bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of metabolic network structures and energy metabolic pattern on E. coli K12 exposed to acoustic field: based on Gene Ontology and KEGG pathway enrichment analysis
Authors: Gu Shaobin , Qiao Suyu , Wu Ying
Published: January 2018

Microorganism is an important part of ecosystems; it is very sensitive to environmental change. In order to study the effects of sound on organisms, it’s meaningful to study mechanism of microbial exposure to sound. In our previous experiments, the effects of different sound intensity and frequency on the growth of E. coli K12 were studied. It was found that in stationary phase the bacteria concentration of sound expose group was higher than control. In this study, we aimed to understand the mechanisms of E. coli underlying sound expose by using Gene Ontology and KEGG Pathway Enrichment Analysis, and established a systematic pathway for the E. coli response to sound expose. At 6 hour, the chemotaxis pathway was significantly up-regulated which responses to the changes of the external environment and leads bacteria to favorable environment. At 12 hour, the glycerophospholipid pathway was significant up-regulated, it is related to the energy metabolism and cell division. At 24 hours, the energy metabolism, nucleotide synthesis and transcriptional translation pathways were significant differences. When bacteria entered the stationary phase (36 hour), in sound exposure group the pathways related to reduce the harmful substances were down-regulated and the pathways about degrade aromatic compounds provides energy were up-regulated, so that the E. coli K12 in sound exposure have a better ability to adapt poor living environment. Comparative transcriptome analysis of sound exposed E. coli K12 can not only reveal the behavior of E. coli K12 response to sound expose, but also lay a foundation for further study the mechanism of prokaryotes response to physical stimulus.
Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
Authors: Santos Liliana , Alves Artur , Alves Rui
Published: January 2018

Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods. Here, we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results. As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS four loci tree as almost equivalent to the five loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion. Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.
MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data
Authors: White III Richard Allen , Panyala Ajay , Glass Kevin , Colby Sean , Glaesemann Kurt R , Jansson Christer , Jansson Janet K
Published: January 2018

MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. Using assembled contigs and raw sequence reads from any platform as input, MerCat performs k-mer counting of any length k, resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST for compositional analysis of whole community shotgun sequencing (e.g., metagenomes and metatranscriptomes).
Phenotypic variation in dorsal fin morphology of coastal bottlenose dolphins (Tursiops truncatus) off Mexico
Authors: Morteo Eduardo , Rocha-Olivares Axayácatl , Morteo Rodrigo , Weller David W
Published: January 2018

Geographic variation in external morphology is thought to reflect an interplay between genotype and the environment. Morphological variation has been well-described for a number of cetacean species, including the bottlenose dolphin (Tursiops truncatus). In this study we analyzed dorsal fin morphometric variation in coastal bottlenose dolphins to search for geographic patterns at different spatial scales. A total of 533 dorsal fin images from 19 available photo-identification catalogs across the three Mexican oceanic regions (Pacific Ocean n=6, Gulf of California n=6 and, Gulf of Mexico n=7) were used in the analysis. Eleven fin shape measurements were analyzed to evaluate fin polymorphism through multivariate tests. Principal Component Analysis on log-transformed standardized ratios explained 94% of the variance. Canonical Discriminant Function Analysis on factor scores showed separation among most study areas (p<0.05) with exception of the Gulf of Mexico where a strong morphometric cline was found. Possible explanations for the observed differences are related to environmental, biological and evolutionary processes. Shape distinction between dorsal fins from the Pacific and those from the Gulf of California were consistent with previously reported differences in skull morphometrics and genetics. Although the functional advantages of dorsal fin shape remains to be assessed, it is not unlikely that over a wide range of environments, fin shape may represent a trade-off among thermoregulatory capacity, hydrodynamic performance and the swimming/hunting behavior of the species.
Towards a metadata-driven multi-community research data management service
Authors: Grunzke Richard , Hartmann Volker , Jejkal Thomas , Prabhune Ajinkya , Herold Hendrik , Deicke Aline , Hoffmann Alexander , Schrade Torsten , Meinel Gotthard , Herres-Pawlis Sonja , Stotzka Rainer , Nagel Wolfgang E.
Published: January 2018

Nowadays, the daily work of many research communities is characterized by an increasing amount and complexity of data. This makes it increasingly difficult to manage, access and utilize to ultimately gain scientific insights based on it. At the same time, domain scientists want to focus on their science instead of IT. The solution is research data management in order to store data in a structured way to enable easy discovery for future reference. An integral part is the use of metadata. With it, data becomes accessible by its content instead of only its name and location. The use of metadata shall be as automatic and seamless as possible in order to foster a high usability.

