Multiple Origins of kdr-type Resistance in the House Fly,Musca domestica

Insecticide resistance is a model phenotype that can be used to investigate evolutionary processes underlying the spread of alleles across a global landscape, while offering valuable insights into solving the problems that resistant pests present to human health and agriculture. Pyrethroids are one of the most widely used classes of insecticides world-wide and they exert their toxic effects through interactions with the voltage-sensitive sodium channel (Vssc). Specific mutations in Vssc (kdr, kdr-his and super-kdr) are known to cause resistance to pyrethroid insecticides in house flies. In order to determine the number of evolutionary origins of kdr, kdr-his and super-kdr, we sequenced a region of Vssc from house flies collected in the USA, Turkey and China. Our phylogenetic analysis of Vssc unequivocally supports the hypothesis of multiple independent origins of kdr, super-kdr and kdr-his on an unprecedented geographic scale. The implications of these evolutionary processes on pest management are discussed.     

KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs

Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way.     

Saccharomyces cerevisiae as a model organism: a comparative study

Background

Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking.

Methodology/Principal Findings

In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes.

Conclusions/Significance

The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.     

Diversity in Chemotaxis Mechanisms among the Bacteria and Archaea

The study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. In bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. Most insights into the processes involved have come from studies of Escherichia coli over the last three decades. However, in the last 10 years, with the sequencing of many prokaryotic genomes, it has become clear that E. coli represents a streamlined example of bacterial chemotaxis. While general features of excitation remain conserved among bacteria and archaea, specific features, such as adaptational processes and hydrolysis of the intracellular signal CheY-P, are quite diverse. The Bacillus subtilis chemotaxis system is considerably more complex and appears to be similar to the one that existed when the bacteria and archaea separated during evolution, so that understanding this mechanism should provide insight into the variety of mechanisms used today by the broad sweep of chemotactic bacteria and archaea. However, processes even beyond those used in E. coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli.     

A useful relationship between epidemiology and queueing theory: The distribution of the number of infectives at the moment of the first detection

In this paper we establish a relation between the spread of infectious diseases and the dynamics of so called M/G/1 queues with processor sharing. The relation between the spread of epidemics and branching processes, which is well known in epidemiology, and the relation between M/G/1 queues and birth death processes, which is well known in queueing theory, will be combined to provide a framework in which results from queueing theory can be used in epidemiology and vice versa.In particular, we consider the number of infectious individuals in a standard SIR epidemic model at the moment of the first detection of the epidemic, where infectious individuals are detected at a constant per capita rate. We use a result from the literature on queueing processes to show that this number of infectious individuals is geometrically distributed.     

Dissecting the function of Cullin-RING ubiquitin ligase complex genes in planarian regeneration

The ubiquitin system plays a role in nearly every aspect of eukaryotic cell biology. The enzymes responsible for transferring ubiquitin onto specific substrates are the E3 ubiquitin ligases, a large and diverse family of proteins, for which biological roles and target substrates remain largely undefined. Studies using model organisms indicate that ubiquitin signaling mediates key steps in developmental processes and tissue regeneration. Here, we used the freshwater planarian, Schmidtea mediterranea, to investigate the role of Cullin-RING ubiquitin ligase (CRL) complexes in stem cell regulation during regeneration. We identified six S. mediterranea cullin genes, and used RNAi to uncover roles for homologs of Cullin-1, ?3 and ?4 in planarian regeneration. The cullin-1 RNAi phenotype included defects in blastema formation, organ regeneration, lesions, and lysis. To further investigate the function of cullin-1-mediated cellular processes in planarians, we examined genes encoding the adaptor protein Skp1 and F-box substrate-recognition proteins that are predicted to partner with Cullin-1. RNAi against skp1 resulted in phenotypes similar to cullin-1 RNAi, and an RNAi screen of the F-box genes identified 19 genes that recapitulated aspects of cullin-1 RNAi, including ones that in mammals are involved in stem cell regulation and cancer biology. Our data provides evidence that CRLs play discrete roles in regenerative processes and provide a platform to investigate how CRLs regulate stem cells in vivo.     

