bluuebunny/crossref_metadata_2025 huggingface dataset:
Variable elements of metacommunity structure across an aquatic-terrestrial ecotone
Authors: Tonkin Jonathan D , Stoll Stefan , Jähnig Sonja C , Haase Peter
Published: January 2018

The Elements of Metacommunity Structure (EMS) framework gives rise to important ecological insights through the distinction of metacommunities into several different idealised structures. We examined the EMS in assemblages occupying a low-mountain river system in central Germany, sampled over three consecutive years. We compared the idealised distributions of assemblages in both the riparian floodplain zone (carabid beetles and spiders) and the benthic instream environment (benthic invertebrates). We further grouped instream organisms into taxonomic and trait groups to examine whether greater competition signal emerges in more similar species groups. We found little evidence of strong competition, even for trait-modality groups, and nestedness was almost non-existent. In addition to random distributions, Gleasonian distributions (indicating clear, but individualistic turnover between sites) were the most commonly identified structure. Clear differences were apparent between different trait groups, particularly between within-trait modalities. These were most evident for different dispersal modes and life cycle durations, with strong dispersers showing possible signs of mass effects. While random distributions may have partly reflected small sample sizes, clearly coherent patterns were evident for many groups, indicating a sufficient gradient in environmental conditions. The prevalence of random distributions suggests many species are responding to a variety of environmental filters in these river-floodplain metacommunities in an anthropogenically-dominated landscape, whereas Gleasonian distributions indicate species are responding idiosyncratically to a primary environmental gradient. Our findings further emphasise the prevalence of context dependency (spatio-temporal variability) in metacommunity studies and emphasise the need to further disentangle the causes of such variation.
DIYlandcover: Crowdsourcing the creation of systematic, accurate landcover maps
Authors: Estes Lyndon , McRitchie Dennis , Choi Jonathan , Debats Stephanie R , Evans Tom , Guthe William , Luo Dee , Ragazzo Gabrielle , Zempleni Reka , Caylor Kelly
Published: January 2018

Accurate landcover maps are fundamental to understanding socio-economic and environmental patterns and processes, but existing datasets contain substantial errors. Crowdsourcing map creation may substantially improve accuracy, but the quality and representativeness of crowdsourced data is hard to verify. We present an open-sourced platform, DIYlandcover, that systematically serves samples of high resolution imagery to an online job market, where workers delineate landcover features of interest. Worker mapping skill is frequently assessed, providing estimates of overall map accuracy and a basis for performance-based payments. An initial trial of DIYlandcover showed that novice workers delineated South African cropland with 91% accuracy, which exceeds current generation global landcover products, while capturing important field geometry data. Given worker payment costs, large area, wall-to-wall mapping may be cost prohibitive, but a potentially promising use of DIYlandcover is to iteratively train and test emerging computer vision algorithms adapted for landcover mapping.
Efficient routes to land conservation given risk of covenant failure
Authors: Schuster Richard , Arcese Peter
Published: January 2018

Conservation initiatives to protect valued species communities in human-dominated landscapes face challenges linked to their potential costs. Conservation covenants on private land may represent a cost-effective alternative to land purchase, although many questions on the long-term monitoring and enforcement costs of covenants and the risk of violation or legal challenges remain unquantified. We explore the cost-effectiveness of conservation covenants, defined here as the fraction of the high-biodiversity landscape potentially protected via investment in covenants versus land purchase. We show that covenant violation and dispute rates substantially affect the estimated long-term cost-effectiveness of a covenant versus land purchase strategy. Our results suggest the long-term cost-effectiveness of conservation covenants may outperform land purchase as a strategy to protect biodiversity as long as disputes and legal challenges are low, but point to a critical need for monitoring data to reduce uncertainty and maximize conservation investment cost-effectiveness.
Context dependency in biodiversity patterns of stream metacommunities
Authors: Tonkin Jonathan D , Heino Jani , Sundermann Andrea , Haase Peter , Jähnig Sonja C
Published: January 2018

Context dependency is a key challenge emerging in metacommunity ecology, which is hindering the development of general ecological theories. River networks and other dendritic systems provide unique systems for examining variation in the processes shaping biodiversity between different metacommunities. We examined biodiversity patterns in five benthic invertebrate datasets, from two drainage basins in central Germany, with the aim of exploring context dependency in these systems. We used variance partitioning to disentangle the variation explained in three biodiversity metrics, including the local contribution to beta diversity (LCBD; a measure of the uniqueness of a site), by proxies of network position (i.e. catchment size and elevation) and local environmental conditions. Contrary to expectation, we found no evidence of a decline in LCBD downstream in our study. Local habitat conditions and catchment land use played a much stronger role than catchment size and elevation in explaining biodiversity metrics. Observed patterns were highly variable between different datasets in our study. These findings suggest that factors shaping biodiversity patterns in these systems are highly context dependent and less related to their position along the river network than local habitat conditions. Given the clear context dependency between datasets, we urge researchers to focus on disentangling the factors driving the high levels of variability between individual systems through the simultaneous study of a number of replicate metacommunities.
Conservation of the critically endangered endemic Malaysian black fighting fish Betta persephone Schaller (Teleostei: Osphronemidae): a brief review
Authors: Chan Kok-Gan
Published: January 2018

