bluuebunny/crossref_metadata_2025 huggingface dataset:
Zeta potential of bacterial cells: Effect of wash buffers
Authors: Ng Wenfa
Published: January 2018

Zeta potential - defined as the electrical charge at the shear plane - is widely used as a proxy for cell surface charge. Consequent of its definition, nonspecific adsorption of ions on the cell surface may alter the value - and polarity - of the measured zeta potential, thereby, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis – where various wash buffers (such as 9 g/L sodium chloride and 0.1M sodium nitrate) help remove ions and charged molecules nonspecifically bound to the cell surface. Nevertheless, little information on the wash buffers’ relative efficacies in removing nonspecifically bound ions hamper the comparison of zeta potential results across laboratories even for the same bacterial strain cultured under identical conditions. Thus, the present study sought to evaluate the effect of various wash buffers on zeta potential of bacterial cells grown in two culture media differing in salt content – thereby, allowing potential differential efficacy of buffers in removing nonspecifically adsorbed ions and metabolites to be discerned. Preliminary data revealed that for Escherichia coli DH5α (ATCC 53868) grown in LB Lennox (supplemented with 2 g/L glucose), the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L sodium chloride, and phosphate buffer saline (PBS) wash buffers. As the glucose supplemented LB medium was a low salt medium without a phosphate buffer, it was unlikely that nonspecific adsorption of ions on the cell surface was extensive – thus, supporting the observation that the various wash buffers used did not have differential effect on zeta potential measurement. On the other hand, the zeta potential-pH profile of E. coli grown in a semi-defined medium with a high capacity phosphate buffer system, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L sodium chloride, 0.1M sodium nitrate, 0.1M sodium acetate, and 0.1M sodium citrate with the extent of difference positively correlated with wash buffers’ ionic strength. A similar relationship was also observed between the measured point of zero charge (pHzpc) and ionic strength of wash buffer, which, taken together, suggested that charge screening might be an important mechanism for removing the adsorbed ions. Collectively, although the experimental data suggests possible use of high ionic strength wash buffer in removing nonspecifically adsorbed ions from bacterial cell surface prior to zeta potential analysis, possible structural damage to the surface from removing intrinsic ions - necessary for stabilizing the bacterial cell wall - could not be discounted.
Zeta potential of bacterial cells: Effect of wash buffers
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Zeta potential - defined as the electrical charge at the shear plane - is widely used as a proxy for cell surface charge. Consequent of its definition, nonspecific adsorption of ions on the cell surface may alter the value - and polarity - of the measured zeta potential, thereby, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis – where various wash buffers (such as 9 g/L sodium chloride and 0.1M sodium nitrate) help remove ions and charged molecules nonspecifically bound to the cell surface. Nevertheless, little information on the wash buffers’ relative efficacies in removing nonspecifically bound ions hamper the comparison of zeta potential results across laboratories even for the same bacterial strain cultured under identical conditions. Thus, the present study sought to evaluate the effect of various wash buffers on zeta potential of bacterial cells grown in two culture media differing in salt content – thereby, allowing potential differential efficacy of buffers in removing nonspecifically adsorbed ions and metabolites to be discerned. Preliminary data revealed that for Escherichia coli DH5α (ATCC 53868) grown in LB Lennox (supplemented with 2 g/L glucose), the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L sodium chloride, and phosphate buffer saline (PBS) wash buffers. As the glucose supplemented LB medium was a low salt medium without a phosphate buffer, it was unlikely that nonspecific adsorption of ions on the cell surface was extensive – thus, supporting the observation that the various wash buffers used did not have differential effect on zeta potential measurement. On the other hand, the zeta potential-pH profile of E. coli grown in a semi-defined medium with a high capacity phosphate buffer system, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L sodium chloride, 0.1M sodium nitrate, 0.1M sodium acetate, and 0.1M sodium citrate with the extent of difference positively correlated with wash buffers’ ionic strength. A similar relationship was also observed between the measured point of zero charge (pHzpc) and ionic strength of wash buffer, which, taken together, suggested that charge screening might be an important mechanism for removing the adsorbed ions. Collectively, although the experimental data suggests possible use of high ionic strength wash buffer in removing nonspecifically adsorbed ions from bacterial cell surface prior to zeta potential analysis, possible structural damage to the surface from removing intrinsic ions - necessary for stabilizing the bacterial cell wall - could not be discounted.
Investigating readiness to use Internet and mobile services of diabetic patients of a middle-income country
Authors: Jafari Javad , Karimi Moonaghi Hossein , Ahmady Soleiman , Zary Nabil , Masiello Italo
Published: January 2018

