A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin
A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species. The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment. The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
Dalby et al. (2014) A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin. PeerJ 2:e655 https://doi.org/10.7717/peerj.655
A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success
In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of sealed brood were assessed in each colony throughout summer and autumn. Samples of honey, beeswax, pollen, and nectar were regularly collected, and samples were analyzed for clothianidin residues. Several of these endpoints were also measured in spring 2013. Overall, colonies were vigorous during and after the exposure period, and we found no effects of exposure to clothianidin seed-treated canola on any endpoint measures. Bees foraged heavily on the test fields during peak bloom and residue analysis indicated that honey bees were exposed to low levels (0.5–2 ppb) of clothianidin in pollen. Low levels of clothianidin were detected in a few pollen samples collected toward the end of the bloom from control hives, illustrating the difficulty of conducting a perfectly controlled field study with free-ranging honey bees in agricultural landscapes. Overwintering success did not differ significantly between treatment and control hives, and was similar to overwintering colony loss rates reported for the winter of 2012–2013 for beekeepers in Ontario and Canada. Our results suggest that exposure to canola grown from seed treated with clothianidin poses low risk to honey bees.
Cutler et al. (2014) A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success. PeerJ 2:e652 https://doi.org/10.7717/peerj.652
Horizontal transfer generates genetic variation in an asexual pathogen
There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS) regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts. We found highly homologous elements in LS regions of each strain; LS regions of V. dahliae strain JR2 are much richer in highly homologous elements than the core genome. In addition, we discovered, in LS regions of JR2, several structural forms of nonhomologous recombination, and two or three homologous sequence types of each form, with almost each sequence type present in an LS region of another strain. A large section of one of the forms is known to be horizontally transferred between V. dahliae strains. We unexpectedly found that 350 kilobases of dynamic LS regions were much more conserved than the core genome between V. dahliae and a closely related species (V. albo-atrum), suggesting that these LS regions were horizontally transferred recently. Our results support the view that genetic variation in LS regions is generated by horizontal transfer between strains, and by chromosomal reshuffling reported previously.
Huang (2014) Horizontal transfer generates genetic variation in an asexual pathogen. PeerJ 2:e650 https://doi.org/10.7717/peerj.650
Comparison of predictor approaches for longitudinal binary outcomes: application to anesthesiology data
Longitudinal data with binary repeated responses are now widespread among clinical studies and standard statistical analysis methods have become inadequate in the answering of clinical hypotheses. Instead of such conventional approaches, statisticians have started proposing better techniques, such as the Generalized Estimating Equations (GEE) approach and Generalized Linear Mixed Models (GLMM) technique. In this research, we undertook a comparative study of modeling binary repeated responses using an anesthesiology dataset which has 375 patient data with clinical variables. We modeled the relationship between hypotension and age, gender, surgical department, positions of patients during surgery, diastolic blood pressure, pulse, electrocardiography and doses of Marcain-heavy, chirocaine, fentanyl, and midazolam. Moreover, parameter estimates between the GEE and the GLMM were compared. The parameter estimates, except time-after, Marcain-Heavy, and Fentanyl from the GLMM, are larger than those from GEE. The standard errors from the GLMM are larger than those from GEE. GLMM appears to be more suitable approach than the GEE approach for the analysis hypotension during spinal anesthesia.
Aktas Samur et al. (2014) Comparison of predictor approaches for longitudinal binary outcomes: application to anesthesiology data. PeerJ 2:e648 https://doi.org/10.7717/peerj.648
Study of the effect on shelter cat intakes and euthanasia from a shelter neuter return project of 10,080 cats from March 2010 to June 2014
Cat impoundments were increasing at the municipal San Jose animal shelter in 2009, despite long-term successful low cost sterilization programs and attempts to lower the euthanasia rate of treatable-rehabilitatable impounds beginning in 2008. San Jose Animal Care and Services implemented a new strategy designed to control overall feral cat reproduction by altering and returning feral cats entering the shelter system, rather than euthanizing the cats. The purpose of this case study was to determine how the program affected the shelter cat intakes over time. In just over four years, 10,080 individual healthy adult feral cats, out of 11,423 impounded at the shelter during this time frame, were altered and returned to their site of capture. Included in the 11,423 cats were 862 cats impounded from one to four additional times for a total of 958 (9.5%) recaptures of the previously altered 10,080 cats. The remaining 385 healthy feral cats were euthanized at the shelter from March 2010 to June 2014. Four years into the program, researchers observed cat and kitten impounds decreased 29.1%; euthanasia decreased from over 70% of intakes in 2009, to 23% in 2014. Euthanasia in the shelter for Upper Respiratory Disease decreased 99%; dead cat pick up off the streets declined 20%. Dog impounds did not similarly decline over the four years. No other laws or program changes were implemented since the beginning of the program.
Johnson et al. (2014) Study of the effect on shelter cat intakes and euthanasia from a shelter neuter return project of 10,080 cats from March 2010 to June 2014. PeerJ 2:e646 https://doi.org/10.7717/peerj.646
No sex-biased dispersal in a primate with an uncommon social system—cooperative polyandry
An influential hypothesis proposed by Greenwood (1980) suggests that different mating systems result in female and male-biased dispersal, respectively, in birds and mammals. However, other aspects of social structure and behavior can also shape sex-biased dispersal. Although sex-specific patterns of kin cooperation are expected to affect the benefits of philopatry and dispersal patterns, empirical evidence is scarce. Unlike many mammals, Saguinus geoffroyi (Geoffroy’s tamarin) has a breeding system in which typically multiple males mate with a single breeding female. Males typically form cooperative reproductive partnerships between relatives, whereas females generally compete for reproductive opportunities. This system of cooperative polyandry is predicted to result in female-biased dispersal, providing an opportunity to test the current hypotheses of sex-biased dispersal. Here we test for evidence of sex-biased dispersal in S. geoffroyi using demographic and genetic data from three populations. We find no sex bias in natal dispersal, contrary to the prediction based on the mating patterns. This pattern was consistent after controlling for the effects of historical population structure. Limited breeding opportunities within social groups likely drive both males and females to disperse, suggesting that dispersal is intimately related to the social context. The integration of genetic and field data revealed that tamarins are another exception to the presumed pattern of male-biased dispersal in mammals. A shift in focus from mating systems to social behavior, which plays a role in most all processes expected to influence sex-bias in dispersal, will be a fruitful target for research both within species and across taxa.
