A Basis for Spatial and Social Patterns in Ant Species: Dynamics and Mechanisms of Aggregation

Aggregation is usually studied in functional terms, forgetting mechanisms. In this paper, experimental results on the ant Lasius niger, complemented by a model, allow us to understand the mechanisms responsible for aggregation and to study the influence of the population density on this phenomenon. The results show (1) a high level of aggregation and the emergence of a large cluster; (2) that aggregation results from an amplification mechanism—the greater the number of ants inside a cluster, the greater the time spent by one ant in this cluster; and (3) that population density has only a weak influence on the aggregation process. This method of analysis and these results can certainly be extended not only in social insects but also in other species, like subsocial arthropods.     

Niche width and niche overlap: a method based on type-2 fuzzy sets

Complicated ecosystems and the high non-linearity of evolution has made biology more adaptable to a variety of environments. The relationship between life and environment demands a dynamic definition of niche and its measurement. In this paper we propose a model of niche with dynamic character based on the “broad band” effect in type-2 fuzzy sets. The niche in this definition is an interval in each ecological dimension which is dynamic in character and depends on the actual environment. We also give formulas for niche width and niche overlap. We compute the niche width and overlap for plants and animals and then compare these results with previous results. The results for niche width in this paper reflect the diversity of resources used by species or communities. The results for niche overlap demonstrate overlap under different environmental conditions. The results are, moreover, intervals, which could provide more information. The model in this paper could therefore be used to describe the state of every resource comprehensively, reflecting the interaction between species and environment.     

Defects in the Error Prevention Oxidized Guanine System Potentiate Stationary-Phase Mutagenesis in Bacillus subtilis

Previous studies showed that a Bacillus subtilis strain deficient in mismatch repair (MMR; encoded by the mutSL operon) promoted the production of stationary-phase-induced mutations. However, overexpression of the mutSL operon did not completely suppress this process, suggesting that additional DNA repair mechanisms are involved in the generation of stationary-phase-associated mutants in this bacterium. In agreement with this hypothesis, the results presented in this work revealed that starved B. subtilis cells lacking a functional error prevention GO (8-oxo-G) system (composed of YtkD, MutM, and YfhQ) had a dramatic propensity to increase the number of stationary-phase-induced revertants. These results strongly suggest that the occurrence of mutations is exacerbated by reactive oxygen species in nondividing cells of B. subtilis having an inactive GO system. Interestingly, overexpression of the MMR system significantly diminished the accumulation of mutations in cells deficient in the GO repair system during stationary phase. These results suggest that the MMR system plays a general role in correcting base mispairing induced by oxidative stress during stationary phase. Thus, the absence or depression of both the MMR and GO systems contributes to the production of stationary-phase mutants in B. subtilis. In conclusion, our results support the idea that oxidative stress is a mechanism that generates genetic diversity in starved cells of B. subtilis, promoting stationary-phase-induced mutagenesis in this soil microorganism.     

Use of nfsB, encoding nitroreductase, as a reporter gene to determine the mutational spectrum of spontaneous mutations in Neisseria gonorrhoeae

Background  

Organisms that are sensitive to nitrofurantoin express a nitroreductase. Since bacterial resistance to this compound results primarily from mutations in the gene encoding nitroreductase, the resulting loss of function of nitroreductase results in a selectable phenotype; resistance to nitrofurantoin. We exploited this direct selection for mutation to study the frequency at which spontaneous mutations arise (transitions and transversions, insertions and deletions).     

