Breaking the Ice and Forging Links: The Importance of Socializing in Research

When meeting someone for the first time—whether another PhD student, or the Founding Editor-in-chief of PLOS Computational Biology—nothing breaks the ice like eating pancakes or having drinks together. A social atmosphere provides a relaxed, informal environment where people can connect, share ideas, and form collaborations. Being able to build a network and thrive in a social environment is crucial to a successful scientific career. This article highlights the importance of bringing people together who speak the same scientific language in an informal setting. Using examples of events held by Regional Student Groups of the ISCB''s Student Council, this article shows that socializing is much more than simply sharing a drink.     

The nucleolar organizer of Plethodon cinereus cinereus (Green)

The lampbrush nucleolar organizers in P. c. cinereus are on the shorter arms of the 7th longest bivalent, near to the centromeres. The organizer consists of a non-chromomeric, Feulgen-negative section of the half bivalent axis inserted between typically chromomeric regions with normal lampbrush loops. The main axis of the organizer may appear double or single. The distributions and lengths of the double regions are variable. The axial strand of the organizer can be broken with DNase. Nucleolus-like objects are attached at irregular intervals along the organizer axis. The attached nucleoli closely resemble the free nucleoli in the same nucleus. Where free and attached nucleoli appear as beaded rings, the general characteristics and range of lengths of the attached rings are similar to those of the free rings. The attached rings occur singly, in pairs, or in clusters. The point of attachment of a ring is sometimes marked by a granule on the organizer axis. Pairs of attached nucleolar rings sometimes form double bridges in which the nucleoli extend linearly across a gap in the organizer axis. The length of the organizer varies from 20 μm to 300 μm, depending, at least in part, on the stage of oocyte development. The difference is a function of the length of the axial strand. Nucleolar organizers similar to that described for P. c. cinereus have been seen on the lampbrush bivalents of 7 other species of Plethodon and 2 species of Eurycea. In all of these, the 2 organizers of the nucleolus bivalents differ in length.     

Gender and performance in athletics

Abstract

A comparison of women's and men's performance in swimming, running, and skating is made based on available world record data. The ratio of women's to men's record times is analyzed as a time series, and the asymptotic value of this ratio is discussed in the context of a model. “Rate of improvement curves” are defined over time and by event in a given sport and are compared across gender. The relationship of record time to event distance is estimated and also analyzed across event and gender boundaries. We make three conclusions: 1. The rate of improvement for women has been extraordinary and is larger for longer distance vents. 2. Law‐like relations emerge for record times and event lengths. These relations have interesting physical interpretations when examined for various sports. 3. The male physiology is more suited to anaerobic strength events while, given increased access and participation, women can be expected to be more on a par with men in some long‐distance aerobic events.     

Variation Among Student Chapters of The Wildlife Society

ABSTRACT Student Chapters of The Wildlife Society serve the parent organization as a source of new members while promoting professional development among aspiring wildlife biologists. However, little is known about the operation of the Student Chapters across North America. I conducted an online survey between March and May 2006 to learn about variation among chapters and to define successful chapters with a quantifiable, objective parameter (e.g., the active members or budgets). I sent chapter advisors and student officers the online survey via e-mail. Of 92 Student Chapters known to the parent Society in 2005, 66 active and one inactive chapters responded. Activities, sizes, and budgets varied greatly among chapters. Additionally, perceived values of membership by survey participants matched the parent Society's goals. No clear definition of a successful chapter (e.g., those with the most money or members) emerged, but chapters faced some evident problems including apathy from students and advisors as well as a lack of support from the parent Society. Based upon the survey, I recommend Student Chapters have strong projects and activities as well as consider collaborating with other professional organizations. I recommend the parent Society continue to expand student programs and incorporate students into the Society.     

Divide and conquer: pattern formation in Drosophila embryonic epidermis

The pattern of differentiated cell types within tissues and organs is often established by organizers, the localized sources of secreted ligands. Although the mechanisms underlying organizer function have been extensively studied, only in a few cases is it clear how an organizer ultimately controls each individual cell's fate across a field of progenitor cells. One of these cases involves the establishment of a precise pattern of cell differentiation across the embryonic epidermis in Drosophila. Here, we review several recent reports that help to elucidate the regulatory principles used to control this pattern. Because organizers are conserved, the same fundamental principles might operate in other organizers.     