Díaz-Muñoz et al. (2014) No sex-biased dispersal in a primate with an uncommon social system—cooperative polyandry. PeerJ 2:e640 https://doi.org/10.7717/peerj.640
Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin–dockerin interactions
Cellulosic waste represents a significant and underutilized carbon source for the biofuel industry. Owing to the recalcitrance of crystalline cellulose to enzymatic degradation, it is necessary to design economical methods of liberating the fermentable sugars required for bioethanol production. One route towards unlocking the potential of cellulosic waste lies in a highly complex class of molecular machines, the cellulosomes. Secreted mainly by anaerobic bacteria, cellulosomes are structurally diverse, cell surface-bound protein assemblies that can contain dozens of catalytic components. The key feature of the cellulosome is its modularity, facilitated by the ultra-high affinity cohesin–dockerin interaction. Due to the enormous number of cohesin and dockerin modules found in a typical cellulolytic organism, a major bottleneck in understanding the biology of cellulosomics is the purification of each cohesin- and dockerin-containing component, prior to analyses of their interaction. As opposed to previous approaches, the present study utilized proteins contained in unpurified whole-cell extracts. This strategy was made possible due to an experimental design that allowed for the relevant proteins to be “purified” via targeted affinity interactions as a function of the binding assay. The approach thus represents a new strategy, appropriate for future medium- to high-throughput screening of whole genomes, to determine the interactions between cohesins and dockerins. We have selected the cellulosome of Acetivibrio cellulolyticus for this work due to its exceptionally complex cellulosome systems and intriguing diversity of its cellulosomal modular components. Containing 41 cohesins and 143 dockerins, A. cellulolyticus has one of the largest number of potential cohesin–dockerin interactions of any organism, and contains unusual and novel cellulosomal features. We have surveyed a representative library of cohesin and dockerin modules spanning the cellulosome’s total cohesin and dockerin sequence diversity, emphasizing the testing of unusual and previously-unknown protein modules. The screen revealed several novel cell-bound cellulosome architectures, thus expanding on those previously known, as well as soluble cellulose systems that are not bound to the bacterial cell surface. This study sets the stage for screening the entire complement of cellulosomal components from A. cellulolyticus and other organisms with large cellulosome systems. The knowledge gained by such efforts brings us closer to understanding the exceptional catalytic abilities of cellulosomes and will allow the use of novel cellulosomal components in artificial assemblies and in enzyme cocktails for sustainable energy-related research programs.
Hamberg et al. (2014) Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin–dockerin interactions. PeerJ 2:e636 https://doi.org/10.7717/peerj.636
The link between immunity and life history traits in scleractinian corals
Immunity is an important biological trait that influences the survival of individuals and the fitness of a species. Immune defenses are costly and likely compete for energy with other life-history traits, such as reproduction and growth, affecting the overall fitness of a species. Competition among these traits in scleractinian corals could influence the dynamics and structural integrity of coral reef communities. Due to variability in biological traits within populations and across species, it is likely that coral colonies within population/species adjust their immune system to the available resources. In corals, the innate immune system is composed of various pathways. The immune system components can be assessed in the absence (constitutive levels) and/or presence of stressors/pathogens (immune response). Comparisons of the constitutive levels of three immune pathways (melanin synthesis, antioxidant and antimicrobial) of closely related species of Scleractinian corals allowed to determine the link between immunity and reproduction and colony growth. First, we explored differences in constitutive immunity among closely related coral species of the genus Meandrina with different reproductive patterns (gonochoric vs. hermaphrodite). We then compared fast-growing branching vs. slow-growing massive Porites to test co-variation between constitutive immunity and growth rates and morphology in corals. Results indicate that there seems to be a relationship between constitutive immunity and sexual pattern with gonochoric species showing significantly higher levels of immunity than hermaphrodites. Therefore, gonochoric species maybe better suited to resist infections and overcome stressors. Constitutive immunity varied in relation with growth rates and colony morphology, but each species showed contrasting trends within the studied immune pathways. Fast-growing branching species appear to invest more in relatively low cost pathways of the immune system than slow-growing massive species. In corals, energetic investments in life-history traits such as reproduction and growth rate (higher energy investment) seem to have a significant impact on their capacity to respond to stressors, including infectious diseases and coral bleaching. These differences in energy investment are critical in the light of the recent environmental challenges linked to global climate change affecting these organisms. Understanding physiological trade-offs, especially those involving the immune system, will improve our understanding as to how corals could/will respond and survive in future adverse environmental conditions associated with climate change.
Pinzón C. et al. (2014) The link between immunity and life history traits in scleractinian corals. PeerJ 2:e628 https://doi.org/10.7717/peerj.628
Are improper kinetic models hampering drug development?
Reproducibility of biological data is a significant problem in research today. One potential contributor to this, which has received little attention, is the over complication of enzyme kinetic inhibition models. The over complication of inhibitory models stems from the common use of the inhibitory term (1 + [I]/Ki), an equilibrium binding term that does not distinguish between inhibitor binding and inhibitory effect. Since its initial appearance in the literature, around a century ago, the perceived mechanistic methods used in its production have spurred countless inhibitory equations. These equations are overly complex and are seldom compared to each other, which has destroyed their usefulness resulting in the proliferation and regulatory acceptance of simpler models such as IC50s for drug characterization. However, empirical analysis of inhibitory data recognizing the clear distinctions between inhibitor binding and inhibitory effect can produce simple logical inhibition models. In contrast to the common divergent practice of generating new inhibitory models for every inhibitory situation that presents itself. The empirical approach to inhibition modeling presented here is broadly applicable allowing easy comparison and rational analysis of drug interactions. To demonstrate this, a simple kinetic model of DAPT, a compound that both activates and inhibits γ-secretase is examined using excel. The empirical kinetic method described here provides an improved way of probing disease mechanisms, expanding the investigation of possible therapeutic interventions.
Walsh (2014) Are improper kinetic models hampering drug development?. PeerJ 2:e649 https://doi.org/10.7717/peerj.649
Use of Twitter to monitor attitudes toward depression and schizophrenia: an exploratory study
Introduction. The paper reports on an exploratory study of the usefulness of Twitter for unobtrusive assessment of stigmatizing attitudes in the community. Materials and Methods. Tweets with the hashtags #depression or #schizophrenia posted on Twitter during a 7-day period were collected. Tweets were categorised based on their content and user information and also on the extent to which they indicated a stigmatising attitude towards depression or schizophrenia (stigmatising, personal experience of stigma, supportive, neutral, or anti-stigma). Tweets that indicated stigmatising attitudes or personal experiences of stigma were further grouped into the following subthemes: social distance, dangerousness, snap out of it, personal weakness, inaccurate beliefs, mocking or trivializing, and self-stigma. Results and Discussion. Tweets on depression mostly related to resources for consumers (34%), or advertised services or products for individuals with depression (20%). The majority of schizophrenia tweets aimed to increase awareness of schizophrenia (29%) or reported on research findings (22%). Tweets on depression were largely supportive (65%) or neutral (27%). A number of tweets were specifically anti-stigma (7%). Less than 1% of tweets reflected stigmatising attitudes (0.7%) or personal experience of stigma (0.1%). More than one third of the tweets which reflected stigmatising attitudes were mocking or trivialising towards individuals with depression (37%). The attitude that individuals with depression should “snap out of it” was evident in 30% of the stigmatising tweets. The majority of tweets relating to schizophrenia were categorised as supportive (42%) or neutral (43%). Almost 10% of tweets were explicitly anti-stigma. The percentage of tweets showing stigmatising attitudes was 5%, while less than 1% of tweets described personal experiences of stigmatising attitudes towards individuals with schizophrenia. Of the tweets that indicated stigmatising attitudes, most reflected inaccurate beliefs about schizophrenia being multiple personality disorder (52%) or mocked or trivialised individuals with schizophrenia (33%). Conclusions. The study supports the use of analysis of Twitter content to unobtrusively measure attitudes towards mental illness, both supportive and stigmatising. The results of the study may be useful in assisting mental health promotion and advocacy organisations to provide information about resources and support, raise awareness and counter common stigmatising attitudes.
