Interhelical angle and distance preferences in globular proteins

Orientational preferences between interacting helices within globular proteins have been studied extensively over the years. A number of classical structural models such as "knobs into holes" and "ridges into grooves" were developed decades ago to explain perceived preferences in interhelical angle distributions. In contrast, relatively recent works have examined statistical biases in angular distributions which result from spherical geometric effects. Those works have concluded that the predictions of classical models are due in large part to these biases. In this article we perform an analysis on the largest set of helix-helix interactions within high-resolution structures of nonhomologous proteins studied to date. We examine the interhelical angle distribution as a function of spatial distance between helix pairs. We show that previous efforts to normalize angle distribution data did not include two important effects: 1), helices can interact with each other in three distinct ways which we refer to as "line-on-line," "endpoint-to-line," and "endpoint-to-endpoint," and each of these interactions has its own geometric effects which must be included in the proper normalization of data; and 2), all normalizations that depend on geometric parameters such as interhelical angle must occur before the data is binned to avoid artifacts of bin size from biasing the conclusions. Taking these two points into account, we find that there are very pronounced preferences for helices to interact at angles of approximately +/-160 and +/-20 degrees in the line-on-line case. This pattern persists when the closest alpha-carbons in the helices vary from 4 to 12 A. The endpoint-to-line and endpoint-to-endpoint cases also exhibit distinct preferences when the data is normalized properly. Analysis of the local structural interactions which give rise to these preferences has not been studied here and is left for future work.     

Size of the fibrillar centres of the nucleoli in the supraoptic nucleus of the rat taking the Swiss cheese effect into account

The size of the fibrillar centres (FC) in nucleoli was investigated taking the Swiss cheese effect into account. Electron microscopy was performed on the neurons of the rat supraoptic nucleus after the secretion of vasopressin had been fully suppressed by water load, after the secretion had been stimulated by water deprival and in normal rats with water ad libitum. When the secretory activity was suppressed from a normal level to approximately no activity, the size of the individual FC was doubled. Moreover, with increasing secretory activity the number of FC per cell increased.     

Variability of bacterial biofilms of the "tina" wood vats used in the ragusano cheese-making process

Ragusano cheese is a "protected denomination of origin" cheese made in the Hyblean region of Sicily from raw milk using traditional wooden tools, without starter. To explore the Ragusano bacterial ecosystem, molecular fingerprinting was conducted at different times during the ripening and biofilms from the wooden vats called "tinas" were investigated. Raw milks collected at two farm sites, one on the mountain and one at sea level, were processed to produce Ragusano cheese. Raw milk, curd before and after cooking, curd at stretching time (cheese 0 time), and cheese samples (4 and 7 months) were analyzed by PCR-temporal temperature gel electrophoresis (PCR-TTGE) and by classical enumeration microbiology. With the use of universal primers, PCR-TTGE revealed many differences between the raw milk profiles, but also notable common bands identified as Streptococcus thermophilus, Lactobacillus lactis, Lactobacillus delbrueckii, and Enterococcus faecium. After the stretching, TTGE profiles revealed three to five dominant species only through the entire process of ripening. In the biofilms of the two tinas used, one to five species were detected, S. thermophilus being predominant in both. Biofilms from five other tinas were also analyzed by PCR-TTGE, PCR-denaturating gradient gel electrophoresis, specific PCR tests, and sequencing, confirming the predominance of lactic acid bacteria (S. thermophilus, L. lactis, and L. delbrueckii subsp. lactis) and the presence of a few high-GC-content species, like coryneform bacteria. The spontaneous acidification of raw milks before and after contact with the five tinas was followed in two independent experiments. The lag period before acidification can be up to 5 h, depending on the raw milk and the specific tina, highlighting the complexity of this natural inoculation system.     

Microbiological quality of Pecorino Siciliano "primosale" cheese on retail sale in the street markets of Palermo, Italy

Pecorino Siciliano (PS) "primosale" is a traditional Sicilian fresh soft cheese made from sheep's milk. Short-ripening time and production from unpasteurized or raw milk can facilitate bacterial contamination of PS "primosale". The microbiological quality of "primosale" on retail sale in the street markets of Palermo, Italy was studied by detecting the common food pathogens Listeria monocytogenes and Staphylococcus aureus and indicator microorganisms, such as Escherichia coli, Enterobacteriaceae and Staphylococcaceae. In our study, 4% and 44% of the samples, respectively, did not comply with the acceptability levels fixed by European regulations for S. aureus and E. coli. A high contamination of bacteria belonging to Enterobacteriaceae and Staphylococcaceae was found in 42% and 50% of the cheeses analyzed, respectively. Such results indicate poor husbandry and poor hygiene practices during milk collection or preservation or during cheese production processes and handling. In addition, the retail sale conditions may have played a role in cheese contamination since a correlation was found between poor microbiological quality and some selling parameters. This study emphasizes the need to improve production hygiene throughout the PS food chain in line with the traditional cheese-making procedures. Labelling of PS with clear information on whether the cheese was prepared from raw milk also requires improvement.     

