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After decades of research and development, synthetic nucleic acids are beginning to enjoy significant success in the clinic. Approved drugs have increased interest in the field, and many basic research studies have focused on synthetic nucleic acids to control the action of messenger RNA and noncoding RNAs. Unfortunately, experimental designs are often inadequate, resulting in misleading interpretation of data and unconvincing work that wastes resources and does little to advance the field. The goal of this commentary is to outline the problems facing many researchers, especially those new to the use of synthetic oligonucleotides. We describe the minimum control experiments necessary to build a strong case for real effects that are likely due to interactions at the intended molecular target. A common set of standards for preparing and judging experiments should facilitate better interpretation of data and publications that contribute positively to using synthetic nucleic acids as tools and drugs. [ABSTRACT FROM AUTHOR]

The aim of the present study was to establish the effect of salt-free - salt diet (SFSD) on the size of antral follicles during salt consumption, the duration of controlled breeding campaign and the fertilities of ewes from the Ile de France breed. The experiment was carried out with 57 ewes, which were divided into 3 groups (19 ewes in each) depending on whether they were subjected to SFSD and their contacts with rams during the first 8 days of the beginning of breeding: Group I - SFSD + ram contact; Group II - only SFSD; Group III - no SFSD, only ram contacts. The first day of the salt diet coincided with the first day of ram contacts. Transrectal ultrasound examinations of the ovaries were done on days 1, 2, 3, 5, 6 and 7. The time of manifestation of estrus (in days), pregnancy rate and fecundity were studied. A significant effect of time (P<0.05) and diet (P<0.01) on the size of follicles was established. The onset of the first estrus, the shortest terms of breeding campaign, the fertility and the fecundity results gave us reason to favour the scheme applied to Group II. A stimulatory effect of the diet in that study was demonstrated, but the pattern was different from our previous studies. [ABSTRACT FROM AUTHOR]

The article offers information on scientific experiment on the screening and identification method for regulated veterinary drug residues in food. Topics discussed include standards for method performance requirements; use of Liquid chromatography-tandem mass spectrometry (LC-MS/MS); and information on routine surveillance for genetically modified product compliance.

Consistent and accurate manipulation of liquids is essential for many biology experiments. Teaching these skills is challenging in the laboratory. I have developed Training Tips, a homemade teaching tool to train students to use micropipettes in the classroom and laboratory. Training Tips provide obvious visual targets that enable inexperienced students to know immediately if they are pipetting accurately. [ABSTRACT FROM AUTHOR]

The centrifuge is an important piece of equipment for any biology lab, necessary for a wide variety of experiments. Cost, however, often prevents the use of centrifuges in many teaching labs, greatly limiting educational experiences for students. As a result, we describe how to construct a "homemade" single-speed mini-centrifuge using inexpensive parts easily acquired online or at hardware or other stores (e.g., a 4.7-quart plastic bowl and lid, standard computer cooling fan, AC/DC adapter, electrical wire, etc.). We further used this design and a commercial mini-centrifuge to pellet 1-mL samples of Tetrahymena thermophila, and we found that the two performed comparably. Finally, because our plans and the materials needed to build this device are all open source, we call our design the OPN Minifuge, and we hope that it will help to expand the scope of experiments that students can run in introductory and upper-level biology teaching labs. [ABSTRACT FROM AUTHOR]

The article offers information on a study which deals with BioBits Explorer kit which enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms. It mentions that the next-generation synthetic biology educational kit described here addresses the need for easy-to-implement, hands-on biology demonstrations in STEM education.

Digital microfluidic is an emerging technology to reduce the cost and time of experiments and improve the flexibility, automate‐ability and correctness of biochemical assays. In many of applications such as drug discovery and DNA profiling, a large number of bio‐operations (e.g. the chemical operations used in biology applications) must be done. In these applications, parallelising the operations will be critical in accuracy and cost of the process and digital microfluidic biochips can be considered as a reasonable platform. In this study, a new microfluidic architecture and the corresponding CAD flow is introduced to parallelise the assays on this platform. The authors implemented the proposed architecture and evaluated it using the large real bioassays. The authors' simulations show that the degree‐of‐parallelism and speed of bioassays are increased more than 4× and the improvements will be better for larger assays. This contribution can open new horizons in drug testing, biology experiments and medical diagnosis operations that contain iterative, time‐consuming and labour experiments. [ABSTRACT FROM AUTHOR]

Despite numerous calls for science education to be driven by authentic investigation, many laboratory experiences continue to consist of disconnected weekly units during which students carry out instructions that lead to some predetermined finding. This study developed and evaluated a pedagogical design for introductory biology labs where students designed, carried out, analyzed, and presented their own experiments. Each lab module was 3 weeks long, allowing students to complete the entire experimental process four times over the course of the semester. Assessment of the pedagogy included pre- and postsurveys, video analysis of group work, exit interviews, analysis of changes in lab reports across the semester, and instructor observations. Students rated their lab experiences highly, became more confident in using scientific process, and improved in terms of scientific process and scientific reasoning. Students also learned science content, though the content varied from student to student. The pedagogical design presented here is relatively time efficient to implement and maintain, and with subtle adjustments could be transferred to other courses and disciplines. [ABSTRACT FROM AUTHOR]