Allochronic isolation and incipient hybrid speciation in tiger swallowtail butterflies

Hybridization leading to reproductively isolated, novel genotypes is poorly understood as a means of speciation and few empirical examples have been studied. In 1999, a previously non-existent delayed flight of what appeared to be the Canadian tiger swallowtail butterfly, Papilio canadensis, was observed in the Battenkill River Valley, USA. Allozyme frequencies and morphology suggest that this delayed flight was the product of hybridization between Papilio canadensis and its sibling species Papilio glaucus. The mitochondrial DNA (mtDNA) restriction fragment length polymorphisms presented here indicate that only P. canadensis-like mtDNA occurs in this population, suggesting that introgression likely occurred from hybrid males mating with P. canadensis females. Preliminary studies of this population indicated that delayed post-diapause pupal emergence in this hybrid genotype was the root cause behind the observed delayed flight, which suggests a potential empirical example of a mechanism leading to reproductive isolation. Here we provide further evidence of the role of adult pupal emergence as a reproductive barrier likely leading to reproductive isolation. In particular, we present results from pupal emergence studies using four different spring and two different winter temperature treatments. The results indicate a clear separation of adult emergences between the hybrid population and both parental species. However, our results indicate that exceptionally hot springs are likely to lead to greater potential for overlap between the local parental species, P. canadensis, and this delayed population with hybrid origins. Conversely, our results also show that warmer winters are likely to increase the temporal separation of the hybrid population and the parental species. Finally, we report recently collected evidence that this hybrid population remains morphologically distinct.     

Research into the oxidation of abietic acid–derived enone with atmospheric oxygen

This work presents results of methyl 7-oxoabiet-13(14)-en-18-oate ( 3 ) self-oxidation with air-oxygen in the presence of various bases such as triethylamine or sodium t-butoxide. While under aerobic conditions, the use of sodium t-butoxide as a base results in the formation of four isomeric alcohols, an addition of triethylamine into reaction medium directs the enone 3 oxidation to hydroperoxides. To clarify this base dependence and to obtain more in-depth information about this reaction additional studies with cyclohexenone as a reference enone have been undertaken. Their results demonstrated the predisposition of abietane hydroperoxides to oxidize α,β-unsaturated ketones to epoxides in the presence of t-butoxide while reducing the hydroperoxide group to hydroxyl. This ability of hydroperoxides to epoxidize conjugated double bonds and confirmed by the present study intermolecular course allowed proposing a plausible mechanism for this reaction.     

Ouabain-dependent potassium-potassium exchange in the toad bladder

Summary Recent results from this laboratory have indicated the existence of two potassium compartments in the isolated toad bladder. Only one of these, containing less than 10% of total intracellular potassium, appears to be related to the sodium transport system, since potassium influx at the serosal border of this compartment is coupled to the sodium efflux which occurs there. Ouabain, which specifically inhibits serosal sodium exit, has no effect on potassium fluxes and compartment sizes in bladders mounted in normal (2.5mm K) Ringer's solution. However, in the presence of this inhibitor, removal of serosal potassium results in a significant decrease in the rate coefficient for potassium efflux into the serosal medium, while an increase in serosal potassium results in a significant rise in this parameter, which appears to saturate at approximately 5mm K. This sensitivity to serosal potassium is seen neither in the absence of ouabain nor when the sodium pump is inactivated by removal of sodium from the mucosal medium. Furosemide, which also inhibits the sodium transport system, both inhibits potassium transport parameters in normal Ringer's and abolishes the potassium-sensitive potassium efflux seen in the presence of ouabain. Thus, the Na–K pump appears to operate as a K–K exchanger when the sodium system is inhibited by ouabain; this K–K exchange mechanism is inhibited by furosemide. One explanation for these results is that ouabain effects an alteration in the affinities of the transport system for sodium and potassium.     

Classifiers for Ischemic Stroke Lesion Segmentation: A Comparison Study

Motivation

Ischemic stroke, triggered by an obstruction in the cerebral blood supply, leads to infarction of the affected brain tissue. An accurate and reproducible automatic segmentation is of high interest, since the lesion volume is an important end-point for clinical trials. However, various factors, such as the high variance in lesion shape, location and appearance, render it a difficult task.