Biotechnology of non-Saccharomyces yeasts—the ascomycetes

Saccharomyces cerevisiae and several other yeast species are among the most important groups of biotechnological organisms. S. cerevisiae and closely related ascomycetous yeasts are the major producer of biotechnology products worldwide, exceeding other groups of industrial microorganisms in productivity and economic revenues. Traditional industrial attributes of the S. cerevisiae group include their primary roles in food fermentations such as beers, cider, wines, sake, distilled spirits, bakery products, cheese, sausages, and other fermented foods. Other long-standing industrial processes involving S. cerevisae yeasts are production of fuel ethanol, single-cell protein (SCP), feeds and fodder, industrial enzymes, and small molecular weight metabolites. More recently, non-Saccharomyces yeasts (non-conventional yeasts) have been utilized as industrial organisms for a variety of biotechnological roles. Non-Saccharomyces yeasts are increasingly being used as hosts for expression of proteins, biocatalysts and multi-enzyme pathways for the synthesis of fine chemicals and small molecular weight compounds of medicinal and nutritional importance. Non-Saccharomyces yeasts also have important roles in agriculture as agents of biocontrol, bioremediation, and as indicators of environmental quality. Several of these products and processes have reached commercial utility, while others are in advanced development. The objective of this mini-review is to describe processes currently used by industry and those in developmental stages and close to commercialization primarily from non-Saccharomyces yeasts with an emphasis on new opportunities. The utility of S. cerevisiae in heterologous production of selected products is also described.     

Transformation of saturated nitrogen-containing heterocyclic compounds by microorganisms

The saturated nitrogen-containing heterocyclic compounds include many drugs and compounds that may be used as synthons for the synthesis of other pharmacologically active substances. The need for new derivatives of saturated nitrogen-containing heterocycles for organic synthesis, biotechnology and the pharmaceutical industry, including optically active derivatives, has increased interest in microbial synthesis. This review provides an overview of microbial technologies that can be valuable to produce new derivatives of saturated nitrogen-containing heterocycles, including hydroxylated derivatives. The chemo-, regio- and enantioselectivity of microbial processes can be indispensable for the synthesis of new compounds. Microbial processes carried out with fungi, including Beauveria bassiana, Cunninghamella verticillata, Penicillium simplicissimum, Aspergillus niger and Saccharomyces cerevisiae, and bacteria, including Pseudomonas sp., Sphingomonas sp. and Rhodococcus erythropolis, biotransform many substrates efficiently. Among the biological activities of saturated nitrogen-containing heterocyclic compounds are antimicrobial, antitumor, antihypertensive and anti-HIV activities; some derivatives are effective for the treatment and prevention of malaria and trypanosomiasis, and others are potent glycosidase inhibitors.     

Holotestoid: a computational model for testing hypotheses about echinoid skeleton form and growth

Regular echinoid skeletons, or tests, comprise plate patterns and overall shapes that have proven challenging to analyse solely on the basis of any one approach or process. Herein, we present a computational model, Holotestoid, that emulates four macrostructural ontogenic processes involved in test growth (plate growth, plate addition, plate interaction, and plate gapping). We devise a geometric representation for analysing tests and describe how we use analogies (bubble interactions and close-packing) to emulate the processes. In the computational model, the emulated processes are used to determine the plate size and plate shape and combined to simulate a growth zone. We simulated growth zones for Arbacia punctulata and for Strongylocentrotus franciscanus by changing the value for one parameter, the ambulacral column angle. We quantitatively compared morphological features for simulated forms to those for real specimens to test the computational model. Additionally, we simulated growth zones for A. punctulata, S. franciscanus, Eucidaris thouarsii, and Mellita quinquiesperforata by changing three parameters, ambulacral column angle, peristome radius to apical system radius ratio, and apical system radius to column length ratio. Holotestoid can be used to explain morphological disparity among echinoid tests.     

Multifractal analysis of K+ channel activity

The Multifractal version of the Detrended Fluctuation Analysis was used for the study of non-stationary dwell time series of Ca²⁺-activated K⁺ channels (K_Ca channels) in cultured kidney Vero cells and of voltage-dependent K⁺ channels (K_v channels) in mollusc (Lymnaea stagnalis) neurons. The data obtained can briefly be summarized as follows: (i) The generalized fluctuation function F _q (l) strongly depends on the index (order) q; for monofractal time series, such dependence is nonexistent; (ii) The relationship between the scaling exponent τ commonly employed in standard multifractal analysis and q is characterized by two slopes and a transitory region, whereas monofractal processes are characterized by the linear dependence; (iii) The relationship between the singularity spectrum f(h) and the Hurst exponent h is bell-shaped, while in the case of monofractal processes it is represented by a single point f(h) = 1. Random mixing of the time series resulted in the narrowing of the spectrum f(h) and a shift of f(h) towards the value more characteristic of stochastic (monofractal) processes (h ～ 0.5). It is concluded that the activities of both K_Ca channels in kidney Vero cells and of K_V channels in mollusc (Lymnaea stagnalis) neurons can be characterized as multifractal processes.     