Reavley et al. (2014) Use of Twitter to monitor attitudes toward depression and schizophrenia: an exploratory study. PeerJ 2:e647 https://doi.org/10.7717/peerj.647
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus
As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the P. eremicus transcriptome. We assay four tissues (kidney, liver, brain, testes) from a single individual and supplement this with population level renal transcriptome sequencing from 15 additional animals. We identified a set of transcripts undergoing both purifying and balancing selection based on estimates of Tajima’s D. In addition, we used the branch-site test to identify a transcript—Slc2a9, likely related to desert osmoregulation—undergoing enhanced selection in P. eremicus relative to a set of related non-desert rodents.
MacManes et al. (2014) Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus. PeerJ 2:e642 https://doi.org/10.7717/peerj.642
Purification and properties of glyceraldehyde-3-phosphate dehydrogenase from the skeletal muscle of the hibernating ground squirrel, Ictidomys tridecemlineatus
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the skeletal muscle of euthermic and torpid Ictidomys tridecemlineatus was purified to electrophoretic homogeneity using a novel method involving Blue-agarose and Phenyl-agarose chromatography. Kinetic analysis of the enzymes isolated from the two conditions suggested the existence of two structurally distinct proteins, with GAPDH V max being 40–60% less for the enzyme from the torpid condition (in both glycolytic and gluconeogenic directions) as compared to the euthermic enzyme form. Thermal denaturation, in part determined by differential scanning fluorimetry, revealed that purified GAPDH from the torpid animals was significantly more stable that the enzyme from the euthermic condition. Mass spectrometry combined with Western blot analyses of purified GAPDH indicate that the cellular GAPDH population is extensively modified, with posttranslational phosphorylation, acetylation and methylation being detected. Global reduction in GAPDH tyrosine phosphorylation during torpor as well as site specific alterations in methylation sites suggests that that the stable changes observed in kinetic and structural GAPDH properties may be due to posttranslational modification of this enzyme during torpor. Taken together, these results suggest a stable suppression of GAPDH (possibly by some reversible posttranslational modification) during ground squirrel torpor, which likely contributes to the overall reduction in carbohydrate metabolism when these animals switch to lipid fuels during dormancy.
Bell et al. (2014) Purification and properties of glyceraldehyde-3-phosphate dehydrogenase from the skeletal muscle of the hibernating ground squirrel, Ictidomys tridecemlineatus. PeerJ 2:e634 https://doi.org/10.7717/peerj.634
Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches
An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.
Asakura et al. (2014) Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches. PeerJ 2:e550 https://doi.org/10.7717/peerj.550
Associating disease-related genetic variants in intergenic regions to the genes they impact
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.
Macintyre et al. (2014) Associating disease-related genetic variants in intergenic regions to the genes they impact. PeerJ 2:e639 https://doi.org/10.7717/peerj.639
What did you choose just now? Chimpanzees’ short-term retention of memories of their own behavior
Many recent comparative studies have addressed “episodic” memory in nonhuman animals, suggesting that birds, rodents, great apes, and others can remember their own behavior after at least a half-day delay. By contrast, despite numerous studies regarding long-term memory, few comparable studies have been conducted on short-term retention for own behavior. In the current study, we addressed the following question: Do chimpanzees remember what they have just done? Four chimpanzees performed matching-to-sample and visual search tasks on a routine basis and were occasionally (every four sessions) given a “recognition” test immediately after their response during visual search trials. Even though these test trials were given very rarely, all four chimpanzees chose the stimulus they selected in the visual search trials immediately before the test trial significantly more frequently than they chose the stimulus they selected in another distractor trial. Subsequent experiments ruled out the possibility that preferences for the specific stimuli accounted for the recognition test results. Thus, chimpanzees remembered their own behavior even within a short-term interval. This type of memory may involve the transfer of episodic information from working memory to long-term episodic-like memory (i.e., an episodic buffer).
Tomonaga et al. (2014) What did you choose just now? Chimpanzees’ short-term retention of memories of their own behavior. PeerJ 2:e637 https://doi.org/10.7717/peerj.637
Chicks change their pecking behaviour towards stationary and mobile food sources over the first 12 weeks of life: improvement and discontinuities
Chicks (Gallus gallus domesticus) learn to peck soon after hatching and then peck in rapid bursts or bouts with intervals of non-pecking activity. The food sources may be static such as seeds and chick crumb, or mobile such as a mealworm. Here, changes with age in pecking toward chick crumb and a mealworm were measured. Chicks were reared in pairs and their pecking of crumb food was video recorded in their pair housed environment, from food presentation, every third day from day 8 (wk 2) to day 65 (wk 10). Peck rate at crumb food reached maximum levels at day 32 (wk 5), and then declined, fitting a quadratic model, with no sex, sex of cagemate, or box order effects. Within bouts the peck rate was higher and it increased to day 41 (wk 6) and then declined, and here males pecked faster than females. A change in dietary protein concentration from 22% to 18% at day 28 (wk 4) had no effect on subsequent peck rate. Pecking at and consumption of a mealworm in pair housed chicks were measured weekly from wks [5 to 12]. The latency to first worm peck and latency to swallow decreased to wk 8 and increased thereafter. The peck rate to first wormpeck and number of pecks to swallow increased to wk 8 and then declined paralleling the changes with crumb food. The increase in peck rate is coupled with an increase in efficiency in worm catching. The results are consistent with the view that the improvement in pecking ability and accuracy compliments change in nutritional requirement best served by an invertebrate food (IF) source requiring speed to achieve feeding success, especially with live prey. When this food source is no longer crucial these associated skill levels decline. An appreciation of the role of domestic fowl in controlling insect populations, at farm level, that are often vectors in disease spread is lacking.
Murphy et al. (2014) Chicks change their pecking behaviour towards stationary and mobile food sources over the first 12 weeks of life: improvement and discontinuities. PeerJ 2:e626 https://doi.org/10.7717/peerj.626
X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov.
We document a new species of ovulate cone (Pararaucaria collinsonae) on the basis of silicified fossils from the Late Jurassic Purbeck Limestone Group of southern England (Tithonian Stage: ca. 145 million years). Our description principally relies on the anatomy of the ovuliferous scales, revealed through X-ray synchrotron microtomography (SRXMT) performed at the Diamond Light Source (UK). This study represents the first application of SRXMT to macro-scale silicified plant fossils, and demonstrates the significant advantages of this approach, which can resolve cellular structure over lab-based X-ray computed microtomography (XMT). The method enabled us to characterize tissues and precisely demarcate their boundaries, elucidating organ shape, and thus allowing an accurate assessment of affinities. The cones are broadly spherical (ca. 1.3 cm diameter), and are structured around a central axis with helically arranged bract/scale complexes, each of which bares a single ovule. A three-lobed ovuliferous scale and ovules enclosed within pocket-forming tissue, demonstrate an affinity with Cheirolepidiaceae. Details of vascular sclerenchyma bundles, integument structure, and the number and attachment of the ovules indicate greatest similarity to P. patagonica and P. carrii. This fossil develops our understanding of the dominant tree element of the Purbeck Fossil Forest, providing the first evidence for ovulate cheirolepidiaceous cones in Europe. Alongside recent discoveries in North America, this significantly extends the known palaeogeographic range of Pararaucaria, supporting a mid-palaeolatitudinal distribution in both Gondwana and Laurasia during the Late Jurassic. Palaeoclimatic interpretations derived from contemporaneous floras, climate sensitive sediments, and general circulation climate models indicate that Pararaucaria was a constituent of low diversity floras in semi-arid Mediterranean-type environments.
