bluuebunny/crossref_metadata_2025 huggingface dataset:
Humoral immunity is the primary means of heterologous Propionibacterium acnes vaccination against Actinobacillus pleuropneumoniae infection in pig
Authors: Li Linxi , Feng Xin , Xie Fang , Gu Jingmin , Gao Yu , Lei Liancheng , Han Wenyu
Published: January 2018

Objective: To analyze the immunoprotection of pigs by heterologous P. acnes vaccination against A. pleuropneumoniae infection, by vaccine and infection in pig. Methods: 12 five-week-old healthy pigs were randomly divided into 2 groups, of which 1 group (n=6) was vaccinated twice with living P. acnes and the other group served as a non-vaccinated control (n=6). Both groups were experimentally infected with A. pleuropneumoniae (serotype 1, 5*107 CFU, CCVC 259) then the clinical symptoms and pathological changes were monitored. Results: Compared to the control group, the vaccination group showed significantly reduced clinical symptoms and pathological changes. The P. acnes-vaccinated group showed a significant increase in the levels of specific serum antibody titer against A. pleuropneumoniae soluble antigen and serum IL-2 and IL-4 concentration. Conclusion: Immunization with heterologous P. acnes enabled an effective humoral immune response against A. pleuropneumoniae infection in pigs.
Comment on Nalliah and Allareddy (2014): Unwarranted conclusions
Authors: Bernhardt Paul C
Published: January 2018

A PeerJ paper by Nalliah and Allareddy (2014) describes improvement in weaker dental students’ scores (and decline in stronger students’ scores) by use of a unique instructional method. I argue that the causal conclusion in their paper cannot be justified because of lack of a comparison group. Regression to the mean is a common confound in test-retest studies such as presented in their paper. Inclusion of a comparison group could be used to rule it out. Other minor issues are raised involving scaling and consistency in the data.
Characterization of artisanal fisheries in Nepal and potential implications for the conservation and management of Ganges River Dolphin (Platanista gangetica gangetica)
Authors: Paudel Shambhu , Levesque Juan C , Saavedra Camilo , Pita Cristina , Pal Prabhat
Published: January 2018

The Ganges River dolphin (Platanista gangetica gangetica) (GRD) is classified as one of the most endangered of all cetaceans in the world and the second scarcest freshwater cetacean. The population is estimated to be less than 2,000 individuals. In Nepal’s Narayani, Sapta Koshi, and Karnali river systems, survival of GRD continues to be threatened by various anthropogenic activities, such as dam construction and interactions with artisanal fisheries. A basic description of the geographic scope, economics, and types of gear used in these fisheries would help managers understand the fishery-dolphin interaction conflict and assist with developing potential solutions to reduce interactions between GRD and local fisheries in Nepal. The main purpose of the study was to collect fishery and socio-economic information by conducting interviews with local fishermen in the Narayani, Sapta Koshi, and Karnali river systems. Based on interviews (n = 163), 79 percent of Nepalese fishermen indicated fishing for local species (e.g., mullet [Rhinomugil corsula] or siloroid catfish [Bagarius bagarius]) was their primary form of income. Fishermen reported fishing effort was greater in summer than winter; greatest in the afternoon (1430 hrs ± 0.27) and during low water level conditions; and gear was set 4.8 ± 0.2 days/week. Fishermen reported using eight different types of monofilament nets (gillnets and cast nets). Sixty percent used gillnets less than 10 m long, and less than one third preferred gillnets between 10 and 100 m long; a few used gillnets longer than 100 m. Fishermen usually set their gear close to their village, and about 50 percent preferred to fish in tributaries followed by the main channel behind sandbars and islands, and the main channel near a bank. Fishermen reported seeing more GRD in the main river stem in winter. In summer, fishermen spotted more GRD in tributaries. Most fishermen told us they believed education, awareness, and changing occupations were important for GRD conservation, but they indicated that occupational options were currently limited in Nepal. Nepalese fishermen acknowledged that fisheries posed a risk to GRD, but they believed water pollution, and dam/irrigation development were the greatest threats.
Getting the most out of RNA-seq data analysis
Authors: Khang Tsung Fei , Lau Ching Yee
Published: January 2018