Here we present the architecture and initial steps of the MASi project with its aim to build a comprehensive research data management service. First, it extends the existing KIT Data Manager framework by a generic programming interface and by a generic graphical web interface. Advanced additional features includes the integration of provenance metadata and persistent identifiers. The MASi service aims at being easily adaptable for arbitrary communities with limited effort. The requirements for the initial use cases within geography, chemistry and digital humanities are elucidated. The MASi research data management service is currently being built up to satisfy these complex and varying requirements in an efficient way.
Phenotypic and biochemical diversity among peach cultivars grown under environmental conditions of Pothohar (salt range) Pakistan
Authors: Qadri Rashad , Ubaid Zeeshan , Saleem Aqib , Iqbal Amjad , Nisar Numrah , Khan Muhammad M , Haq Imran U , Hanif Asif , Khan Imran , Feroz Aqeel , Azam Muhammad , Ahmad Saeed , Yang yaodong
Published: January 2018

Background. Peaches are the prominent species among the fruits due to having diverse germplasm around the globe with largest number of commercial genotypes. Pakistan is also rich in various cultivars of peaches that are rarely studied for its genetic diversity. An attempt was, therefore, made to study the phenotypic variation in peach tree and fruit characteristic of 7 desirable cultivars (namely A669, Texas y-455, Florida King, Arctic Fantacy, Spring Creast, Micholea and Swanee). Methods. All cultivars were grown at the Experimental Peach Block at Barani Agriculture Research Institute (BARI), Chakwal, Punjab-Pakistan. Tree traits such as growth habit, leaf characteristics, flower characteristics, morphological and biochemical fruit traits were evaluated by using IBPGR peach descriptors. Results. Extensive variation was found among the cultivars for various traits, including tree growth (weeping, compact or open whereas), leaf length (9.0 ± 0.8 to 12.0 ± 0.4 cm), leaf width (2.6 ± 0.1 to 3.3 ± 0.2 cm), fruit weight (45.6 ±3.3 to 107 ± 8.8 g) and stone weight (4.3 ± 0.2 to 7.5 ± 0.4 g). Besides, a significant variation among the various cultivars has also been observed regarding, titratable acidity (0.64 ± 0.02 to 1.19 ± 0.04%), °Brix (7.17 ± 0.62 to 11.27 ± 0.21), ripening index (6.02 ± 0.72 to 17.2 ± 0.44), Vitamin C (75.3 ± 15 to 116.1 ± 10.5 mg 100 g-1), total sugar (13.52 ± 0.50 to 20.84 ± 1.23%), reducing sugar (5.68 ± 0.11 to 7.25 ± 0.51%), non-reducing sugar (4.12 ± 0.45 to 10.77 ± 0.8%), total phenolics (176.20 ± 7.18 to 317.72 ± 4.66 mg GAE 100 g-1), radical scavenging activity (44.25 ± 0.28 to 78.17 ± 1.43%) and reducing power (0.12 ± 0.1 to 0.22 ± 0.03). Similarly, a significant correlation was noticed between many tested traits.
Open Science strategies for NIH data management, sharing, and citation
Authors: Clark Tim , Cousijn Helena , Katz Daniel S , Fenner Martin
Published: January 2018

This document summarizes a series of authoritative views on research data management, sharing and citation, developed in Expert Groups, Working Groups, and other activities organized through FORCE11 (http://force11.org), an international community of over 2,000 members dedicated to advancing research communications and e-scholarship. It was prepared in response to NIH Request for Information (RFI) NOT-OD-17-015 (URL: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-015.html), and was reviewed and approved by the FORCE11 Board of Directors on January 19, 2017.
Why do jellyfish bloom in Norwegian waters and what can be done to recover the ecosystems in the North Sea and on the Norwegian coast?
Authors: Hamre Johannes
Published: January 2018