Malaysian black fighting fish Betta persephone Schaller (Teleostei: Osphronemidae) is economically and ecologically important fish in South East Asia notably in Malaysia. The locals keep this fish as ornemental fish as well as biocontrol for mosquitoes larvae. But due to rapid deterioriration of its habitats and economy activities, hence this fish population is decreasing at an alarming level. If this goes unnoticed, the fish may face the risk of extinction. In this review, the author performed a systematic approach to analyse the issues, and propose the ways forward to preserve and sustain this fish both in captivity as well as in its natural habitat.
The transplanting of Posidonia oceanica: best practices for Italy
Authors: Bacci Tiziano , Rende Sante Francesco , La Porta Barbara , Paganelli Daniela
Published: January 2018

In the last decades Posidonia oceanica meadows have been undergoing a strong regression phenomena mainly due to a rapid and high overexploitation of coastal zones (e.g. urban encroachment, waste dumping), that significantly altered their natural characteristics and heavily affected marine ecosystems in the whole Mediterranean Basin. As P. oceanica meadows are protected as priority habitat according to Habitat Directive 1992/43/CEE and Barcelona Convention (16.02.1976) and play an important role within some European Directives (WFD: 2000/60/EC and MSFD: 2008/56/EC) each type of human pressure that potentially produces impacts or changes on Posidonia meadows must be deeply assessed to avoid any negative effect on this sensitive habitat. In this contest, transplant of P. oceanica plants may be necessary to reduce meadow regression or to facilitate meadow recovery, reducing the sacrifice of those portions of meadows destroyed by infrastructural works. The Italian National Institute for Environmental Protection and Research (ISPRA) published the technical volume “Preservation and management of coastal-marine ecosystems: The transplanting of Posidonia oceanica" (in Italian language) with the aim to provide a useful tool for operators and Public Administrators involved in this topic at different levels. The manual contains all available information on transplant of P. oceanica derived from a critical analysis of the existing technical and scientific literature and reports, the legal aspects of this issue as well as the main biological characteristics of P. oceanica meadows. Moreover specific details about different transplant techniques and their results over time in some case studies in Italy, have been presented in specific datasheets enclosed to the manual.
Pinna nobilis mapping in Posidonia oceanica meadows by video-photographic techniques in the Gulf of Oristano, Sardinia
Authors: Rende Sante Francesco , Penna Marina , Trabucco Benedetta , Bacci Tiziano , Coppa Stefania , De Lucia Andrea , Camedda Andrea , Massaro Giorgio , Marra Stefano , Perilli Angelo , Cicero Anna Maria
Published: January 2018

Pinna nobilis spatial distribution have been analysed trough a video - photographic approach in a Posidonia oceanica meadow in the Gulf of Oristano (Sardinia, Italy). In situ visual censuses and 2D/3D georeferenced vertical photographic survey were conducted by SCUBA diving in different sampling transect. The experimental procedure was carried out in the summer of 2014. Data have been processed using the photogrammetric techniques, in particular, in this work we presented the procedure and processing techniques to realize the orthographic planar micro cartography mosaics from photo sequences. Results of this study, although preliminary, showed the time-cost effectiveness of this approach to map the benthic species.
Cymodocea nodosa response to simulated CO2-driven ocean acidification: a first insight from global transcriptome profiling
Authors: Ruocco Miriam , Gabriele Procaccini , Musacchia Francesco , Sanges Remo , Olivé Irene , Costa Monya M , Barrote Isabel , Santos Rui , Silva João
Published: January 2018