Steart et al. (2014) X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov.. PeerJ 2:e624 https://doi.org/10.7717/peerj.624
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell–cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein–protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
Mournetas et al. (2014) Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells. PeerJ 2:e618 https://doi.org/10.7717/peerj.618
15-LOX metabolites and angiogenesis: angiostatic effect of 15(S)-HPETE involves induction of apoptosis in adipose endothelial cells
Inflammation is critical in the dysregulated growth of adipose tissue and associated vascular dysfunctions. 15-Lipoxygenase metabolites, important mediators of inflammation in adipose tissue during obese conditions, may contribute to codependence of inflammation and angiogenesis in adipose tissue. We have already reported the pro-angiogenic effect of 15(S)-HETE in adipose tissue. The present study was designed to understand the effect of 15(S)-HPETE, precursor of 15(S)-HETE, on angiogenesis in adipose tissue. Results showed that 15(S)-HPETE exerts an anti-angiogenic effect in adipose tissue. This was evidenced from decreased endothelial sprouting in adipose tissue explants, inhibition of angiogenic phenotype in adipose endothelial cells, decreased production of CD31 and VEGF in endothelial cells treated with 15(S)-HPETE. Further studies to examine the molecular mechanism of anti-angiogenic effect of 15(S)-HPETE showed that it inhibited cell survival signaling molecule Akt and anti-apoptotic Bcl-2 and also activated caspase-3 in adipose endothelial cells. These observations indicate that 15(S)-HPETE exerts its angiostatic effect in adipose tissue by inducing apoptosis of endothelial cells.
Soumya et al. (2014) 15-LOX metabolites and angiogenesis: angiostatic effect of 15(S)-HPETE involves induction of apoptosis in adipose endothelial cells. PeerJ 2:e635 https://doi.org/10.7717/peerj.635
Gender differences in conference presentations: a consequence of self-selection?
Women continue to be under-represented in the sciences, with their representation declining at each progressive academic level. These differences persist despite long-running policies to ameliorate gender inequity. We compared gender differences in exposure and visibility at an evolutionary biology conference for attendees at two different academic levels: student and post-PhD academic. Despite there being almost exactly a 1:1 ratio of women and men attending the conference, we found that when considering only those who presented talks, women spoke for far less time than men of an equivalent academic level: on average student women presented for 23% less time than student men, and academic women presented for 17% less time than academic men. We conducted more detailed analyses to tease apart whether this gender difference was caused by decisions made by the attendees or through bias in evaluation of the abstracts. At both academic levels, women and men were equally likely to request a presentation. However, women were more likely than men to prefer a short talk, regardless of academic level. We discuss potential underlying reasons for this gender bias, and provide recommendations to avoid similar gender biases at future conferences.
Jones et al. (2014) Gender differences in conference presentations: a consequence of self-selection?. PeerJ 2:e627 https://doi.org/10.7717/peerj.627
Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins
The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds (Paraves). Results of aerodynamic testing are mapped phylogenetically to examine how maneuvering characteristics correspond to tail shortening, forewing elaboration, and other morphological features. In the evolution of Paraves we observe shifts from static stability to inherently unstable aerial planforms; control effectiveness also migrated from tails to the forewings. These shifts suggest that a some degree of aerodynamic control and capacity for maneuvering preceded the evolution of a strong power stroke. The timing of shifts also suggests features normally considered in light of development of a power stroke may play important roles in control.
Evangelista et al. (2014) Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins. PeerJ 2:e632 https://doi.org/10.7717/peerj.632
The role of macrobiota in structuring microbial communities along rocky shores
Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.
Pfister et al. (2014) The role of macrobiota in structuring microbial communities along rocky shores. PeerJ 2:e631 https://doi.org/10.7717/peerj.631
Stable hydrogen isotopes record the summering grounds of eastern red bats (Lasiurus borealis)
Bats face numerous threats associated with global environmental change, including the rapid expansion of wind-energy facilities, emerging infectious disease, and habitat loss. An understanding of the movement and migration patterns of these highly dispersive animals would help reveal how spatially localized the impacts from these threats are likely to be on bat populations, thus aiding in their conservation. Stable hydrogen isotope ratios (δ2H) can be used to infer regions where bats have foraged during the summer molt season, thus allowing an assessment of summering location and distance of movement of bats sampled during other times of year. However, a major impediment to the application of δ2H for inference of bat movements is that the relationship between δ2H of bat hair and precipitation tends to be species specific and is still unknown for some key species of conservation concern. We addressed this issue by using geo-referenced museum specimens to calibrate the relationship between δ2H of hair (δ2Hhair) and long-term δ2H of growing-season precipitation (δ2HGSprecip) at the site of collection for eastern red bats (Lasiurus borealis), one of the main species of bats experiencing large numbers of fatalities at wind-energy facilities in North America. Based on comparison of δ2Hhair and δ2HGSprecip values for males we estimated a period of molt of June 14–August 7. Within this period, male and female red bats exhibited a significant positive relationship between δ2Hhair and δ2HGSprecip. These results establish the relationship between δ2Hhair and δ2HGSprecip for red bats, which is necessary for the use of δ2Hhair to infer the movement and migration patterns of this important species. These results provide a critical resource to conservation biologists working to assess the impacts of environmental change on bat populations.
Pylant et al. (2014) Stable hydrogen isotopes record the summering grounds of eastern red bats (Lasiurus borealis). PeerJ 2:e629 https://doi.org/10.7717/peerj.629
A randomized trial in a massive online open course shows people don’t know what a statistically significant relationship looks like, but they can learn
Scatterplots are the most common way for statisticians, scientists, and the public to visually detect relationships between measured variables. At the same time, and despite widely publicized controversy, P-values remain the most commonly used measure to statistically justify relationships identified between variables. Here we measure the ability to detect statistically significant relationships from scatterplots in a randomized trial of 2,039 students in a statistics massive open online course (MOOC). Each subject was shown a random set of scatterplots and asked to visually determine if the underlying relationships were statistically significant at the P < 0.05 level. Subjects correctly classified only 47.4% (95% CI [45.1%–49.7%]) of statistically significant relationships, and 74.6% (95% CI [72.5%–76.6%]) of non-significant relationships. Adding visual aids such as a best fit line or scatterplot smooth increased the probability a relationship was called significant, regardless of whether the relationship was actually significant. Classification of statistically significant relationships improved on repeat attempts of the survey, although classification of non-significant relationships did not. Our results suggest: (1) that evidence-based data analysis can be used to identify weaknesses in theoretical procedures in the hands of average users, (2) data analysts can be trained to improve detection of statistically significant results with practice, but (3) data analysts have incorrect intuition about what statistically significant relationships look like, particularly for small effects. We have built a web tool for people to compare scatterplots with their corresponding p-values which is available here: http://glimmer.rstudio.com/afisher/EDA/.