Essential oil variations in different Perilla L. accessions: chemotaxonomic implications

Three processes play an important role in plant speciation: isolation, hybridization and polyploidization. Galapagos endemic Opuntia display putatively all of these processes. On this archipelago most islands are inhabited by a single Opuntia taxon. Santa Cruz, however, houses two morphologically distinct O. echios varieties (echios and gigantea). Morphological intermediates are found where these two geographically isolated varieties meet. Here we used ten microsatellite loci to reveal the population genetic structure of this system. In contrast to earlier studies, we found high genetic variability within localities. Genetic structuring was weak and no evidence for the existence of hybrids was found. The reasons for this weak genetic structure may include: the species’ hexaploid nature, high levels of gene flow, recent colonization, and the lack of geographic barriers. This first detailed genetic study on these threatened species will be important for further conservation planning.     

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.     

Thermostability of Fumonisin B1, a Mycotoxin from Fusarium moniliforme, in Corn

Fumonisin B₁ (FB₁) is a mycotoxin from Fusarium moniliforme that is frequently associated with corn. Thermal treatments are used in many processes concerning this cereal and its derivatives. The thermostability of this toxin in dry contaminated corn, resulting from F. moniliforme culture, was studied in different time-temperature combinations. FB₁ was quantified by instrumentalized thin-layer chromatography after a two-step sequential development and postchromatographic derivatization by p-anisaldehyde. The identity of FB₁ in extracts, before and after heat treatments, was confirmed by high-pressure liquid chromatography. For each temperature, the natural logarithm of the ratio of resulting FB₁ on initial content (In C/C₀) is linearly correlated to exposure time. The calculated half-lives (L₅₀), corresponding to the 50% value, were 10 min, 38 min, 175 min, and 8 h at 150, 125, 100, and 75°C, respectively. There is a linear relationship between calculated L₅₀s on a logarithmic scale and temperature. Therefore FB₁ is not significantly destroyed by the main drying processes of corn or thermal treatments used for its derivatives. Other associated means are required for detoxification.     

Stochastic Actin Polymerization and Steady Retrograde Flow Determine Growth Cone Advancement

Neuronal growth is an extremely complex yet reliable process that is directed by a dynamic lamellipodial structure at the tip of every growing neurite, called the growth cone. Lamellipodial edge fluctuations are controlled by the interplay between actin polymerization pushing the edge forward and molecular motor driven retrograde actin flow retracting the actin network. The leading edge switches randomly between extension and retraction processes. We identify switching of “on/off” states in actin polymerization as the main determinant of lamellipodial advancement. Our analysis of motility statistics allows for a prediction of growth direction. This was used in simulations explaining the amazing signal detection capabilities of neuronal growth by the experimentally found biased stochastic processes. Our measurements show that the intensity of stochastic fluctuations depend on changes in the underlying active intracellular processes and we find a power law η = a^∗x^α with exponent α = 2.63 ± 0.12 between noise intensity η and growth cone activity x, defined as the sum of protrusion and retraction velocity. Differences in the lamellipodial dynamics between primary neurons and a neuronal cell line further suggests that active processes tune the observed stochastic fluctuations. This hints at a possible role of noise intensity in determining signal detection sensitivity.     

Hystrichokolpoma from pleistocene sediments in Okinawa-Jima,Japan

Three species of Hystrichokolpoma (Dinophyceae) are described from lower Pleistocene sediments of Okinawa-jima in the Ryukyu-Islands, Southwest Japan. Hystrichokolpoma pacifica and H. okinawaia are new. H. pacifica is characterized by subconical to short cylindrical, large processes with rectangular or pentagonal bases, and H wokinawaia by short cylindrical to tubiform, large processes with denticulate to foliate distal extremities. The paratabulation of Hystrichokolpoma is discussed.     