Global climate changes are imposing multiple pressures to marine organisms. The rising atmospheric CO2 concentration is causing substantial changes in ocean physics, chemistry and biology. At least three synergic environmental stressors have been recognized as primary driven by CO2 emissions: ocean warming, oxygen loss and ocean acidification. The effects of CO2-driven ocean acidification on seagrass metabolism remain largely understudied. A few studies have been conducted near submarine volcanic vents, which mimic the future ocean acidification scenarios, allowing researchers to investigate the performance of marine organisms under long-term exposure to high-CO2 levels. Apart from these, some mesocosm-based experiments have investigated growth and physiological responses to high CO2. For this work, we built an outdoor mesocosm facility at the Centre of Marine Sciences’ field station in Algarve, Portugal, to experimentally manipulate CO2 levels and investigate the effects of high-CO2/low pH on seagrass metabolism and underlying molecular mechanisms. Cymodocea nodosa plants were collected in Cadiz Bay at the end of January 2014 and transported to the mesocosm facility. After a one week acclimation period, C. nodosa were either kept under normal (400 ppm) or elevated (1200 ppm) CO2 concentration for 12 days. Water physico-chemical parameters, irradiance, and chlorophyll-fluorescence-derived photosynthetic parameters were monitored on a daily basis. Here we present, for the first time in this species, results obtained using Illumina RNAseq technology and de-novo transcriptome assembly. Using C. nodosa RNAs extracted at the beginning and the end of the experiment, we assembled more than 70 thousands unique transcripts and were able to annotate more than 90% of them using the Annocript pipeline. Differential expression analysis revealed about 500 transcripts significantly differentially regulated between plants kept under control and high-CO2 conditions. Pathways showing largest changes in gene expression included isoprenoid and amino-acid biosynthesis, porphyrin-containing compound metabolism, amine and polyamine biosynthesis, lipid and carbohydrate metabolism. Transcriptome sequencing also significantly increases the molecular resources available for C. nodosa, almost completely absent before this study.
Circadian fluctuation of gene expression along a bathymetric cline in the marine angiosperm Posidonia oceanica
Authors: Dattolo Emanuela , Lauritano Chiara , Ruocco Miriam , Procaccini Gabriele
Published: January 2018

Plants developed several mechanisms to sense light and to cope with its natural diel and seasonal fluctuation. Many species use an endogenous clock to predict signals from the environment and to anticipate circadian light change. Changes in circadian clock genes allow plants to synchronize their physiology with local light and temperature conditions and to adapt to changes in light regimes occurring across environmental gradient (e.g. across latitudes). Understanding the genetic and physiological basis of plants response to the seasonal and daily variation in environmental conditions, could allow to predict the effects on plant physiology of environmental perturbations that could happen in the future, due to anthropogenic pressure and climatic changes. Most of the recently identified genes, associated with endogenous clock in plants, are themselves circadian regulated, with expression peaks phased to occur at a specific time of the day. Here we explore daily variations in the expression of clock genes in the marine angiosperm Posidonia oceanica along its bathymetric distribution, where plants are exposed to a natural cline of light and temperature. To do that, we measured genes expression (by RT-qPCR) of photoreceptors and components of the plant clock at two target depths (5 and 25 meter depth) and at six time points during the day. Sampling was performed in a continuous meadow located in the Bay of Calvi, Corsica (thanks to the ESF Cost Action 0906). We discuss the effects of the influence of the distinct light environments on the peak expression occurring at a specific time of the day between the two depths. Further, we discuss the potential adaptive relevance of these results on P. oceanica fitness and survival.
Changing paradigms in the supply of sanitation to marginalised groups - 30 years of challenges in Mumbai
Authors: Singh Mahesh Nath , Singh Aditya , Jagtap Anand , Pranjali Pragya
Published: January 2018

Water-borne and poor sanitation related diseases still account for much of the morbidity and mortality in India. Out of the 300 million urban dwellers in India, 22.6% reside in slums. This paper aims to examine the sanitation conditions of slums in the city of Mumbai. About 6.9 million slum dwellers are residing in almost 2000 slum pockets in Mumbai, which constitutes 54% of the population of the city. Most of the slum households depend on inadequate public toilet facilities of very poor quality. Efforts and investments in sanitation have failed to alleviate the situation, as the local population has not been involved. Only recently a demand-driven approach has been applied largely inspired by experiences in rural sanitation programmes. Still supply-driven initiatives by short-term political interests are, to some extent, eroding the resources available for sanitation. However, experiences from the last decade locally and globally, reveal that the demand-driven model is a way forward.
Seagrasses or caged mussels to bioassess the contamination rate of Mediterranean coastal waters? That is the question
Authors: Richir Jonathan , Galgani François , Benedicto José , Andral Bruno , Lejeune Pierre , Salivas-Decaux Maylis , Lafabrie Céline , Lopez y Royo Cecilia , Pergent Gérard , Pergent-Martini Christine , Gobert Sylvie
Published: January 2018