Background: Diabetes mellitus is increasing worldwide, especially in developing countries, as a consequence of urbanization. The use of the Internet and mobile service are increasing as well. The independent use of the Internet and mobile technologies by the patients could be a key step towards self-care management of the disease. Methods: A validated questionnaire with two parts was used and was completed by patients who came to two diabetic clinics for routine checkup. The first part consisted of 16 items collecting demographics information. The second part contained 26 items about the specific use of the Internet and mobile services to access information. Results: 407 questionnaires were completed. 108 (26,5 %) had routine access to Internet, of which 95,4 % had routine access to mobile services and 77,8 % were positive to the use of a Persian website for medical information. Yet, 55 % of respondents preferred to get information from TV, radio and educational courses. Conclusions: Data suggest that most diabetic patients who use the Internet in this study were willing to receive educational material by the Internet. However, many still prefer traditional means of information. Our future research is going to focus on early adopters.
Customization of psychosocial stress effects on human health: An intrapersonal conflict perspective
Authors: Sandoz Patrick
Published: January 2018

From etiologic, clinical or public health perspectives, differences in psychosocial stress responses remain a huge scientific and medical challenge. We address the customization of psychosocial stress responses in humans by considering our dual character of independent organisms and interdependent social group members as a source of intrapersonal conflicts.

By challenging our subjective representations on our social identity, psychosocial stress triggers or exhibits intrapersonal conflicts and may enhance divergence between physiologically-driven and psycho-sociologically-driven internal forces. In this perspective, our individual-specific brain development constitutes a major cause of interindividual variability since it impacts the overall stress-to-disease links.

We propose a two-step stress-to-disease etiological chain: i) stress perception and appraisal and ii) response to actually perceived stress. We argue that the first step of stress perception and appraisal is more affected by interindividual variability than the second step of response to actually perceived stress. A psychocognitive approach correlating symptoms with actually perceived stress is proposed to address the epidemiology of psychosocial stress effects. The ability of this approach to reduce interindividual variability biases is discussed.

From this perspective, pathological effects of psychosocial stress might be questioned as possible conflict responses internally emerging as the lesser evil, thus corresponding to adaptation attempts.
The impact of threat of shock on the framing effect and temporal discounting: executive functions unperturbed by acute stress?
Authors: Robinson Oliver J , Bond Rebecca L , Roiser Jonathan P
Published: January 2018

Anxiety and stress-related disorders constitute a large global health burden, but are still poorly understood. Prior work has demonstrated clear impacts of stress upon basic cognitive function: biasing attention towards unexpected and potentially threatening information and instantiating a negative affective bias. However, the impact that these changes have on higher-order, executive, decision-making processes is unclear. In this study we examined the impact of a translational within-subjects stress induction (threat of unpredictable shock) on two well-established executive decision-making biases: the framing effect (N=83), and temporal discounting (N=36). In both studies, we demonstrate a) clear subjective effects of stress, and b) clear executive decision-making biases but c) no impact of stress on these decision-making biases. Indeed, Bayes factor analyses confirmed substantial preference for decision-making models that did not include stress. We posit that while stress may induce subjective mood change and alter low-level perceptual and action processes (Robinson et al., 2013b) , some higher-level executive processes remain unperturbed by these impacts. As such, although stress can induce a transient affective biases and altered mood, these need not result in poor financial decision-making.
Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY
Authors: Kumar Abhishek
Published: January 2018

The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins can be conveniently classified into six groups (V1-V6), based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system, using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have less than 10 serpins, which expanded into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 ) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, the phylogenetic history and genomic characteristics of vertebrate serpins were revisited.
Exploring the attitudes of medical faculty members and students in Pakistan towards plagiarism: a cross sectional survey
Authors: Rathore Farooq A , Waqas Ahmed , Zia Ahmad Marjan , Mavrinac Martina , Farooq Fareeha
Published: January 2018

Objective:The objective of this survey was to explore the attitudes towards plagiarism of faculty members and medical students in Pakistan.

Methods:The attitudes toward plagiarism questionnaire (ATPQ) was modified and distributed among 550 medical students and 130 faculty members in 7 medical colleges of Lahore and Rawalpindi. Data was entered in the SPSS v.20 and descriptive statistics were analyzed. The questionnaire was validated by principal axis factoring analysis.