Exemplary for social insects,Temnothoraxants allow for various hands-on investigations in biology classes. The aim of this study was to provide a quantitative and qualitative analysis of secondary school students’ learning achievement after teaching units with ants lasting between one and six weeks. The questionnaires included transfer and factual knowledge tasks divided into eight fields of knowledge. Students (N  =  459) from 22 classes participated in the study and received different treatments: The experimental group (n  =  366) started their investigations by initial observation using stereo microscopes, while the control group (n  =  93) conducted ant research without this introductory teaching unit. We investigated the influence of class level, gender and time period of participation on knowledge acquisition. Independent of class level, factual learning achievement was observed for all fields of knowledge except ecology. We did not find a positive correlation between time period of participation and basic ant knowledge acquisition. The findings suggest that ant research may be implemented within the framework of a progressive curriculum for all secondary school students. However, attentive and detailed observation of ant colonies with stereo microscopes and continuous repetition of technical terms seem to be inevitable preconditions for learning achievement. [ABSTRACT FROM AUTHOR]

Background: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. Results: This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. Conclusions: An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments. [ABSTRACT FROM AUTHOR]

Human-assisted, trans-generational exposure to ocean warming and acidification has been proposed as a conservation and/or restoration tool to produce resilient offspring. To improve our understanding of the need for and the efficacy of this approach, we characterized life-history and physiological responses in offspring of the marine polychaete Ophryotrocha labronica exposed to predicted ocean warming ( OW: + 3°C), ocean acidification ( OA: pH −0.5) and their combination ( OWA: + 3°C, pH −0.5), following the exposure of their parents to either control conditions ( within-generational exposure) or the same conditions ( trans-generational exposure). Trans-generational exposure to OW fully alleviated the negative effects of within-generational exposure to OW on fecundity and egg volume and was accompanied by increased metabolic activity. While within-generational exposure to OA reduced juvenile growth rates and egg volume, trans-generational exposure alleviated the former but could not restore the latter. Surprisingly, exposure to OWA had no negative impacts within- or trans-generationally. Our results highlight the potential for trans-generational laboratory experiments in producing offspring that are resilient to OW and OA. However, trans-generational exposure does not always appear to improve traits and therefore may not be a universally useful tool for all species in the face of global change. [ABSTRACT FROM AUTHOR]

Various types of restraint collars have been used for research animals, and the Elizabethan collar (E-collar) is the most commonly used. However, animals can be choked by the E-collar or they tend to remove it; furthermore, repeated rubbing and scratching of the collar may chafe the neck. We developed a new restraint collar with a vest to overcome these limitations. The vest-collar (V-collar) can be worn similarly to a vest, in contrast to the E-collar, which is fixed around the neck. A cone-shaped collar is attached to the vest in the V-collar and is made of Eva foam to surround the chest softly, accompanied by a transparent polyvinyl chloride (PVC) film for visibility. To evaluate the performance of the V-collar, we conducted experiments with mice wearing the V-collar and the E-collar. Both groups showed normal weight gain and food intake. Glucose and stress hormone levels showed no significant differences, and no stress-associated leukocyte profiles were observed during the experiments. However, despite the short experimental duration, more than half of the mice in the E-collar group showed injury to the skin on the neck, with increased thickness of the epidermal and keratin layers. Moreover, inflammatory cell counts were higher in the E-collar group than in the V-collar group. In conclusion, the V-collar, in contrast to the E-collar, does not cause skin injuries in animals and is thus beneficial for animals and investigators. Investigators can effectively use the V-collar to enhance laboratory animal welfare. [ABSTRACT FROM AUTHOR]

Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems biology. In particular, examples reviewed in this paper suggest that rigorous mathematical expressions of design principles, imported primarily from engineering, could produce experimentally confirmable predictions of the regulatory properties of small biological networks. But this is not enough for contemporary systems biologists who adopt the holistic aspirations of early systemologists, seeking high-level organizing principles that could provide insights into problems of biological complexity at the whole-system level. While the presented evidence is not conclusive about whether this strategy could lead to the realization of the lofty goal of a comprehensive explanatory integration, it suggests that the ongoing quest for organizing principles is pragmatically advantageous for systems biologists. The formalisms postulated in the course of this process can serve as bridges between system-theoretic concepts and the results of molecular experimentation: they constitute theoretical tools for generalizing molecular data, thus producing increasingly accurate explanations of system-wide phenomena. [ABSTRACT FROM AUTHOR]

Central to the attempt to develop a biosemiotics has been the discussion of what it means to be scientific. In Marcello Barbieri's latest argument for leaving Peircean biosemiotics and creating an alternative code-biology the definition of what it means to be scientific plays a major role. For Barbieri “scientific knowledge is obtained by building machine-like models of what we observe in nature”. Barbieri interestingly claims that – in combination with the empirical and experimental basis – mechanism is virtually equivalent to the scientific method. The consequences of this statement seem to be that the optimal type of knowledge science can produce about living system is to model them as machines. But the explicit goal of a Peircean semiotically based biosemiotics is (also) to model living systems as cognitive and communicative systems working on the basis of meaning and signification. These two concepts are not part of the mechanistic models of natural science today, not even of cognitive science. Barbieri tries to solve this problem by introducing a new concept of biological meaning that is separate from the Peircean biosemiotics and then add Peirce's semiotics on top. This article argues why this view is inconsistent on the grounds that Peirce's semiotic paradigm only gives meaning in its pragmaticist conception of a fallibilist view of science, which again is intrinsic connected to its non-mechanistic metaphysics of Tychism, Synechism and Agapism. The core of the biosemiotic enterprise is to establish another type of trans- and interdisciplinary wissenschaft than the received view of “science”. [ABSTRACT FROM AUTHOR]