Background: A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally or use them for downstream systems biology analysis. Producing a coherent differential expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to the biologist. Results: Using two large public RNA-seq data sets - one representing strong, and another mild, biological response, we simulated different replicate size scenarios and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. Our results suggest that if the biological response of interest in the different phenotype classes is expected to be mild, then RNA-seq experiments should focus on validation of differentially expressed gene candidates. At least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value such as NOISeq or GFOLD. In contrast, for strong biological response, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean positive predictive value, an increase of more than 30-fold compared to the case of mild biological response. Among methods with good positive predictive value performance, having triplicates or more substantially improved mean positive predictive value to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. We found DESeq2 to be the most reasonable method to call differentially expressed genes for systems level analysis as it showed the best PPV and sensitivity trade-off (mean PPV and mean sensitivity ∼ 65% at replicate size of six). Conclusion: When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for validation work. Having triplicates or more enables DESeq2 to detect sufficiently large numbers of reliable gene candidates for downstream systems level analysis. When biological effect size is weak, systems level investigation is not possible, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of candidates with good validation potential when triplicates or more are available.
Evidence for embodied predictive coding: the anterior insula coordinates cortical processing of tactile deviancy
Authors: Allen Micah , Fardo Francesca , Dietz Martin , Hillebrandt Hauke F , Rees Geraint , Roepstorff Andreas
Published: January 2018

Embodied awareness is the pervasive, multimodal self-awareness that is thought to form the foundation of emotion. This awareness was recently proposed to rely on the anterior insular cortex (AIC) comparing expected and actual bodily signals arising in prefrontal and sensory cortices. To investigate this possibility in the somatosensory domain, we measured brain activity using functional magnetic resonance imaging while healthy participants discriminated tactile stimuli in a roving oddball design. Dynamic Causal Modelling revealed that unexpected stimuli increased the strength of forward connections in a caudal to rostral ascending hierarchy from thalamic and somatosensory regions towards insula, cingulate and prefrontal cortices, consistent with hierarchical predictive coding. Within this feed-forward flow of neural coupling, the AIC increased both forwards and backwards connections with prefrontal and somatosensory cortex, supporting a comparator role. Further, we found that greater prefrontal to AIC connectivity predicted subjective ratings of stimulus discrimination difficulty. These results are interpreted in light of embodied predictive coding, suggesting that the AIC coordinates global cortical processing of tactile changes to support body awareness.
The atherosclerosis of the sinus node artery is associated with an increased history of supra-ventricular arrhythmias: A retrospective study on 541 standard coronary angiograms
Authors: Ciulla Michele M , Astuti Matteo , Carugo Stefano
Published: January 2018

BACKGROUND: The ischemic damage of the sinus node (SN) is a well known cause of cardiac arrhythmias and can be a consequence of any flow abnormality in the sinus node artery (SNA). Accordingly we aimed this retrospective study to: 1. evaluate the suitability of the standard coronary angiography to study the SNA and 2. determine if the percentage of subjects with a positive retrospective history of supra-ventricular arrhythmias (SVA) differs in patients with normal and diseased SNA ascertained at the time of coronary angiography. METHODS and RESULTS: out of the 541 coronary angiograms reviewed the SNA was visible for its entire course in 486 cases (89.8%). It was found to arise from the right side of the coronary circulation in 266 cases (54.7%) slightly more often than from the left, 219 cases (45.1%). One patient had 2 distinct SNA arising from either side of the coronary circulation. For the second objective we studied the 333 patients with: a. coronary artery disease (CAD), b. properly evaluable SNA and c. complete clinical history available. In 51 (15.3%) a SNA disease was found, the 41.2% of them had a positive SVA history, mainly atrial fibrillation (AF), whereas only the 7.4% of patients with a positive history of SVA could be found in the non-SNA diseased. This difference was statistically significant (P< 0.001). CONCLUSIONS: 1- The evaluation of the SNA is feasible in clinical practice during a standard coronary angiography; 2- this may be relevant since angiographically detectable SNA disease was significantly associated with a positive history of SVA .
Integrating motion sensing technology in radiographic examination
Authors: Lai Christopher , Li Chun-Fai Ellis
Published: January 2018

Background: In the daily operation of X-ray machine, radiation technologists need to have direct close contact with patients with known or potential infectious disease, resulting in environmental contamination by pathogens if hand hygiene was not properly observed. In the last 15 decades, the method for inputting computer commands has evolved from using keyboard, mouse and to touchscreen and a touch-less method: motion sensing technology. Therefore in the present study, we aim to explore the feasibility of using motion-sensing technology to replace several computer-inputting commands that were frequently used during radiographic examination in order to reduce the chance of pathogen contamination to the radiographic equipment and accessories.