Biological indicators have the capacity to integrate the temporal changes of contaminants, concentrations or fluxes over various time-scales, and are thus considered as interesting tools for water quality biomonitoring. Since the mid-70ies, French programs have developed water monitoring approaches based on the use of bivalve molluscs; and recently the natural background and the extent of water contamination were bioassessed at the scale of the whole western Mediterranean. But even if bivalve molluscs are viewed as reliable bioindicators, their use is not always made easy as a result of their absence in numerous coastal regions that force their transplantation (cages) during several months before their sampling and analysis. This weakness led several scientists to evaluate the bioindicator abilities of other marine organisms. Seagrasses, whose ability to bioaccumulate contaminants proportionally to environmental contamination levels has been clearly demonstrated, have thus been proposed as an appropriate alternative tool for coastal water quality assessment. Very little studies have however so far considered the combined utilization of these two groups of bioindicator organisms, i.e. caged bivalve molluscs and seagrasses. In the framework of the STARECAPMED project, we therefore compared and discussed the bioaccumulation of trace elements in the Neptune grass Posidonia oceanica and in caged Mediterranean mussels Mytilus galloprovincialis. The sampling was performed at the scale of the western Mediterranean. The two species told two contamination stories which, although sometimes different, showed to be complementary. P. oceanica and M. galloprovincialis bioaccumulated dissolved trace elements from the water column and thus provided information regarding trace element contamination severity integrated over several days to a few months. Seagrasses, strongly rooted in the sediments, reflected the long-term exposure to trace elements since sediments offer a degree of time integration over several years to decades. Caged mussels, as filter feeder artificially maintained in the water column, bioaccumulated trace elements from their particulate phase, and therefore gave valuable information regarding continental-terrigenous inputs to coastal waters. In conclusion, seagrasses and mussels should neither supplant, nor substitute, but rather complement each other in order to provide the full time- and space-integrated coastal contamination story of the Mediterranean.
Molecular modeling of the Plasmodium falciparum pre-mRNA splicing and nuclear export factor PfU52
Authors: Newo Soufo Alain Narcisse
Published: January 2018

UAP56/SUB2 is a DExD/H-box RNA helicase that is critically involved in pre-mRNA splicing and mRNA nuclear export. This helicase is broadly conserved and essential in many eukaryotic lineages, including protozoan and metazoan parasites. Previous research suggests that helicases from parasites could be promising drug targets for treating parasitic diseases. Accordingly, characterizing the structure and function of these proteins is of interest for structure-based, de novo design of new lead compounds. Here, we used homology modeling to construct a three-dimensional structure of PfU52 (PMDB ID: PM0079288), the Plasmodium falciparum ortholog of UAP56/SUB2. Comparative in silico analysis revealed that although PfU52 shared many physicochemical, structural and dynamic similarities with its human homolog, it also displayed some unique features that could be exploited for drug design.
The more things change the more they stay the same: Assessing the immediate impact of the licensing act (2004) on attendances to accident & emergency departments
Authors: Patton Robert , Strang John , Birtles Catherine , Crawford Mike
Published: January 2018

This paper reports on a survey of 39 Accident and Emergency departments (AED) in England regarding presentations over a three month time period before and after the changes in the Licensing Act (2003) which came into force in November 2005. The time periods reported are January – March 2005 (the PRE period) and January – March 2006 (the POST period). Our data indicated NO significant change in the number of attendances that could be related to alcohol consumption (hereafter referred to as ‘attendances’) in the first two months following increased availability. In the third month there was a significant decrease in ‘attendances’. There was considerable variation in the changes in ‘attendances’ between participating AEDs. The pattern of ‘attendances’ on weekdays (Monday – Thursday) was unchanged. Following increased availability ‘attendances’ on Saturday fell, but increased on Fridays and Sundays. There were no changes in the pattern of ‘attendances’ across the 24 hour period, with most patients presenting at around Midday. Rates of ‘attendances’ for Assault and Head Injury fell significantly following the change in availability. The number of ‘attendances’ where alcohol was specifically mentioned increased significantly during the POST period. Prior to the increase in availability, the number of ‘attendances’ where alcohol was specifically mentioned peaked sharply around Midnight. Following the change in the law, there was a general increase in such ‘attendances’ from 11PM through to 3AM. Although there was a general increase in alcohol specified ‘attendances’ across the week, there was a significant increase in such ‘attendances’ on a Sunday. Data from one Northern and one Southern Local Ambulance Service was provided to complement the data obtained from individual AEDs. The number of alcohol related ambulance call outs for the LAS and NEAS increased following the change in the law.
The blue-green eggs of dinosaurs: How fossil metabolites provide insights into the evolution of bird reproduction
Authors: Wiemann Jasmina , Yang Tzu-Ruei , Sander Philipp N. N , Schneider Marion , Engeser Marianne , Kath-Schorr Stephanie , Müller Christa E , Sander P. Martin
Published: January 2018

