High-mass-resolution direct-tissue MALDI-FTMS reveals broad conservation of three neuropeptides (APSGFLGMRamide, GYRKPPFNGSIFamide and pQDLDHVFLRFamide) across members of seven decapod crustaean infraorders

Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) has become an important method for identifying peptides in neural tissues. The ultra-high-mass resolution and mass accuracy of MALDI-FTMS, in combination with in-cell accumulation techniques, can be used to advantage for the analysis of complex mixtures of peptides directly from tissue fragments or extracts. Given the diversity within the decapods, as well as the large number of extant species readily available for analysis, this group of animals represents an optimal model in which to examine phylogenetic conservation and evolution of neuropeptides and neuropeptide families. Surprisingly, no large comparative studies have previously been undertaken. Here, we have initiated such an investigation, which encompasses 32 species spanning seven decapod infraorders. Two peptides, APSGFLGMRamide and pQDLDHVFLRFamide, were detected in all species. A third peptide, GYRKPPFNGSIFamide, was detected in all species except members of the Astacidean genus Homarus, where a Val(1) variant was present. Our finding that these peptides are ubiquitously (or nearly ubiquitously) conserved in decapod neural tissues not only suggests important conserved functions for them, but also provides an intrinsic calibrant set for future MALDI-FTMS assessments of other peptides in this crustacean order.     

Rheological behaviour of some antibiotic biosynthesis liquids

This paper prsents the results of teh study of rheological behaviour of antibiotic biosynthesis liquids obtained by submerged aerobic cultivation of microorganisms belonging to the actinomycete and fungi classes, in stirred tank bioreactors with turbine impellers. These liquids have a non-Newtonian behaviour which follows the power-law rhcological model with a correlation index of over 0.95. The studied liquids are pseudoplastic, and alter their rheological properties, such as consistency index, (K), flow index, (n), apparent viscosity, (η_a), maximum Newtonian viscosity (η₀), with the culture age, microrganism strain and batch conditions. Also, these liquids are time dependent, exhibiting thixotropy. The most viscous liquids are produced by Streptomyces aureofaciens and Streptomyces rimosus cultivation, while that produced by Streptomyces griseus is the least viscous. A higher pseudoplasticity appears after 30 hours culture age. Since all these biosynthesis are aerobic, a careful observation of the rhelogical behaviour dynamics is necessary to avoid the oxygen culture supply limitation and the decrease of the bioreactor performance during biosynthesis.     

24-hour lock mass protection

The positive role and application of highly accurate mass measurements in proteomics is well documented. The new generation of hybrid FTMS and Q-TOF instruments, including the LTQ-Orbitrap (OT), is remarkable in their ability to routinely produce single-digit to subppm statistical mass accuracy while maintaining high analytical sensitivity. The use of mass calibrants (lock masses) to reduce the systematic error of mass-to-charge measurements has also been reported and, in some cases, incorporated in the instrument control software by the instrument manufacturers. We evaluated the use of one such calibrant in the OT (e.g., polydimethylcyclosiloxane, PCM) to study its impact on the rate of phosphopeptide annotation and found it to lack robustness under normal laboratory conditions. Therefore, we devised a strategy to improve its performance by increasing the external abundance of calibrant molecules in laboratory air. This resulted in a more robust performance of the preprogrammed lock mass recalibration feature as evidenced by improvements in both statistical mass accuracy and peptide annotation rates.     

Capillary Filling at the Microscale: Control of Fluid Front Using Geometry

We propose an experimental and theoretical framework for the study of capillary filling at the micro-scale. Our methodology enables us to control the fluid flow regime so that we can characterise properties of Newtonian fluids such as their viscosity. In particular, we study a viscous, non-inertial, non-Washburn regime in which the position of the fluid front increases linearly with time for the whole duration of the experiment. The operating shear-rate range of our apparatus extends over nearly two orders of magnitude. Further, we analyse the advancement of a fluid front within a microcapillary in a system of two immiscible Newtonian liquids. We observe a non-Washburn regime in which the front can accelerate or decelerate depending on the viscosity contrast between the two liquids. We then propose a theoretical model which enables us to study and explain both non-Washburn regimes. Furthermore, our theoretical model allows us to put forward ways to control the emergence of these regimes by means of geometrical parameters of the experimental set-up. Our methodology allows us to design and calibrate a micro-viscosimetre which works at constant pressure.     

