Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA-DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA-DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA-DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA-DNA hybridization.

How large are actor and partner effects of personality on relationship satisfaction? The importance of controlling for shared method variance

Previous research suggests that the personality of a relationship partner predicts not only the individual’s own satisfaction with the relationship but also the partner’s satisfaction. Based on the actor–partner interdependence model, the present research tested whether actor and partner effects of personality are biased when the same method (e.g., self-report) is used for the assessment of personality and relationship satisfaction and, consequently, shared method variance is not controlled for. Data came from 186 couples, of whom both partners provided self- and partner reports on the Big Five personality traits. Depending on the research design, actor effects were larger than partner effects (when using only self-reports), smaller than partner effects (when using only partner reports), or of about the same size as partner effects (when using self- and partner reports). The findings attest to the importance of controlling for shared method variance in dyadic data analysis.

Patient classification system: An integrated method for measuring nursing intensity and optimizing resource allocation

A patient classification system was developed integrating a patient acuity instrument with a computerized nursing distribution method based on a linear programming model. The system was designed for real-time measurement of patient acuity (workload) and allocation of nursing personnel to optimize the utilization of resources.^ The acuity instrument was a prototype tool with eight categories of patients defined by patient severity and nursing intensity parameters. From this tool, the demand for nursing care was defined in patient points with one point equal to one hour of RN time. Validity and reliability of the instrument was determined as follows: (1) Content validity by a panel of expert nurses; (2) predictive validity through a paired t-test analysis of preshift and postshift categorization of patients; (3) initial reliability by a one month pilot of the instrument in a practice setting; and (4) interrater reliability by the Kappa statistic.^ The nursing distribution system was a linear programming model using a branch and bound technique for obtaining integer solutions. The objective function was to minimize the total number of nursing personnel used by optimally assigning the staff to meet the acuity needs of the units. A penalty weight was used as a coefficient of the objective function variables to define priorities for allocation of staff.^ The demand constraints were requirements to meet the total acuity points needed for each unit and to have a minimum number of RNs on each unit. Supply constraints were: (1) total availability of each type of staff and the value of that staff member (value was determined relative to that type of staff's ability to perform the job function of an RN (i.e., value for eight hours RN = 8 points, LVN = 6 points); (2) number of personnel available for floating between units.^ The capability of the model to assign staff quantitatively and qualitatively equal to the manual method was established by a thirty day comparison. Sensitivity testing demonstrated appropriate adjustment of the optimal solution to changes in penalty coefficients in the objective function and to acuity totals in the demand constraints.^ Further investigation of the model documented: correct adjustment of assignments in response to staff value changes; and cost minimization by an addition of a dollar coefficient to the objective function. ^

A new method to measure higher visual functions in an immersive environment

BACKGROUND: Higher visual functions can be defined as cognitive processes responsible for object recognition, color and shape perception, and motion detection. People with impaired higher visual functions after unilateral brain lesion are often tested with paper pencil tests, but such tests do not assess the degree of interaction between the healthy brain hemisphere and the impaired one. Hence, visual functions are not tested separately in the contralesional and ipsilesional visual hemifields. METHODS: A new measurement setup, that involves real-time comparisons of shape and size of objects, orientation of lines, speed and direction of moving patterns, in the right or left visual hemifield, has been developed. The setup was implemented in an immersive environment like a hemisphere to take into account the effects of peripheral and central vision, and eventual visual field losses. Due to the non-flat screen of the hemisphere, a distortion algorithm was needed to adapt the projected images to the surface. Several approaches were studied and, based on a comparison between projected images and original ones, the best one was used for the implementation of the test. Fifty-seven healthy volunteers were then tested in a pilot study. A Satisfaction Questionnaire was used to assess the usability of the new measurement setup. RESULTS: The results of the distortion algorithm showed a structural similarity between the warped images and the original ones higher than 97%. The results of the pilot study showed an accuracy in comparing images in the two visual hemifields of 0.18 visual degrees and 0.19 visual degrees for size and shape discrimination, respectively, 2.56° for line orientation, 0.33 visual degrees/s for speed perception and 7.41° for recognition of motion direction. The outcome of the Satisfaction Questionnaire showed a high acceptance of the battery by the participants. CONCLUSIONS: A new method to measure higher visual functions in an immersive environment was presented. The study focused on the usability of the developed battery rather than the performance at the visual tasks. A battery of five subtasks to study the perception of size, shape, orientation, speed and motion direction was developed. The test setup is now ready to be tested in neurological patients.