Open-nesting birds use biological pigments in eggshell to camouflage their unhatched offspring, varying the colour to account for the nesting environment and location. The tetrapyrrolic pigments protoporphyrin (PP) and biliverdin (BV), which both participate in the haem metabolism, are responsible for the reddish brown of chicken eggs and the brilliant blue of robin and emu eggs. However, eggshell pigmentation correlates with the nest type in a wide range of avian species and suggests that coloured eggs are basal to the avian lineage, extending back to their non-avian dinosaur origins. Detecting preserved eggshell pigments could thus shed light on dinosaur nesting behaviour. Using HPLC separation coupled to ESI-Q-TOF mass spectrometry, we here provide the first record of the eggshell pigments PP and BV preserved in fossils from three different localities, in 66 million year-old oviraptorid eggshell (Macroolithus yaotunensis). These eggs were presumably laid in at least partially open nests by the oviraptorid Heyuannia huangi and camouflaged by an originally blue-greenish egg colouration. Such a blue-greenish eggshell pigmentation hints at increased paternal care in Heyuannia. Shell porosity measurements, preserved clutches and parental animals support an open nesting behaviour for oviraptorid dinosaurs. Furthermore, the detection of PP, together with supporting microscopic observations, represents the first evidence for cuticle preservation in fossil eggshell. Our study demonstrates that molecular biomarkers, such as preserved metabolites, can be used to trace the evolution of modern avian traits, and to provide insights into dinosaur reproductive biology and the preservation of endogenous organic matter in fossil vertebrates.
Measuring the well-being of health care professionals in the Punjab: a psychometric evaluation of the Warwick-Edinburgh Mental Well-being Scale in a Pakistani population
Authors: Waqas Ahmed , Ahmad Waqas , Haddad Mark , Taggart Frances , Muhammad Zerwah , Bukhari Muhammad Hamza HB , Sami Shahzad Ahmed , Batool Sayyeda Mehak , Najeeb Fiza , Hanif Ayesha , Rizvi Zehra Ali , Ejaz Sumbul
Published: January 2018

Background: There is growing awareness of the public health importance of the mental well-being of population in general. This study was carried out to examine the wellbeing of Pakistani healthcare professionals, and to evaluate the psychometric properties of Warwick-Edinburgh Mental Well-being Scale in in this population. The well-being of health professionals is likely to influence their care delivery. Methods: A cross-sectional survey was carried out from June, 2013 to December, 2014 among 1271 Pakistani health personnel (HCPs) belonging to seven different cities of Punjab province, Pakistan, to examine the acceptability, internal consistency, test-retest reliability and the content and construct validity of the English version of the Warwick-Edinburgh Mental Well-being Scale in a Pakistani population sample. All data were analyzed in SPSS v.21. Results: Our analysis demonstrated a unidimensional construct, a high internal consistency (0.89) and test-retest reliability, good convergent validity and easy readability of WEMBS among Pakistani HCPs. The mean on WEMWBS score was 48.1 (9.4) which is lower than general population sample in other nations. Male healthcare professionals scored significantly higher on WEMWBS than their female counterparts (P < .05), and older respondents had higher scores. Conclusion: The WEMBS appears feasible and acceptable for use in the Pakistani healthcare professionals, and findings from this study indicate its validity and internal consistency. The well-being scores of the health professional respondents were lower than those identified in general population surveys in the UK.
The role of information technologies in medical curriculum harmonisation
Authors: Komenda Martin , Schwarz Daniel , Dušek Ladislav
Published: January 2018

In this contribution a new comprehensive approach describing medical curriculum harmonisation will be introduced. Behind the whole concept stays original methodological background, which is trending towards an outcome-based paradigm, together with an engineering and development of new curriculum management system intended for for curriculum designers, guarantors and faculty management. It provides a clear and transparent composition of compulsory and optional courses, and easy identification of potential duplicities and overlaps across a domain of medical and healthcare education. For students, it means an absolutely new way of how to understand what is really taught during a learning period, including all necessary meta information such as type and range of teaching, related MeSH keywords and list of essential terms presented in particular lecture, seminar or clinical practice. Moreover it brings a new communication channel between all involved stakeholders including students at institution level. The broad overview shows that various existing curriculum management systems focus on the outcome-based paradigm only from a certain perspective offering the agenda together with selected functionalities. However, they are unable to cater all the needs on curriculum harmonisation of the today’s higher education institutions. This is the reason why we decided to develop own web-based platform supporting guaranteed and more transparent building of curriculum including a control mechanisms in the form of deep inspection. Furthermore we will introduce a set of data mining and statistical methods in compliance with standardized and approved approaches, which are used for content analysis of a huge dataset extracted from a curriculum management system. These results may assist to identify potentially problematic areas and construct comprehensive overview of defined curriculum, because from the perspective of human cognition abilities, it is not possible to carefully read, verify and understand all learning units with all their linkages and co-dependencies.
The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles
Authors: Bahar Ofir , Pruitt Rory N , Luu Dee Dee , Schwessinger Benjamin , Ruan Randy , Fontaine-Bodin Lisa , Koebnik Ralf , Ronald Pamela
Published: January 2018