The ecosystems with their relationships between fish species and stocks, have been established by evolution for millions of years, but during the last 50 years, the ecosystems in the North Sea and along the Norwegian coast have been changed fundamentally by fisheries. The North Sea mackerel stock has been depleted and its feeding grounds have been invaded by the Western mackerel which spawns west of Ireland. This stock is now very rich in numbers and occupies the North Sea, the Norwegian Sea and the western Barents Sea. If the trend continues, mackerel may outcompete many of the other fish stocks in the area. Traditionally and until the beginning of the 1970s, there was a large stock of sandeel spawning in the North Sea and on the Norwegian coast. Sandeel juveniles was an important food source for a wide range of species, including sea mammals and birds. The fact that this stock has also been overfished, may explain many changes observed in the ecosystem on the west coast of Norway, for example a large reduction in the populations of sea birds. There are several instances where ecosystems shift to sustain jellyfish blooms in response to depletion of forage fish stocks. This was registered in Namibia in the 1990’s, where the pilchard stock was decimated and the biomass of jellyfish soon became overwhelming. On the west-coast of Norway, there are now frequent blooms of jellyfish, yet another indication that a controlling factor is missing in the system, in this case sandeel, which is a key species in the transfer of nutrients from zooplankton to higher trophic levels in the area. In this paper, I give a description of the situation and some suggested measures that should be taken in fisheries management.
ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data
Authors: White III Richard Allen , Brown Joseph , Colby Sean , Overall Christopher C , Lee Joon-Yong , Zucker Jeremy , Glaesemann Kurt R , Jansson Christer , Jansson Janet K
Published: January 2018

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein-coding open reading frames (ORFs) rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.
Towards a dashboard environment for repeating and reusing research
Authors: Taylor Ian , Nabrzyski Jarek
Published: January 2018

Over the past 18 months, we have been working on a dashboard concept that enables researchers a means of interacting with existing research. This work was motivated by the National Data Service (NDS), which is an emerging vision of how scientists and researchers across all disciplines can find, reuse, and publish data. NDS intends to provide an international federation of data providers, data aggregators, community-specific federations, publishers, and cyberinfrastructure providers by linking data archiving and sharing efforts together with a common set of tools. This abstract provides a status of the two existing proof-of-concept pilot dashboard implementations and how we plan to evolve this work. At a high level, the researcher dashboard aims to provide an intuitive Web-based interface to expose fully interactive research containers that support the lifecycle of scholarly communication. Research containers enable executable and repeatable research by supporting methods, source code, and data within dynamically created Docker containers.
Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance
Authors: Kleiner Manuel
Published: January 2018

Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental microbiologists have started using metatranscriptomics and metaproteomics to look at gene expression differences between different environments or conditions. This has been mostly done by using makeshift adaptations of pure culture focused differential transcriptomics and proteomics approaches. However, since meta-omics data has many more variables attached to it as compared to pure culture derived data, such makeshift adaptations are problematic at best. One particular challenge is posed by the data normalization strategies used to account for technical and biological variables in meta-omic data. Here I discuss the most common normalization strategy for transcriptomic and proteomic data and why it is not valid by itself for meta-omic data. I provide logical proof that variation in species abundances between samples is an additional variable that must be accounted for during normalization of meta-omic data. Finally, I show how the existing normalization methods for transcriptomic and proteomic data can be augmented to be applicable to meta-omic data.
The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning
Authors: Conrado Ana C , Arruda Hugo , Stanton David , James Samuel W , Kille Peter , Brown George , Silva Elodie D , Dupont Lise , Taheri Shabnam , Morgan Andrew J , Simoes Nelson , Rodrigues Armindo , Montiel Rafael , Cunha Luis
Published: January 2018

Pontoscolex corethrurus (Müller, 1857) plays an important role in soil terrestrial ecosystems and has been widely used as an animal model for a large variety of ecological studies, in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm Pontoscolex corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG), 2 rRNA genes and 22 tRNA genes). It has the same gene content and structure as in other sequenced earthworms, but unusual among invertebrates it has several overlapping open reading frames. All genes are encoded on the same strand, most of the PCGs use ATG as the start codon except for NAD3, which uses GTG as the start codon. The T+A content of the mitochondrial genome is 59.9% (31.9% A, 27.9% T, 14.9% G, and 25.3% for C). The annotated genome sequence has been deposited in GenBank under the accession number KT988053.
Effects of zinc supplementation on growth and colouration of the scleractinian coral Stylophora pistillata
Authors: Tijssen Jennifer , Wijgerde Tim , Leal Miguel C , Osinga Ronald
Published: January 2018