The genes for ribosomal RNA in diploid and polytene chromosomes of Drosophila melanogaster

The proportion of the Drosophila genome coding for ribosomal RNA was examined in DNA from both diploid and polytene tissues of Drosophila melanogaster by rRNA-DNA hybridization. Measurements were made on larvae with one, two, three and four nucleolus organizer regions per genome. In DNA from diploid tissues the percent rDNA (coding for 28S and 18S ribosomal DNA) was found to be in proportion to the number of nucleolus organizers present. The number of rRNA genes within a nucleolus organizer therefore does not vary in response to changes in the number of nucleolus organizers. On the other hand, in DNA from cells with polytene chromosomes the percent rDNA remained at a level of about 0.1% (two to six times lower than the diploid values), regardless of either the number of nucleolus organizers per genome or whether the nucleolus organizers were carried by the X or Y chromosomes. This independence of polytene rDNA content from the number of nucleolus organizers is presumably due to the autonomous polytenization of this region of the chromosome. When the rDNA content of DNA from whole flies is examined, both the rDNA additivity of the diploid cells and the rDNA independence of polytene cells will affect the results. This is a possible explanation for the relative rDNA increase known to occur in X0 flies, but probably not for the phenomenon of rDNA magnification. — In further studies on DNA from larval diploid tissues, the following findings were made: 1) the Ybb-chromosome carries no rDNA; 2) flies carrying four nucleolus organizers do not tend to lose rDNA, even after eleven generations, and 3) the nucleolus organizer on the wild type Y chromosome may have significantly less rDNA than does that on the corresponding X chromosome.     

The Regional Student Group Program of the ISCB Student Council: Stories from the Road

The International Society for Computational Biology (ISCB) Student Council was launched in 2004 to facilitate interaction between young scientists in the fields of bioinformatics and computational biology. Since then, the Student Council has successfully run events and programs to promote the development of the next generation of computational biologists. However, in its early years, the Student Council faced a major challenge, in that students from different geographical regions had different needs; no single activity or event could address the needs of all students. To overcome this challenge, the Student Council created the Regional Student Group (RSG) program. The program consists of locally organised and run student groups that address the specific needs of students in their region. These groups usually encompass a given country, and, via affiliation with the international Student Council, are provided with financial support, organisational support, and the ability to share information with other RSGs. In the last five years, RSGs have been created all over the world and organised activities that have helped develop dynamic bioinformatics student communities. In this article series, we present common themes emerging from RSG initiatives, explain their goals, and highlight the challenges and rewards through specific examples. This article, the first in the series, introduces the Student Council and provides a high-level overview of RSG activities. Our hope is that the article series will be a valuable source of information and inspiration for initiating similar activities in other regions and scientific communities.     

The Spirit of Competition: To Win or Not To Win

A competition is a contest between individuals or groups. The gain is often an award or recognition, which serves as a catalyst to motivate individuals to put forth their very best. Such events for recognition and success are part of many International Society for Computational Biology (ISCB) Student Council Regional Student Groups (RSGs) activities. These include a popular science article contest, a Wikipedia article competition, travel grants, poster and oral presentation awards during conferences, and quizzes at social events. Organizing competitions is no different than any other event; they require a lot of hard work to be successful. Each event gives remarkable organizational and social experience for students running it, while at the same time the participants of the competitions are rewarded by prizes and recognition. It gives everybody involved an opportunity to demonstrate their extraordinary talents and skills. Competitions are unique because they bring out both the best and worst in people.     

Bias in phylogenetic measurements of extinction and a case study of end‐Permian tetrapods

Extinction risk in the modern world and extinction in the geological past are often linked to aspects of life history or other facets of biology that are phylogenetically conserved within clades. These links can result in phylogenetic clustering of extinction, a measurement comparable across different clades and time periods that can be made in the absence of detailed trait data. This phylogenetic approach is particularly suitable for vertebrate taxa, which often have fragmentary fossil records, but robust, cladistically‐inferred trees. Here we use simulations to investigate the adequacy of measures of phylogenetic clustering of extinction when applied to phylogenies of fossil taxa while assuming a Brownian motion model of trait evolution. We characterize expected biases under a variety of evolutionary and analytical scenarios. Recovery of accurate estimates of extinction clustering depends heavily on the sampling rate, and results can be highly variable across topologies. Clustering is often underestimated at low sampling rates, whereas at high sampling rates it is always overestimated. Sampling rate dictates which cladogram timescaling method will produce the most accurate results, as well as how much of a bias ancestor–descendant pairs introduce. We illustrate this approach by applying two phylogenetic metrics of extinction clustering (Fritz and Purvis's D and Moran's I) to three tetrapod clades across an interval including the Permo‐Triassic mass extinction event. These groups consistently show phylogenetic clustering of extinction, unrelated to change in other quantitative metrics such as taxonomic diversity or extinction intensity.     