Refractory heart failure

Any patient with so-called "refractory" heart failure should be looked upon as suboptimally handled. The patient should be studied for possible development of new disturbances, either inside or outside the vascular system, which, at the same time, have a bearing upon the heart failure.The entire therapeutic program should be reviewed to be sure that all aspects of therapy have been evaluated satisfactorily and established optimally. If diuretics, especially mercurial diuretics, have been given, the possible complications of such therapy, particularly in terms of electrolyte imbalance, should be considered. It is only through a general survey of the patient for an evaluation of these factors that they may be found and therapy instituted to minimize or eliminate them.     

CALIFORNIA MEDICAL ASSOCIATION

Any patient with so-called “refractory” heart failure should be looked upon as suboptimally handled. The patient should be studied for possible development of new disturbances, either inside or outside the vascular system, which, at the same time, have a bearing upon the heart failure.The entire therapeutic program should be reviewed to be sure that all aspects of therapy have been evaluated satisfactorily and established optimally. If diuretics, especially mercurial diuretics, have been given, the possible complications of such therapy, particularly in terms of electrolyte imbalance, should be considered. It is only through a general survey of the patient for an evaluation of these factors that they may be found and therapy instituted to minimize or eliminate them.     

Evaluation of the accuracy of precipitation methods for HDL cholesterol determination

Several methods for HDL-Cholesterol determination have been proposed; the over-floating cholesterol evaluation after non-HDL lipoproteins precipitation by polyanions with bivalent cations or neutral polymers is practical and not expensive, but it's accuracy and precision must be strictly control led. The Authors, after a review and a quality-check of the most used methods, conclude that the best accuracy for HDL-Cholesterol determination is provided by Dextransulphate-Mg-chloride and Phosphotungstate-Mg-chloride at pH 7,5.     

Is multiple-sequence alignment required for accurate inference of phylogeny?

The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.     

Particle rosettes and microtubular ridges on the plasma membrane of Chara

We have examined the plasma membrane of cortical and internodal cells of Chara globularis var. capillacea (Thuill.) Zanev. using rapid-freezing and freeze-fracturing techniques. The non-etched image of the protoplasmic face reveals particle rosettes, and also reveals ridges which can be correlated with cortical microtubules. Since both rosettes and microtubular ridges can thus be viewed simultaneously, we have looked for a spatial relationship between them, but have found them to be essentially independent. We have found that the density of particle rosettes is a function of age and of type of cell. Groups of pits may represent the complementary exoplasmic component of the rosettes.     

Optimization and use of peptide mass measurement accuracy in shotgun proteomics

Mass spectrometers that provide high mass accuracy such as FT-ICR instruments are increasingly used in proteomic studies. Although the importance of accurately determined molecular masses for the identification of biomolecules is generally accepted, its role in the analysis of shotgun proteomic data has not been thoroughly studied. To gain insight into this role, we used a hybrid linear quadrupole ion trap/FT-ICR (LTQ FT) mass spectrometer for LC-MS/MS analysis of a highly complex peptide mixture derived from a fraction of the yeast proteome. We applied three data-dependent MS/MS acquisition methods. The FT-ICR part of the hybrid mass spectrometer was either not exploited, used only for survey MS scans, or also used for acquiring selected ion monitoring scans to optimize mass accuracy. MS/MS data were assigned with the SEQUEST algorithm, and peptide identifications were validated by estimating the number of incorrect assignments using the composite target/decoy database search strategy. We developed a simple mass calibration strategy exploiting polydimethylcyclosiloxane background ions as calibrant ions. This strategy allowed us to substantially improve mass accuracy without reducing the number of MS/MS spectra acquired in an LC-MS/MS run. The benefits of high mass accuracy were greatest for assigning MS/MS spectra with low signal-to-noise ratios and for assigning phosphopeptides. Confident peptide identification rates from these data sets could be doubled by the use of mass accuracy information. It was also shown that improving mass accuracy at a cost to the MS/MS acquisition rate substantially lowered the sensitivity of LC-MS/MS analyses. The use of FT-ICR selected ion monitoring scans to maximize mass accuracy reduced the number of protein identifications by 40%.     