Method: In this study, two sets of gesture commands that can encompass the most frequently used computer commands for image manipulation and x-ray acquisition during radiographic examination were carefully designed. Then, the proposed gesture commands were detected by the Leap Motion Controller using motion sensing technology under a controlled experimental environment. Using Leap Motion Diagnostic Visualizer, the recognition performance, practicability and feasibility of the gesture commands were assessed by 4 different trained operators.

Results: In our proposed gesture commands, the horizontal movement of the thumb (when performing right click and exposure release command) and the vertical movement of the index finger (when performing left click, scrolling up and scrolling down command) were the key sensing component that govern and trigger the gesture command. In general, the magnitude of these key sensing fingertip movement was consistent within an operator, but was varies from operator to operator because each of the operator was allowed to achieve the proposed gesture commands with certain extent of flexibility.

Discussion and conclusion: Motion-sensing technology could practicably for image manipulation and making X-ray exposure. As a high variability exists among different operators, the application of an individual operator dependent threshold value rather than a single threshold value in the magnitude of key sensing fingertip movement of gesture commands is recommended. Also, although the implementation motion sensing technology in radiographic examination may inevitably slow down the examination throughput, it could possibly reduce pathogen contamination to the radiographic equipment and accessories, in particular under nosocomial outbreak of epidemic diseases.
By-catch in a recreational fishery: an unmonitored source of mortality.
Authors: McCallum Malcolm L , Worley Gina M , Safi Barroq , Dickens Kris , Jones Jason , McCallum Jamie L
Published: January 2018

The purpose of this study was to infer the possible impact of unmonitored discard of by-catch on a recreational fishery. We recorded by-catch of fishes at a recreational fishery in Northeast Texas, statistically analyzed them, and then projected estimates of mortality if our observations represent a general pattern of behavior. Anglers discarded nine species of fishes during our study. The most frequently discarded fish were Gizzard Shad and Freshwater Drum. Four species of game fish were among the discarded species, but only Channel Catfish and Hybrid Striped Bass composed a large portion of the discarded fishes. Based on our observations, recreational fishing can produce a large amount of by-catch throughout the year and potentially pose an important unmonitored source of fish mortality.
Samples and data accessibility in research biobanks: an explorative survey
Authors: Capocasa Marco , Anagnostou Paolo , D'Abramo Flavio , Matteucci Giulia , Dominici Valentina , Destro Bisol Giovanni , Rufo Fabrizio
Published: January 2018

Biobanks hold human biological samples and/or data giving a crucial contribution to the progress of biomedical research. However, the effective and efficient exploitation of these resources depends on their accessibility. In fact, making bio-resources promptly accessible to all, can favour collaboration among research groups as well as multidisciplinarity. Although this has become a rather common belief, several laboratories still apply secrecy and withholding of samples and data. In this study we conducted a questionnaire based survey in order to investigate sample and data accessibility in research biobanks operating all over the world. 46 out of the 238 contacted biobanks have decided to participate. Most of them provide permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seems not to be a common practice. The analysis of the biobanks guidelines regarding the accessibility of their resources reveal the importance of three aspects: (i) request for applicants to explain what they would like to do with the required resources; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sharing of samples and data stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of the requirements for accessing to biobanks’ resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where biobanks operate.
Relationship of clinical service intensity to hospitalist clinician‐educator evaluations by internal medicine clerkship students
Authors: Robinson Robert
Published: January 2018