Variation of the detergent-binding capacity and phospholipid content of membrane proteins when purified in different detergents.

Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches.

Effect of a Traditional Processing Method on the Chemical Composition of Local White Lupin (Lupinus albus L.) Seed in North-Western Ethiopia

The effect of a traditional Ethiopian lupin processing method on the chemical composition of lupin seed samples was studied. Two sampling districts, namely Mecha and Sekela, representing the mid- and high-altitude areas of north-western Ethiopia, respectively, were randomly selected. Different types of traditionally processed and marketed lupin seed samples (raw, roasted, and fi nished) were collected in six replications from each district. Raw samples are unprocessed, and roasted samples are roasted using fi rewood. Finished samples are those ready for human consumption as snack. Thousand seed weight for raw and roasted samples within a study district was similar (P > 0.05), but it was lower (P < 0.01) for fi nished samples compared to raw and roasted samples. The crude fi bre content of fi nished lupin seed sample from Mecha was lower (P < 0.01) than that of raw and roasted samples. However, the different lupin samples from Sekela had similar crude fi bre content (P > 0.05). The crude protein and crude fat contents of fi nished samples within a study district were higher (P < 0.01) than those of raw and roasted samples, respectively. Roasting had no effect on the crude protein content of lupin seed samples. The crude ash content of raw and roasted lupin samples within a study district was higher (P < 0.01) than that of fi nished lupin samples of the respective study districts. The content of quinolizidine alkaloids of fi nished lupin samples was lower than that of raw and roasted samples. There was also an interaction effect between location and lupin sample type. The traditional processing method of lupin seeds in Ethiopia has a positive contribution improving the crude protein and crude fat content, and lowering the alkaloid content of the fi nished product. The study showed the possibility of adopting the traditional processing method to process bitter white lupin for the use as protein supplement in livestock feed in Ethiopia, but further work has to be done on the processing method and animal evaluation.

What’s the best method? Comparison of different short forms oft he Pathological Narcissism Inventory

Recent research emphasizes the various facets of narcissism. As a consequence, newly developed questionnaires for narcissism have a large number of subscales and items. However, for the daily use in research and practice, short measures are crucial. In this study we compare different short forms of the Pathological Narcissism Questionnaire, a 54 item measure with seven subscales. In different samples (total N>2000) we applied different theoretical models to construct short forms of approximately 20 items. In particular, we compared IRT, item-total correlation, and factor loading based short forms and versions based on content validity and random selection. In all versions the original subscale structure was preserved. Results show that the short forms all have high correlations with the original version. Furthermore, correlations with criterion validation measures were comparable. We conclude that the item number can be reduced substantially without loosing information. Pros and cons of the different reduction methods are discussed.

The sequence comparison index: A novel method for comparing proteins and proteomes

Historically morphological features were used as the primary means to classify organisms. However, the age of molecular genetics has allowed us to approach this field from the perspective of the organism's genetic code. Early work used highly conserved sequences, such as ribosomal RNA. The increasing number of complete genomes in the public data repositories provides the opportunity to look not only at a single gene, but at organisms' entire parts list. ^ Here the Sequence Comparison Index (SCI) and the Organism Comparison Index (OCI), algorithms and methods to compare proteins and proteomes, are presented. The complete proteomes of 104 sequenced organisms were compared. Over 280 million full Smith-Waterman alignments were performed on sequence pairs which had a reasonable expectation of being related. From these alignments a whole proteome phylogenetic tree was constructed. This method was also used to compare the small subunit (SSU) rRNA from each organism and a tree constructed from these results. The SSU rRNA tree by the SCI/OCI method looks very much like accepted SSU rRNA trees from sources such as the Ribosomal Database Project, thus validating the method. The SCI/OCI proteome tree showed a number of small but significant differences when compared to the SSU rRNA tree and proteome trees constructed by other methods. Horizontal gene transfer does not appear to affect the SCI/OCI trees until the transferred genes make up a large portion of the proteome. ^ As part of this work, the Database of Related Local Alignments (DaRLA) was created and contains over 81 million rows of sequence alignment information. DaRLA, while primarily used to build the whole proteome trees, can also be applied shared gene content analysis, gene order analysis, and creating individual protein trees. ^ Finally, the standard BLAST method for analyzing shared gene content was compared to the SCI method using 4 spirochetes. The SCI system performed flawlessly, finding all proteins from one organism against itself and finding all the ribosomal proteins between organisms. The BLAST system missed some proteins from its respective organism and failed to detect small ribosomal proteins between organisms. ^