Vicariance events shaping Southern South American insect distributions

The main goal of this study is to use multiple insect phylogenies along with geographical information to test known vicariance hypotheses for Southern South America. We analysed the phylogenies and geographical distributions of seven insect genera endemic to southern South America using Hovenkamp's ( 1997 ) protocol, which have been in part implemented in software (vicariance inference program). Using this software, we were able to hypothesize 55 traceable vicariance events; among these, we recognized four supported vicariance events (i.e. confirmed by more than a single sister group). The first supported vicariance event consisted of an East/West separation of the faunas in all analysed trees; the second supported vicariance event is a North/South separation of the fauna located East of the Andes; the third supported vicariance event was found in the southernmost fauna located East of the Andes, which separates allopatric Patagonian species in a North/South direction; and finally, the fourth supported vicariance event separates in a North/South direction clades of the Central Chilean fauna located West of the Andes. Our results suggest that these four supported vicariance events could be correlated with the uplifting of the Andes and the marine ingressions that occurred during the Cenozoic that is the estimated age at which these events occurred. Finally, we discuss that current software implementation of Hovenkamp's ideas need to be expanded, particularly regarding the automated selection of traceable vicariance events.     

The nucleolus organizers of Plethodon and Aneides located by in situ nucleic acid hybridization with Xenopus 3H-ribosomal RNA

The main clusters of ribosomal genes, or nucleolus organizers, have been located by in situ nucleic acid hybridization of Xenopus laevis ³H labelled ribosomal RNA to mitotic chromosomes in squash preparations of intestinal epithelium from 7 species of Plethodon and 3 species of Aneides. The species used were chosen on account of having well known karyotypes and genome sizes. The Plethodon species covered a range of genome size of 20–69.4 pg. The locations of those nucleolus organizers that could be detected by autoradiography after in situ hybridization varied from species to species, and in Aneides there were differences between two populations of the same species. On the other hand, some distantly related species of Plethodon, with widely different genome sizes, had nucleolus organizers at corresponding positions. The results are discussed in relation to ideas on karyotype stability, homosequentiality and chromosome repatterning.     

Leaf gas exchange and water status responses of a native and non-native grass to precipitation across contrasting soil surfaces in the Sonoran Desert

Arid and semi-arid ecosystems of the southwestern US are undergoing changes in vegetation composition and are predicted to experience shifts in climate. To understand implications of these current and predicted changes, we conducted a precipitation manipulation experiment on the Santa Rita Experimental Range in southeastern Arizona. The objectives of our study were to determine how soil surface and seasonal timing of rainfall events mediate the dynamics of leaf-level photosynthesis and plant water status of a native and non-native grass species in response to precipitation pulse events. We followed a simulated precipitation event (pulse) that occurred prior to the onset of the North American monsoon (in June) and at the peak of the monsoon (in August) for 2002 and 2003. We measured responses of pre-dawn water potential, photosynthetic rate, and stomatal conductance of native (Heteropogon contortus) and non-native (Eragrostis lehmanniana) C₄ bunchgrasses on sandy and clay-rich soil surfaces. Soil surface did not always amplify differences in plant response to a pulse event. A June pulse event lead to an increase in plant water status and photosynthesis. Whereas the August pulse did not lead to an increase in plant water status and photosynthesis, due to favorable soil moisture conditions facilitating high plant performance during this period. E. lehmanniana did not demonstrate heightened photosynthetic performance over the native species in response to pulses across both soil surfaces. Overall accumulated leaf-level CO₂ response to a pulse event was dependent on antecedent soil moisture during the August pulse event, but not during the June pulse event. This work highlights the need to understand how desert species respond to pulse events across contrasting soil surfaces in water-limited systems that are predicted to experience changes in climate.     

Memory for events and their spatial context: models and experiments

The computational role of the hippocampus in memory has been characterized as: (i) an index to disparate neocortical storage sites; (ii) a time-limited store supporting neocortical long-term memory; and (iii) a content-addressable associative memory. These ideas are reviewed and related to several general aspects of episodic memory, including the differences between episodic, recognition and semantic memory, and whether hippocampal lesions differentially affect recent or remote memories. Some outstanding questions remain, such as: what characterizes episodic retrieval as opposed to other forms of read-out from memory; what triggers the storage of an event memory; and what are the neural mechanisms involved? To address these questions a neural-level model of the medial temporal and parietal roles in retrieval of the spatial context of an event is presented. This model combines the idea that retrieval of the rich context of real-life events is a central characteristic of episodic memory, and the idea that medial temporal allocentric representations are used in long-term storage while parietal egocentric representations are used to imagine, manipulate and re-experience the products of retrieval. The model is consistent with the known neural representation of spatial information in the brain, and provides an explanation for the involvement of Papez''s circuit in both the representation of heading direction and in the recollection of episodic information. Two experiments relating to the model are briefly described. A functional neuroimaging study of memory for the spatial context of life-like events in virtual reality provides support for the model''s functional localization. A neuropsychological experiment suggests that the hippocampus does store an allocentric representation of spatial locations.     