Summary We recently published genetic lineage-tracing experiments using the Fezf2 and Cux2 loci. These experiments demonstrated that at both the clonal and population levels Fezf2 + RGCs are multipotent and that at the population level Cux2 + RGCs are multipotent. Here, we extend our work on the lineages of Fezf2 + and Cux2 + RGCs. Clonal analysis of E10.5 neocortical progenitors suggests that most, if not all, Cux2 + and Fezf2 + RGCs generate diverse projection neuron subtypes located throughout layers 2–6. These results support our previous conclusion that both Fezf2 + and Cux2 + RGCs are multipotent neocortical progenitors. This Matters Arising Response paper addresses the Gil-Sanz et al. (2015) Matters Arising paper, published concurrently in Neuron . [ABSTRACT FROM AUTHOR]

Sperm competition ( SC) occurs when the sperm of two or more males compete for the same set of ova. Theoretical models and experimental observations indicate that the presence of rival males causes focal males to adjust sperm allocation in a given copulation. Males allocate more sperm when they perceive the presence of one rival male ( SC risk), either before or during mating, or when they perceive the presence of multiple rival males before mating (previous SC intensity). Conversely, males are expected to allocate fewer sperm when they perceive the presence of rival males during mating (current SC intensity). Here, we varied male perception of SC by manipulating the number of rival males, both before mating (from emergence to mating) and during mating (at the time of mating) to examine their effects on mating latency, copulation duration, and sperm allocation in the South American fruit fly Anastrepha fraterculus. We showed that exposure to rival males at the time of mating decreased mating latency. However, in contrast to the theory, exposure to multiple rivals at the time of mating increased sperm allocation. Female and male size were significant predictors of mating latency, copulation duration, and sperm allocation. Our results showed that there is a plastic response of males to the level of perceived SC through the number of rival males. Current levels of SC intensity are important in shaping male responses to SC, although the patterns in this species are opposite to predictions from the existing theory. We propose that female preference for males forming leks could explain lower sperm counts when encountering only one or two males. [ABSTRACT FROM AUTHOR]

Leeches are fascinating creatures: they have simple modular nervous circuitry yet exhibit a rich spectrum of behavioural modes. Leeches could be ideal blue-prints for designing flexible soft robots which are modular, multi-functional, fault-tolerant, easy to control, capable for navigating using optical, mechanical and chemical sensorial inputs, have autonomous inter-segmental coordination and adaptive decision-making. With future designs of leech-robots in mind we study how leeches behave in geometrically constrained spaces. Core results of the paper deal with leeches exploring a row of rooms arranged along a narrow corridor. In laboratory experiments we find that rooms closer to ends of the corridor are explored by leeches more often than rooms in the middle of the corridor. Also, in series of scoping experiments, we evaluate leeches capabilities to navigating in mazes towards sources of vibration and chemo-attraction. We believe our results lay foundation for future developments of robots mimicking behaviour of leeches. [ABSTRACT FROM AUTHOR]

Soluble expression of de novo-designed proteins in Escherichia coli ( E. coli ) remains empirical. For given experimental conditions expression success is determined in part by protein primary sequence. This has been previously explored with varying success using a variety of statistical solubility prediction tools though without taking fold stability into account. In the present study, the three-dimensional structure of proteins in molecular dynamics (MD) simulations is used to predict expression as a new approach with a set of four-helix bundles. Stability-related parameters for ten structures were determined in a thermal unfolding MD simulation and used to build statistical models with a support vector machine (SVM) classifier. The most accurate models were identified by their performance on five independent four-helix bundle sequences. The final model provided accurate classification prediction for this test set and was successfully applied in a model challenge with two newly designed sequences. The combination of simulation-derived parameters and an SVM classifier has potential to predict recombinant expression outcome for this set of four-helix bundles. With further development, this approach of utilizing higher-dimensional protein structural information to predict expression may have potential to advance recombinant biotechnology through modern computational and statistical science. [ABSTRACT FROM AUTHOR]

In this essay I explore how Soviet policymakers, biologists, and writers negotiated the borderline dividing the human and animal domains and conceptualized the animal world for ideological purposes. I link the classic Soviet clash between stikhiinost' (spontaneity) and soznatel'nost' (consciousness) with biological experiments of the 1920s that were set to deconstruct the human-animal hierarchy and to create a vision of "classless" biology. I show why Dzhan, one of Andrei Platonov's first earnest attempts to evolve into a socialist realist writer glorifying the Soviet state's firm strides toward the communist future, fails to achieve the semantic certitude of the Stalinist text. Various recurrent and profoundly unconventional themes, often connected with animality and corporeality, drastically muddle the ideological coordinates of the text and preclude the possibility of a clear passage from stikhiinost' to soznatel'nost'. The (a)political status of the Dzhan people as a newly formed Soviet collective body manifests itself in the complex interplay between two rather commonplace categories: body and soul. The body acquires abstract political qualities by becoming collective, while the soul, as a designator for the Dzhan people and as a category, gains flesh. The novella reveals the "Turkmen" nation as a site of bare life itself in its indestructible corporeal glory. [ABSTRACT FROM AUTHOR]