The relationship between supermarket nutrient movements and the mortality rates from fat-associated and non-fat-associated cardiovascular disease: Development of an ecologic method for determining community food patterns

Supermarket nutrient movement, a community food consumption measure, aggregated 1,023 high-fat foods, representing 100% of visible fats and approximately 44% of hidden fats in the food supply (FAO, 1980). Fatty acid and cholesterol content of foods shipped from the warehouse to 47 supermarkets located in the Houston area were calculated over a 6 month period. These stores were located in census tracts with over 50% of a given ethnicity: Hispanic, black non-Hispanic, or white non-Hispanic. Categorizing the supermarket census tracts by predominant ethnicity, significant differences were found by ANOVA in the proportion of specific fatty acids and cholesterol content of the foods examined. Using ecological regression, ethnicity, income, and median age predicted supermarket lipid movements while residential stability did not. No associations were found between lipid movements and cardiovascular disease mortality, making further validation necessary for epidemiological application of this method. However, it has been shown to be a non-reactive and cost-effective method appropriate for tracking target foods in populations of groups, and for assessing the impact of mass media nutrition education, legislation, and fortification on community food and nutrient purchase patterns. ^

Chlorophyll a content, protist biomass and experimental plankton growth and mortality in West Greenland water samples

We evaluated the role of microzooplankton (sensu latto, grazers <500 µm) in determining the fate of phytoplankton production (PP) along a glacier-to-open sea transect in the Greenland subarctic fjord, Godthabfjord. Based on the distribution of size fractionated chlorophyll a (chl a) concentrations we established 4 zones: (1) Fyllas Bank, characterized by deep chl a maxima (ca. 30 to 40 m) consisting of large cells, (2) the mouth and main branch of the fjord, where phytoplankton was relatively homogeneously distributed in the upper 30 m layer, (3) inner waters influenced by glacial melt water and upwelling, with high chl a concentrations (up to 12 µg/l) in the >10 µm fraction within a narrow (2 m) subsurface layer, and (4) the Kapisigdlit branch of the fjord, ice-free, and characterized with a thick and deep chl a maximum layer. Overall, microzooplankton grazing impact on primary production was variable and seldom significant in the Fyllas Bank and mouth of the fjord, quite intensive (up to >100% potential PP consumed daily) in the middle part of the main and Kapisigdlit branches of the fjord, and rather low and unable to control the fast growing phytoplankton population inhabiting the nutrient rich waters in the upwelling area in the vicinity of the glacier. Most of the grazing impact was on the <10 µm phytoplankton fraction, and the major grazers of the system seem to be >20 µm microzooplankton, as deducted from additional dilution experiments removing this size fraction. Overall, little or no export of phytoplankton out of the fjord to the Fyllas Bank can be determined from our data.

Geochemistry and radionuclide content of sediment and water samples obtained from the Ob and Irtysh river, Russia

This paper reports the results of the investigations of 2006-2007 on the distribution and migration forms of artificial radionuclides and chemical elements in the Ob-Irtysh water system. Three regions were studied. One of them is a local segment of the Ob River upstream from the confluence with the Irtysh River; its investigation allowed us to estimate the general radioecological state of the aquatic environment affected by the activity of the Tomsk 7 plant. The second region is a local segment of the Irtysh River upstream from its confluence with the Ob River, where the influence of emissions from the NPO Mayak could be estimated. The third region is the water area of the Ob River after its confluence with the Irtysh River. It characterizes the real level of radioactive and chemical contamination of the middle reaches of the Ob River. In order to explain horizontal variations in the distribution of radionuclides in the upper layer of bottom sediments collected at various sites, the results of sorption-kinetic experiments with radioactive tracers in the precipitate-solution system were used. The investigation of the migration forms of trace elements and radionuclides occurring in river water was based on the method of tangential-flow membrane filtration. Chemical element contents were determined in 400-ml water samples. A set of Millipore polysulfone membranes with pore sizes of 8, 1.2, 0.45, 0.1, and 0.025 µm was employed. Taking into account the ultralow specific concentrations of radionuclides in the water, they were analyzed in 300-500 litre samples using Millipore polysulfone membranes with pore sizes of 0.45 µm and 15 kDa. This allowed us to estimate the percentages of cesium-137 and plutonium-239, 240 in the suspended particulate fraction, colloids, and dissolved species.