Fisher et al. (2014) A randomized trial in a massive online open course shows people don’t know what a statistically significant relationship looks like, but they can learn. PeerJ 2:e589 https://doi.org/10.7717/peerj.589
Complex groundwater flow systems as traveling agent models
Analyzing field data from pumping tests, we show that as with many other natural phenomena, groundwater flow exhibits complex dynamics described by 1/f power spectrum. This result is theoretically studied within an agent perspective. Using a traveling agent model, we prove that this statistical behavior emerges when the medium is complex. Some heuristic reasoning is provided to justify both spatial and dynamic complexity, as the result of the superposition of an infinite number of stochastic processes. Even more, we show that this implies that non-Kolmogorovian probability is needed for its study, and provide a set of new partial differential equations for groundwater flow.
López Corona et al. (2014) Complex groundwater flow systems as traveling agent models. PeerJ 2:e557 https://doi.org/10.7717/peerj.557
Occurrence of the megatoothed sharks (Lamniformes: Otodontidae) in Alabama, USA
The Otodontidae include some of the largest sharks to ever live in the world’s oceans (i.e., Carcharocles megalodon). Here we report on Paleocene and Eocene occurrences of Otodus obliquus and Carcharocles auriculatus from Alabama, USA. Teeth of Otodus are rarely encountered in the Gulf Coastal Plain and this report is one of the first records for Alabama. Carcharocles auriculatus is more common in the Eocene deposits of Alabama, but its occurrence has been largely overlooked in the literature. We also refute the occurrence of the Oligocene Carcharocles angustidens in the state. Raised awareness and increased collecting of under-sampled geologic formations in Alabama will likely increase sample sizes of O. obliquus and C. auriculatus and also might unearth other otodontids, such as C. megalodon and C. chubutensis.
Ehret et al. (2014) Occurrence of the megatoothed sharks (Lamniformes: Otodontidae) in Alabama, USA. PeerJ 2:e625 https://doi.org/10.7717/peerj.625
An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella
Comparative genomics based on whole genome sequencing (WGS) is increasingly being applied to investigate questions within evolutionary and molecular biology, as well as questions concerning public health (e.g., pathogen outbreaks). Given the impact that conclusions derived from such analyses may have, we have evaluated the robustness of clustering individuals based on WGS data to three key factors: (1) next-generation sequencing (NGS) platform (HiSeq, MiSeq, IonTorrent, 454, and SOLiD), (2) algorithms used to construct a SNP (single nucleotide polymorphism) matrix (reference-based and reference-free), and (3) phylogenetic inference method (FastTreeMP, GARLI, and RAxML). We carried out these analyses on 194 whole genome sequences representing 107 unique Salmonella enterica subsp. enterica ser. Montevideo strains. Reference-based approaches for identifying SNPs produced trees that were significantly more similar to one another than those produced under the reference-free approach. Topologies inferred using a core matrix (i.e., no missing data) were significantly more discordant than those inferred using a non-core matrix that allows for some missing data. However, allowing for too much missing data likely results in a high false discovery rate of SNPs. When analyzing the same SNP matrix, we observed that the more thorough inference methods implemented in GARLI and RAxML produced more similar topologies than FastTreeMP. Our results also confirm that reproducibility varies among NGS platforms where the MiSeq had the lowest number of pairwise differences among replicate runs. Our investigation into the robustness of clustering patterns illustrates the importance of carefully considering how data from different platforms are combined and analyzed. We found clear differences in the topologies inferred, and certain methods performed significantly better than others for discriminating between the highly clonal organisms investigated here. The methods supported by our results represent a preliminary set of guidelines and a step towards developing validated standards for clustering based on whole genome sequence data.
Pettengill et al. (2014) An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ 2:e620 https://doi.org/10.7717/peerj.620
Hair is a filamentous biomaterial consisting mainly of proteins in particular keratin. The structure of human hair is well known: the medulla is a loosely packed, disordered region near the centre of the hair surrounded by the cortex, which contains the major part of the fibre mass, mainly consisting of keratin proteins and structural lipids. The cortex is surrounded by the cuticle, a layer of dead, overlapping cells forming a protective layer around the hair. The corresponding structures have been studied extensively using a variety of different techniques, such as light, electron and atomic force microscopes, and also X-ray diffraction. We were interested in the question how much the molecular hair structure differs from person to person, between male and female hair, hair of different appearances such as colour and waviness. We included hair from parent and child, identical and fraternal twins in the study to see if genetically similar hair would show similar structural features. The molecular structure of the hair samples was studied using high-resolution X-ray diffraction, which covers length scales from molecules up to the organization of secondary structures. Signals due to the coiled-coil phase of α-helical keratin proteins, intermediate keratin filaments in the cortex and from the lipid layers in the cell membrane complex were observed in the specimen of all individuals, with very small deviations. Despite the relatively small number of individuals (12) included in this study, some conclusions can be drawn. While the general features were observed in all individuals and the corresponding molecular structures were almost identical, additional signals were observed in some specimen and assigned to different types of lipids in the cell membrane complex. Genetics seem to play a role in this composition as identical patterns were observed in hair from father and daughter and identical twins, however, not for fraternal twins. Identification and characterization of these features is an important step towards the detection of abnormalities in the molecular structure of hair as a potential diagnostic tool for certain diseases.
Yang et al. (2014) The structure of people’s hair. PeerJ 2:e619 https://doi.org/10.7717/peerj.619
VERO cells harbor a poly-ADP-ribose belt partnering their epithelial adhesion belt
Poly-ADP-ribose (PAR) is a polymer of up to 400 ADP-ribose units synthesized by poly-ADP-ribose-polymerases (PARPs) and degraded by poly-ADP-ribose-glycohydrolase (PARG). Nuclear PAR modulates chromatin compaction, affecting nuclear functions (gene expression, DNA repair). Diverse defined PARP cytoplasmic allocation patterns contrast with the yet still imprecise PAR distribution and still unclear functions. Based on previous evidence from other models, we hypothesized that PAR could be present in epithelial cells where cadherin-based adherens junctions are linked with the actin cytoskeleton (constituting the adhesion belt). In the present work, we have examined through immunofluorescence and confocal microscopy, the subcellular localization of PAR in an epithelial monkey kidney cell line (VERO). PAR was distinguished colocalizing with actin and vinculin in the epithelial belt, a location that has not been previously reported. Actin filaments disruption with cytochalasin D was paralleled by PAR belt disruption. Conversely, PARP inhibitors 3-aminobenzamide, PJ34 or XAV 939, affected PAR belt synthesis, actin distribution, cell shape and adhesion. Extracellular calcium chelation displayed similar effects. Our results demonstrate the existence of PAR in a novel subcellular localization. An initial interpretation of all the available evidence points towards TNKS-1 as the most probable PAR belt architect, although TNKS-2 involvement cannot be discarded. Forthcoming research will test this hypothesis as well as explore the existence of the PAR belt in other epithelial cells and deepen into its functional implications.