BACKGROUND: Hospitalists play a significant role in medical student education and have been shown to be satisfactory and effective teachers in several observational studies. We hypothesized that the clinical productivity demands placed on academic hospitalists may influence medical student evaluations, which has the potential to impact the promotion and retention of hospitalist faculty. METHODS: Retrospective review with correlation analysis of clinical productivity and medical student evaluations of faculty during the 2009 to 2013 academic years for the hospitalists at SIU‐SOM. RESULTS: A total of 32 sets of annual learner evaluations and clinical intensity data were reviewed, representing data for 18 individual hospitalists. Significant correlations between long term measures of service intensity such as annual work RVUs, total patient encounters, and duty days with lower teaching evaluations in many areas were identified. CONCLUSIONS: These results suggest that medical student evaluations of hospitalist faculty are negatively influenced by higher clinical service intensity measured in terms of annual work RVUs, patient encounters, and duty days when measured on an annual basis.
CAUSA 2.0: accurate and consistent evolutionary analysis of proteins using codon and amino acid unified sequence alignments
Authors: Wang Xiaolong , Yang Chao
Published: January 2018

Multiple sequence alignment (MSA) is widely used to reveal structural and functional changes leading to genetic differences among species, and to reconstruct evolutionary histories of related genes, proteins and genomes. Traditionally, proteins and their coding sequences (CDSs) are aligned and analyzed separately, but often drastically different conclusions were drawn on a same set of data. Here we present a new alignment strategy, Codon and Amino Acid Unified Sequence Alignment (CAUSA) 2.0, which aligns proteins and their coding sequences simultaneously. CAUSA 2.0 optimizes the alignment of CDSs at both codon and amino acid level efficiently. Theoretical analysis showed that CAUSA 2.0 enhances the entropy information content of MSA. Empirical data analysis demonstrated that CAUSA 2.0 is more accurate and consistent than nucleotide, protein or codon level alignments. CAUSA 2.0 locates in-frame indels more accurately, makes the alignment of coding sequences biologically more significant, and reveals several novel mutation mechanisms that relate to some genetic diseases. CAUSA 2.0 is available in website www.DNAPlusPro.com .
S-nitrosylation-impaired autophagy: An alternative mechanism underlying aging?
Authors: Zeng Qing-Ping
Published: January 2018

Aging is mysterious with unknown managing patterns. A surprising finding on the tune mode of autophagy by S-nitrosylation is a distinctive step towards the interpretation of the mechanism underlying aging and age-related diseases. This commentary article will discuss, in a wider sense, the implications of S-nitrosylation- and nitration-switched dysfunction of proteins/enzymes in neurodegenerative disorders including Alzheimer's disease (AD), Huntington's diseases (HD) and Parkinson's disease (PD).
Protofeathers were likely to have existed within the common ancestor of dinosaurs
Authors: Yun Chan-gyu
Published: January 2018

In this paper, I comment on Barrett et al. (2015) "Evolution of dinosaur epidermal structures". Though the original authors made some very interesting results, the conclusions made by them are likely influenced by inappropriate or incorrect assumptions such as very little preserved skin fragments represent whole body covering or dinosaurian integumentary structures might represent a degraded collagen fibres. Therefore, their result might represent small size of current datas or preservational bias rather than actual evolutionary history of dinosaurian feathers.
Urban/rural disparities in cancer incidence in New York State, 2008-2012
Authors: Conwell Timothy , Boscoe Francis P
Published: January 2018

We measured urban/rural disparities in cancer incidence in New York State using a data set with more than 500,000 tumors diagnosed among New York State residents between 2008-2012 geocoded to the census tract level. Using poisson regression, we computed the site and stage-specific relative risks of cancer by level of urbanicity after adjustment for age, sex, socioeconomic status and race/ethnicity. 18 of the 23 cancer sites analyzed showed some form of significant association between cancer incidence and urbanicity, although the risk differences were generally small. Differences in risk of 50% or more were seen for stomach, liver, distant-stage uterine, and thyroid cancers (each higher in New York City than in rural areas); esophagus, distant-stage kidney, and distant-stage lung (each lower in New York City than in rural areas); and distant-stage prostate cancer (higher in rural areas).
Understanding text-based persuasion and support tactics of concerned significant others
Authors: van Stolk-Cooke Katherine , Hayes Marie , Baumel Amit , Muench Frederick
Published: January 2018