Results:Response rate was 93% and 73% respectively. Principal axis factoring analysis confirmed one factor structure of ATPQ in the present sample. It had an acceptable Cronbach’s alpha value of 0.73. There were 421 medical students (218 (52%) female, 46% 3rd year MBBS students, mean age of 20.93 ± 1.4 years) and 95 faculty members (54.7% female, mean age 34.5 ± 8.9 years). One fifth of the students (19.7%) trained in medical writing (19.7%), research ethics (25.2%) or were currently involved in medical writing (17.6%). Most of the faculty members were demonstrators (66) or assistant professors (20) with work experience between 1-10 years. Most of them had trained in medical writing (68), research ethics (64) and were currently involved in medical writing (64). Medical students and faculty members had a mean score of 43.21 (7.1) and 48.4 (5.9) respectively on ATPQ. Most of the respondents did not consider that they worked in a plagiarism free environment and reported that self-plagiarism should not be punishable in the same way as plagiarism. Opinion regarding leniency in punishment of younger researchers who were just learning medical writing was divided.

Conclusions:The general attitudes of Pakistani medical faculty members and medical students as assessed by ATPQ were positive. We propose training in medical writing and research ethics as part of the under and post graduate medical curriculum.
Origin of the unique ventilatory apparatus of turtles
Authors: Lyson Tyler , Schachner Emma R , Botha-Brink Jennifer , Scheyer Torsten , Lambertz Markus , Bever Gaberiel , Rubidge Bruce , de Queiroz Kevin
Published: January 2018

Background. The turtle body plan differs markedly from that of other vertebrates and serves as a model system for studying structural and developmental evolution. Incorporation of the ribs into the iconic turtle shell negates the rib movements that effect lung ventilation in the majority of air-breathing amniotes (the clade encompassing mammals, lizards, turtles, birds, and crocodilians). Instead, turtles have a novel abdominal-muscle-based ventilatory apparatus whose evolutionary origin remains a mystery. Methods. Here we show through broadly comparative anatomical and histological analyses that the earliest stem-group turtle form the middle Permian (260 mya), Eunotosaurus africanus, has several turtle-specific lung ventilation characters: rigid ribcage, inferred loss of intercostal muscles which drive costal ventilation in all other amniotes, and histological correlates for the primary muscle, M. transverses, used in exhalation. Results. Our results place the origin of the unique lung ventilatory apparatus of extant turtles shortly after the divergence of turtles from other reptiles and approximately 50 million years before the oldest known fully developed shell. Discussion. These data indicate that it was an easing of structural constraints through division of function (divergent specialization) between the ribs and abdominal musculature that facilitated the evolution of both the novel turtle lung ventilation mechanism and the turtle shell.
Building social networks: a Web microportal to promote ADHD monitoring
Authors: Seta Luciano , Chifari Antonella , Di Giuseppe Onofrio , Denaro Paola , Ferreira Manuela , Santos Miguel A.
Published: January 2018

The WHAAM (Web Health Application for Adhd Monitoring) project, funded by the European LLP program, aims at spreading a multimodal and comprehensive cognitive-behavioral treatment for the ADHD. The main deliverable of this project was the WHAAM app, a digital environment designed to support parents, teachers and health professionals in the monitoring children’s behaviors throughout different contexts: home, school and social interaction with peers. A web microportal was developed to introduce potential users both to the methodology and the main characteristics underlying this environment. The aims of the microportal were to illustrate the use of the WHAAM application and describe the ideas underlying the WHAAM approach. The web interface is divided into two areas: the first, introduces users to a short tour in the core functionalities of the application, the latter guides users to keep information around four principal themes, which are ADHD overview, Observation, Intervention and Training. Each of them respects the main steps of an approach based on the careful analysis of the behavior's functions in the main life contexts of the child. This second area permits both horizontal and vertical navigation. In the first modality, users can explore the contents very quickly, obtaining a fresh and simple picture of the most important concepts of the approach used in the project. Otherwise, in the vertical one, users can examine in depth many ADHD resources, some of which are internal to the microportal, and other external. Authors have paid special attention to the use of a simple terminology, avoiding specialized and obscure terms and concepts. Besides, they carefully filtered any sensible information and examined ethical issues related to the health information management. The final version of the microportal will be available in four languages.
Prioritization of actions needed to develop IT skills among healthcare workforce
Authors: Li Sisi , Bamidis Panagiotis D , Konstantinidis Stathis , Traver Vicente , Zary Nabil
Published: January 2018