Analysis of some Filipino perspectives on ethical issues in multi-country collaborative research: a case of deep listening

The discussion on ethical issues, it is said, should not be confined to experts but should be extended to patients and local communities, because of the real need to engage stakeholders and non-stakeholders alike not only in carrying out any biomedical research project, but also in the drafting and legislation of bioethics instruments. Several local and inter-country consultations have already been conducted in furtherance of this goal, but there is much left to be desired in them. The consultations may have helped in articulating local principles, but not in making the instruments embody these principles. As such, instruments turn incompossible, i.e. the principles and actions they legitimate are not performable. In an ethnographic study conducted in the Philippines, for example, paragraphs 29 and 30 of the Declaration of Helsinki and CIOMS guidelines 8 and 15 are construed as not only contradictory to one another but also to local principles. This problem can be solved by taking deliberate steps to ensure that consultations are grounded in ethnographic data about local principles, which the instruments would embody. A steering committee can be of help in gathering ethnographic data, in conducting consultations at the local level, and in providing a venue for discourse on various bioethical issues.     

Explaining the Non-Newtonian Character of Aggregating Monoclonal Antibody Solutions Using Small-Angle Neutron Scattering

A monoclonal antibody solution displays an increase in low shear rate viscosity upon aggregation after prolonged incubation at 40°C. The morphology and interactions leading to the formation of the aggregates responsible for this non-Newtonian character are resolved using small-angle neutron scattering. Our data show a weak repulsive barrier before proteins aggregate reversibly, unless a favorable contact with high binding energy occurs. Two types of aggregates were identified after incubation at 40°C: oligomers with radius of gyration ∼10 nm and fractal submicrometer particles formed by a slow reaction-limited aggregation process, consistent with monomers colliding many times before finding a favorable strong interaction site. Before incubation, these antibody solutions are Newtonian liquids with no increase in low shear rate viscosity and no upturn in scattering at low wavevector, whereas aggregated solutions under the same conditions have both of these features. These results demonstrate that fractal submicrometer particles are responsible for the increase in low shear rate viscosity and low wavevector upturn in scattered intensity of aggregated antibody solutions; both are removed from aggregated samples by filtering.     

Explaining the Non-Newtonian Character of Aggregating Monoclonal Antibody Solutions Using Small-Angle Neutron Scattering

A monoclonal antibody solution displays an increase in low shear rate viscosity upon aggregation after prolonged incubation at 40°C. The morphology and interactions leading to the formation of the aggregates responsible for this non-Newtonian character are resolved using small-angle neutron scattering. Our data show a weak repulsive barrier before proteins aggregate reversibly, unless a favorable contact with high binding energy occurs. Two types of aggregates were identified after incubation at 40°C: oligomers with radius of gyration ∼10 nm and fractal submicrometer particles formed by a slow reaction-limited aggregation process, consistent with monomers colliding many times before finding a favorable strong interaction site. Before incubation, these antibody solutions are Newtonian liquids with no increase in low shear rate viscosity and no upturn in scattering at low wavevector, whereas aggregated solutions under the same conditions have both of these features. These results demonstrate that fractal submicrometer particles are responsible for the increase in low shear rate viscosity and low wavevector upturn in scattered intensity of aggregated antibody solutions; both are removed from aggregated samples by filtering.     