Pattern recognition receptors (PRRs) play an important role in detecting invading pathogens and mounting a robust defense response to restrict infection. In rice, one of the best characterized PRRs is XA21, a leucine rich repeat receptor-like kinase that confers broad-spectrum resistance to multiple strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). In 2009 we reported that an Xoo protein, called Ax21, was secreted by a type I-secretion system and that it served to a ctivate X A 21 -mediated immunity. This report has recently been retracted. Here we present data that corrects our previous model. We first show that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. We further show that Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles. Finally, we provide data showing that ax21 knockout strains do not overcome XA21-mediated immunity.
Secondary nucleation overcomes seeding template in amyloid-like fibril formation
Authors: Milto Katažyna , Šneideris Tomas , Smirnovas Vytautas
Published: January 2018

Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features of amyloid strains is the ability to self-propagate, maintaining a constant set of physical properties despite being propagated under conditions different from those that allowed initial formation of the strain. Here we report a cross-seeding experiment using strains formed under different conditions. Using high concentrations of seeds results in rapid elongation and new fibrils preserve the properties of the seeding fibrils. At low seed concentrations secondary nucleation plays the major role and new fibrils gain properties predicted by the environment rather than the structure of the seeds. Our findings could explain conformational switching between amyloid strains observed in a wide variety of in vivo and in vitro experiments.
Social, and social networking media: A biomedical science department experience in training health professionals at the University of Technology, Jamaica
Authors: Grannum Joseph C , McLaughlin Pamela , Osbourne Danisha R , Bullock Patricia , Sands Caryn
Published: January 2018

Background: In a region of Caribbean states with limited human and financial resources institutions of higher education must use the technology available to reach its students across the region and allow professionals in the Biomedical Sciences to teach, interact and follow students from first year to their professional registration. This paper shares the journey of our students’ progression across island states using Social Networking and Social media academic delivery. Objective: Using Information Communication Technology to delivery and monitor students across. Collect the data of their academic success and monitor their the use of knowledge over the 4 years of training so see if there was a link between the success at board examinations and the use and participation of the technology. Method: Accounts were opened with groups of students from the different islands. The research team was made managers of the account. Lectures, tutorials and labs were discussed. After completion of the module clinical cases were discussed building on a student’s foundation knowledge. Control group used Moodle and at the end of were allowed to progress without for the next cohort. Results: Students who remained active in a Social and Social Networking Group after completing their modules had a higher rate of success in their professional registration examinations. Conclusions: Social and Social Networking Media had a very positive and lasting effect in the learning process than the control group using Moodle who were allowed to progress after they completed each modules. The quality of performance in the registration/board examinations was also better.
Essential amino acid provisioning by termite-associated gut microbiota
Authors: Ayayee Paul A , Jones Susan C , Sabree Zakee L
Published: January 2018

Gut-associated microbes of many insects provide a variety of beneficial nutritive functions to their hosts such as the provisioning of essential amino acids (EAAs) to those that feed on diets limited in assimilable nitrogen (i.e., wood). We investigated this function by the gut microbiota of the eastern subterranean termite (Reticulitermes flavipes) using 13C-stable isotope analysis of EAAs in the diet and termite samples. Evidence of possible microbe input was revealed by 13C-depletion of termite carcass (-27.0 ± 0.43‰, mean ± s.e.), and termite gut filtrate samples (-27.3 ± 0.58‰) relative to their wood diet (-26.0 ± 0.48‰) (F (2, 63) = 6.2, P < 0.004). An investigation of the identity of non-dietary EAA sources determined that termites predominantly incorporated EAAs derived from bacteria, with minor fungal input. The most likely means of EAA acquisition is through proctodeal trophallaxis (mouth-anus feeding), a well-established feature of termite colony nestmates, and subsequent digestion of the microbial fraction in the transferred food. Our study provides empirical data in support of the gut microbial EAA provisioning function in termites by using 13C-stable isotopes to determine the microbial origins of incorporated EAAs in termite tissues.
Zeta potential of bacterial cells: Effect of wash buffers
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy parameter for bacterial cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured zeta potential, 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 NaCl, 0.001M KCl, and 0.1M NaNO3) are routinely used for removing (by charge screening) ions and charged molecules that bind nonspecifically to the cell surface. Using Escherichia coli DH5α grown in LB Lennox (with 2 g/L glucose), experiment data showed that the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L NaCl, and phosphate buffer saline (PBS) wash buffers. As LB Lennox is a low salt medium without a phosphate buffer, it was likely that the extent of nonspecific adsorption of ions on the cell surface was not severe, and the different wash buffers would correspondingly not exert much effect on measured zeta potential. Zeta potential-pH profiles for E. coli grown in a semi-defined medium (with a high capacity phosphate buffer system), on the other hand, was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L NaCl, 0.1M NaNO3, 0.1M sodium acetate, and 0.1M sodium citrate wash buffers with the deviation positively correlated with wash buffer’s ionic strength. Furthermore, the point of zero charge (pHzpc) for E. coli grown in the semi-defined medium varies between 1.5 and 3, in an ionic strength dependent manner, for the various wash buffers tested. Collectively, this preliminary study highlights the importance of wash buffer ionic strength in affecting removal efficiency of non-specifically absorbed ions on bacterial cell surface, where a threshold exists (0.15M) for charge screening to be effective. At the upper bound, 0.6M ionic strength might remove cations intrinsic to the cell envelope, leading to possible cell surface damage and erroneous measurements.
An unusual archosauriform tooth increases known tetrapod diversity in the lower Chinle Formation (Late Triassic) of southeastern Utah
Authors: Lopez Andres , St. Aude Isabella , Alderete David , Alvarez David , Aultman Hannah , Busch Dominique , Bustamante Rogelio , Cirks Leah , Lopez Martin , Moncada Adriana , Ortega Elizabeth , Verdugo Carlos , Gay Robert J
Published: January 2018