Background: Health related information and communication technology is globally an important and growing sector. With the promise of more efficient and cost-effective care, eHealth is becoming a key priority to address the current challenges faced by health systems worldwide. Addressing IT skills for health care workforce is seen as an important element of achieving greater social inclusion. Objective: To identify and prioritize the actions needed to improve the IT skills of health care workforce across the EU from different perspectives of experts in health care. Methods: A diverse group of experts, representing different fields of expertise in health care and geographical locations participated in the study. A scientific priority-setting methodology was used to systematically list and score actions that would improve IT skills among health care workforce. The participants evaluated the actions using several criteria: feasibility, effectiveness, deliverability, and maximum impact on IT skills improvement. Results: The actions that scored highest were related to appropriate training, integrating eHealth in curriculum, involving health care workforce in the eHealth solution development, improving awareness of eHealth as well as learning arrangement. The actions that scored lowest were related to the workforce management, identification of IT skills competences needed, joint funding for training program and training on potential workforce. Conclusion: To maintain highly IT skilled health care workforce, eHealth related knowledge and skills in current curricula, improving awareness of eHealth and continuous training according to the different professionals’ needs should be addressed. In addition, healthcare workforce should be actively and continuously included in the development of eHealth solutions.
Distribution, structure and state of seagrass habitats in the SW Black Sea (Burgas Bay, Bulgaria)
Authors: Berov Dimitar , Deyanova Diana , Klayn Stefania , Karamfilov Ventzislav
Published: January 2018

Seagrass habitats play an important role in maintaining the biodiversity and functions of coastal marine ecosystems of the Black Sea. Еutrophication pressures in the 1970s and 1980s had a severe impact on phytobenthic communities, including deterioration, decrease in geographical and depth distribution and disappearance from certain areas. The state of Zostera spp. habitats in the SW Black Sea has not been studied since the 1970s. The purpose of this study is to evaluate the current distribution, structure and overall condition of seagrasses in Burgas Bay, Bulgaria. Historical sites with seagrass meadows were surveyed by SCUBA diving between 2009 and 2014, using destructive sampling and georeferenced digital photogrammetry. Nutrient concentrations in water were measured seasonally at selected sites to study the effects of eutrophication on seagrasses. Seagrass biomass, shoot density, leaf length and leaf area index were measured. Species diversity and biomass of zoobenthic organisms were also determined. Community structure was analyzed with multivariate statistical methods based on photo and destructive samples.The geographical extent of the meadows was mapped in GIS on recent satellite images, then verified by georeferenced photo samples. Results indicate that most of the seagrass meadows reported in the area in the late 1970s are present today. A decrease in the depth limit of the habitat was established in areas under local eutrophication pressures. A clear depth-related change in community structure was observed, where Zostera noltei dominated the 1-3 m depth range, followed by a mixed Z. noltei – Zannichellia palustris - Zostera marina community (3-4 m) , and dominance of Z. marina between 4 and 7 m. Zoobenthic communities within seagrass meadows were dominated by the gastropods Bittium reticulatum and Rissoa sp., the bivalve Loripes lucinalis, and oligochaetes. Abundance and species richness, as well as faunal dominance were significantly higher in seagrass meadows than in adjacent unvegetated sediments. Biometric parameters of Z. noltei showed significant correlations with measured eutrophication pressures (nutrient concentrations, LUSI index, sediment organic matter content). The ecological quality status of selected meadows was evaluated by using a multimeric indicator based on Z. noltei phenology data, which also showed clear correlation with anthropogenic pressures.
Designing patient education with distance learning
Authors: Franssen Bastiaan , Jafari Javad , Zary Nabil , Masiello Italo
Published: January 2018

Background: Self-management is crucial for patients with chronic diseases. The development of an online learning platform, incorporating a knowledge-driven decision support system, could increase the level of self-management by tailoring education to the patient needs. This leads to better patient understanding and increasing awareness of the importance of self-management. Objective: Describing the needs and requirements of type 2 diabetics for the development of an education platform. The study tried to analyse whether patients like to use a full knowledge driven decision support platform over classic patient centric education. Methods: A qualitative approach for this study used 6 participants, aged 30 to 65 years old. They were diagnosed with type 2 diabetes not earlier than 6 months ago and had no further secondary diabetic complications. They participated in an interview on the several topics related to diabetes. The interview was based on using Diabetes Self-Management Education (DSME). The interview contained both structured and unstructured questions, and was performed with a high-level of involvement to let participants provide consistent information throughout the data-collection. Results: Participants preferred to receive education that is changing to their needs. The incorporation of multimedia was highly recommended, and the method of receiving education was recommended to change per subject. Overall, patient-centric learning was preferred, but knowledge driven learning was welcomed as an addition to some subjects. Conclusion: The education offered is limited to providing basic understanding of self-management. Participants felt the need for follow-up education, but could not be provided with this. The proposed platform, with possibilities to access knowledge whenever the patients needed, was seen as a welcoming addition to the current education. Using patient-centric learning, combined with the integration of knowledge driven decision support, could significantly increase self-management among diabetics.
The biological side of randomness
Authors: Ciulla Michele M
Published: January 2018