The behavior of concerned significant others (CSOs) can have a measurable impact on the health and wellness of individuals attempting to meet behavioral and health goals, and research is needed to better understand the attributes of text-based CSO language when encouraging target significant others (TSOs) to achieve those goals. In an effort to inform the development of interventions for CSOs, this study examined the language content of brief text-based messages generated by CSOs to motivate TSOs to achieve a behavioral goal. CSOs generated brief text-based messages for TSOs for three scenarios: (1) to help TSOs achieve the goal, (2) in the event that the TSO is struggling to meet the goal, and (3) in the event that the TSO has given up on meeting the goal. Results indicate that there was a significant relationship between the tone and compassion of messages generated by CSOs, the CSOs’ perceptions of TSO motivation, and their expectation of a grateful or annoyed reaction by the TSO to their feedback or support. Results underscore the importance of attending to patterns in language when CSOs communicate with TSOs about goal achievement or failure, and how certain variables in the CSOs’ perceptions of their TSOs affect these characteristics.
Learning by teaching in dental informatics: An explorative study
Authors: Athanasopoulou Christina , Bamidis Panagiotis
Published: January 2018

An intriguing educational approach, learning by teaching, was applied in the course of dental informatics. The aim of this study was to investigate the effect that teaching expectancy (preparation to teach) and actually teaching, have on skills and knowledge that students are expected to acquire during the course. In order to assess the applicability of this method to various forms of educational materials, students were asked to prepare and present educational objects that would be part of the current semester's curriculum. These were short lectures, computer laboratory exercises and virtual patient cases. The instructors evaluated their content and presentation fulfillment. Focus group sessions were held so as to capture the students' perception of the pedagogic technique. The results indicate that learning by teaching can enhance the quality of knowledge in Dental Informatics and increase computer, research, communication and cognitive skills of the involved students.
Evidence for the s count macrogene
Authors: Schexnayder Russell
Published: January 2018

Background: A macrogene is defined here as a gene on which successive mutations incrementing a repeat count produces successive punctuated evolutionary events in species that are homogeneous for it. The set of repeat count on the asp (abnormal spindle) family of gene is thought to affect brain size in mammals. Corticogenesis requires two integer valued (quantum) variables, the f and s counts, to determine the number of division cycles during the first and second phases, respectively, of neuron production in the cerebral cortex. Quantum ‘extra’ neuron theory hypothesizes that increments in a quantum variable, the n count, cause punctuated encephalization events in species that are homogenous for it. There is evidence in six pairs of inbred mice strains for one or more major genes affecting brain size. Results: The s count is probably equal to the n count plus a positive integer. The calculated n counts are different in three of the four pairs of strains studied where encephalization data has been previously published. Five different n counts have been found in eleven mouse strains. The difference between the n counts of humans and mice is about 25. Conclusions: Encephalization in mammals may be caused by a macrogene that determines the s count. This theory can be tested by determining the s counts of the various mice strains. However, the asp family of gene is probably not the s count macrogene because the difference in the asp counts of humans and mice of 13 (= 74 – 61) is much smaller than the difference in their s counts of around 25.
Information-feed pathways in biological systems as evidence for occurrence of non-natural stimulus-functional response pairing
Authors: Jeff-Eke Imadol V
Published: January 2018

This paper explores a possible underlying tenet of classical information-feed pathways (feedback and feedforward) as seen in metabolism and signaling in biological systems. We intend to determine whether information-feed pathways derive from spatial and temporal overlap of event occurrences involving connection points of the information-feed loop. We shall revisit three known and established biological phenomena involving information-feed, in an attempt to deduce the principles governing such phenomena. We propose that such principles involve anticipatory associations.
State-dependent behavior and alternative behavioral strategies in brown trout (Salmo trutta L.) fry
Authors: Näslund Joacim , Johnsson Jörgen I
Published: January 2018