Fate of Mycobacterium avium subsp. paratuberculosis in Swiss hard and semihard cheese manufactured from raw milk

Raw milk was artificially contaminated with declumped cells of Mycobacterium avium subsp. paratuberculosis at a concentration of 10(4) to 10(5) CFU/ml and was used to manufacture model hard (Swiss Emmentaler) and semihard (Swiss Tisliter) cheese. Two different strains of M. avium subsp. paratuberculosis were tested, and for each strain, two model hard and semihard cheeses were produced. The survival of M. avium subsp. paratuberculosis cells was monitored over a ripening period of 120 days by plating out homogenized cheese samples onto 7H10-PANTA agar. In both the hard and the semihard cheeses, counts decreased steadily but slowly during cheese ripening. Nevertheless, viable cells could still be detected in 120-day cheese. D values were calculated at 27.8 days for hard and 45.5 days for semihard cheese. The most important factors responsible for the death of M. avium subsp. paratuberculosis in cheese were the temperatures applied during cheese manufacture and the low pH at the early stages of cheese ripening. Since the ripening period for these raw milk cheeses lasts at least 90 to 120 days, the D values found indicate that 10(3) to 10(4) cells of M. avium subsp. paratuberculosis per g will be inactivated.     

Influence of the Volume Fraction,Size and Surface Coating of Hard Spheres on the Microstructure and Rheological Properties of Model Mozzarella Cheese

This study investigated the influence of model filler particles (glass beads) on the microstructure and rheological properties of Mozzarella cheese. Model Mozzarella cheese composites with increasing volume fractions of glass beads of various sizes and surface properties were processed in a Rapid Visco Analyser (RVA). Confocal laser scanning microscope images showed that all the hard spheres were dispersed in the protein phase, rather than in the fat phase. Dynamic oscillatory rheology revealed that the volume fraction of the glass beads had a major influence on the complex modulus (G*) of the cheese composites, whereas the size and the coating of the glass beads had no influence. However, the zero shear viscosity (η ₀), measured using the creep-compliance test, was affected by both the size and the volume fraction of the glass beads. This indicated that there were some interactions between the glass beads and the cheese matrix. Filler–matrix interactions played a major role in the fracture properties of the cheese composites. The fracture stress (σ _f ) was highly dependent on the coating and the size of the glass beads. Simple equations for filled gels from the literature fitted well with the experimental results and could be successfully applied for future predictions. According to this study, the transfer of knowledge from filled polymer composites to model cheese appears relevant. This can provide a good basis for designing new dairy product structures.     

Minimal size of Nitrobacter membrane frangments retaining nitrite oxidizing activity

Summary The minimal size of active membrane fragments from sonic homogenates of a Nitrobacter cell suspension is about 22 m. Nitrite oxidizing activity is absent from particles smaller than that although the distribution of cytochrome a, a link in the respiratory chain responsible for nitrite oxidation, does not show any abnormality below the critical size indicated.Two independent estimates of the parameters of the cumulative distribution function for particle size in sonic homogenates have been made using either statistics from electron micrographs or sedimentation pattern observed after density gradient centrifugation. The distribution function was found to be of the log-normal type which was considered to be a consequence of the observed kinetics of sonic comminution. Another estimate of the parameters of the distribution function was made by fixed angle centrifugation, a method much less accurate with respect to size determination but which allowed a rapid estimate of nitrite oxidizing capacity remaining in particles smaller than the given size.Results from the first two determinations of the distribution function for particle size and of its parameters were then used for correcting the error in the estimate of the critical size from the activity found in supernatants from centrifugations in fixed angle rotors.     