Zinc levels in artificial seawater are often unnaturally elevated, and thus potentially toxic to aquacultured corals. However, our knowledge of how zinc affects corals is still limited. We tested the effects of zinc supplementation (0, 1, 10 and 100 µg L–1) on health, growth, NDVI (a proxy for chlorophyll a) and overall colouration of the stony coral Stylophora pistillata. After two weeks, no signs of necrosis were observed in any of the treatments. However, at 100 µg L–1, we detected a considerable ~62% growth reduction compared to zinc levels of 0 to 10 µg L–1. In addition, NDVI was significantly reduced by ~36% at 100 µg L–1 zinc, indicating loss of chlorophyll a. Zinc did not affect coral colouration in general, although reflection intensity increased markedly at 100 µg L–1, most likely due to a loss of chlorophyll a. In conclusion, the No Observed Effect Concentration (NOEC) after a two–week zinc exposure was 10 µg L–1 for S. pistillata. Our results show that potentially toxic metals such as zinc, found in commercial sea salts and supplements, can have detrimental effects on corals. Therefore, we recommend regular monitoring and restrained supplementation of zinc in coral aquaculture systems.
On the connection between supersaturation in the upper airways and «humid-rainy» and «cold-dry» seasonal patterns of influenza
Authors: Ishmatov Aleksandr N
Published: January 2018

We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.

We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:

- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;

- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;

- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.

Thus, the effect of supersaturation and condensational growth can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.
Snake classification from images
Authors: James Alex
Published: January 2018

Incorrect snake identification from the observable visual traits is a major reason of death resulting from snake bites. So far no automatic classification method has been proposed to distinguish snakes by deciphering the taxonomy features of snake for the two major species of snakes i.e. Elapidae and Viperidae. We present a parallel processed inter-feature product similarity fusion based automatic classification of Spectacled Cobra, Russel's Viper, King Cobra, Common Krait, Saw Scaled Viper, Hump nosed Pit Viper. We identify 31 different taxonomically relevant features from snake images for automated snake classification studies. The scalability and real-time implementation of the classifier is analyzed through GPU enabled parallel computing environment. The developed systems finds application in wild life studies, analysis of snake bites and in management of snake population.
Ananke: Temporal clustering reveals ecological dynamics of microbial communities
Authors: Hall Michael W , Rohwer Robin R , Perrie Jonathan , McMahon Katherine D , Beiko Robert G
Published: January 2018

Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that clusters marker-gene data based on time-series profiles and provides interactive visualization of clusters. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.
Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars
Authors: Fang Zhigang , Lou Laiqing , Tai Zhenglan , Wang Yufeng , Yang Lei , Hu Zhubing , Cai Qingsheng
Published: January 2018

Cadmium (Cd) is one of the most toxic heavy metals and is difficult to remove from contaminated soil and water. Italian ryegrass (Lolium multiflorum), as an energy crop, exhibits a valuable potential to develop Cd polluted sites due to its use as a biofuel rather than as food and forage. Previously, via a screening for Cd-tolerant ryegrass, the two most extreme cultivars (IdyII and Harukaze) with high and low Cd tolerance during seed germination, respectively, were selected. However, the underlying mechanism for Cd tolerance was not well investigated. In this study, we comparatively investigated the growth, physiological responses, and Cd uptake and translocation of IdyII and Harukaze when the seedlings were exposed to a Cd (0-100 µM) solution for 12 days. As expected, excess Cd inhibited seedling growth and was accompanied by an accumulation of malondialdehyde (MDA) and reduced photosynthetic pigments in both cultivars. The effects of Cd on the uptake and translocation of other nutrient elements (Zn, Fe, Mn and Mg) were dependent on Cd concentrations, cultivars, plant tissues and elements. Compared with Harukaze, IdyII exhibited better performance with less MDA and higher pigment content. Furthermore, IdyII was less efficient in Cd uptake and translocation compared to Harukaze, which might be explained by the higher NPT (non-protein thiols) content in its roots. Taken together, our data indicate that IdyII is more tolerant than Harukaze, which partially resulted from the differences in Cd uptake and translocation.
The influence of storage time and temperature on propofol concentrations in canine blood and plasma
Authors: Cox Sherry , Bailey Joan , Okafor Chika , Seddighi Reza , Doherty Tom
Published: January 2018