Lafon-Hughes et al. (2014) VERO cells harbor a poly-ADP-ribose belt partnering their epithelial adhesion belt. PeerJ 2:e617 https://doi.org/10.7717/peerj.617
Representing connectivity: quantifying effective habitat availability based on area and connectivity for conservation status assessment and recovery
We apply a comprehensive suite of graph theoretic metrics to illustrate how landscape connectivity can be effectively incorporated into conservation status assessments and in setting conservation objectives. These metrics allow conservation practitioners to evaluate and quantify connectivity in terms of representation, resiliency, and redundancy and the approach can be applied in spite of incomplete knowledge of species-specific biology and dispersal processes. We demonstrate utility of the graph metrics by evaluating changes in distribution and connectivity that would result from implementing two conservation plans for three endangered plant species (Erigeron parishii, Acanthoscyphus parishii var. goodmaniana, and Eriogonum ovalifolium var. vineum) relative to connectivity under current conditions. Although distributions of the species differ from one another in terms of extent and specific location of occupied patches within the study landscape, the spatial scale of potential connectivity in existing networks were strikingly similar for Erigeron and Eriogonum, but differed for Acanthoscyphus. Specifically, patches of the first two species were more regularly distributed whereas subsets of patches of Acanthoscyphus were clustered into more isolated components. Reserves based on US Fish and Wildlife Service critical habitat designation would not greatly contribute to maintain connectivity; they include 83–91% of the extant occurrences and >92% of the aerial extent of each species. Effective connectivity remains within 10% of that in the whole network for all species. A Forest Service habitat management strategy excluded up to 40% of the occupied habitat of each species resulting in both range reductions and loss of occurrences from the central portions of each species’ distribution. Overall effective network connectivity was reduced to 62–74% of the full networks. The distance at which each CHMS network first became fully connected was reduced relative to the full network in Erigeron and Acanthoscyphus due to exclusion of peripheral patches, but was slightly increased for Eriogonum. Distances at which networks were sensitive to loss of connectivity due to presence non-redundant connections were affected mostly for Acanthoscyphos. Of most concern was that the range of distances at which lack of redundancy yielded high risk was much greater than in the full network. Through this in-depth example evaluating connectivity using a comprehensive suite of developed graph theoretic metrics, we establish an approach as well as provide sample interpretations of subtle variations in connectivity that conservation managers can incorporate into planning.
Spatial and Geographic Information Science
Neel et al. (2014) Representing connectivity: quantifying effective habitat availability based on area and connectivity for conservation status assessment and recovery. PeerJ 2:e622 https://doi.org/10.7717/peerj.622
A vision physiological estimation of ultraviolet window marking visibility to birds
Billions of birds are estimated to be killed in window collisions every year, worldwide. A popular solution to this problem may lie in marking the glass with ultraviolet reflective or absorbing patterns, which the birds, but not humans, would see. Elegant as this remedy may seem at first glance, few of its proponents have taken into consideration how stark the contrasts between ultraviolet and human visible light reflections or transmissions must be to be visible to a bird under natural conditions. Complicating matters is that diurnal birds differ strongly in how their photoreceptors absorb ultraviolet and to a lesser degree blue light. We have used a physiological model of avian colour vision to estimate the chromatic contrasts of ultraviolet markings against a natural scene reflected and transmitted by ordinary window glass. Ultraviolets markings may be clearly visible under a range of lighting conditions, but only to birds with a UVS type of ultraviolet vision, such as many passerines. To bird species with the common VS type of vision, ultraviolet markings should only be visible if they produce almost perfect ultraviolet contrasts and are viewed against a scene with low chromatic variation but high ultraviolet content.
Håstad et al. (2014) A vision physiological estimation of ultraviolet window marking visibility to birds. PeerJ 2:e621 https://doi.org/10.7717/peerj.621
Using observation-level random effects to model overdispersion in count data in ecology and evolution
Overdispersion is common in models of count data in ecology and evolutionary biology, and can occur due to missing covariates, non-independent (aggregated) data, or an excess frequency of zeroes (zero-inflation). Accounting for overdispersion in such models is vital, as failing to do so can lead to biased parameter estimates, and false conclusions regarding hypotheses of interest. Observation-level random effects (OLRE), where each data point receives a unique level of a random effect that models the extra-Poisson variation present in the data, are commonly employed to cope with overdispersion in count data. However studies investigating the efficacy of observation-level random effects as a means to deal with overdispersion are scarce. Here I use simulations to show that in cases where overdispersion is caused by random extra-Poisson noise, or aggregation in the count data, observation-level random effects yield more accurate parameter estimates compared to when overdispersion is simply ignored. Conversely, OLRE fail to reduce bias in zero-inflated data, and in some cases increase bias at high levels of overdispersion. There was a positive relationship between the magnitude of overdispersion and the degree of bias in parameter estimates. Critically, the simulations reveal that failing to account for overdispersion in mixed models can erroneously inflate measures of explained variance (r2), which may lead to researchers overestimating the predictive power of variables of interest. This work suggests use of observation-level random effects provides a simple and robust means to account for overdispersion in count data, but also that their ability to minimise bias is not uniform across all types of overdispersion and must be applied judiciously.
Harrison (2014) Using observation-level random effects to model overdispersion in count data in ecology and evolution. PeerJ 2:e616 https://doi.org/10.7717/peerj.616
Pure oxygen ventilation during general anaesthesia does not result in increased postoperative respiratory morbidity but decreases surgical site infection. An observational clinical study
Background. Pure oxygen ventilation during anaesthesia is debatable, as it may lead to development of atelectasis. Rationale of the study was to demonstrate the harmlessness of ventilation with pure oxygen. Methods. This is a single-centre, one-department observational trial. Prospectively collected routine-data of 76,784 patients undergoing general, gynaecological, orthopaedic, and vascular surgery during 1995–2009 were retrospectively analysed. Postoperative hypoxia, unplanned ICU-admission, surgical site infection (SSI), postoperative nausea and vomiting (PONV), and hospital mortality were continuously recorded. During 1996 the anaesthetic ventilation for all patients was changed from 30% oxygen plus 70% nitrous oxide to 100% oxygen in low-flow mode. Therefore, in order to minimize the potential of confounding due to a variety of treatments being used, we directly compared years 1995 (30% oxygen) and 1997 (100%), whereas the period 1998 to 2009 is simply described. Results. Comparing 1995 to 1997 pure oxygen ventilation led to a decreased incidence of postoperative hypoxic events (4.3 to 3.0%; p < 0.0001) and hospital mortality (2.1 to 1.6%; p = 0.088) as well as SSI (8.0 to 5.0%; p < 0.0001) and PONV (21.6 to 17.5%; p < 0.0001). There was no effect on unplanned ICU-admission (1.1 to 0.9; p = 0.18). Conclusions. The observed effects may be partly due to pure oxygen ventilation, abandonment of nitrous oxide, and application of low-flow anesthesia. Pure oxygen ventilation during general anaesthesia is harmless, as long as certain standards are adhered to. It makes anaesthesia simpler and safer and may reduce clinical morbidity, such as postoperative hypoxia and surgical site infection.
von Bormann et al. (2014) Pure oxygen ventilation during general anaesthesia does not result in increased postoperative respiratory morbidity but decreases surgical site infection. An observational clinical study. PeerJ 2:e613 https://doi.org/10.7717/peerj.613
Construction and comparison of gene co-expression networks shows complex plant immune responses
Gene co-expression networks (GCNs) are graphic representations that depict the coordinated transcription of genes in response to certain stimuli. GCNs provide functional annotations of genes whose function is unknown and are further used in studies of translational functional genomics among species. In this work, a methodology for the reconstruction and comparison of GCNs is presented. This approach was applied using gene expression data that were obtained from immunity experiments in Arabidopsis thaliana, rice, soybean, tomato and cassava. After the evaluation of diverse similarity metrics for the GCN reconstruction, we recommended the mutual information coefficient measurement and a clustering coefficient-based method for similarity threshold selection. To compare GCNs, we proposed a multivariate approach based on the Principal Component Analysis (PCA). Branches of plant immunity that were exemplified by each experiment were analyzed in conjunction with the PCA results, suggesting both the robustness and the dynamic nature of the cellular responses. The dynamic of molecular plant responses produced networks with different characteristics that are differentiable using our methodology. The comparison of GCNs from plant pathosystems, showed that in response to similar pathogens plants could activate conserved signaling pathways. The results confirmed that the closeness of GCNs projected on the principal component space is an indicative of similarity among GCNs. This also can be used to understand global patterns of events triggered during plant immune responses.