Enhancing ATP-based bacteria and biofilm detection by enzymatic pyrophosphate regeneration

The manufacturing processes of many electronic and medical products demand the use of high-quality water. Hence the water supply systems for these processes are required to be examined regularly for the presence of microorganisms and microbial biofilms. Among commonly used bacteria detection approaches, the ATP luminescence assay is a rapid, sensitive, and easy to perform method. The aim of this study is to investigate whether ATP regeneration from inorganic pyrophosphate, a product of the ATP luminescence assay, can stabilize the bioluminescence signals in ATP detection. ADPglc pyrophosphorylase (AGPPase), which catalyzes the synthesis of ATP from PP_i in the presence of ADPglc, was selected because the system yields much lower luminescence background than the commercially available ATP sulfurylase/adenosine 5′-phosphosulfate (APS) system which was broadly used in pyrosequencing technology. The AGPPase-based assay could be used to measure both PP_i and ATP quantitatively and shows 1.5- to 4.0-fold slight increases in a 10-min assay. The method could also be used to stabilize the luminescence signals in detection of Escherichia coli, Pseudomonas aeruginosa, and Bacillus cereus in either broth or biofilm. These findings suggest that the AGPPase-based ATP regeneration system will find many practical applications such as detection of bacterial biofilm in water pipelines.     

Statistical properties of estimators for continuous time Markov branching processes with varying and random environments

Asymptotic properties are established for estimators of time dependent intensities in Markov branching processes with varying and random environments. For the varying environment model, the estimators are shown to be uniformly strongly consistent on bounded intervals as the initial population size X₀ → ∞, and, when considered as empirical stochastic processes, to converge weakly to Gaussian processes with independent increments. For random environments, the estimators are shown to be asymptotically normal as t → ∞, where t is the time parameter.     

Change Is Good: Variations in Common Biological Mechanisms in the Epsilonproteobacterial Genera Campylobacter and Helicobacter

Summary: Microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. The epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. Many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. Some epsilonproteobacteria, such as Campylobacter jejuni and Helicobacter pylori, are common pathogens of humans that inhabit specific regions of the gastrointestinal tract. As such, the biological processes of pathogenic Campylobacter and Helicobacter spp. are often modeled after those of common enteric pathogens such as Salmonella spp. and Escherichia coli. While many exquisite biological mechanisms involving biochemical processes, genetic regulatory pathways, and pathogenesis of disease have been elucidated from studies of Salmonella spp. and E. coli, these paradigms often do not apply to the same processes in the epsilonproteobacteria. Instead, these bacteria often display extensive variation in common biological mechanisms relative to those of other prototypical bacteria. In this review, five biological processes of commonly studied model bacterial species are compared to those of the epsilonproteobacteria C. jejuni and H. pylori. Distinct differences in the processes of flagellar biosynthesis, DNA uptake and recombination, iron homeostasis, interaction with epithelial cells, and protein glycosylation are highlighted. Collectively, these studies support a broader view of the vast repertoire of biological mechanisms employed by bacteria and suggest that future studies of the epsilonproteobacteria will continue to provide novel and interesting information regarding prokaryotic cellular biology.     

Insertionally inactivated and inducible recA alleles for use in Neisseria

Two classes of recA mutations have been constructed for use in Neisseria gonorrhoeae: three insertionally inactivated (`knockout') mutations and three LacI-regulatable constructs that can be shifted between Rec⁻ and Rec⁺ by the removal or addition of IPTG. The effects of regulating recA expression on the processes of DNA transformation, DNA repair and pilin-phase variation are described. These regulatable cassettes can also be used to control the expression of any chromosomal gene.     

Green bioprocess of degumming of jute fibers and bioscouring of cotton fabric by recombinant pectin methylesterase and pectate lyases from Clostridium thermocellum

Enzymatic processes are emerging as important green biotechnological processes in textile industry. The application of recombinant pectin methylesterase (CtPME) and pectate lyase (CtPL1B) from Clostridium thermocellum for enzymatic degumming of jute or bioscouring of cotton was evaluated. The effectiveness of processes by combination of two enzymes were evaluated that effective degumming of jute and bioscouring of cotton as compared with individual enzyme. The optimum concentrations of two enzymes mixture for both processes, degumming of jute and bio scouring of cotton were 5 mg/mL (2.1 U/mL) of CtPME and 5 mg/mL (3.0 U/mL) of CtPL1B under optimized conditions of 60 min, 100 rpm and 50 °C. FESEM images showed more effective removal of pectin from jute fiber and cotton fabric by enzyme mixture, nevertheless similar to NaOH treatment. Wettability analysis showed mixture of enzymes and NaOH treated cotton fabric absorbed a water drop in 10 s and 8 s, respectively. UTM analysis showed higher tensile strength and Young’s modulus for jute fiber and cotton fabric treated with enzyme mixture than untreated and were similar to those of NaOH treated. These results showed that the CtPME and CtPL1B mixture can be used for replacing the chemical process by green bioprocess in textile industry.