Methods

In this article, nine classification methods (e.g. Generalized Linear Models, Random Decision Forests and Convolutional Neural Networks) are evaluated and compared with each other using 37 multiparametric MRI datasets of ischemic stroke patients in the sub-acute phase in terms of their accuracy and reliability for ischemic stroke lesion segmentation. Within this context, a multi-spectral classification approach is compared against mono-spectral classification performance using only FLAIR MRI datasets and two sets of expert segmentations are used for inter-observer agreement evaluation.

Results and Conclusion

The results of this study reveal that high-level machine learning methods lead to significantly better segmentation results compared to the rather simple classification methods, pointing towards a difficult non-linear problem. The overall best segmentation results were achieved by a Random Decision Forest and a Convolutional Neural Networks classification approach, even outperforming all previously published results. However, none of the methods tested in this work are capable of achieving results in the range of the human observer agreement and the automatic ischemic stroke lesion segmentation remains a complicated problem that needs to be explored in more detail to improve the segmentation results.     

Different forms of phototropic response induced by microbeam irradiation of discrete regions of an organ

Abstract Continuous unilateral microbeam (1 mm) irradiation of coleoptiles of Avena saliva L. produces growth responses in non-irradiated regions of the organ. Irradiation of the apex is followed by differential growth which commences in the apical zone, but then moves in a basipetal direction and results in positive curvature. Irradiation of the base also results in differential growth which commences at the apex and moves basipetally. However, the growth differential in this case results in negative curvature. The results of basal irradiation suggest the likely occurrence of acropetal transmission of the phototropic signal. The rate of movement of this signal is faster than the documented rate of auxin transport.     

A Contact-Network-Based Formulation of a Preferential Mixing Model

Heterogeneity in the number of potentially infectious contacts and connectivity correlations (“like attaches to like” i.e., assortatively mixed or “opposites attract” i.e., disassortatively mixed) have important implications for the value of the basic reproduction ratio R ₀ and final epidemic size. In this paper, we present a contact-network-based derivation of a simple differential equation model that accounts for preferential mixing based on the number of contacts. We show that results based on this model are in good qualitative agreement with results obtained from preferential mixing models used in the context of sexually transmitted diseases (STDs). This simple model can accommodate any mixing pattern ranging from completely disassortative to completely assortative and allows the derivation of a series of analytical results.     

Evidence against the use of fecal pellet size for age determination in European wild rabbits

Techniques for estimating the age of wild animals are crucial to many aspects of the study of population biology. Accurate estimates of the proportion of different age classes in wild rabbit populations would be very useful, and the possibility that it could be obtained from the pellet size holds great appeal. However, this suggestion has created controversy in the literature as this technique has not been validated. This study involved assessment of whether threshold fecal pellet diameters could be used to differentiate adult and juvenile rabbits. The proportion of adults in four wild rabbit populations living in semi-natural conditions was compared with the proportion of animal pellets greater than threshold diameters of 6 mm and 4 mm. Our results suggest that inferring a relationship between the proportion of pellets >6 mm diameter and the proportion of adults in a population is not applicable to European wild rabbits, and that the use of this method could produce erroneous interpretations. The use of a 4 mm pellet diameter threshold appeared to produce even more inaccurate results. Studies that use this technique should include validation, as the results can vary greatly among individuals and populations.     

Oral Bioavailability of Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans in Industrial Soils

In this study, the oral bioavailabilities of numerous 2,3,7,8-PCDD/F congeners were evaluated in soil samples from an industrial site. The purpose of this study is several-fold: (1) to compare the soil bioavailability results of the different PCDD/F congeners; (2) to evaluate the consistency of the bioavailability results with those obtained in an in vitro bioaccessibility study with simulated GI tract fluids; and (3) to develop quantitative bioavailability measurements that are appropriate for use in a health risk assessment for this site. Soil samples containing PCDD/F toxic equivalent (TEQ) concentrations ranging from 0.53–45.2 ng/g were administered to female Sprague Dawley rats via oral gavage. Reference formulations of PCDD/Fs were administered intravenously or by oral gavage. The overall relative bioavailability of PCDD/Fs in the soil samples on a TEQ basis ranged from 17 to 51%, with a mean of 38%. The results of the in vitro bioaccessibility study were consistent with the bioavailability results (mean extracted TEQ of 22%). Because of the clear relationship between increasing chlorination and decreasing bioavailability and bioaccessibility observed in this study, we suggest that simply extrapolating results from one congener to another may be associated with a high degree of uncertainty.     

