normal range. Horses received lactated Ringer’s solution 5 mL kg^?1 hour^?1, dobutamine <1.25 μg kg^?1 minute^?1 and colloids if required. Inspired and exhaled gases, heart rate and mean arterial blood pressure (MAP) were monitored continuously; pH and arterial blood gases were measured every 30 minutes. Recovery was timed and scored. Data were analyzed using two way repeated measures anova, independent t-tests or Mann–Whitney Rank Sum test (p < 0.05).ResultsThere was no difference between groups with respect to anaesthesia duration, end-tidal isoflurane (MB: mean 1.06 ± SD 0.11, M: 1.05 ± 0.1%), MAP (MB: 88 ± 9, M: 87 ± 7 mmHg), heart rate (MB: 33 ± 6, M: 35 ± 8 beats minute^?1), pH, PaO₂ (MB: 19.2 ± 6.6, M: 18.2 ± 6.6 kPa) or PaCO_2. Recovery times and quality did not differ between groups, but the time to extubation was significantly longer in group MB (26.9 ± 10.9 minutes) than in group M (20.4 ± 9.4 minutes).Conclusion and clinical relevanceButorphanol CRI at the dose used does not decrease isoflurane requirements in horses anaesthetised with medetomidine–isoflurane and has no influence on cardiopulmonary function or recovery.     

Mercury Concentrations in Largemouth BASS (Micropterus Salmoides) from Five South Carolina Reservoirs

Mercury concentrations in largemouth bass (Micropterus salmoides) bass were compared among five reservoirs in South Carolina. Three of these reservoirs (Lake Russell, Lake Thurmond, and Lake Marion) are accessible to the public and two (L-Lake and Par Pond) are located on the U.S. Department of Energy's Savannah River Site (SRS), which is closed to public access. Age-adjusted mercury concentrations were significantly higher in SRS bass compared to the offsite reservoirs. In addition, mercury concentrations were significantly higher in bass from Par Pond compared to L-Lake and in bass from Lakes Russell and Thurmond compared to Lake Marion. No mercury concentrations in excess of the U.S. Food and Drug Administration action level (1.0 mg?kg^?1) were found in any bass from the public-accessible reservoirs. However, the majority of fish from these reservoirs had mercury concentrations that fall into or exceed the U.S. Environmental Protection Agency consumption category of “no more than one per week". In addition, most fish from these reservoirs had mercury levels in excess of those believed to be detrimental to sensitive avian species.     

Supercritical extraction of essential oil from aniseed (Pimpinella anisum L) using CO2: solubility,kinetics, and composition data

Supercritical fluid extraction (SFE) from aniseed using carbon dioxide was performed at 30 degrees C and pressures of 80-180 bar. The chemical composition of the SFE extract was determined by GC-MS; the quantitative analysis was done by GC-FID and TLC. The total amount of extractable substances or global yield (mass of extract/mass of feed) for the SFE process varied from 3.13 to 10.67% (mass). The solubilities of the anise essential oil in CO(2) were 0.0110, 0.0277, 0.0143, and 0.0182 kg of solute/kg of CO(2) at 80, 100, 140, and 180 bar, respectively. The major compounds identified and quantified in the extracts were anethole ( approximately 90%), gamma-himachalene (2-4%), p-anisaldehyde (<1%), methylchavicol (0.9-1.5%), cis-pseudoisoeugenyl 2-methylbutyrate ( approximately 3%), and trans-pseudoisoeugenyl 2-methylbutyrate ( approximately 1.3%). The Sovová model described quite well the experimental overall extraction curves.     

Nutritive evaluation of the seed,germinated seed,and string bean of Erythrina americana and the detoxification of the material by boiling

The nutritive and toxicological values of the dry seeds, germinated seeds, and string beans of Erythrina americana were studied using raw and boiled samples. Raw germinated seeds had a higher protein content and lower fiber content than dry seeds. The whole string bean had lower protein content and higher fiber content. However, the seeds of the green pod showed the same protein concentration as the dry seeds (dry basis). Boiling and elimination of broth was beneficial in diminishing the alkaloid concentration in all the samples. The trypsin inhibitors, lectins, and tannins were also diminished as was expected. The raw string bean showed the lowest LD(50). Although the total essential amino acids content of the boiled germinated seeds was increased, the quality of protein, protein efficiency ratio (PER), was lower than in boiled dry seeds, and in these, the PER was similar to the control (casein). The present results suggest that for the protein quality and low alkaloid content, the boiled dry seeds and string beans could be used for animal feeding. It could be interesting to test the raw string beans in ruminants since in this stage E. americana showed the lowest toxicity.     

Wasserhaushalt und Dickenwachstum von Kiefern in Abhängigkeit des Grundwasserflurabstandes

Water budget and annual ring growth of pines for different groundwater depth conditions Relation between annual ring width and water supply was examined for different groundwater depth in an old pine stand on a sandy soil. The quotient Ereal/Epot is a suitable parameter to quantify water stress. Multiple regression analyses were used to describe the dependence between annual ring width and water stress. Mean growth of basal area can be expressed by Ereal/Epot of the actual and previous year. This site specific function was used to quantify growth reduction affected by ground-water lowering for various soil conditions.     

A novel series of O,O-diethyl O-(1,3-disubstituted-1,2,4-triazol-5-yl) phosphorothioates. Part II. Quantitative structure–activity relationships

The in-vivo toxicity data of 33 O,O-diethyl O-(1-alkyl-3-R″-1,2,4-triazol-5-yl) phosphorothioates, reported in Part I of this series, were subjected to multiregression analyses for the following organisms: Leptinotarsa decemlineata (larvae), Macrosiphum euphorbiae (aphids), Culex pipiens (adults), Spodoptera littoralis (larvae) and the rat. The activities were found to depend mainly on the steric parameters of R″, these being best expressed by the values L, B₁ and B₄ of the computer program STERIMOL. It was shown that there were different steric requirements for each species and these are discussed. The predictive values of the best equations were also estimated.