Granulometry, biogenic silica content, magnetic susceptibility and bulk densities of ODP Site 188-1165

The Prydz Bay area is a key region for studying and understanding the history of the eastern Antarctic Continental Ice Sheet (O'Brien, Cooper, Richter, et al., 2001, doi:10.2973/odp.proc.ir.188.2001). Ocean Drilling Program (ODP) Site 1165 is situated in a water depth of 3357 m on the continental rise offshore from Prydz Bay and lies in front of the outlet for the Lambert Glacier-Amery Ice Shelf system that today drains 22% of East Antarctica. The site was drilled into mixed pelagic and hemipelagic sediments from the southwestern side of the Wild Drift. The drift is an elongate sediment body formed by the interaction of sediment supplied from continental shelf and slope with westward-flowing bottom currents. The sedimentary sequence is characterized by alternations between a generally gray to dark gray facies and a green to greenish gray facies. The greenish facies are structureless diatom-bearing clays with common bioturbation and larger amounts (>15%-20%) of biogenic silica, dispersed clasts, and lonestones than the dark gray facies, which are mostly less bioturbated clay with some silt laminations (Shipboard Scientific Party, 2001, doi:10.2973/odp.proc.ir.188.103.2001). High-quality advanced piston corer and extended core barrel cores containing nearly complete sections of middle Miocene to early Pliocene age allow a detailed characterization of sedimentary cycles and can provide indications for ice advances of the Lambert Glacier system into Prydz Bay, for the extent of sea ice, and for changes in oceanic circulation. The purpose of this work is to provide a data set of coarse-fraction mass percentage (>63, >125, and >250 µm) and biogenic silica content measured on sediments of late Miocene to early Pliocene age drilled at Site 1165. Additionally, high-resolution records of magnetic susceptibility (MS) and gamma ray attenuation (GRA) bulk density are presented. These shipboard data sets were edited postcruise. Furthermore, I provide a high-resolution dry bulk density record that is derived from GRA bulk density and can be used for the calculation of mass accumulation rates. These sedimentological and physical parameters will be used in future work to understand the depositional pattern of alternating biogenic and terrigenous sediments that was observed at Site 1165 (Shipboard Scientific Party, 2001, doi:10.2973/odp.proc.ir.188.103.2001).

Radiocarbon ages, d13C values and rare earth element content of sediment cores BP00-23/07 and BP00-07/06

Two bottom sediment cores (BP00-23/7 and BP00-7/6) recovered from the Yenisei transect in the southern Kara Sea are described. Data on their grain size composition, clay and heavy mineral assemblages, and distribution of a large group of chemical elements are presented. Radiocarbon dates based on AMS C-14 method suggest the Holocene age of sediments in the cores. Literature data on physical properties and foraminifers have also been analyzed. The facies affiliation of the lithostratigraphic subdivisions has been unraveled. History of the Yenisei River runoff in the Holocene has been reconstructed on the basis of different indicators.

Hydrate, ice and quartz content of eight holes of Leg 204

The state of preservation of natural gas hydrate samples, recovered from 6 sites drilled during ODP Leg 204 at southern summit of Hydrate Ridge, Oregon Margin, has been investigated by X-ray diffraction (XRD) and cryo-scanning-electron-microscopy (cryo-SEM) techniques. A detailed characterization of the state of decomposition of gas hydrates is necessary since no pressurized autoclave tools were used for sampling and partial dissociation must have occurred during recovery prior to the quench and storage in liquid nitrogen. Samples from 16 distinct horizons have been investigated by synchrotron X-ray diffraction measurements at HASYLAB/ Hamburg. A full profile fitting analysis ("Rietveld method") of synchrotron XRD data provides quantitative phase determinations of the major sample constituents such as gas hydrate structure I (sI), hexagonal ice (Ih) and quartz. The ice content (Ih) in each sample is related to frozen water composed of both original existing pore water and the water from decomposed hydrates. Hydrate contents as measured by diffraction vary between 0 and 68 wt.% in the samples we measured. Samples with low hydrate content usually show micro-structural features in cryo-SEM ascribed to extensive decomposition. Comparing the appearance of hydrates at different scales, the grade of preservation seems to be primarily correlated with the contiguous volume of the original existing hydrate; the dissociation front appears to be indicated by micrometer-sized pores in a dense ice matrix.