The in-chlorophyll centre waveband (ICCW) (640–680 nm) is the specific chlorophyll (Chl) absorption band, but the reflectance in this band has not been used as an optimal index for non-destructive determination of plant Chl content in recent decades. This study develops a new spectral index based solely on the ICCW for robust retrieval of leaf Chl content for the first time. A glasshouse experiment for solution-culture of one chlorophyll-deficient rice mutant and six wild types of rice genotypes was conducted, and the leaf reflectance (400–900 nm) was measured with a high spectral resolution (1 nm) spectrophotometer and the contents of chlorophyll a (Chla), chlorophyll b (Chlb) and chlorophyll a+b (Chlt) of the rice leaves were determined. It was found that the reflectance curves from 640 nm to 674 nm and from 675 nm to 680 nm of the low-chlorophyll mutant leaf were drastically steeper than that of the wild types in the ICCW. The new index based on the reflectance variation within ICCW, the difference of the first derivative sum within the ICCW (DFDS_ICCW), was highly sensitive (r = −0.77, n = 93, P<0.01) to Chlt while the mean reflectance (R_ICCW) in the ICCW became insensitive (r = −0.12, n = 93, P>0.05) to Chlt when the leaf Chlt was higher than 200 mg/m2. The best equations of R-ICCW and DFDS_ICCW yielded an RMSE of 78.7, 32.9 and 107.3 mg/m2, and an RMSE of 37.4, 16.0 and 45.3 mg/m−2, respectively, for predicting Chla, Chlb and Chlt. The new index could rank in the top 10 for prediction of Chla and Chlt as compared with the 55 existing indices. Additionally, most of the 55 existing Chl-related VIs performed robustly or strongly in simultaneous prediction of leaf Chla, Chlb and Chlt. [ABSTRACT FROM AUTHOR]

As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard designs for ChIP-seq experiments employ a paired control per ChIP-seq sample. Genomic coverage for control experiments is often sacrificed to increase the resources for ChIP samples. However, the quality of ChIP-enriched regions identifiable from a ChIP-seq experiment depends on the quality and the coverage of the control experiments. Insufficient coverage leads to loss of power in detecting enrichment. We investigate the effect of in silico pooling of control samples within multiple biological replicates, multiple treatment conditions, and multiple cell lines and tissues across multiple datasets with varying levels of genomic coverage. Our computational studies suggest guidelines for performing in silico pooling of control experiments. Using vast amounts of ENCODE data, we show that pairwise correlations between control samples originating from multiple biological replicates, treatments, and cell lines/tissues can be grouped into two classes representing whether or not in silico pooling leads to power gain in detecting enrichment between the ChIP and the control samples. Our findings have important implications for multiplexing samples. [ABSTRACT FROM AUTHOR]

Hiring committees address the glut of highly qualified applicants for faculty positions by experimenting with new evaluation methods and adapting their expectations for today’s increasingly competitive academic environment. [ABSTRACT FROM AUTHOR]

Many biogenic minerals are composed of aggregated particles at the nanoscale. These minerals usually form through the transformation of amorphous precursors into single crystals inside a privileged space controlled by the organism. Here, in vitro experiments aimed at understanding the factors responsible for producing such single crystals with aggregated particle texture are presented. Crystallization is achieved by a two-step reaction in which amorphous calcium carbonate (ACC) is first precipitated and then transformed into calcite in small volumes of water and in the presence of additives. The additives used are gel-forming molecules, phosphate ions, and the organic extract from sea urchin embryonic spicules - all are present in various biogenic crystals that grow via the transformation of ACC. Remarkably, this procedure yields faceted single-crystals of calcite that maintain the nanoparticle texture. The crystals grow predominantly by the accretion of ACC nanoparticles, which subsequently crystallize. Gels and phosphate ions stabilize ACC via a different mechanism than sea urchin spicule macromolecules. It is concluded that the unique nanoparticle texture of biogenic minerals results from formation pathways that may differ from one another, but given the appropriate precursor and micro-environment, share a common particle accretion mechanism. [ABSTRACT FROM AUTHOR]

It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems. [ABSTRACT FROM AUTHOR]

Abstract: Human Epithelial type 2 (HEp-2) cells play an important role in the diagnosis of autoimmune disorder. Traditional approach relies on specialists to observe HEp-2 slides via the fluorescence microscope, which suffers from a number of shortcomings like being subjective and labor intensive. Pattern recognition techniques have been recently introduced to this research issue to make the process automatic. However, performances of current systems available in literature are not satisfying. We propose in this paper a framework using intensity order pooling based gradient feature and bag of words for HEp-2 classification. By pooling the gradient features based on the intensity orders of local grid points, the pooled feature is rotationally invariant without requirement of orientation estimation. The proposed approach was fully tested using publicly available ICPR dataset and our own SZU dataset. Experimental results show that the propose method significantly outperformed widely used SIFT feature and the winner of ICPR contest 2012. Encouraging 100% image level accuracy was achieved on the SZU dataset. [Copyright &y& Elsevier]

The article lists the members of the periodical's advisory and editorial board including editor-in-chief Mike Tipton, deputy editor-in-chief Michael White and senior editor Greti Aguilera, along with information on the periodical's disclaimer, copyright and copying, and ethics of experimentation.