First evidence of lysogeny in Propionibacterium freudenreichii subsp. shermanii

Dairy propionic acid bacteria, particularly the species Propionibacterium freudenreichii, play a major role in the ripening of Swiss type cheese. Isometric and filamentous bacteriophages infecting P. freudenreichii have previously been isolated from cheese. In order to determine the origin of these bacteriophages, lysogeny of P. freudenreichii was determined by isometric bacteriophage type analysis. The genomic DNA of 76 strains were hybridized with the DNA of nine bacteriophages isolated from Swiss type cheeses, and the DNA of 25 strains exhibited strong hybridization. Three of these strains released bacteriophage particules following UV irradiation (254 nm) or treatment with low concentrations of mitomycin C. A prophage-cured derivative of P. freudenreichii was readily isolated and subsequently relysogenized. Lysogeny was therefore formally demonstrated in P. freudenreichii.     

Spatial distribution of bacterial colonies in a model cheese

In most ripened cheeses, bacteria are responsible for the ripening process. Immobilized in the cheese matrix, they grow as colonies. Therefore, their distribution as well as the distance between them are of major importance for ripening steps since metabolites diffuse within the cheese matrix. No data are available to date about the spatial distribution of bacterial colonies in cheese. This is the first study to model the distribution of bacterial colonies in a food-type matrix using nondestructive techniques. We compared (i) the mean theoretical three-dimensional (3D) distances between colonies calculated on the basis of inoculation levels and considering colony distribution to be random and (ii) experimental measurements using confocal microscopy photographs of fluorescent colonies of a Lactococcus lactis strain producing green fluorescent protein (GFP) inoculated, at different levels, into a model cheese made by ultrafiltration (UF). Enumerations showed that the final numbers of cells were identical whatever the inoculation level (10(4) to 10(7) CFU/g). Bacterial colonies were shown to be randomly distributed, fitting Poisson's model. The initial inoculation level strongly influenced the mean distances between colonies (from 25 μm to 250 μm) and also their mean diameters. The lower the inoculation level, the larger the colonies were and the further away from each other. Multiplying the inoculation level by 50 multiplied the interfacial area of exchange with the cheese matrix by 7 for the same cell biomass. We finally suggested that final cell numbers should be discussed together with inoculation levels to take into account the distribution and, consequently, the interfacial area of colonies, which can have a significant influence on the cheese-ripening process on a microscopic scale.     

USE OF PURCHASE PREFERENCE OPTIONS TO INCREASE "NO PREFERENCE" FREQUENCIES IN PLACEBO PREFERENCE TESTS

Besides responses to the different stimuli being tested in a paired preference test, responses to identical "placebo" stimuli can be used as a screening tool to identify biased consumers. Those consumers who give preference responses to identical stimuli can be assumed to be biased. Accordingly, only the data from unbiased consumers need to be considered for the different stimuli. The problem with this procedure is that the sample size is reduced. The goal of the present research was to see whether using options associated with purchase intent, elicited a greater number of "No Preference" responses to identical "placebo" stimuli. It was found that they did. The increase was large when the preference options implied exclusivity. In conditions where the preference strength options were not so strong, the frequency of "No Preference" responses dropped accordingly.

PRACTICAL APPLICATIONS

A problem with paired preference testing is the tendency of consumers to give false preferences, which produces the seriously misleading overestimation of the proportion of consumers who have preferences for one or other of the products being assessed. The "placebo" condition is an important control for alleviating this problem. The statistical analysis can be improved by finding a protocol that maximizes the proportion of "No Preference" responses in the placebo condition. The key finding here is that using purchase intent questions rather than preference questions may possibly provide a way of achieving this aim.     

Influence of the hole geometry on the flow distribution in ventricular catheters for hydrocephalus

Background

Hydrocephalus is a medical condition consisting of an abnormal accumulation of cerebrospinal fluid within the brain. A catheter is inserted in one of the brain ventricles and then connected to an external valve to drain the excess of cerebrospinal fluid. The main drawback of this technique is that, over time, the ventricular catheter ends up getting blocked by the cells and macromolecules present in the cerebrospinal fluid. A crucial factor influencing this obstruction is a non-uniform flow pattern through the catheter, since it facilitates adhesion of suspended particles to the walls. In this paper we focus on the effects that tilted holes as well as conical holes have on the flow distribution and shear stress.

Methods

We have carried out 3D computational simulations to study the effect of the hole geometry on the cerebrospinal fluid flow through ventricular catheters. All the simulations were done with the OpenFOAM® toolbox. In particular, three different groups of models were investigated by varying (i) the tilt angles of the holes, (ii) the inner and outer diameters of the holes, and (iii) the distances between the so-called hole segments.