This is my comment to an article that was recently published by Science (see ref.1) raising several issues. In this brief note I will not address the methodological issue, as the main merit of the article is to have questioned the preventive medicine as a strategy by undermining its foundations with the randomness of disease, in this case, the cancer. To understand the scope of this refutation we must remember that the preventive strategy was developed since the introduction of the concept of risk factor, that date back to the Framingham Heart Study (FHS) started in 1948. Indeed, prior to the FHS, doctors were still engaged in the study of causation by following the established paradigm of aetiology, and had not yet focused on the concept of prevention or prophylaxis. After having metabolised the concept of risk factor for disease and having made prevention of risk factors the main strategy to fight multifactorial diseases for years, today, in a Western world that is aging, we are facing a new challenge since prevention seems to be no longer enough to cope with diseases such as cancer and, possibly, we need new strategies that we still have not. And this why? Possibly because the randomness appears ever more like the engine that drives the physical universe even if, for living organisms, we must admit several deterministic or, at least, very reproducible events since they are able to actively interact with the environment.
Adhesive root hairs facilitate Posidonia oceanica seedling settlement on rocky substrates
Authors: Alagna Adriana , Vega Fernández Tomás , D'Anna Giovanni , Fici Silvio , Magliola Carlo , Badalamenti Fabio
Published: January 2018

Posidonia oceanica, the dominant Mediterranean seagrass, has been historically described as a species typically growing on mobile substrates whose development requires precursor communities. During more than 10 years of direct observations, we noticed that P. oceanica seedlings were often firmly anchored to rocky reefs, even at exposed sites. Thus, we analysed the ultrastructural features of seedling root systems to identify specific traits that may represent adaptations for early seedling anchorage on rocky bottoms. Subapical sections of adventitious roots were obtained from 2-3 months old specimens collected in the field and were observed at SEM revealing an extensive coverage of adhesive root hairs with a maximum length of 2400 µm. Hairs were provided with an enlarged tips with a maximum width of 78.3 µm, which extended the contact area between the hair tip and the substrate. To test whether adhesive root hairs may facilitate P. oceanica seedlings establishment on rocky substrates, a manipulative experiment was performed. 360 seedlings were reared for 5 months in a land-based culture facility under simulated natural hydrodynamic conditions to identify suitable substrates for early seedling anchorage. Two main substrate features were investigated: firmness (i.e., sand vs. rock) and complexity (i.e., size of interstitial spaces between rocks). Anchorage was strongly influenced by substrate firmness and occurred only on rocks through adhesion by sticky root hairs. Percentage of anchored seedlings on rocks was as high as 89%. The minimum force required to dislodge plantlets attached to rocky substrates reached 23.8 N, which would potentially allow many plantlets to overcome winter storms in the field. The ability of rocky substrates to retain seedlings increased with their complexity. The interstitial spaces between rocks provided appropriate microsites for seedling settlement, as seeds were successfully retained and a suitable substrate for anchorage was available. Adhesive root hairs allowed fast and strong seedling anchorage to consolidated substrates when the root system was not yet developed. This mechanism could favour plant recruitment on rocky substrates with respect to mobile ones, in contrast with traditional paradigms. Such an adaptation leads to hypothesize a new microsite driven bottleneck in P. oceanica seedling survival linked to substrate features.
Divergent thermal specialisation of two South African entomopathogenic nematodes
Authors: Hill Matthew P , Malan Antoinette P , Terblanche John S
Published: January 2018

Thermal physiology of entomopathogenic nematodes (EPN) is a critical aspect of field performance and fitness. Thermal limits for survival and activity, and the ability of these limits to adjust (i.e. show phenotypic flexibility) depending on recent thermal history, are generally poorly established, especially for non-model nematode species. Here we report the acute thermal limits for survival, and the thermal acclimation-related plasticity thereof for two key endemic South African EPN species, Steinernema yirgalemense and Heterorhabditis zealandica. Results including LT50 indicate S. yirgalemense (LT50 = 40.8±0.3°C) has greater high temperature tolerance than H. zealandica (LT50 = 36.7±0.2°C), but S. yirgalemense (LT50 = -2.4±0°C) has poorer low temperature tolerance in comparison to H. zealandica (LT50 = -9.7±0.3°C), suggesting these two EPN species occupy divergent thermal niches to one another.