Dynamic choices are most accurate in small groups

According to the classic results of Galton and Condorcet, as well as in modern decision-making models, accuracy in groups increases with group size. However, these studies do not consider the naturally occurring situation in which individuals dynamically re-evaluate their decision with a possible change of opinion. The dynamics of re-evaluation in groups are very different to individual re-evaluation because individuals influence the group and the group influences the individual. We find that individual accuracy in a group is higher when individuals re-evaluate because all members have more access to social information, while in single decisions, those deciding first have less. This improvement is smaller in large groups as in this case errors can cascade across the members of the group before re-evaluation can correct them. The net result is a maximal accuracy at a small group size. We also analyzed the case in which individuals are influenced only by a small number of the other individuals. In this case, cascading errors affect the interacting subgroups but are very unlikely to reach the whole group. This results in a local optimum at a small group size but also an optimum at a very large size. We thus suggest that re-evaluation dynamics can make small and very large groups optimal. Also, features that may be seen as limitations, like an influence from only a small number of individuals, may turn to be beneficial when considering local animal interactions, here filtering out cascading of errors in the group when reconsideration dynamics takes place.     

扬子鳄的起源

介绍了现存鳄彼此间的亲缘关系、扬子鳄起源的时间和地点。主要结论可归纳如下：①现存鳄类在科、属、种分类上都存在不同意见;②扬子鳄与密河鳄被分在同一属内,但两者之间的亲缘关系存在争议,两者在形态、生化、细胞、分子生物学上差异很大;③Stell认为扬子鳄在中新世开始出现,作者认为它可能起源于渐新世或中新世早期;④Stell认为分布于北美的汤氏鳄（A.thomsoni)可能是扬子鳄的祖先类型,而另一些学者认为扬子鳄起源于亚洲的可能性更大些。     

Bubble rise velocities and drag coefficients in non-Newtonian polysaccharide solutions.

Microbially produced polysaccharides have properties which are extremely useful in different applications. Polysaccharide producing fermentations start with liquid broths having Newtonian rheology and end as highly viscous non-Newtonian solutions. Since aerobic microorganisms are used to produce these polysaccharides, it is of great importance to know the mass transfer rate of oxygen from a rising air bubble to the liquid phase, where the microorganisms need the oxygen to grow. One of the most important parameters determining the oxygen transfer rate is the terminal rise velocity of air bubble. The dynamics of the rise of air bubbles in the aqueous solutions of different, mostly microbially produced polysaccharides was studied in this work. Solutions with a wide variety of polysaccharide concentrations and rheological properties were studied. The bubble sizes varied between 0.01 mm3 and 10 cm3. The terminal rise velocities as a function of air bubble volume were studied for 21 different polysaccharide solutions with different rheological properties. It was found that the terminal velocities reached a plateau at higher bubble volumes, and the value of the plateau was nearly constant, between 23 and 27 cm/s, for all solutions studied. The data were analyzed to produce the functional relationship between the drag coefficient and Reynolds number (drag curves). It was found out that all the experimental data obtained from 21 polysaccharide solutions (431 experimental points), can be represented by a new single drag curve. At low values of Reynolds numbers, below 1.0, this curve could be described by the modofoed Hadamard-Rybczynski model, while at Re > 60 the drag coefficient was a constant, equal to 0.95. The latter finding is similar to that observed for bubble rise in Newtonian liquids which was explained on the basis of the "solid bubble" approach.     

Assessing the accuracy of small satellite transmitters on free‐living flying‐foxes

Satellite telemetry using ARGOS platform transmitter terminals (PTTs) is widely used to track the movements of animals, but little is known of the accuracy of these systems when used on active terrestrial mammals. An accurate estimate of the error, and therefore the limitations of the data, is critical when assessing the level of confidence in results. ARGOS provides published 68th percentile error estimates for the three most accurate location classes (LCs), but studies have shown that the errors can be far greater when the devices are attached to free‐living animals. Here we use data from a study looking at the habitat use of the spectacled flying‐fox in the wet tropics of Queensland to calculate these errors for all LCs in free‐living terrestrial mammals, and use these results to assess what level of confidence we would have in habitat use assignment in the study area. The results showed that our calculated 68th percentile errors were larger than the published ARGOS errors for all LCs, and that for all classes the error frequency had a very long tail. Habitat use results showed that the size of the error compared with the scale of the habitat the study was conducted in makes it unlikely that our data can be used to assess habitat use with great confidence. Overall, our results show that while satellite telemetry results are useful for assessing large scale movements of animals, in complex landscapes they may not be accurate enough to be used for finer scale analysis including habitat use assessment.     