Leal et al. (2014) Construction and comparison of gene co-expression networks shows complex plant immune responses. PeerJ 2:e610 https://doi.org/10.7717/peerj.610
Stimulation of glucose uptake in murine soleus muscle and adipocytes by 5-(4-phenoxybutoxy)psoralen (PAP-1) may be mediated by Kv1.5 rather than Kv1.3
Kv1 channels are shaker-related potassium channels that influence insulin sensitivity. Kv1.3−/− mice are protected from diet-induced insulin resistance and some studies suggest that Kv1.3 inhibitors provide similar protection. However, it is unclear whether blockade of Kv1.3 in adipocytes or skeletal muscle increases glucose uptake. There is no evidence that the related channel Kv1.5 has any influence on insulin sensitivity and its expression in adipose tissue has not been reported. PAP-1 is a selective inhibitor of Kv1.3, with 23-fold, 32-fold and 125-fold lower potencies as an inhibitor of Kv1.5, Kv1.1 and Kv1.2 respectively. Soleus muscles from wild-type and genetically obese ob/ob mice were incubated with 2-deoxy[1-14C]-glucose for 45 min and formation of 2-deoxy[1-14C]-glucose-6-phosphate was measured. White adipocytes were incubated with D-[U-14C]-glucose for 1 h. TNFα and Il-6 secretion from white adipose tissue pieces were measured by enzyme-linked-immunoassay. In the absence of insulin, a high concentration (3 µM) of PAP-1 stimulated 2-deoxy[1-14C]-glucose uptake in soleus muscle of wild-type and obese mice by 30% and 40% respectively, and in adipocytes by 20% and 50% respectively. PAP-1 also stimulated glucose uptake by adipocytes at the lower concentration of 1 µM, but at 300 nM, which is still 150-fold higher than its EC50 value for inhibition of the Kv1.3 channel, it had no effect. In the presence of insulin, PAP-1 (3 µM) had a significant effect only in adipocytes from obese mice. PAP-1 (3 µM) reduced the secretion of TNFα by adipose tissue but had no effect on the secretion of IL-6. Expression of Kv1.1, Kv1.2, Kv1.3 and Kv1.5 was determined by RT-PCR. Kv1.3 and Kv1.5 mRNA were detected in liver, gastrocnemius muscle, soleus muscle and white adipose tissue from wild-type and ob/ob mice, except that Kv1.3 could not be detected in gastrocnemius muscle, nor Kv1.5 in liver, of wild-type mice. Expression of both genes was generally higher in liver and muscle of ob/ob mice compared to wild-type mice. Kv1.5 appeared to be expressed more highly than Kv1.3 in soleus muscle, adipose tissue and adipocytes of wild-type mice. Expression of Kv1.2 appeared to be similar to that of Kv1.3 in soleus muscle and adipose tissue, but Kv1.2 was undetectable in adipocytes. Kv1.1 could not be detected in soleus muscle, adipose tissue or adipocytes. We conclude that inhibition of Kv1 channels by PAP-1 stimulates glucose uptake by adipocytes and soleus muscle of wild-type and ob/ob mice, and reduces the secretion of TNFα by adipose tissue. However, these effects are more likely due to inhibition of Kv1.5 than to inhibition of Kv1.3 channels.
Ngala et al. (2014) Stimulation of glucose uptake in murine soleus muscle and adipocytes by 5-(4-phenoxybutoxy)psoralen (PAP-1) may be mediated by Kv1.5 rather than Kv1.3. PeerJ 2:e614 https://doi.org/10.7717/peerj.614
Synthesis and anti-tubercular activity of 3-substituted benzo[b]thiophene-1,1-dioxides
We demonstrated that the 3-substituted benzothiophene-1,1-dioxide class of compounds are effective inhibitors of Mycobacterium tuberculosis growth under aerobic conditions. We examined substitution at the C-3 position of the benzothiophene-1,1-dioxide series systematically to delineate structure–activity relationships influencing potency and cytotoxicity. Compounds were tested for inhibitory activity against virulent M. tuberculosis and eukaryotic cells. The tetrazole substituent was most potent, with a minimum inhibitory concentration (MIC) of 2.6 µM. However, cytotoxicity was noted with even more potency (Vero cell TC50 = 0.1 µM). Oxadiazoles had good anti-tubercular activity (MICs of 3–8 µM), but imidazoles, thiadiazoles and thiazoles had little activity. Cytotoxicity did not track with anti-tubercular activity, suggesting different targets or mode of action between bacterial and eukaryotic cells. However, we were unable to derive analogs without cytotoxicity; all compounds synthesized were cytotoxic (TC50 of 0.1–5 µM). We conclude that cytotoxicity is a liability in this series precluding it from further development. However, the series has potent anti-tubercular activity and future efforts towards identifying the mode of action could result in the identification of novel drug targets.
Chandrasekera et al. (2014) Synthesis and anti-tubercular activity of 3-substituted benzo[b]thiophene-1,1-dioxides. PeerJ 2:e612 https://doi.org/10.7717/peerj.612
Butyrate and other short-chain fatty acids increase the rate of lipolysis in 3T3-L1 adipocytes
We determined the effect of butyrate and other short-chain fatty acids (SCFA) on rates of lipolysis in 3T3-L1 adipocytes. Prolonged treatment with butyrate (5 mM) increased the rate of lipolysis approximately 2–3-fold. Aminobutyric acid and acetate had little or no effect on lipolysis, however propionate stimulated lipolysis, suggesting that butyrate and propionate act through their shared activity as histone deacetylase (HDAC) inhibitors. Consistent with this, the HDAC inhibitor trichostatin A (1 µM) also stimulated lipolysis to a similar extent as did butyrate. Western blot data suggested that neither mitogen-activated protein kinase (MAPK) activation nor perilipin down-regulation are necessary for SCFA-induced lipolysis. Stimulation of lipolysis with butyrate and trichostatin A was glucose-dependent. Changes in AMP-activated protein kinase (AMPK) phosphorylation mediated by glucose were independent of changes in rates of lipolysis. The glycolytic inhibitor iodoacetate prevented both butyrate- and tumor necrosis factor-alpha-(TNF-α) mediated increases in rates of lipolysis indicating glucose metabolism is required. However, unlike TNF-α– , butyrate-stimulated lipolysis was not associated with increased lactate release or inhibited by activation of pyruvate dehydrogenase (PDH) with dichloroacetate. These data demonstrate an important relationship between lipolytic activity and reported HDAC inhibitory activity of butyrate, other short-chain fatty acids and trichostatin A. Given that HDAC inhibitors are presently being evaluated for the treatment of diabetes and other disorders, more work will be essential to determine if these effects on lipolysis are due to inhibition of HDAC.