Animals generally adjust their behavior in response to bodily state (e.g. size and energy reserves) to optimize energy intake in relation to mortality risk, weighing predation probability against starvation. Here we investigated whether brown trout adjust their behavior in relation to feeding history (energetic status) and body size during a major early-life selection bottleneck, when fast growth also appear to be important. We manipulated growth using different food ration schemes over two consecutive time periods (P1 = 12 days, P2 = 23 days), excluding social effects through individual isolation. During these experimental periods the fish were fed either high or low food rations in a crossed design. In behavioral trials following the treatment, where acute hunger levels were standardized among all treatments, fish that were initially fed high rations (P1) and thereafter low rations (P2) had on average 15-21% higher swimming activity than the other groups, but large within-treatment variation rendered only weak statistical support for the effect. Furthermore, fish on low ration during P2 tended to be more aggressive than fish on high ration. Size was related to behavioral expression, with larger fish being more active and aggressive. Swimming activity and active aggression were positively correlated, forming a behavioral syndrome in the studied population. Based on these behavioral traits we could also distinguish two behavioral clusters, one consisting of more active and aggressive individuals, and the other consisting of less active and aggressive individuals. This indicates that two behavioral strategies may exist in young brown trout.
Developing science gateways for drug discovery in a grid environment
Authors: Pérez-Sánchez Horacio , Rezaei Tabar Vahid , Mezhuyev Vitaliy , Man Duhu , Peña-García Jorge Jpg , den-Haan Helena , Gesing Sandra
Published: January 2018

Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life-sciences with a convenient tool for high-throughput virtual screening (HTVS) on distributed computing resources. To this end, we recently integrated the biophysics-based drug screening program FlexScreen into a service applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation, based on Pipeline Pilot and Simple Object Access Protocol (SOAP) provides an easy-to-use graphical user interface to construct complex workflows which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.
Modulatory interactions between the default mode network and task positive networks in resting-state
Authors: Di Xin , Biswal Bharat B.
Published: January 2018

The two major brain networks, i.e. the default mode network (DMN) and the task positive network, typically reveal negative and variable connectivity in resting-state. In the present study, we examined whether the connectivity between the DMN and different components of the task positive network were modulated by other brain regions by using physiophysiological interaction (PPI) on resting-state functional magnetic resonance imaging data. Spatial independent component analysis was first conducted to identify components that represented networks of interest, including the anterior and posterior DMNs, salience, dorsal attention, left and right executive networks. PPI analysis was conducted between pairs of these networks to identify networks or regions that showed modulatory interactions with the two networks. Both network-wise and voxel-wise analyses revealed reciprocal positive modulatory interactions between the DMN, salience, and executive networks. Together with the anatomical properties of the salience network regions, the results suggest that the salience network may modulate the relationship between the DMN and executive networks. In addition, voxel-wise analysis demonstrated that the basal ganglia and thalamus positively interacted with the salience network and the dorsal attention network, and negatively interacted with the salience network and the DMN. The results demonstrated complex modulatory interactions among the DMNs and task positive networks in resting-state, and suggested that communications between these networks may be modulated by some critical brain structures such as the salience network, basal ganglia, and thalamus.
Responses of microbial community from tropical pristine coastal soil to crude oil contamination
Authors: Morais Daniel , Pylro Victor , Clark Ian M , Hirsch Penny R , Tótola Marcos
Published: January 2018

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic Islands near these areas represent sensitive environments, where changes in microbial communities due to oil contamination could cause the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided into two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg-1), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for high-throughput target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20x the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed a rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales in oil contaminated microcosms. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that may be required.
Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling
Authors: Wasowicz Pawel , Pauwels Maxime , Pasierbinski Andrzej , Przedpelska-Wasowicz Ewa M , Babst-Kostecka Alicja A. , Saumitou-Laprade Pierre , Rostanski Adam
Published: January 2018

The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe, to propose hypotheses explaining the emergence of these patterns and to formulate hypotheses on the formation of the present day range of A. halleri in the region. 1281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results suggest that the species might have not survived the last glacial maximum in the Carpathians and Sudetes and that its range during the last glacial maximum might have consisted of at least two major parts: (1) a northern refugium consisting of vast refugial areas north and northeast of the Alps and (2) a southern refugium located in the Dinaric Alps and Balkan Mts. We postulate that the Sudetes and Western Carpathians were colonised mainly by plants originating from the northern refugium, whereas populations from the Eastern Carpathians originate from southern refugium. We also discuss our results in relation to the problematic taxonomy of the species.
Does intrinsically disordered caldesmon bind calmodulin via the “buttons on a string” mechanism?
Authors: Permyakov Sergei E , Permyakov Eugene A , Uversky Vladimir N
Published: January 2018