Propofol is an intravenous anesthetic commonly used due to its favorable pharmacokinetic and pharmacodynamic profile. There are discrepancies in the literature about the most appropriate sample for determining propofol concentrations. Although plasma has been used for determining propofol concentrations, whole blood has been the preferred sample because propofol is significantly bound to erythrocytes. There is also a lack of consistency in the literature on the effect of storage time and temperature on propofol concentrations and this may lead to errors in the design of pharmacokinetic/pharmacodynamics studies. The purpose of this study was to determine the difference in propofol concentrations in whole blood versus plasma and to evaluate the influence of storage time (56 days) and temperature (4°C, -20°C, -80°C) on the stability of propofol concentrations in blood and plasma samples. Results from the study indicate that whole blood and plasma samples containing propofol were stable for at least 56 days when stored at -80°C; thus, -80°C is the most appropriate temperature for propofol sample storage out of the three temperatures evaluated. Plasma propofol concentrations were consistently higher than whole blood for all 3 storage temperatures. Consequently, plasma is the most appropriate sample for propofol analysis due to its consistent determinations.
How to be a great dad: Parental care in a flock of greater flamingo (Phoenicopterus roseus)
Authors: Sandri Camillo , Vallarin Vittoria , Sammarini Carolina , Regaiolli Barbara , Piccirillo Alessandra , Spiezio Caterina
Published: January 2018

The zoo-science literature on flamingos, and avian species in general, is lacking. However, this kind of research is important to improve the knowledge on these species and to improve their ex-situ and in-situ conservation. The aims of the present study were to assess the welfare of a captive colony of greater flamingo hosted at Parco Natura Viva, an Italian zoological garden, through ethological parameters and to improve the knowledge on this species in zoological gardens. In particular, the present study investigated and compared the parental care of females and males in 35 breeding pairs of greater flamingos. For each pair, we collected data on the parental care behaviour of both females and males, recording their position in relation to the nest (near the nest, on the nest, away from the nest) and the behavioural category that was performed. The main results were that males spent more time than females on the nest and near it and were more aggressive toward other flamingos. Therefore, male flamingos seem to be more involved in incubation duties and nest protection than females. Greater flamingos of this study performed species-specific behaviours. Both parents were involved in parental care and displayed all the activities reported in the wild. Therefore, the study flock of greater flamingos seems to be in a good welfare. This kind of research is important not only to expand the knowledge on bird species such as flamingos, but also to improve their husbandry and breeding in controlled environment.
Neuroethics of death in the United States
Authors: Sifuentes Mikaela
Published: January 2018

The search for a universal definition of death is a relatively new objective in human history, framed by complex biological, technological, and socio-political factors. While it is widely understood that “life” and “death” describe inverse states of being, what separates these two states has been vigorously debated by scientists, ethicists, and theologians. Far from merely an academic distinction, the definition of death has implications that extend to end-of-life healthcare, organ transplantation, and inheritance law. This review explores the historical and current definitions of death in the United States, the role of technological advances, and the resultant social and legal applications.
The salt flats fighter: agonistic survival of Liolaemus fabiani in the Salar de Atacama
Authors: Marambio-Alfaro Yery , Álvarez Gabriel , Cortés Araya Marcos , Serrano Antonio E.
Published: January 2018

Liolaemus fabiani is a lizard that lives in the Salar de Atacama, located in the center of the Atacama Desert, northern Chile, one of the driest places on the planet. Likely due to the extreme environmental conditions of their habitat, L. fabiani has colonized all watercourse shores of the Puilar pond where the primary source of food, flies, are confined. By ‘owning’ these shores, they can retain resources, explaining their natural sense of territory and their world-renowned aggressive territorial behavior. From the perspective of the lizard, the battlefield is a narrow stretch between mountains of halite salt and the water, which leads to a winner-take-all type territory. The winning lizard is rewarded with control of the food supply, access to females and a privileged space to survive. This modern gladiator faces his opponent with an unmatched ferocity, although there are rarely, if ever, deaths between the contenders. Like other vertebrates, the defense of the territory is a cooperative job with the alpha female. She releases pheromone compounds, conferring an advantage to her partner to proceed ruthlessly to attack the intruder, on land or in water, in order to obtain victory. The victorious lizard gains ownership of the land, leaving no doubts of his claim to other would-be challengers.
Chemical monitoring of Swedish coastal waters indicates common exceedances of environmental thresholds, both for individual substances as well as their mixtures
Authors: Gustavsson Mikael B , Magnér Jörgen , Carney Almroth Bethanie , Eriksson Martin K , Sturve Joachim , Backhaus Thomas
Published: January 2018