Rumberger et al. (2014) Butyrate and other short-chain fatty acids increase the rate of lipolysis in 3T3-L1 adipocytes. PeerJ 2:e611 https://doi.org/10.7717/peerj.611
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology
Orthology inference and other sequence analyses across multiple genomes typically start by performing exhaustive pairwise sequence comparisons, a process referred to as “all-against-all”. As this process scales quadratically in terms of the number of sequences analysed, this step can become a bottleneck, thus limiting the number of genomes that can be simultaneously analysed. Here, we explored ways of speeding-up the all-against-all step while maintaining its sensitivity. By exploiting the transitivity of homology and, crucially, ensuring that homology is defined in terms of consistent protein subsequences, our proof-of-concept resulted in a 4× speedup while recovering >99.6% of all homologs identified by the full all-against-all procedure on empirical sequences sets. In comparison, state-of-the-art k-mer approaches are orders of magnitude faster but only recover 3–14% of all homologous pairs. We also outline ideas to further improve the speed and recall of the new approach. An open source implementation is provided as part of the OMA standalone software at http://omabrowser.org/standalone.
Wittwer et al. (2014) Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PeerJ 2:e607 https://doi.org/10.7717/peerj.607
Computed tomography analysis of guinea pig bone: architecture, bone thickness and dimensions throughout development
The domestic guinea pig, Cavia aperea f. porcellus, belongs to the Caviidae family of rodents. It is an important species as a pet, a source of food and in medical research. Adult weight is achieved at 8–12 months and life expectancy is ∼5–6 years. Our aim was to map bone local thickness, structure and dimensions across developmental stages in the normal animal. Guinea pigs (n = 23) that had died of natural causes were collected and the bones manually extracted and cleaned. Institutional ethical permission was given under the UK Home Office guidelines and the Veterinary Surgeons Act. X-ray Micro Computed Tomography (microCT) was undertaken on the left and right scapula, humerus and femur from each animal to ascertain bone local thickness. Images were also used to undertake manual and automated bone measurements, volumes and surface areas, identify and describe nutrient, supratrochlear and supracondylar foramina. Statistical analysis between groups was carried out using ANOVA with post-hoc testing. Our data mapped a number of dimensions, and mean and maximum bone thickness of the scapula, humerus and femur in guinea pigs aged 0–1 month, 1–3 months, 3–6 months, 6 months–1 year and 1–4 years. Bone dimensions, growth rates and local bone thicknesses differed between ages and between the scapula, humerus and femur. The microCT and imaging software technology showed very distinct differences between the relative local bone thickness across the structure of the bones. Only one bone showed a singular nutrient foramen, every other bone had between 2 and 5, and every nutrient canal ran in an oblique direction. In contrast to other species, a supratrochlear foramen was observed in every humerus whereas the supracondylar foramen was always absent. Our data showed the bone local thickness, bone structure and measurements of guinea pig bones from birth to 4 years old. Importantly it showed that bone development continued after 1 year, the point at which most guinea pigs have reached full weight. This study is the first to show the high abundance (100% in this study) of the supratrochlear foramen within the guinea pig humerus and the complete absence of a supracondylar foramen, which is different to many other species and may also affect potential fracture points and frequencies. Understanding bone morphology and growth is essential in not only understanding the requirements of the healthy guinea pig, but also necessary in order to investigate disease states.
Witkowska et al. (2014) Computed tomography analysis of guinea pig bone: architecture, bone thickness and dimensions throughout development. PeerJ 2:e615 https://doi.org/10.7717/peerj.615
A cross-sectional study of self-reported general health, lifestyle factors, and disease: the Hordaland Health Study
Background. Information on self-reported health is important for health professionals, and the aim of this study was to examine associations between lifestyle factors and self-reported health and the mediating effect of disease in a Norwegian population. Methods and Materials. The data collection was conducted as part of the Hordaland Health Study (HUSK) 1997–99, which was a cross-sectional epidemiological study. All individuals in Hordaland county born in 1953–1957 were invited to participate (aged 40–44 years). Complete information for the present study was obtained from 12,883 individuals (44% response rate). Height and weight were measured at a physical examination. Information on lifestyle factors, self-reported health, disease (heart attack, apoplexy, angina pectoris, and diabetes), and socio-demographic variables was obtained from a self-administered questionnaire. Self-reported health was measured with a one-item question. Odds ratios for fair or poor self-reported health were calculated using multiple logistic regression analyses adjusted for disease and socio-demographic variables. Results. Respondents reporting adverse lifestyle behaviours (obesity (odds ratio (OR) 1.7, p < 0.001), smoking (OR 1.2, p < 0.001), or excessive intake of alcohol (OR 3.3, p < 0.001)) showed an increased risk of poor self-reported health. Furthermore, a moderate intake of wine (OR 0.6, p < 0.001) or strenuous physical activity (OR 0.5, p < 0.001) decreased the risk of poor health. Disease did not mediate the effect. Conclusion. A one-item question measuring self-reported health may be a suitable measure for health professionals to identify levels of subjective health and reveal a need to target lifestyle factors in relatively young individuals with or without disease.
Jepsen et al. (2014) A cross-sectional study of self-reported general health, lifestyle factors, and disease: the Hordaland Health Study. PeerJ 2:e609 https://doi.org/10.7717/peerj.609
The cranial osteology of Tyrannoneustes lythrodectikos (Crocodylomorpha: Metriorhynchidae) from the Middle Jurassic of Europe
Tyrannoneustes lythrodectikos is one of numerous metriorhynchid crocodylomorph species known from the Oxford Clay Formation of England (Callovian-Oxfordian; Middle-Late Jurassic). This taxon is of evolutionary importance, as it is the oldest and most basal known macrophagous metriorhynchid. It has a mosaic of plesiomorphic and derived feeding related characteristics, including: teeth with microscopic, poorly formed and non-contiguous denticles; increased tooth apicobasal length; ventrally displaced dentary tooth row (increased gape); reduced dentary tooth count; and a proportionally long mandibular symphysis. However the type specimen, and current referred specimens, all lack a preserved cranium. As such, the craniofacial morphology of this taxon, and its potential feeding ecology, remains poorly understood. Here we describe two skulls and two lower jaws which we refer to T. lythrodectikos. Previously these specimens were referred to ‘Metriorhynchus’ brachyrhynchus. They share with the T. lythrodectikos holotype: the in-line reception pits on the dentary, dorsal margin of the surangular is strongly concave in lateral view, and the most of the angular ventral margin is strongly convex. Based on our description of these specimens, the skull of T. lythrodectikos has three autapomorphies: very long posterior processes of the premaxilla terminating in line with the 4th or 5th maxillary alveoli, deep lateral notches on the lateral surface of the maxillary with reception pits for dentary teeth, and the premaxilla forms the anterior margin of the first maxillary alveoli. Our description of the cranial anatomy of Tyrannoneustes lythrodectikos confirms that some macrophagous characteristics evolved during the Middle Jurassic, and were not exclusive to the clade Geosaurini. Moreover, the skulls further highlight the mosaic nature of Tyrannoneustes lythrodectikos and wide-gape macrophagous evolution in Geosaurinae.
Foffa et al. (2014) The cranial osteology of Tyrannoneustes lythrodectikos (Crocodylomorpha: Metriorhynchidae) from the Middle Jurassic of Europe. PeerJ 2:e608 https://doi.org/10.7717/peerj.608