We outline a set of experiments that engage students in testing the effects of readily available household chemicals on maize seed germination and shoot growth, with three alcohols as examples. Proposing possible experimental outcomes, exposure to quantitative approaches, data recording, and the statistical analysis of data provide students with an experience that reflects the nature of modern scientific investigation. [ABSTRACT FROM AUTHOR]

Highlights: [•] Tissue specificity of DNA repair is not well understood and is understudied. [•] TNR instability is ideal to study DNA repair in different tissues. [•] Chromatin, repair rates, and protein levels may account for this tissue specificity. [•] System-level experiments will improve understanding of tissue-specific DNA repair. [ABSTRACT FROM AUTHOR]

Highlights: [•] G-CSF can modestly alleviate experimental NIHL in guinea pigs. [•] G-CSF can protect hair cells in experimental NIHL model. [•] G-CSF can reduce the rate of missing hair cells in experimental NIHL model. [ABSTRACT FROM AUTHOR]

Abstract: Mathematical descriptions of birth–death–movement processes are often calibrated to measurements from cell biology experiments to quantify tissue growth rates. Here we describe and analyze a discrete model of a birth–death–movement process applied to a typical two-dimensional cell biology experiment. We present three different descriptions of the system: (i) a standard mean-field description which neglects correlation effects and clustering; (ii) a moment dynamics description which approximately incorporates correlation and clustering effects; and (iii) averaged data from repeated discrete simulations which directly incorporates correlation and clustering effects. Comparing these three descriptions indicates that the mean-field and moment dynamics approaches are valid only for certain parameter regimes, and that both these descriptions fail to make accurate predictions of the system for sufficiently fast birth and death rates where the effects of spatial correlations and clustering are sufficiently strong. Without any method to distinguish between the parameter regimes where these three descriptions are valid, it is possible that either the mean-field or moment dynamics model could be calibrated to experimental data under inappropriate conditions, leading to errors in parameter estimation. In this work we demonstrate that a simple measurement of agent clustering and correlation, based on coordination number data, provides an indirect measure of agent correlation and clustering effects, and can therefore be used to make a distinction between the validity of the different descriptions of the birth–death–movement process. [Copyright &y& Elsevier]

Aim The challenge for phylogeography, like other observational sciences, is to extract general relationships representing causes and effects from complex natural data. I describe comparisons of synchronously diverging co-distributed ( SDC) taxa, including sympatric sister species, to help meet this challenge. Location Global. Methods As an example, using narrative and best evidence synthesis, I re-evaluate ad hoc aggregate analyses relating population genetic structure ( FST) to dispersal potential. I deconstruct an aggregate global analysis to generate a regional subset of data which I compare with datasets describing co-distributed taxa, SDC species and sympatric sister species. Results A weak negative relationship between FST and dispersal potential is implied by aggregate global analysis (0.1 ≤ R2 ≤ 0.29). In contrast, regional datasets of co-distributed species show strong correlation between FST and dispersal potential (0.78 ≤ R2 ≤ 0.85). Comparisons between SDC and sympatric sister species consistently evince higher gene flow in species with higher dispersal potential. Main conclusions Ad hoc aggregate analyses can be compromised by multiple sources of error. Comparisons of SDC taxa, including sympatric sister species, adapt the experimental scientific method to natural situations, providing robust and repeatable tests of phylogeographic hypotheses and accurate estimates of effect sizes. To make strong inferences about phylogeography we should seek out the hidden wealth of natural experiments that provide particularly clear opportunities to study the factors that influence patterns of biodiversity. The SDC framework enables independent tests of existing hypotheses, integration of independent studies in meta-analyses across taxa and regions, and identification of general trends versus location- or taxon-specific phenomena. Coupled with advances in statistical phylogeography, species distribution modelling and palaeoecology, the SDC framework bridges the long-standing gap between observational and experimental sciences. [ABSTRACT FROM AUTHOR]

Highlights: [•] Establish a transferring efficiency model. [•] The model gave the relationship between transfer efficiency and ultrasound conditions. [•] The numerical results were fit well to the cell experimental results in several literatures. [•] Bring forward the ultrasound technology for drug/gene transferring into cells. [ABSTRACT FROM AUTHOR]