Disruption of a Conserved CAP-D3 Threonine Alters Condensin Loading on Mitotic Chromosomes Leading to Chromosome Hypercondensation

The condensin complex plays a key role in organizing mitotic chromosomes. In vertebrates, there are two condensin complexes that have independent and cooperative roles in folding mitotic chromosomes. In this study, we dissect the role of a putative Cdk1 site on the condensin II subunit CAP-D3 in chicken DT40 cells. This conserved site has been shown to activate condensin II during prophase in human cells, and facilitate further phosphorylation by polo-like kinase I. We examined the functional significance of this phosphorylation mark by mutating the orthologous site of CAP-D3 (CAP-D3^T1403A) in chicken DT40 cells. We show that this mutation is a gain of function mutant in chicken cells; it disrupts prophase, results in a dramatic shortening of the mitotic chromosome axis, and leads to abnormal INCENP localization. Our results imply phosphorylation of CAP-D3 acts to limit condensin II binding onto mitotic chromosomes. We present the first in vivo example that alters the ratio of condensin I:II on mitotic chromosomes. Our results demonstrate this ratio is a critical determinant in shaping mitotic chromosomes.     

Metallothionein-bound cadmium in the gut of the insect Orchesella cincta (Collembola) in relation to dietary cadmium exposure

Metallothionein is considered to be a potential biomarker for heavy metal exposure in the terrestrial environment. However, limited information is available on metallothioneins from insects, a major class of terrestrial invertebrates. In this study we have quantified metallothioneins in the springtail Orchesella cincta by determining metallothionein-bound cadmium after separation of these proteins using gel filtration and reversed phase chromatography from total body homogenates of animals dietary exposed to different concentrations of cadmium. Furthermore, we have studied in more detail where cadmium and metallothionein-bound cadmium is located within this animal. The concentration of metallothionein-bound cadmium increases with the exposure concentration in the same way as the total internal concentration. Both reach a plateau at an exposure concentration of approximately 1.0 μmol Cd/dry food. Cadmium is primarily located within the gut of O. cincta and isolation of metallothionein from this organ gives results identical to isolations from total bodies. Based on this results an estimation of the metallothionein level at the highest exposure concentration results in a concentration of about 115 μg metallothionein/g fresh gut. The O. cincta metallothionein gives the possibility of using this protein as a biomarker for heavy metal exposure in soil insects.     

LabPush: A Pilot Study of Providing Remote Clinics with Laboratory Results via Short Message Service (SMS) in Swaziland,Africa

Background

Turnaround time (TAT) is an important indicator of laboratory performance. It is often difficult to achieve fast TAT for blood tests conducted at clinics in developing countries. This is because clinics where the patient is treated are often far away from the laboratory, and transporting blood samples and test results between the two locations creates significant delay.Recent efforts have sought to mitigate this problem by using Short Message Service (SMS) to reduce TAT. Studies reporting the impact of this technique have not been published in scientific literature however. In this paper we present a study of LabPush, a system developed to test whether SMS delivery of HIV related laboratory results to clinics could shorten TAT time significantly.

Method

LapPush was implemented in six clinics of the Kingdom of Swaziland. SMS results were sent out from the laboratory as a supplement to normal transport of paper results. Each clinic was equipped with a mobile phone to receive SMS results. The laboratory that processes the blood tests was equipped with a system for digital input of results, and transmission of results via SMS to the clinics.

