Tuning the HNN experiment: generation of serine–threonine check points

We describe here the tunability of the HNN experiment to obtain certain residue specific peak patterns in the spectra of (¹⁵N, ¹³C) labeled proteins. This is achieved by tuning a band-selective 180° pulse on the carbon channel in the pulse sequence, whereby one can tamper with the C^α–C^β coupling evolutions for the different residues. Specifically, we generate distinctive peak patterns for serine and threonine and their neighbors in the different planes of the three dimensional spectrum. These provide useful anchor points during sequential assignment of backbone resonances. The performance of this experiment, referred to as HNN-ST here, is demonstrated using two proteins, one properly folded and the other completely denatured. With the availability of high field spectrometers, techniques such as TROSY, and ever increasing sensitivities in the probes, this experiment with its large number of check points has a great potential for rapid and unambiguous backbone resonance assignment in large proteins.     

Four points on Lennart von Post and the invention of “Pollen Statistics”

This essay is a contribution to the historiography of Lennart von Post and the early development of quantitative pollen analysis. Based on von Post’s own publications and source material from the archives of Stockholm University College, where he was appointed professor in 1929, the essay offers four points on von Post’s scientific identity and the collective work through which quantitative pollen analysis, or “pollen statistics”, came into being. The four points are, first, that von Post made his career as a geologist; second, that he framed pollen analysis as a means to tackle Quaternary geological issues; third, that his work benefitted from collective work, both in the field and in the laboratory; and fourth, that quantitative pollen analysis was not accepted without criticism, taking some years to break through beyond the Geological Survey, where von Post worked before he became professor.     

Predicting the points of interaction of small molecules in the NF-κB pathway

Background  

The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway.     

Crucial points within the pore as determinants of K⁺ channel conductance and gating

While selective for K⁺, K⁺ channels vary significantly among their rate of ion permeation. Here, we probe the effect of steric hindrance and electrostatics within the ion conduction pathway on K⁺ permeation in the MthK K⁺ channel using structure-based mutagenesis combined with single-channel electrophysiology and X-ray crystallography. We demonstrate that changes in side-chain size and polarity at Ala88, which forms the constriction point of the open MthK pore, have profound effects on single-channel conductance as well as open probability. We also reveal that the negatively charged Glu92s at the intracellular entrance of the open pore form an electrostatic trap, which stabilizes a hydrated K⁺ and facilitates ion permeation. This electrostatic attraction is also responsible for intracellular divalent blockage, which renders the channel inward rectified in the presence of Ca²⁺. In light of the high structural conservation of the selectivity filter, the size and chemical environment differences within the portion of the ion conduction pathway other than the filter are likely the determinants for the conductance variations among K⁺ channels.     

Spectrographic analysis points to source–filter coupling in rutting roars of Iberian red deer

Source–filter coupling is the rarest acoustic phenomenon not only in Iberian red deer, but in any mammal. In most mammals, sound production can be well described in the framework of source–filter theory. The vocal output is the result of combined work of the larynx (the source) and of the supralaryngeal vocal tract (the filter). The source–filter theory suggests the independence of source and filter. Thus, vocal tract filtering should not affect the fundamental frequency (f0) of the sound created in the larynx. Spectrographically, the source is mostly characterized by the f0 and its harmonics, while the filter by the vocal tract resonances, i.e., formant frequencies. Nevertheless, a non-independent (coupled) source and filter can be proposed when the vocal folds start oscillating at one of the formant frequencies. Coupling between source and filter has been found in human singers and predicted for red deer Cervus elaphus by a computer modeling approach. This study describes different modes of phonation in a natural bout of rutting calls of Iberian red deer Cervus elaphus hispanicus and the transition from a chaotic mode to a probable source–filter coupling mode. This phenomenon might be involved in the production of extremely high-frequency bugles of North American and Asian subspecies of C. elaphus.     

Starting points for small mammal population recovery after wildfire: recolonisation or residual populations?