Abstract: Information about the roles of both sexes in pair formation is required to better understand the mechanisms involved in sexual selection. Mate choice could depend on the courtship behavior, involving chemical, tactile and visual signals. We determined if Neohelice granulata mate choice is based on female or male choice, considering visual and chemical with contact and without contact signals between partners and different categories of individuals: receptive and unreceptive females; and large, small, mated or unmated males. Experiments showed that mate selection was based on receptive female's choice using chemical signals, but not visual ones. Since copulation occurs during high and low tides, water-borne chemical signals would be preferentially used during high tide, while contact ones during low tide. Females preferred large and unmated males, while males did not seem to recognize receptive females using chemical neither visual signals. Females were capable of detecting the presence of the chemical signals released by large and unmated males, but not its amount. It is proposed that small and mated males are probably releasing different types of chemical signals, not attractive to females, or that they are not emitting any signal. [Copyright &y& Elsevier]

The heterodimer of the ecdysone receptor (EcR) and ultraspiracle (Usp), members of the nuclear receptors superfamily, regulates gene expression associated with molting and metamorphosis in insects. The DNA binding domains (DBDs) of the Usp and EcR play an important role in their DNA-dependent heterodimerization. Analysis of the crystal structure of the UspDBD/EcRDBD heterocomplex from Drosophila melanogaster on the hsp27 gene response element, suggested an appreciable similarity between both DBDs. However, the chemical denaturation experiments showed a categorically lower stability for the EcRDBD in contrast to the UspDBD. The aim of our study was an elucidation of the molecular basis of this intriguing instability. Toward this end, we mapped the EcRDBD amino acid sequence positions which have an impact on the stability of the EcRDBD. The computational protein design and in vitro analyses of the EcRDBD mutants indicate that non-conserved residues within the α-helix 2, forming the EcRDBD hydrophobic core, represent a specific structural element that contributes to instability. In particular, the L58 appears to be a key residue which differentiates the hydrophobic cores of UspDBD and EcRDBD and is the main reason for the low stability of the EcRDBD. Our results might serve as a benchmark for further studies of the intricate nature of the EcR molecule. [ABSTRACT FROM AUTHOR]

Many investigations have studied the effects of prédation risk and competition over vigilance and feeding success, but they have proven to be difficult to discriminate. Moreover, none of the studies that have avoided the confusion has considered all the vigilance variables, food intake rate and time spent in the foraging patch. In this study, we designed an experiment with Eurasian siskins Carduelis spinus foraging on three bird table feeders: one with low prédation risk and competition, one with low prédation risk and high competition and one with high prédation risk and intermediate competition. Birds responded to increasing interference competition by increasing mean scan durations (probably due to the birds having to be vigilant for both other flock members and predators) and maintaining the length of mean inter-scan durations, while they responded to increasing prédation risk by reducing mean inter-scan durations (probably in order to detect the predator sooner) while maintaining similar length of mean scan durations. Birds were often ejected from the feeder or departed because of disturbances, so time spent on feeders was reduced both because of competition and prédation risk. Pecking rates were affected by competition but not by prédation risk. Our results clearly show that birds vigilance strategy while foraging might be very different when they are mainly concerned with scanning for predators or when they primarily monitor competing flock companions. In addition, they stress the importance of recording all the vigilance and feeding variables when studying the effect of ecological factors over the foraging behaviour of birds. [ABSTRACT FROM AUTHOR]

Highlights: [•] We explore the flexibility of model-building practices in integrative systems biology. [•] We document the coupling of experimentation and simulation in a case study. [•] We show the affordances of coupling for handling complex problem-solving tasks. [•] We provide a comparison with unimodal (pure modeling) approaches. [Copyright &y& Elsevier]

Humans are the dominant ecological and evolutionary force on the planet today, transforming habitats, polluting environments, changing climates, introducing new species, and causing other species to decline in number or go extinct. These worrying anthropogenic impacts, collectively termed global change, are often viewed as a confounding factor to minimize in basic studies and a problem to resolve or quantify in applied studies. However, these 'accidental experiments' also represent opportunities to gain fundamental insight into ecological and evolutionary processes, especially when they result in perturbations that are large or long in duration and difficult or unethical to impose experimentally. We demonstrate this by describing important fundamental insights already gained from studies which utilize global change factors as accidental experiments. In doing so, we highlight why accidental experiments are sometimes more likely to yield insights than traditional approaches. Next, we argue that emerging environmental problems can provide even more opportunities for scientific discovery in the future, and provide both examples and guidelines for moving forward. We recommend 1) a greater flow of information between basic and applied subfields of ecology and evolution to identify emerging opportunities; 2) considering the advantages of the 'accidental experiment' approach relative to more traditional approaches; and 3) planning for the challenges inherent to uncontrolled accidental experiments. We emphasize that we do not view the accidental experiments provided by global change as replacements for scientific studies quantifying the magnitude of anthropogenic impacts or outlining strategies for mitigating impacts. Instead, we believe that accidental experiments are uniquely situated to provide insights into evolutionary and ecological processes that ultimately allow us to better predict and manage change on our human-dominated planet. Synthesis Humans have an increasingly large impact on the planet. In response, ecologists and evolutionary biologists are dedicating increasing scientific attention to global change, largely with studies documenting biological effects and testing strategies to avoid or reverse negative impacts. In this article, we analyze global change from a different perspective, and suggest that human impacts on the environment also serve as valuable 'accidental experiments' that can provide fundamental scientific insight. We highlight and synthesize examples of studies taking this approach, and give guidance for gaining future insights from these unfortunate 'accidental experiments'. [ABSTRACT FROM AUTHOR]