Results

The replacement of cylindrical holes by conical holes was found to have a strong influence on the flow distribution and to lower slightly the shear stress. Tilted holes did not involve flow distribution changes when the hole segments are sufficiently separated, but the mean shear stress was certainly reduced.

Conclusions

The authors present new results about the behavior of the fluid flow through ventricular catheters. These results complete earlier work on this topic by adding the influence of the hole geometry. The overall objective pursued by this research is to provide guidelines to improve existing commercially available ventricular catheters.

     

Angle distribution of foliage in individual Chamaecyparis obtusa canopies and effect of angle on diffuse light penetration

 The vertical distribution of foliage angle and area of three Chamaecyparis obtusa trees was determined by the triangle method, which calculates foliage geometry using measured coordinates of the leaf ”corners”, in a 43-year-old plantation in central Japan. Vertical distribution patterns of leaf area were different depending on tree size, but the boundary heights, which divide the canopy into sunlit and shaded parts, were similar in the three sample trees. The value of the average foliage angle [I(Z)] at a given depth (Z) from the tip of the stem decreased continually from the upper to lower layers within the canopy. The vertical patterns of changes in I(Z) were different among the three trees, but could be expressed by the following allometric equation as a function of depth.

Fate of Mycobacterium avium subsp. paratuberculosis in Swiss Hard and Semihard Cheese Manufactured from Raw Milk

Raw milk was artificially contaminated with declumped cells of Mycobacterium avium subsp. paratuberculosis at a concentration of 10⁴ to 10⁵ CFU/ml and was used to manufacture model hard (Swiss Emmentaler) and semihard (Swiss Tisliter) cheese. Two different strains of M. avium subsp. paratuberculosis were tested, and for each strain, two model hard and semihard cheeses were produced. The survival of M. avium subsp. paratuberculosis cells was monitored over a ripening period of 120 days by plating out homogenized cheese samples onto 7H10-PANTA agar. In both the hard and the semihard cheeses, counts decreased steadily but slowly during cheese ripening. Nevertheless, viable cells could still be detected in 120-day cheese. D values were calculated at 27.8 days for hard and 45.5 days for semihard cheese. The most important factors responsible for the death of M. avium subsp. paratuberculosis in cheese were the temperatures applied during cheese manufacture and the low pH at the early stages of cheese ripening. Since the ripening period for these raw milk cheeses lasts at least 90 to 120 days, the D values found indicate that 10³ to 10⁴ cells of M. avium subsp. paratuberculosis per g will be inactivated.     

Isolation of histamine-producing Lactobacillus buchneri from Swiss cheese implicated in a food poisoning outbreak.

A histamine-producing strain of Lactobacillus buchneri was isolated from Swiss cheese that had been implicated in an outbreak of histamine poisoning. It produced up to 4,070 nmol of histamine per ml in MRS broth supplemented with 0.1% histidine. The identification of this isolate was based on its biochemical, bacteriological, and DNA characterizations.     

Localization of Active Microorganisms in Cheese by Autoradiography

By using an autoradiographic technique, one can follow, during ripening of a cheese, the distribution, size, and metabolic activity of microcolonies. Fragments of cheese were labeled with [³H]leucine, fixed, and mounted in epoxy resin. After exposure and development, sections were examined by optical microscopy. In Camembert cheese, bacterial microcolonies synthesized protein rapidly during the beginning of the ripening process. At the end of the ripening process, active bacterial clusters were scarcer and of two types: (i) large microcolonies with reduced labeling, and (ii) microcolonies having the same size as those observed at the beginning of the ripening process, but with slight or no labeling.     