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636-771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A, W707A, and W737A) and a double tryptophan mutant (W674A/W707A) suggested that although the interaction of CaD136 with calmodulin (CaM) can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136 tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be described as the “buttons on a charged string” model, where the electrostatic attraction between the intrinsically disordered CaD136 and the CaM is solidified in a “snapping buttons” manner by specific packing of the CaD136 “pliable buttons” (which are the short segments of fluctuating local structure condensed around the tryptophan residues) at the CaD136-CaM interface. Our data also show that all three “buttons” are important for binding, since mutation of any of the tryptophans affects CaD136-CaM binding and since CaD136 remains CaM-buttoned even when two of the three tryptophans are mutated to alanines.
My flipped classroom: what I did and how I did it
Authors: Jensen Jan H.
Published: January 2018

In this chapter I describe my own personal experiences with the flipped classroom approach (e.g. lectures at home, problem solving in class) called peer instruction. I describe both the technical aspects such as making video lectures, practical aspects such how to get started, and pedagogical aspects such as curriculum design and how to write good peer instruction questions. Additional and updated material, including short tutorial videos and many additional links to extra material can be found at tinyurl.com/janstips.
Climate change enlarges China’s Great Bustards’ (Otis tarda dybowskii) suitable wintering distribution in the 21st century
Authors: Mi Chunrong , Falk Huettmann , Guo Yumin
Published: January 2018

Rapidly changing climate makes humans realize that there is a critical need to rethink the current conservation and incorporate climate change adaptation into conservation planning. Whether Great Bustards’ (Otis tarda dybowskii), a globally endangered species whose population is approximately 1,500~2,200 individuals in China, would survive in a changing climate environment is an important protection issue. In this study, we selected the most suitable species distribution model for bustards from four machine learning models, combining two modelling approaches (TreeNet and Random Forest) with two sets of variables (correlated variables removed or not), using common evaluation methods (AUC, Kappa and TSS) and independent testing data. We found Random Forest with all environmental variables outperformed in all assessment methods. Projected the best model to the latest IPCC-CMIP5 climate scenarios (RCP 2.6, 4.5 and 8.5 in BCC-CSM1-1), we found suitable wintering habitats in the current bustards distribution would increase during the 21st century, and dramatically extend eastwards, lightly northwards and westwards, with ongoing climate change. Northeast Plain and the south of North China and the North of East China would become two major suitable wintering habitats of bustards. However, some current suitable habitats will experience a reduction, such as in Middle and Lower Yangtze. Although our results suggest the habitats quantity and quality would widen with climate changing, greater efforts should be undertaken on human disturbance, such as pollution, hunting, unsuitable agriculture development, infrastructure construction, habitat fragmentation, oil and mine exploitation. All of which are negatively and intensely linked with global change.
Age, growth, and recruitment patterns of juvenile ladyfish (Elops sp) from the east coast of Florida (USA)
Authors: Levesque Juan C
Published: January 2018

Ladyfish (Elops sp) are a common and economically valuable coastal nearshore species found along coastal beaches, bays, and estuaries of the southeastern United States, and subtropical and tropical regions worldwide. Previously, ladyfish were a substantial bycatch in Florida’s commercial fisheries, but changes in regulations significantly reduced commercial landings. Today, ladyfish are still taken in commercial fisheries in Florida, but many are also taken by recreational anglers. Life-history information and research interest in ladyfish is almost non-existent, especially information on age and growth. Thus, the overarching purpose of this study was to expand our understanding of ladyfish age and growth characteristics. The specific objectives were to describe, for the first time, age, growth, and recruitment patterns of juvenile ladyfish from the east coast of Florida (USA). In the Indian River Lagoon (IRL), annual monthly length-frequency distributions were confounded because a few small individuals recruited throughout the year; monthly length-frequency data generally demonstrated a cyclical pattern. The smallest were collected in September and the largest in May. Post-hoc analysis showed no significant difference in length between August and May, or among the other months. In Volusia County (VC), annual monthly length-frequency distribution demonstrated growth generally occurred from late-winter and spring to summer. The smallest ladyfish were collected in February and the largest in August. On average, the absolute growth rate in the IRL was 36.3 mm in 60 days or 0.605 mm day-1. Cohort-specific daily growth rates, elevations, and coincidentals were similar among sampling years. Cohort-specific growth rates ranged from 1.807 in 1993 to 1.811 mm day-1 in 1994. Overall, growth was best (i.e., goodness of fit) described by exponential regression. On average, the absolute growth rate in VC was 28 mm in 150 days or 0.1866 mm day-1. Cohort-specific daily growth rates were significantly different among sampling years; however, the elevations and coincidentals were similar. Cohort-specific growth rates ranged from 1.741 in 1994 to 1.933 mm day-1 in 1993. Mean ladyfish growth was best described by linear regression; however, natural growth was explained better by exponential regression. In the IRL, the corrected exponential growth equation yielded a size-at-age 1 of 156.0 mm SL, which corresponded to an estimated growth rate of 0.4356 mm day-1. In VC, the corrected exponential growth equation yielded a size-at-age 1 of 80 mm SL corresponding to an estimated growth rate of 0.2361 mm day-1.
Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene
Authors: Verstraelen Hans , Vilchez-Vargas Ramiro , Desimpel Fabian , Jauregui Ruy , Vankeirsbilck Nele , Weyers Steven , Verhelst Rita , De Sutter Petra , Pieper Dietmar H , Van De Wiele Tom
Published: January 2018

Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar in as much B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.
Anvi’o: An advanced analysis and visualization platform for ‘omics data
Authors: Eren A. Murat , Esen Özcan C , Quince Christopher , Vineis Joseph H , Sogin Mitchell L , Delmont Tom O
Published: January 2018

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi’o, an advanced analysis and visualization platform for ‘omics data, and its assembly-based metagenomic workflow. Anvi’o’s interactive interface facilitates the management of contigs and associated metadata for automatic or human-guided identification of genome bins, and their curation. Its extensible visualization approach distills multiple dimensions of information about each contig into a single, intuitive display, offering a dynamic and unified work environment for data exploration, manipulation and reporting. Beyond its easy-to-use interface, the advanced modular architecture of anvi’o as a platform allows users with programming skills to implement and test novel ideas with minimal effort. To demonstrate anvi’o’s capabilities, we re-analyzed a metagenomic time-series data from an infant gut microbiome. Through the anvi’o interface we identified near-complete draft genomes, and explored temporal genomic changes within the abundant microbial populations through de novo characterization of subtle nucleotide variations. We also used anvi’o to re-analyze a collection of datasets from multiple investigators who studied microbial responses to the Deepwater Horizon oil spill. We linked metagenomic, metatranscriptomic, and single-cell genomic data from the water plume, and used the holistic perspective anvi’o provides to identify the draft genome of a previously uncharacterized, active population of Oceanospirillales. We also linked environmental isolates with metagenomes recovered from an oil-contaminated beach, and identified 56 near-complete draft genomes including abundant oil degraders whose functional features suggested an oceanic origin.
Stress-induced production of lipids in oleaginous microalgae for novel biofuel optimization
Authors: Teichner Eric M
Published: January 2018

Emerging concerns over energy security and accelerating climate change have led to a global interest in developing a sustainable biofuel. Recently, it was determined that algal biofuels can be possibly cultured in a wastewater medium due to high levels of nutrients nitrogen, phosphorus, and potassium (NPK), reducing economic costs. Further efforts are needed in strain selection for cultivation in wastewater or inexpensive fertilizer. Common algal strains Nannochloropsis sp. and Chlorella sp. were studied to determine effects. Both strains were exposed to standard nutrients, which acted as controls, and high levels of NPK to simulate wastewater. The results revealed that NPK had a positive effect on turbidity and dissolved oxygen while decreasing the lipid productivities (measured via hexane solvent extraction) by an average of 36.5%. Specifically, Nannochloropsis sp. had overall higher values for all dependent variables. It is believed that under nutrient limiting conditions the cells deposited fatty acids in a triacylglycerol pathway. A follow-up experiment was performed using salinity as a novel method of decreasing biomass while maintaining lipid viability. Results revealed that freshwater algae can be cultivated in salinity levels between 10-15 ppt in order to increase lipid production. It is believed that while salinity osmotically interfered with the cell, lipid content increased, acting as a protective mechanism. Future research should focus on optimizing lipid production under stressed conditions using genetic manipulation of the TAG biosynthesis pathway.