Wildfire is a major driver of spatio‐temporal variation in terrestrial ecosystems. Large wildfires are predicted to occur more frequently due to climate change. The mechanisms by which post‐fire recovery proceeds are influenced by the abundance of survivors, and their distribution in relation to habitat variability and refugia. Thus, characterising early post‐fire demographic processes is critical to understanding the demographic and community‐level responses of ecosystems to fire. The Black Saturday fires of February 2009 burnt an area of approximately 3500 km² in Victoria, Australia. We quantified the effects of this high severity forest fire on the habitat, abundance, sex ratio and body mass of two small mammal species, the agile antechinus Antechinus agilis and bush rat Rattus fuscipes. We developed a hypothetical framework to distinguish in situ survival and rapid recolonisation as the processes underlying short‐term post‐fire distributions. These hypotheses were based on expected patterns of abundance over increasing distances from unburnt sources, and the estimated recolonisation capabilities of each species and sex. The agile antechinus and bush rat were present in burnt sites at 30% and 12% of the density observed in unburnt sites. In situ survival, and not recolonisation, was the most plausible explanation for our findings. Abundance and body mass data indicated a greater effect of fire on the bush rat than the agile antechinus. The bush rat showed a shift in topographic association, whereby drainage lines acted as post‐fire refugia. Our findings suggest these species do not depend on recolonisation for recovery, and that the bush rat will follow a nucleated recovery, expanding from topographic refugia. Thus, connectivity‐reducing management activities, such as salvage logging and firebreak and road construction, may not affect the early stages of population recovery in remaining stands of burnt forest. Rather, ongoing recovery is likely to be limited by demographic rates and resource availability.     

Connecting species’ geographical distributions to environmental variables: range maps versus observed points of occurrence

Connecting the geographical occurrence of a species with underlying environmental variables is fundamental for many analyses of life history evolution and for modeling species distributions for both basic and practical ends. However, raw distributional information comes principally in two forms: points of occurrence (specific geographical coordinates where a species has been observed), and expert-prepared range maps. Each form has potential short-comings: range maps tend to overestimate the true occurrence of a species, whereas occurrence points (because of their frequent non-random spatial distribution) tend to underestimate it. Whereas previous comparisons of the two forms have focused on how they may differ when estimating species richness, less attention has been paid to the extent to which the two forms actually differ in their representation of a species’ environmental associations. We assess such differences using the globally distributed avian order Galliformes (294 species). For each species we overlaid range maps obtained from IUCN and point-of-occurrence data obtained from GBIF on global maps of four climate variables and elevation. Over all species, the median difference in distribution centroids was 234 km, and median values of all five environmental variables were highly correlated, although there were a few species outliers for each variable. We also acquired species’ elevational distribution mid-points (mid-point between minimum and maximum elevational extent) from the literature; median elevations from point occurrences and ranges were consistently lower (median −420 m) than mid-points. We concluded that in most cases occurrence points were likely to produce better estimates of underlying environmental variables than range maps, although differences were often slight. We also concluded that elevational range mid-points were biased high, and that elevation distributions based on either points or range maps provided better estimates.     

Natural products as starting points for future anti-malarial therapies: going back to our roots?

Background

Population movements along the Thailand-Cambodia border, particularly among highly mobile and hard-to-access migrant groups from Cambodia and Myanmar, are assumed to play a key role in the spread of artemisinin resistance. Data on treatment-seeking behaviours, knowledge and perceptions about malaria, and use of preventive measures is lacking as characteristics of this population prevent them from being represented in routine surveillance and the lack of a sampling frame makes reliable surveys challenging.

Methods

A survey of migrant populations from Cambodia and Myanmar was implemented in five selected rural locations in Thailand along the Thai-Cambodian border using respondent driven sampling (RDS) to determine demographic characteristics of the population, migratory patterns, knowledge about malaria, and health-care -seeking behaviours.

Results

The majority of migrants from Myanmar are long-term residents (98%) with no plans to move back to Myanmar, understand spoken Thai (77%) and can therefore benefit from health messages in Thai, have Thai health insurance (99%) and accessed public health services in Thailand (63%) for their last illness. In comparison, the majority of Cambodian migrants are short-term (72%). Of the short-term Cambodian migrants, 92% work in agriculture, 18% speak Thai, 3.4% have Thai health insurance, and the majority returned to Cambodia for treatment (45%), self-treated (11%), or did not seek treatment for their last illness (27%).

Conclusion

Most highly mobile migrants along the Thai-Cambodia border are not accessing health messages or health treatment in Thailand, increasing their risk of malaria and facilitating the spread of potentially resistant Plasmodium falciparum as they return to Cambodia to seek treatment. Reaching out to highly mobile migrants with health messaging they can understand and malaria diagnosis and treatment services they can access is imperative in the effort to contain the spread of artemisinin-resistant P. falciparum.     

