Video-supported Analysis of Beggiatoa Filament Growth, Breakage, and Movement

A marine Beggiatoa sp. was cultured in semi-solid agar with opposing oxygen-sulfide gradients. Growth pattern, breakage of filaments for multiplication, and movement directions of Beggiatoa filaments in the transparent agar were investigated by time-lapse video recording. The initial doubling time of cells was 15.7 ± 1.3 h (mean ± SD) at room temperature. Filaments grew up to an average length of 1.7 ± 0.2 mm, but filaments of up to approximately 6 mm were also present. First breakages of filaments occurred approximately 19 h after inoculation, and time-lapse movies illustrated that a parent filament could break into several daughter filaments within a few hours. In >20% of the cases, filament breakage occurred at the tip of a former loop. As filament breakage is accomplished by the presence of sacrificial cells, loop formation and the presence of sacrificial cells must coincide. We hypothesize that sacrificial cells enhance the chance of loop formation by interrupting the communication between two parts of one filament. With communication interrupted, these two parts of one filament can randomly move toward each other forming the tip of a loop at the sacrificial cell

The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens

Urine is the CDC-recommended specimen for STI testing. It was unknown if the bacterial communities (microbiomes) in urine reflected those in the distal male urethra. We compared microbiomes of 32 paired urine and urethral swab specimens obtained from adult men attending an STD clinic, by 16S rRNA PCR and deep pyrosequencing. Microbiomes of urine and swabs were remarkably similar, regardless of STI status of the subjects. Thus, urine can be used to characterize urethral microbiomes when swabs are undesirable, such as in population-based studies of the urethral microbiome or where multiple sampling of participants is required

Local alignment of generalized k-base encoded DNA sequence

<p>Abstract</p> <p>Background</p> <p>DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base individually. The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence.</p> <p>Results</p> <p>Although two-base encoding is currently used in practice, many other encoding schemes are possible, whereby two ore more bases are encoded at a time. A generalized <it>k</it>-base encoding scheme is presented, whereby feasible higher order encodings are better able to differentiate errors in the encoded sequence from true DNA sequence variants. A generalized version of the previous two-base encoding DNA sequence comparison algorithm is used to compare a <it>k</it>-base encoded sequence to a DNA reference sequence. Finally, simulations are performed to evaluate the power, the false positive and false negative SNP discovery rates, and the performance time of <it>k</it>-base encoding compared to previous methods as well as to the standard DNA sequence comparison algorithm.</p> <p>Conclusions</p> <p>The novel generalized <it>k</it>-base encoding scheme and resulting local alignment algorithm permits the development of higher fidelity ligation-based next generation sequencing technology. This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time.</p

The Citation Field of Evolutionary Economics

Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal that is indispensable in the exchange of expert knowledge on topics and using approaches that relate naturally with it. Analyzing citation data for the relevant academic field for the Journal of Evolutionary Economics, we use insights from scientometrics and social network analysis to find that, indeed, the JEE is a central player in this interdisciplinary field aiming mostly at understanding technological and regional dynamics. It does not, however, link firmly with the natural sciences (including biology) nor to management sciences, entrepreneurship, and organization studies. Another journal that could be perceived to have evolutionary acumen, the Journal of Economic Issues, does relate to heterodox economics journals and is relatively more involved in discussing issues of firm and industry organization. The JEE seems most keen to develop theoretical insights

Engaging Undergraduates in Science Research: Not Just About Faculty Willingness.

Despite the many benefits of involving undergraduates in research and the growing number of undergraduate research programs, few scholars have investigated the factors that affect faculty members' decisions to involve undergraduates in their research projects. We investigated the individual factors and institutional contexts that predict faculty members' likelihood of engaging undergraduates in their research project(s). Using data from the Higher Education Research Institute's 2007-2008 Faculty Survey, we employ hierarchical generalized linear modeling to analyze data from 4,832 science, technology, engineering, and mathematics (STEM) faculty across 194 institutions to examine how organizational citizenship behavior theory and social exchange theory relate to mentoring students in research. Key findings show that faculty who work in the life sciences and those who receive government funding for their research are more likely to involve undergraduates in their research project(s). In addition, faculty at liberal arts or historically Black colleges are significantly more likely to involve undergraduate students in research. Implications for advancing undergraduate research opportunities are discussed

Appointing Women to Boards: Is There a Cultural Bias?

Companies that are serious about corporate governance and business ethics are turning their attention to gender diversity at the most senior levels of business (Institute of Business Ethics, Business Ethics Briefing 21:1, 2011). Board gender diversity has been the subject of several studies carried out by international organizations such as Catalyst (Increasing gender diversity on boards: Current index of formal approaches, 2012), the World Economic Forum (Hausmann et al., The global gender gap report, 2010), and the European Board Diversity Analysis (Is it getting easier to find women on European boards? 2010). They all lead to reports confirming the overall relatively low proportion of women on boards and the slow pace at which more women are being appointed. Furthermore, the proportion of women on corporate boards varies much across countries. Based on institutional theory, this study hypothesizes and tests whether this variation can be attributed to differences in cultural settings across countries. Our analysis of the representation of women on boards for 32 countries during 2010 reveals that two cultural characteristics are indeed associated with the observed differences. We use the cultural dimensions proposed by Hofstede (Culture’s consequences: International differences in work-related values, 1980) to measure this construct. Results show that countries which have the greatest tolerance for inequalities in the distribution of power and those that tend to value the role of men generally exhibit lower representations of women on boards

Neural processing of criticism and positive comments from relatives in individuals with schizotypal personality traits

Objectives. High negative expressed emotion by family members towards schizophrenia patients increases the risk of subsequent relapse. The study aimed to determine whether individuals with high schizotypy (HS) and low schizotypy (LS) would differ in activation of brain areas involved in cognitive control when listening to relative criticism

A green fluorescent protein-expressing murine tumour but not its wild-type counterpart is cured by photodynamic therapy

The ideal cancer treatment should both destroy the primary tumour and at the same time educate the immune system to recognise the tumour as foreign so that distant metastases will also be eradicated. Photodynamic therapy (PDT) involves the i.v. administration of photosensitisers followed by illumination of the tumour with red light producing reactive oxygen species that eventually cause vascular shutdown and tumour cell death by apoptosis and necrosis. Anti-tumour immunity is stimulated after PDT due to the acute inflammatory response, generation of tumour-specific antigens, and induction of heat-shock proteins. Green fluorescent protein (GFP) is used as an optical reporter to noninvasively image the progression of mouse tumours, and in addition, may act as a foreign (jellyfish) antigen. We asked whether GFP-expressing tumours could be used to monitor the response of tumour-bearing mice to PDT, and whether the tumour response differed when a nonimmunogenic tumour cell line was transduced with GFP. We injected RIF-1 or RIF-1 EGFP (stably transduced with a retroviral vector) cells in the leg of C3H/HeN mice and both the cells and tumour grew equally well. We used PDT with benzoporphyrin derivative and a short drug-light interval. There were complete cures and 100% mouse survival of RIF-1 EGFP while RIF-1 wild-type tumours all recurred. Cured mice were resistant to rechallenge with RIF-1 EGFP cells and a rechallenge with wild-type RIF-1 cells grew significantly slower. There was also slower RIF-1 EGFP rechallenge growth but no rejection when RIF-1 EGFP tumours were surgically removed. There was a low rate of PDT cure of tumours when RIF-1 cells were transduced with an empty retroviral vector. The presence of antibodies against EGFP in mouse serum suggests EGFP can act as a foreign antigen and PDT can then stimulate a long-term memory immune response