Extreme streams: species persistence and genomic change in montane insect populations across a flooding gradient

The ecological and evolutionary consequences of extreme events are poorly understood. Here, we tested predictions about species persistence and population genomic change in aquatic insects in 14 Colorado mountain streams across a hydrological disturbance gradient caused by a one in 500‐year rainfall event. Taxa persistence ranged from 39 to 77% across sites and declined with increasing disturbance in relation to species' resistance and resilience traits. For taxa with mobile larvae and terrestrial adult stages present at the time of the flood, average persistence was 84% compared to 25% for immobile taxa that lacked terrestrial adults. For two of six species analysed, genomic diversity (allelic richness) declined after the event. For one species it greatly expanded, suggesting resilience via re‐colonisation from upstream populations. Thus, while resistance and resilience traits can explain species persistence to extreme disturbance, population genomic change varies among species, challenging generalisations about evolutionary responses to extreme events at landscape scales.     

Are MDs more intent on maintaining their elite status than in promoting public good?

The message that philosopher John Ralston Saul delivered during a recent CMA policy conference may have been unpopular with many physicians, but it wasn''t intended to win their support. Instead, organizers wanted him to provide food for thought. Charlotte Gray reports that he did just that.     

Neutrophil transendothelial migration in vitro to Streptococcus pneumoniae is pneumolysin dependent

The recruitment of polymorphonuclear leukocytes (PMN) from the vascular space to the alveolar air space is an early event in host defense against pneumococcal pneumonia. Pneumolysin is a virulence factor for Streptococcus pneumoniae, but a specific role for pneumolysin in neutrophil-endothelial cell interactions has not been investigated. Using a Transwell system, we studied in vitro migration of PMNs across a monolayer of human pulmonary microvascular endothelial cells in response to wild-type S. pneumoniae (D39) and a pneumolysin-deficient mutant (plnA(-)) incubated on the abluminal surface of the monolayer. S. pneumoniae induction of PMN migration was dose dependent and elicited by > or =10(5) D39. Mutants lacking pneumolysin had dramatically reduced potency for eliciting PMN migration compared with the parent strain (5 x 10(6) plnA(-) elicits 18.6% PMN migration vs. 55.5% for 5 x 10(6) D39). The disparity between D39 and plnA(-) persisted in ethanol-fixed bacteria, consistent with the properties of pneumolysin. Neither conditioned medium from D39 nor purified pneumolysin elicited PMN migration to the same extent as the intact D39, suggesting that the role of pneumolysin in eliciting PMN migration requires a more complex interaction between the organism, the endothelium, and the PMN. Both D39 and plnA(-) adhered to, and translocated across, the endothelium in the abluminal to luminal direction and elicited similar levels of IL-8 production. Neither strain elicited upregulation of the endothelial adhesion molecules ICAM-1, VCAM-1, or E-selectin, and they did not cause translocation of NF-kappaB to the nucleus. These findings demonstrate a novel role for pneumolysin in pneumococcus-induced PMN recruitment across the pulmonary endothelium.     

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS''s multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.     

Patterns of contraceptive pill taking in an inner city practice.

A total of 161 patients completed a questionnaire about their pattern of taking the oral contraceptive pill. Only 28% (45) of patients were taking the pill according to the manufacturer''s instructions, and in the event of the pill being missed only 26% of patients would use a sheath. A tenth of the patients believed that amenorrhoea always indicated pregnancy, but 35% believed that amenorrhoea was harmful to the body. This group did not differ in their pill taking from the remaining 65% of patients.     

Les psychodysleptiques: II. Quelques problèmes relatifs à leur usage

In the first part of this paper, a classification was proposed which divided dysleptic drugs into two categories. Further evidence in support of this classification is drawn from the variability of the clinical picture in schizophrenics elicited by mescaline or allied substances, whereas dysleptics with potent anticholinergic properties always induce the same symptomatology. If the therapeutic usefulness of LSD-25 for instance still may be argued, dysleptics belonging to the second group seem to have no therapeutic usefulness. The dysleptics of the first group include in their chemical formula an aromatic or an indole nucleus; the second group is characterized by a phenylglycolate group. The classification proposed here may be compared with Henri Ey''s ideas: in this Jacksonian perspective, dysleptics like LSD would impair the superior strata of the psycho-organic structure whereas Ditran (in the second group) would act at a lower level.