There are two issues in balancing a stick pivoting on a finger tip (or mechanically on a moving cart): maintaining the stick angle near to vertical and maintaining the horizontal position within the bounds of reach or cart track. The (linearised) dynamics of the angle are second order (although driven by pivot acceleration), and so, as in human standing, control of the angle is not, by itself very difficult. However, once the angle is under control, the position dynamics are, in general, fourth order. This makes control quite difficult for humans (and even an engineering control system requires careful design). Recently, three of the authors have experimentally demonstrated that humans control the stick angle in a special way: the closed-loop inverted pendulum behaves as a non-inverted pendulum with a virtual pivot somewhere between the stick centre and tip and with increased gravity. Moreover, they suggest that the virtual pivot lies at the radius of gyration (about the mass centre) above the mass centre. This paper gives a continuous-time control-theoretical interpretation of the virtual-pendulum approach. In particular, by using a novel cascade control structure, it is shown that the horizontal control of the virtual pivot becomes a second-order problem which is much easier to solve than the generic fourth-order problem. Hence, the use of the virtual pivot approach allows the control problem to be perceived by the subject as two separate second-order problems rather than a single fourth-order problem, and the control problem is therefore simplified. The theoretical predictions are verified using the data previously presented by three of the authors and analysed using a standard parameter estimation method. The experimental data indicate that although all subjects adopt the virtual pivot approach, the less expert subjects exhibit larger amplitude angular motion and poorly controlled translational motion. It is known that human control systems are delayed and intermittent, and therefore, the continuous-time strategy cannot be correct. However, the model of intermittent control used in this paper is based on the virtual pivot continuous-time control scheme, handles time delays and moreover masquerades as the underlying continuous-time controller. In addition, the event-driven properties of intermittent control can explain experimentally observed variability. [ABSTRACT FROM AUTHOR]

The lack of a suitable infection model remains an important obstacle for the pathophysiological understanding of Bartonella spp. The following pilot study was designed to determine whether cell culture-grown Bartonella henselae SA2 and Bartonella vinsonii subsp. berkhoffii genotype III would cause persistent bacteremia in dogs. Pre-inoculation screening established that two laboratory-raised Golden retrievers were naturally-infected with Bartonella koehlerae. Despite prior infection, one dog each was inoculated subcutaneously with 5×104 B. henselae (SA2 strain) or 3×104 B. vinsonii subsp. berkhoffii genotype III. Dogs were bled weekly for serological testing and culture using Bartonella alpha proteobacteria growth medium (BAPGM) diagnostic platform. Dog 1 seroconverted to B. henselae and Dog 2 seroconverted to B. vinsonii subsp. berkhoffii genotype III. Throughout the study period, Bartonella spp. DNA was neither amplified nor isolated in ante-mortem BAPGM enrichment blood cultures. B. henselae SA2 was isolated from a postmortem bone marrow from Dog 1 and B. koehlerae DNA was amplified from postmortem lung from Dog 2 following BAPGM enrichment culture. Limitations include lack of uninfected controls, a potentially suboptimal B. vinsonii subsp. berkhoffii inoculum and a relatively short duration of study. We conclude that following intradermal infection, sequestration of Bartonella spp. in tissues may limit diagnostic detection of these bacteria in dog blood samples. [ABSTRACT FROM AUTHOR]

Abstract: The purpose of this study was to compare clinical and virological differences between non-cytopathic (ncp) bovine viral diarrhea virus (BVDV)-1 and ncp BVDV-2 isolated from Korean field cases. Each five naïve calves were experimentally infected with Korean ncp BVDV-1 or BVDV-2 isolates. Two additional age-matched animals were used as uninfected controls. Leukocyte, lymphocyte, and platelet counts declined in all infected calves, but were significantly lower and remained decreased longer in calves infected with ncp BVDV-2 isolate. The number of monocytes was greater in calves infected with ncp BVDV-2. Flow cytometric assay showed that lymphocyte apoptosis occurred with an increase of annexin-V positive cells in all infected calves by day 6. Tumor necrosis factor alpha (TNF-α) concentration in all infected calves was lower than in control calves. In ncp BVDV-1 infected calves, interferon gamma (IFN-γ) levels in the serum were increased by day 6 compared to calves infected with ncp BVDV-2. These results demonstrated that the Korean ncp BVDV-2 isolate shows a reduced IFN-γ production, indicating prevention of the antiviral activity, and therefore promotes the development of pathological effects. [Copyright &y& Elsevier]

I describe two traditions of philosophical accounts of evidence: one characterizes the notion in terms of signs of success, the other characterizes the notion in terms of conditions of success. The best examples of the former rely on the probability calculus, and have the virtues of generality and theoretical simplicity. The best examples of the latter describe the features of evidence which scientists appeal to in practice, which include general features of methods, such as quality and relevance, and general features of evidence, such as patterns in data, concordance with other evidence, and believability of the evidence. Two infamous episodes from biomedical research help to illustrate these features. Philosophical characterization of these latter features-conditions of success-has the virtue of potential relevance to, and descriptive accuracy of, practices of experimental scientists. [ABSTRACT FROM AUTHOR]