Comparison of mathematically determined blood lactate and heart rate “threshold” points and relationship with performance

The purpose of this study was to investigate the relationship between threshold points for heart rate (Thfc) and blood lactate (Thla) as determined by two objective mathematical models. The models used were the mono-segmental exponential (EXP) model of Hughson et al. and the log-log (LOG) model of Beaver et al. Inter-correlations of these threshold points and correlations with performance were also studied. Seventeen elite runners (mean, SD = 27.5, 6.5 years; 1.73, 0.05 m; 63.8, 7.3 kg; and maximum oxygen consumption of 67.8, 3.7 ml.kg-1.min-1) performed two maximal multistage running field tests on a 183.9-m indoor track with inclined turns. The initial speed of 9 km.h-1 (2.5 m.s-1) was increased by 0.5 km.h-1 (0.14 m.s-1) every lap for the fc test and by 1 km.h-1 (0.28 m.s-1) every 4 min for the la test. After fitting the la or the fc data to the two mathematical models, the threshold speed was assessed in the LOG model from the intersection of the two linear segments (LOG-la; LOG-fc) and in the EXP model from a tangent point (TI-la; TI-fc). Thla and Thfc speeds computed with the two models were significantly different (P less than 0.001) and poorly correlated (LOG-la vs LOG-fc: r = 0.36, TI-la vs TI-fc: r = 0.13). In general, Thfc were less well correlated with performance than Thla. With two different objective mathematical models, this study has shown significant differences and poor correlations between Thla and Thfc.(ABSTRACT TRUNCATED AT 250 WORDS)     

Automation et robotique préanalytique points forts et zones sensibles d’un nouveau développement

Cet article est la première partie d’un dossier relatif à l’Automation et à la Robotique. Elle est plus théorique. Elle sera suivie d’une deuxième partie pratique, réalisée en lien avec des installations effectives.     

Intervention points for community- acquired methicillin–resistant <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> colonization and load in healthy population of lesser Himalayan Belt,South Asia,India

Objectives

To trace the critical practicing, clinical and epidemiological risk factors in bacterial load and points of intervention in spread of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) in healthy community.

Study Design

2872 individuals with no prominent clinical features were enrolled and administered a pre-tested questionnaire prepared on the basis of outcome of a prior pilot study in same region. Swab samples from skin, throat and nasal nares were tested for MRSA and molecular identification was done to track the strains moving from hospital to community.

Methods

Swab samples from skin, throat and nasal nares were tested for MRSA culture followed by molecular characterization of isolates and antimicrobial resistance pattern. Bacterial load was estimated to better understand the burden in different categories. Statistical analysis was done using SPSS 16.0 version.

Results

History of prior infection (OR 3.9, 95% CI 1.363 – 5.793), habit of self remedy (OR 3.2, 95% CI 0.991 – 1.473) and incomplete treatment (OR 0.26, 95% CI 0.08 – 0.80) (P < 0.05 for each) were the predominant factors that contributed to spread of CA-MRSA. Increased drug resistance in CA-MRSA was observed for 4 different clones: SCCmec ⁺ IVa/PVL ⁺, SCCmec ⁺ IVa/PVL ^? and SCCmec ⁺ IVc/PVL ⁺, SCCmec ⁺ IVc/PVL ^?. Bacterial load was found significantly high in below poverty line dwellers and drug abusers (P < 0.05).

Conclusion

We identified habit of self remedy, drug abusing and incomplete treatment as practicing risk factors where interventions can be made to manage the dissemination of CA-MRSA in rural population.

     

Determining tipping points in aquatic ecosystems: The case of biodiversity and chlorophyll α relations in fish pond systems

The management of biodiversity in aquatic ecosystems requires knowing the state of water quality linked to regime shifts in various taxonomic groups. We examine this question by studying the fish ponds in the Dombes region, France. These waterbodies are characterized by a high diversity of species. High levels of nutrients due to certain fish farming practices may cause significant eutrophication leading to loss in biodiversity and a shift from high coverage of aquatic vegetation to phytoplankton dominance may also be observed. The aim of this study is to assess tipping points, thresholds for effect, along a gradient of chlorophyll α in different taxonomic groups: aquatic vascular plants, phytoplankton, dragonflies and aquatic macro-invertebrates. Tipping points are analyzed with three different statistical methods: a method which evaluates tipping points with a difference in the mean (TMEAN), a second method which evaluates tipping point by comparing the mean and linear regressions before and after the tipping point (FSTAT) and third a method which evaluates linear regressions with a pivotal tipping point (SEGMENTED). We also compare tipping points for the different taxonomic groups using five different diversity indices: Observed richness, Jackknife first order, Fisher's alpha, Simpson index and Evenness.Our results show that there is an important variation in tipping points following the three statistical methods, but the SEGMENTED is the best method for evaluating tipping points. We observe a high difference of tipping point values for the different taxonomic groups depending on the diversity indices used. Jackknife first order has a better performance to evaluate a eutrophic change according to the diversity than the other indices.In all taxonomic groups, aquatic vascular plants are the most impacted by the chlorophyll α and almost all their tipping points are observed around 60 μg/L chlorophyll α concentrations. No significant relationship is found between chlorophyll α and phytoplankton diversity, while the two other groups, dragonflies and macro-invertebrates, are both impacted by the chlorophyll α but their relevant tipping points are situated in higher values than aquatic vascular plants.