Acclimation had both negative and positive effects on temperature stress survival of both species, although the overall variation meant that many of these effects were non-significant. There was no indication of a consistent loss of plasticity with improved basal thermal tolerance for either species at upper lethal temperatures. At lower temperatures measured for H. zealandica, the 5°C acclimation lowered survival until below -12.5°C, where after it increased survival. Such results indicate that the thermal niche breadth of EPN species can differ significantly depending on recent thermal conditions, and should be characterized across a broad range of species to understand the evolution of thermal limits to performance and survival in this group.
1001 - A tool for binary representations of unordered multistate characters (with examples from genomic data)
Authors: Mavrodiev Evgeny V
Published: January 2018

In modern molecular systematics, matrices of unordered multistate characters, such as DNA sequence alignments, are used for analysis with no further re-coding procedures nor any a priori determination of character polarity. Here we present 1001, a simple freely available Python-based tool that helps re-code matrices of non-additive characters as different types of binary matrices. Despite to the historical basis, our analytical approach to DNA and protein data has never been properly investigated since the beginning of the molecular age. The polarized matrices produced by 1001 can be used as the proper inputs for Cladistic analysis, as well as used as inputs for future three-taxon permutations. The 1001 binary representations of molecular data (not necessary polarized) may also be used as inputs for different parametric software. This may help to reduce the complicated sets of assumptions that normally precede either Bayesian or Maximum Likelihood analyses.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 1
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Sufficient quantities of cells of consistent characteristics are needed for studying biological processes (at the population level) in many areas of applied microbiology research. However, generating the requisite biomass amount by cell culture is usually the rate-limiting step of the experiment given the relatively low biomass yield of many commercial culture media in shake flasks. This work reports the formulation of a semi-defined medium that enabled aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium (FM) comprises: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L); vitamins and trace elements (yeast extract: 12.0 g/L); salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L); and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium are: high buffer capacity (89 mM phosphate), 1:1 molar ratio between D-Glucose and NH4Cl, and yeast extract providing trace elements and a secondary source of carbon and nitrogen. Preliminary data revealed that an OD600nm of 9 was attained after 24 hours of cultivation at 37 oC, with glucose and NH4Cl as the main nutritional sources. At 48 hours, the OD600nm reached a maximal value of 11 with yeast extract providing the necessary nutrients for cell growth and biomass formation. The broth’s pH varied between 5.5 and 7.8 during cultivation. For comparison, the maximum OD600nm of E. coli grown in three commonly used complex media: Nutrient Broth, LB Lennox, and Tryptic Soy Broth (TSB) were 1.4, 3.2 and 9.2, respectively, under identical culture conditions. Finally, FM maintained the viability of a larger population of cells for three days - compared to a population collapse observed in TSB after one day. Collectively, the present findings suggest that the formulated medium may find use as a high cell density aerobic growth medium for E. coli in shake flasks. Part 2 of this work describes improvements in medium performance - specifically, higher cell yield as well as a shorter diauxic lag phase and total culture period – achieved through a small reduction in D-Glucose and NH4Cl concentrations in the medium composition. A preprint of the work is available at https://peerj.com/preprints/117/.
Towards a global dataset of seagrass occurrences: current progress, knowledge gaps and challenges
Authors: Weatherdon Lauren , Martin Corinne S , Mcowen Chris , Thomas Hannah
Published: January 2018

For a number of years, the United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC) has collaborated with Dr. Frederic Short (SeagrassNet, University of New Hampshire) and other seagrass experts worldwide to compile a global georeferenced dataset of seagrass occurrences. More than 184,000 point and polygon records have been collated to date. The GIS dataset and associated metadata can be downloaded from UNEP-WCMC’s Ocean Data Viewer, thereby providing ready-for-use information on the location of this critical habitat to policy-makers, conservationists, and scientists. This knowledge is necessary to inform better decisions regarding marine conservation (e.g., marine spatial planning) and to ensure the sustainable use of our ocean’s resources (e.g., ecosystem service valuation). This and other similar datasets on the distribution of key marine habitats—e.g., saltmarshes, mangroves, and corals (also curated and distributed by UNEP-WCMC)—have been used in numerous global and regional studies that examine the status of sensitive marine biodiversity and related impacts. Occurrence datasets such as these are also used to inform predictive models aimed at filling spatial gaps in knowledge. Moreover, such a global dataset can support analyses that explore the contribution of seagrass and other ‘blue carbon’ ecosystems (e.g. saltmarsh, mangrove) to carbon sequestration, thereby aiding climate change mitigation. As part of an interactive session, we will: 1. Present current progress towards collating a global dataset of seagrass occurrences, highlighting the achievements of such collaborative endeavours and the relevance of this dataset to global science, conservation, and policy initiatives; and 2. Facilitate a discussion with Mediterranean seagrass experts to develop recommendations for addressing the knowledge gaps and challenges (e.g. licensing issues) that have been identified. In particular, this session will focus on improving our collective knowledge of the spatial distribution of seagrass ecosystems in data-poor regions of the Mediterranean by drawing from local and regional expertise. Given the importance of these ecosystems to sustaining marine biodiversity, regulating carbon, and supporting global fisheries, such contributions towards developing a comprehensive and accurate dataset can help to ensure that scientists, conservationists, policy-makers and other decision-makers have the appropriate information to make better-informed analyses and decisions.
Reconstructing the evolutionary and ecological history of the sea skaters Halobates spp. (Heteroptera: Gerridae)
Authors: Román Palacios Cristian , Moraga Lopez Daniela
Published: January 2018