Results

Laboratory results were received for 1041 different clinical cases. The total number of SMS records received (1032) was higher than that of paper records (965), indicating a higher loss rate for paper records. A statistical comparison of TAT for SMS and paper reports indicates a statistically significant improvement for SMS. Results were more positive for more rural clinics, and an urban clinic with high workload.

Conclusion

SMS can be used to reduce TAT for blood tests taken at clinics in developing countries. Benefits are likely to be greater at clinics that are further away from laboratories, due to the difficulties this imposes on transport of paper records.     

Crystal Structure of Hcp from Acinetobacter baumannii: A Component of the Type VI Secretion System

The type VI secretion system (T6SS) is a bacterial macromolecular machine widely distributed in Gram-negative bacteria, which transports effector proteins into eukaryotic host cells or other bacteria. Membrane complexes and a central tubular structure, which resembles the tail of contractile bacteriophages, compose the T6SS. One of the proteins forming this tube is the hemolysin co-regulated protein (Hcp), which acts as virulence factor, as transporter of effectors and as a chaperone. In this study, we present the structure of Hcp from Acinetobacter baumannii, together with functional and oligomerization studies. The structure of this protein exhibits a tight β barrel formed by two β sheets and flanked at one side by a short α-helix. Six Hcp molecules associate to form a donut-shaped hexamer, as observed in both the crystal structure and solution. These results emphasize the importance of this oligomerization state in this family of proteins, despite the low similarity of sequence among them. The structure presented in this study is the first one for a protein forming part of a functional T6SS from A. baumannii. These results will help us to understand the mechanism and function of this secretion system in this opportunistic nosocomial pathogen.     

A rapidly new-typed detection of norovirus based on F<Subscript>0</Subscript>F<Subscript>1</Subscript>-ATPase molecular motor biosensor

In order to adapt port rapid detection of food borne norovirus, presently we developed a new typed detection method based on F₀F₁-ATPase molecular motor biosensor. A specific probe was encompassed the conservative region of norovirus and F₀F₁-ATPase within chromatophore was constructed as a molecular motor biosensor through the “ε-subunit antibody-streptomycin-biotin-probe” system. Norovirus was captured based on probe-RNA specific binding. Our results demonstrated that the Limit of Quantification (LOQ) is 0.005 ng/mL for NV RNA and also demonstrated that this method possesses specificity and none cross-reaction for food borne virus. What’s more, the experiment used this method could be accomplished in 1 h. We detected 10 samples by using this method and the results were consistent with RT-PCR results. Overall, based on F₀F₁-ATPase molecular motors biosensor system we firstly established a new typed detection method for norovirus detection and demonstrated that this method is sensitive and specific and can be used in the rapid detection for food borne virus.     

MADAM - An open source meta-analysis toolbox for R and Bioconductor

Background  

Meta-analysis is a major theme in biomedical research. In the present paper we introduce a package for R and Bioconductor that provides useful tools for performing this type of work. One idea behind the development of MADAM was that many meta-analysis methods, which are available in R, are not able to use the capacities of parallel computing yet. In this first version, we implemented one meta-analysis method in such a parallel manner. Additionally, we provide tools for combining the results from a set of methods in an ensemble approach. Functionality for visualization of results is also provided.     

Consensus Statement for the Management and Communication of High Risk Laboratory Results

Ineffective test follow-up is a major source of harm for patients around the world. Unreliable communication from medical laboratories (henceforth termed ‘laboratories’) to clinicians of results that represent critical or significant risk to patients (collectively termed ‘high risk results’) is a contributing factor to this problem. Throughout Australasia, management practices for such results vary considerably. The recommendations presented in this document are based on best practice derived from the published literature and follow consultation with a wide range of stakeholders. These recommendations were created to harmonise Australasian practices by guiding laboratories in the design and implementation of safe and effective communication procedures for managing high risk results which require timely notification.