An unusual tetrapod tooth was discovered in the Late Triassic Chinle Formation of southeastern Utah. The tooth was originally thought to belong to Revueltosaurus but further investigations have rejected that hypothesis. In this paper we compare MNA V10668 to other known fossil teeth found in the Chinle Formation and identify the least inclusive clade it may belongs to. Using data found in other publications and pictures of other teeth, we compare this specimen to other Triassic dental taxa. MNA V10668 shares some similarities with Crosbysaurus, Tecovasaurus, and several other named taxa but possesses unique characteristics not found in other diapsid teeth. We conclude that it is most likely an archosauromorph and probably an archosauriform. This increases the known diversity of tetrapods from the Chinle Formation and represents the first tooth morphotype completely unique to Utah in the Late Triassic Period.
The Life “SeResto” project: A new strategic approach to meet HD and WFD objectives by SEagrass RESTOration
Authors: Buosi Alessandro , Facca Chiara , Ponis Emanuele , Bonometto Andrea , Boscolo Rossella , Parravicini Massimo , Centanni Elena , Siega Andrea , Volpe Valerio , Sfriso Adriano
Published: January 2018

Pristine conditions in transitional water ecosystems are characterized by the dominance of aquatic angiosperms. Aquatic plants consolidate bottoms, prevent erosion, support benthic and fish communities as nursery and food areas, and favour the bird presence. Hence, they may contribute to the achievement of a good ecological status as required by the WFD (2000/60/EC). Their reduction or disappearance is a symptom of environmental deterioration. Over the past few decades, the aquatic angiosperms have shown a significant decrease on a worldwide scale and in some areas of Venice Lagoon (Adriatic Sea), particularly in the central and Northern basins, as a consequence of anthropogenic activities.

At present, most of the anthropogenic pressures which caused their decline or disappearance in Venice Lagoon have significantly decreased creating the ecological conditions for a new colonization. In this context, the project SeResto (LIFE12 NAT/IT/000331), funded by the European Commission, aims at restoring the angiosperm meadows in the Northern basin of Venice Lagoon where the natural seed spreading is hampered by the presence of island, tidal marsh barriers and long residence times.

The project has two main strengths: i) the widespread transplantations of small angiosperm sods and manual dispersion of rhizomes and seeds and based on a low costs and low impact on donor sites approach, ii) the participation of fishermen and hunters daily living the lagoon for recreational purposes. Thirty-five sites have been selected and in each one 9 sod-bearing plants (diameter: 30 cm), supplied by fish farms where angiosperm meadows are almost natural, have been transplanted. In addition, the plant spreading is enhanced by the dissemination of hundreds of rhizomes, 1500 at minimum in each area during the project period (52 months).

In 8 sites, out of the 35, biological and chemico-physical conditions are being monitored monthly during the first and last year and quarterly in the intermediate period. Ecological indices, based on the study of macrophytes, macrobenthic fauna and fish fauna (Biological Quality Elements), as required by the WFD 2000/60/EC, will allow to assess changes in the Ecological Status of the study sites. Preliminary results are encouraging in great part of the selected areas although some difficulties have been recorded in areas with high water turbidity and the presence of thionitrophilous macroalgae, especially Ulvaceae, favoured by the unexpected weather conditions of summer 2014. Information on the restoration effectiveness and the relationship between the angiosperm presence/growth and the environmental conditions can be employed for interventions in other lagoon areas and can be exported in other similar transitional environments.
A taste for exotic food: Neotropical land planarians feeding on an invasive flatworm
Authors: Boll Piter K , Rossi Ilana , Amaral Silvana V , Leal-Zanchet Ana
Published: January 2018