The genus Halobates includes the only five insect species that have been successful in a pelagic marine environment. Different scenarios of independent colonization events of that environment have been proposed, considering the appearance of pelagic distribution in several non-sister clades in the phylogeny of the genus. In this paper, we aim to update the phylogenetic hypothesis under the criterion of Bayesian inference, calibrate a molecular clock using the only fossil described in the genus and also analyze the diversity pattern of the lineage since its divergence. High support values were found in the phylogenetic reconstruction, which tend to decrease with an increase of the distances from the root. Low supports for the most derived clades or relatively recent divergences cast doubt on the delimitation of some species. Although the divergence time for Halobates was estimated at 42.01 mya (± 8.13) the emergence of the lineage probably happened a few million years before, so the estimated time of divergence probably also marked the start of diversification of the marine lineages of this genus. Since divergence, the richness of genus showed continuous linear growth for approximately 24.4 my, when the lineages began to diversify more quickly with a significantly lower extinction rate.The colonization of the pelagic environment which occurred nearly 42 mya, could also have been the starting point of the colonization of the marine pelagic environment when changes in their morphology, physiology and behaviour enabled them to exploit novel ecological niches. Ancestors of pelagic marine insects probably inhabited areas close to the seacoast more than 41 mya ago. The ecological history of Halobates was probably not limited to a pair of open water colonization events as indicated by earlier proposals. We hypothesize instead that at least three independent events of open water colonization by Halobates species have occurred. In this sense, the ecological character of coastal or pelagic distribution is considered to be a homoplasic character without direct implications on the net diversification of Halobates.
Genetic structure of the Crown-of-Thorns seastar in the Pacific Ocean, with focus on Guam
Authors: Tusso Sergio , Morcinek Kerstin , Vogler Catherine , Schupp Peter J , Caballes Ciemon F , Vargas Sergio , Woerheide Gert
Published: January 2018

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The most stark divergence of these groupings from previous studies is the lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island. These findings suggest potential long-range dispersal of COTS in the Pacific, and highlight the importance of ecological determinants in shaping genetic structure.
A native beetle fond of exotic plants. Characteristics that contribute to invasive success in Costelytra zealandica (Scarabaeidae: Melolonthinae)
Authors: Lefort Marie-Caroline , Boyer Stéphane , Vereijssen Jessica , Glare Travis R , Worner Susan P
Published: January 2018

Widespread replacement of native ecosystems by productive land sometimes results in the outbreak of a native species. In New Zealand, the introduction of exotic pastoral plants has resulted in the diet alteration of the native coleopteran species, Costelytra zealandica (White) (Scarabaeidae) such that this insect has reached the status of pest. In contrast, C. brunneum (Broun), a close congeneric species, has not developed such a relationship with these ‘new’ host plants. This study investigated the feeding preferences and fitness performance of these two closely related scarab beetles to increase fundamental knowledge about the mechanisms responsible for the development of invasive characteristics in native insects. To this end the feeding preferences of larvae of both Costelytra species were investigated under controlled conditions and the survival and larval growth of the invasive species C. zealandica were compared on native and exotic host plants. Costelytra zealandica, when sampled from exotic pastures, was unable to fully utilise its ancestral native host and showed better performance on exotic plants. In contrast, C. zealandica sampled from native grasslands did not perform significantly better on either host and showed similar feeding preferences to C. brunneum. This study suggests the possibility of strong intra-specific variation, in the ability of C. zealandica to exploit native or exotic plants, supporting the hypothesis that such ability underpins the existence of distinct host-races in this species.
LecoS - A QGIS plugin for automated landscape ecology analysis
Authors: Jung Martin
Published: January 2018