A simple observation is the basis of the development of BioArena system: according to the first observations during the biological incubation after inoculation there is formaldehyde (HCHO) emission from the chromatographic spots; in this emission process, the level of HCHO molecules decreases time dependently. In fact, the antibiotic effect of an antibiotic-like compound decreases in parallel with the HCHO emission. The investigations demonstrated clearly a unique function and role of endogenous HCHO and its one main reaction product, ozone (O3), in the antiproliferative (e.g., antimicrobial) effect of different molecules with diverse chemical structures. The results in BioArena can be extended for in vivo conditions (e.g., greenhouse experiments), as well. For the pretreatment with different doses of inducers (immunostimulation-inducing molecules) there are always four bioequivalent immunostimulating response ranges (quadruple bioequivalent immune response system) in plants. The inducers (e.g., N-methylated basic amino acids, salicylic acid, cinnamic acid, and trace elements) do not participate directly in the induction of the immunostimulating effect. These new findings support a statement that HCHO and its reaction products (mainly O3), as bioreactive small molecules, are responsible for the immunostimulating activity (in vivo conditions), as well. [ABSTRACT FROM AUTHOR]

Abstract: Cerebellar long-term depression (LTD) is induced by short-lasting synaptic activities, progressively expressed, and then maintained for hours or longer. Short-lasting events, such as calcium transients, are activated and required for the induction of LTD. Further, a positive-feedback kinase loop was shown to follow the transient events and to aid the transition between LTD induction and prolonged synaptic depression. Yet, it is not entirely clear as to how LTD is maintained and how the maintenance mechanisms are activated, mainly because of a lack of experimental studies regarding this topic, while an idea has been theoretically proposed. A new analysis of the experimental results suggests that early maintenance mechanisms display a threshold behavior and that they may be of stochastic nature. This suggestion is conceptually consistent with an idea from a computational study, which postulates that other bistable switch systems are required for LTD maintenance. We thus propose that cellular mechanisms showing a threshold behavior and a stochastic nature maintain LTD, and that future experimental studies in search of such mechanisms would be an important step toward fully understanding the time course of LTD. [Copyright &y& Elsevier]

Prediction of the three-dimensional structure of a protein from its amino acid sequence can be considered as a global optimization problem. In this paper, the Chaotic Artificial Bee Colony (CABC) algorithm was introduced and applied to 3D protein structure prediction. Based on the 3D off-lattice AB model, the CABC algorithm combines global search and local search of the Artificial Bee Colony (ABC) algorithm with the chaotic search algorithm to avoid the problem of premature convergence and easily trapping the local optimum solution. The experiments carried out with the popular Fibonacci sequences demonstrate that the proposed algorithm provides an effective and high-performance method for protein structure prediction. [ABSTRACT FROM AUTHOR]

Pichia pastoris is commonly used for the production of recombinant proteins due to its preferential secretion of recombinant proteins, resulting in lower production costs and increased yields of target proteins. However, not all recombinant proteins can be successfully secreted in P. pastoris. A computational method that predicts the likelihood of a protein being secreted into the supernatant would be of considerable value; however, to the best of our knowledge, no such tool has yet been developed. We present a machine-learning approach called Presep to assess the likelihood of a recombinant protein being secreted by P. pastoris based on its pseudo amino acid composition (PseAA). Using a 20-fold cross validation, Presep demonstrated a high degree of accuracy, with Matthews correlation coefficient (MCC) and overall accuracy (Q2) scores of 0.78 and 95%, respectively. Computational results were validated experimentally, with six β-galactosidase genes expressed in P. pastoris strain GS115 to verify Presep model predictions. A strong correlation (R2 = 0.967) was observed between Presep prediction secretion propensity and the experimental secretion percentage. Together, these results demonstrate the ability of the Presep model for predicting the secretion propensity of P. pastoris for a given protein. This model may serve as a valuable tool for determining the utility of P. pastoris as a host organism prior to initiating biological experiments. The Presep prediction tool can be freely downloaded at http://www.mobioinfor.cn/Presep. [ABSTRACT FROM AUTHOR]

Abstract: In the present research we explored the role of the dorsolateral prefrontal cortex (DLPFC) in memory retrieval process of positive vs. negative emotional stimulus, as a function of the anxiety levels. Anxiety behavior showed a consistent attentional bias toward negative and aversive memories, induced by a right frontal cortical superiority. This effect was analyzed by using a rTMS paradigm that induced a cortical activation of the left DLPFC. Subjects, who were divided in two different groups depending on their anxiety level (high/low-anxiety, State-Trait-Anxiety-Inventory, STAI), were required to perform a task consisting of two experimental phases: an encoding-phase, where some lists composed by positive and negative emotional words were presented to the subjects; and a retrieval-phase, where the old stimuli and new stimuli were presented for a recognition performance. We found that the rTMS stimulation affects the memory retrieval of emotional material. High-anxiety subjects benefit in greater measure from the left DLPFC stimulation with a reduced negative bias. This result suggested that left DLPFC activation favors the memory retrieval of positive emotional information and might limit the “unbalance effect” induced by a right hemispheric superiority at a high level of anxiety. The potentiality of TMS for anxiety behavior modulation was also discussed. [Copyright &y& Elsevier]