Invasive species establish successfully in new habitats especially due to their generalist diet and release of natural enemies. However, native species may also adapt to use new elements in their ecosystem. The planarian Endeavouria septemlineata, first recorded in Hawaii, was later registered in Australia and Brazil. Recently we found it in human-disturbed areas in southern Brazil and here we investigate its interactions with other invertebrates both in the field and in the laboratory. We observed the species in the field during collecting activities and maintained some specimens alive in small terraria in the laboratory, where we offered different invertebrate species as potential prey and also put them in contact with native land planarians in order to examine their interaction. Both in the field and in the laboratory, E. septemlineata showed a gregarious behavior and was found feeding on woodlice, millipedes, earwigs and gastropods. In the laboratory, specimens did not attack live prey, but immediately approached dead specimens, indicating a scavenging behavior. Four native land planarians of the genus Obama and two of the genus Paraba attacked and consumed E. septemlineata, which, after the beginning of the attack, tried to escape by tumbling or using autotomy. As a scavenger, E. septemlineata would impact the populations of species used as food, but could possibly exclude native scavengers by competition. On the other hand, its consumption by native land planarians may control its spread and thus reduce its impact on the ecosystems.
Pan-genomics: Unmasking the gene diversity hidden in the bacteria species
Authors: Alcaraz Luis David
Published: January 2018

The dramatic increase in genome sequencing during the last years has changed our ideas about bacterial diversity, from single gene to whole community DNA surveys; we have learned that nature's lagest gene repository resides in bacteria resides in bacteria. Comparison of bacteria genomes has contributed to understand the flexibility in size and gene content as well as the gene movement due to gene family expansions and Horizontal Gene Transfer. Bacteria species are currently defined by means of 16S rRNA sequence comparisons and some limited phenotypic traits. There is an ongoing debate about the biological and evolutive significance of the bacteria species, and thus the need to refine the definition of it using the most of the genomic shared information across any taxonomic range. When comparing multiple genomes of related strains we can distinguish a set of common shared features which are known as the core genome. In the other hand, the set of strain specific genes are known as accessory genome. The accessory and core genome conform the total of the genetic composition, and are known as pan-genome. Here we present the possibilities using pan-genomics as a workhorse to describe both taxonomical and functional diversity within bacteria.
Predicting cortical bone adaptation to axial loading in the mouse tibia
Authors: Pereira Andre F , Javaheri Behzad , Pitsillides Andrew , Shefelbine Sandra
Published: January 2018

The development of predictive mathematical models can contribute to a deeper understanding of the specific stages of bone mechanobiology and the process by which bone adapts to mechanical forces. The objective of this work was to predict, with spatial accuracy, cortical bone adaptation to mechanical load, in order to better understand the mechanical cues that might be driving adaptation.

The axial tibial loading model was used to trigger cortical bone adaptation in C57BL/6 mice and provide relevant biological and biomechanical information. A method for mapping cortical thickness in the mouse tibia diaphysis was developed, allowing for a thorough spatial description of where bone adaptation occurs.

Poroelastic finite-element (FE) models were used to determine the structural response of the tibia upon axial loading and interstitial fluid velocity as the mechanical stimulus. FE models were coupled with mechanobiological governing equations, which accounted for non-static loads and assumed that bone responds instantly to local mechanical cues in an on-off manner.

The presented formulation was able to simulate the areas of adaptation and accurately reproduce the distributions of cortical thickening observed in the experimental data with a statistically significant positive correlation (Kendall's tau rank coefficient \(\tau = 0.51\), \(p<0.001\)).

This work demonstrates that computational models can spatially predict cortical bone mechanoadaptation to time variant stimulus. Such models could be used in the design of more efficient loading protocols and drugs therapies that target the relevant physiological mechanisms.
Photos provide information on age, but not kinship, of Andean bear
Authors: Van Horn Russell C , Zug Becky , Appleton Robyn D , Velez-Liendo Ximena , Paisley Susanna L , LaCombe Corrin
Published: January 2018

Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs < 6 months old, we evaluated the degree to which visual information may be used to estimate bears’ ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤ 6 months old may be estimated from their size relative to their mothers with an average error of < 0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥ 10 years old may be estimated from the proportion of their nose that is pink with an average error of < 0.01 ± 3.5 years (n = 41). We also show that similarity among the bears’ natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R2 < 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species.
Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs
Authors: Bates Karl , Maidment Susannah C.R. , Schachner Emma R. , Barrett Paul M
Published: January 2018

In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group’s >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction-adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction-adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g. muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.