The quantification of landscape structures is an important part in many ecological analysis dealing with GIS derived satellite data. This paper introduces a new free and open-source tool for conducting landscape ecology analysis. LecoS is able to compute a variety of basic and advanced landscape metrics in an automatized way by iterating through an optional provided vector layer. It is integrated into the QGIS processing framework and can thus be used as a stand-alone tool or within bigger complex models. Finally a potential case-study is demonstrated, which tries to quantify pollinators responses on landscape derived metrics at various scales.
New occurrences of fossilized feathers: systematics, taphonomy, and paleoecology of the Santana Formation of the Araripe Basin (Cretaceous), NE, Brazil
Authors: Prado Gustavo M. E. M. , Anelli Luiz Eduardo , Romero Guilherme Raffaelli
Published: January 2018

Feathers are the most complex and diversified integuments in vertebrates. Their complexity are provided by the different forms and functions, and they occur both in non-avian and avian-dinosaurs. Despite their rareness, feathers are found throughout the world, and the Santana Formation (comprised by Crato and Romualdo formations) of the Araripe Basin is responsible for the majority of these records in Brazil. Most occurrences is consisted by isolated feathers, where downy-feathers is the recurrent morphotype, two coelurosaurs and one enantiornithe bird. The sedimentary deposition of this unit is consisted by a lacustrine (Crato Fm) and lagoonal (Romualdo Fm) environments, where reducing conditions prevailed, precluding the activity of bottom dwelling organisms that favored the exquisite preservation. Despite the arid and hot conditions during the Cretaceous, life teemed in the adjacency of both paleolakes, however, feathered non-avian dinosaurs were not found yet in the Crato Member. By the great diversity of life that existed in the paleolake surroundings, is possible to recognize, through the fossil record, that a complex and diversified trophic chain was well established during the time period of sedimentation of this unit. When the remains reached the bottom of the paleolakes, the subsequent isolation from the environment allowed their preservation. In this work, three fossilized feathers, consisted of two downy and one contour feather, extracted from the laminated limestone of the Crato Member of the Santana Formation, were described and identified according to morphological and evolutionary models. We also used the terminology commonly applied to extant organisms. Relying on the fossil record of this unit and the adjacencies formations and basins (by autochthonous condition), taxonomic inferences can be made when the lowest hierarchy level is considered, and hence, is possible to propose the plausible taxa that could bear these elements. Taphonomic and paleoecological aspects, such as the preservation of these structures, and the presence of dinosaurs, were also reviewed, as well as the future perspectives about the study of these elements. Despite the virtual low significance, the pragmatical study of fossilized feathers, can help with the understanding of the evolution and paleobiology of dinosaurs, especially on the South Hemisphere.
Assessment of seagrass communities in the northern Gulf of Aqaba: Mapping their distribution
Authors: Winters Gidon , Shem Tov Rachamim , Elmaliach Tal , Edelist Dor , Rilov Gil
Published: January 2018

Within the Gulf of Aqaba, coral reefs have been considered the dominating ecosystem, attracting not only scientific attention, but also restoration efforts, aquarium exhibits and outreach educational programs. Seagrasses, which are known worldwide as a highly important ecosystem, have not received much attention by the public, scientists or authorities involved in conservation and management in this region. This is surprising considering the value of ecosystem services associated with seagarsses and the fact that many of these services are important to adjacent coral reefs. The absence of comprehensive seagrass maps for this region, prohibits other downstream activities such as evaluations of the associated ecosystem services and implementation of potential conservation and management tools. Here we present efforts to map seagrass meadows along the Israeli coast of the northern Gulf of Aqaba. Mapping was done by snorkeling with a GPS and a handheld echo-sounder. Transects perpendicular to the shore were conducted with measurements taken every 10-20 m that included water depth, GPS position and percent of seagrass cover estimated visually up to 13-23 m depending on visibility. In addition to these transects, we also tracked the shallow boundary of the meadows parallel to shore, usually at 3-5 m depth. Both data sets were then fed into Arc-GIS to create an interpolated GIS layer. Out of 11 km available shoreline, we swam along 9.7 km and collected a total of 2830 data points. Seagrasses were found growing along 7.5 km of these shores, with seagrass meadows covering 707,000 sqm2.estimated to be worth = US$ 2,000,000 year-1 in associated ecosystem services. In addition to mapping the seagrass meadows themselvs, we also mapped the potential dangers to seagrasses in the region. Disturbances were ranked as low, medium or high according to severity and frequency. We expect that these maps (GIS layers) will allow us to not only understand the current distribution of seagrasses in the area, but also to develop a GIS-based tool that will improve our understanding of how changes in the Gulf could affect the cover and state of seagrasses, and thus improve conservation efforts in the region.