Vertebrate defense against parasites: Interactions between avoidance,resistance, and tolerance

Hosts can utilize different types of defense against the effects of parasitism, including avoidance, resistance, and tolerance. Typically, there is tremendous heterogeneity among hosts in these defense mechanisms that may be rooted in the costs associated with defense and lead to trade‐offs with other life‐history traits. Trade‐offs may also exist between the defense mechanisms, but the relationships between avoidance, resistance, and tolerance have rarely been studied. Here, we assessed these three defense traits under common garden conditions in a natural host–parasite system, the trematode eye‐fluke Diplostomum pseudospathaceum and its second intermediate fish host. We looked at host individuals originating from four genetically distinct populations of two closely related salmonid species (Atlantic salmon, Salmo salar and sea trout, Salmo trutta trutta) to estimate the magnitude of variation in these defense traits and the relationships among them. We show species‐specific variation in resistance and tolerance and population‐specific variation in resistance. Further, we demonstrate evidence for a trade‐off between resistance and tolerance. Our results suggest that the variation in host defense can at least partly result from a compromise between different interacting defense traits, the relative importance of which is likely to be shaped by environmental components. Overall, this study emphasizes the importance of considering different components of the host defense system when making predictions on the outcome of host–parasite interactions.     

Contrast inversion in the epifluorescence of cholesterol-phospholipid monolayers

A number of dihydrocholesterol-phospholipid mixtures have been examined using the epifluorescence microscopy of monolayers at the air-water interface. These mixtures form two coexisting liquids. Fluorescence contrast was provided using a variety of different lipid probes. With increasing monolayer pressure, all of the charged probes show contrast inversion at higher dihydrocholesterol concentrations. That is, with increasing pressure the charged probes transfer from one liquid to the other, reversing the fluorescence contrast. A wide variety of phospholipids were studied, and the inversion was seen in all cases. In the inverted state and at the higher dihydrocholesterol concentrations, the immiscibility persists to the highest pressures employed, 30-40 mN/m. The data show that binary dihydrocholesterol-phospholipid mixtures can form three distinct liquids, one of which is interpreted as a phase rich in condensed complex.     

Traction on the retina induced by saccadic eye movements in the presence of posterior vitreous detachment

Posterior vitreous detachment is a fairly common condition in elderly people. Tractions exerted by the detached vitreous on the retina may result in retinal tears and detachments. We studied how these tractions can arise from saccadic eye movements. Numerical simulations have been performed on a two-dimensional model of the vitreous chamber within a rigid spherical sclera, subjected to prescribed finite-amplitude rotations about a vertical axis. The vitreous chamber was assumed to be split into two regions: one occupied by the detached vitreous, modeled as an elastic viscous solid, and the other occupied by the separated liquefied vitreous, modeled as a Newtonian fluid. At the interface between the two phases, we also considered the presence of the vitreous cortex, modeled as an elastic membrane. We tested several different configurations of the interface. In all cases, we found that eye rotations generate large tractions on the retina close to the attachment points of the membrane. Comparing them, we identified configurations of the vitreous detachment that exhibit higher tractions. We also investigated how the response to saccadic movements depends on some physical parameters, in particular on the rheological properties of the solid phase and the membrane. The numerical simulations show that the generated tractions may be of the same order of magnitude as the adhesive force between the retina and the pigment epithelium. Therefore, the model provides a sound physical justification for the hypothesis that saccadic movements, in the presence of posterior vitreous detachment, could be responsible for high tractions on the retina, which may trigger retinal tear formation.