On-line sterilization of cheese whey using ultraviolet radiation

The effectiveness of ultraviolet radiation for on-line sterilization of cheese whey was investigated. The effects of flow rate and residence time on the performance of three UV reactors having different gap sizes (18, 13, and 6 mm) were studied. Six flow rates and six residence times were tested with the three UV reactors. The cheese whey used in this study had a very high turbidity (4317 NTU), very poor transmittance in the UV radiation germicidal range ( approximately 0%), and high percentage of large solid particles ( approximately 20% > 100 microm). Although the cheese whey physical characteristics showed low probability of sterilization using UV radiation, the study showed that UV radiation can be used on-line to sterilize cheese whey if the proper reactor gap size and the appropriate residence time are used. There were combined effects of the flow rate and gap size. The cell removal efficiency increased with increases in residence time and decreases in the UV reactor gap size. Removal efficiency of 100% was not achieved in this study with the first UV reactor (18-mm gap size), whereas 100% removal efficiency was achieved with the second (13-mm gap size) and third (6-mm gap size) UV reactors at residence times of 2.0 and 0.5 h, respectively. The microbial decay rates achieved in this study were 4.94, 7.62, and 20.9 h(-)(1) using the first, second, and third UV reactor, respectively. Residence times of 3.3, 2.1, and 0.8 h would be required to completely destruct a microbial population of 5.95 x 10(6) cells/mL using the first, second, and third UV reactors, respectively. Although cheese whey sterilization using UV radiation seems to be a good alternative to pasteurization, increases in cheese whey temperature resulted in lamp fouling. If online sterilization is to be used, the fouling problem should be investigated and a maintenance scheme for the UV reactor should be developed.     

Isolation of histamine-producing Lactobacillus buchneri from Swiss cheese implicated in a food poisoning outbreak

A histamine-producing strain of Lactobacillus buchneri was isolated from Swiss cheese that had been implicated in an outbreak of histamine poisoning. It produced up to 4,070 nmol of histamine per ml in MRS broth supplemented with 0.1% histidine. The identification of this isolate was based on its biochemical, bacteriological, and DNA characterizations.     

Alpine glacial relict species losing out to climate change: The case of the fragmented mountain hare population (Lepus timidus) in the Alps

Alpine and Arctic species are considered to be particularly vulnerable to climate change, which is expected to cause habitat loss, fragmentation and—ultimately—extinction of cold‐adapted species. However, the impact of climate change on glacial relict populations is not well understood, and specific recommendations for adaptive conservation management are lacking. We focused on the mountain hare (Lepus timidus) as a model species and modelled species distribution in combination with patch and landscape‐based connectivity metrics. They were derived from graph‐theory models to quantify changes in species distribution and to estimate the current and future importance of habitat patches for overall population connectivity. Models were calibrated based on 1,046 locations of species presence distributed across three biogeographic regions in the Swiss Alps and extrapolated according to two IPCC scenarios of climate change (RCP 4.5 & 8.5), each represented by three downscaled global climate models. The models predicted an average habitat loss of 35% (22%–55%) by 2100, mainly due to an increase in temperature during the reproductive season. An increase in habitat fragmentation was reflected in a 43% decrease in patch size, a 17% increase in the number of habitat patches and a 34% increase in inter‐patch distance. However, the predicted changes in habitat availability and connectivity varied considerably between biogeographic regions: Whereas the greatest habitat losses with an increase in inter‐patch distance were predicted at the southern and northern edges of the species’ Alpine distribution, the greatest increase in patch number and decrease in patch size is expected in the central Swiss Alps. Finally, both the number of isolated habitat patches and the number of patches crucial for maintaining the habitat network increased under the different variants of climate change. Focusing conservation action on the central Swiss Alps may help mitigate the predicted effects of climate change on population connectivity.     

"Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as "ant" and "grasshopper" strategies of resource utilization. Interestingly, a strain may be "ant" in one medium and "grasshopper" in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective.     

Involvement of an N-Acetylglucosaminidase in Autolysis of Propionibacterium freudenreichii CNRZ 725

Propionibacterium freudenreichii plays an important role in Swiss cheese ripening (it produces propionic acid, acetic acid, and CO₂). Moreover, autolysis of this organism certainly contributes to proteolysis and lipolysis of the curd because intracellular enzymes are released. By varying external factors, we determined the following conditions which promoted autolysis of both whole cells and isolated cell walls of P. freudenreichii CNRZ 725: (i) 0.1 M potassium phosphate buffer (pH 5.8) at 40°C and (ii) 0.05 to 0.1 M KCl at 40°C. We found that early-exponential-phase cells possessed the highest autolytic activity. It should be emphasized that the pH of Swiss cheese curd (pH 5.5 to 5.7) is near the optimal pH which we determined. Ultrastructural observations by electron microscopy revealed a 16-nm-thick homogeneous cell wall, as well as degradation of the cell wall that occurred concomitantly with cell autolysis. In the presence of 0.05 M potassium chloride, there was a great deal of isolated cell wall autolysis (the optical density at 650 nm decreased 77.5% ± 7.3% in 3 h), and one-half of the peptidoglycan material was released. Finally, the main autolytic activity was due to an N-acetylglucosaminidase activity.