Chemical pollution was monitored and assessed along the Swedish west coast. 62 of 172 analyzed organic chemicals were detected in the water phase of at least one of five monitored sites. A Concentration Addition based screening-level risk assessment indicates that all sites are put at risk from chemical contamination, with total risk quotients between 2 and 9. Only at one site did none of the individual chemicals exceeded its individual environmental threshold (PNEC, EQS). The monitoring data thus demonstrate a widespread blanket of diffuse pollution, with no clear trends amongst sites. Further issues critical for the environmental chemical risk assessment include the challenges to achieve sufficiently low levels of detection especially for hormones and cybermethrin (a pyrethroid insecticide), the appropriate consideration of non-detects and the limited availability of reliable PNECs and EQS values.
Can pond dyes help to control mosquitoes in urban gardens?
Authors: Ortiz Perea Natali , Callaghan Amanda
Published: January 2018

Background British mosquito population distribution, abundance, species composition and potential for mosquito disease transmission are intimately linked to the physical environment. The presence of ponds and water storage can significantly increase the density of particular mosquito species in the garden. Culex pipiens is the mosquito most commonly found in UK gardens and a potential vector of West Nile Virus WNV, although the current risk of transmission is low. However any factors that significantly change the distribution and population of Cx pipiens are likely to impact subsequent risk of disease transmission. Pond dyes are used to control algal growth and improve aesthetics of still water reflecting surrounding planting. However it is well documented that females of some species of mosquito prefer to lay eggs in dark water and/or containers of different colours and we predict that dyed ponds will be attractive to Culex mosquitoes.

Methods Black pond dye was used in oviposition choice tests using wild-caught gravid Cx pipiens. Larvae from wild-caught Cx pipiens were also reared in the pond dye to determine whether it had any impact on survival. An emergence trap caught any adults that emerged from the water. Water butts (80L) were positioned around university glasshouses and woodland and treated with black pond dye or left undyed. Weekly sampling over a 6 month period through summer and autumn was performed to quantified numbers of larvae and pupae in each treatment and habitat.

Results Gravid female Culex mosquitoes preferred to lay eggs in dyed water. This was highly significant in tests conducted under laboratory conditions and in a semi-field choice test. Despite this, survivorship in black dyed water was significantly reduced compared to undyed water. Seasonal analysis of wild larval and pupal numbers in two habitats with and without dye showed no impact of dye but a significant impact of season and habitat. Mosquitoes were more successful, with significantly higher numbers of pupae, in the habitat where they had vegetation cover and shade.

Discussion Our study has raised some interesting possibilities. One is that where used, pond dyes may be encouraging mosquitoes to breed in gardens in close proximity to people. Considering the concerns over potential future spread of disease in urban environments, this as well as shading of ponds and water butts, should inform future advice over reducing mosquito breeding and spread.
Impact of chemicals, plant extracts and their combination on bacterial blight of cotton
Authors: Sajid Muhammad , Sahi Shahabaz Talib , Atiq Muhammad , Abid Muhammad , Perveen Rashida , Bashir Muhammad Rizwan , Anwaar Hafiz Arslan
Published: January 2018

Five chemicals, incuding Flare, Plant Protector, Mancozeb, Agrimycine, and Copper oxychloride, and five plant extracts including N. tabacum, A. indica, M. oleifera, D. alba and C. longa were evaluated against bacterial blight of cotton caused by Xanthomonas citri pv. malvacearum (a bacterium). The impact of chemicals and plant extracts on bacterial development was tested in laboratory while on disease reduction was tested in green house and field experiments. Laboratory experiments showed that maximum inhibition zone of bacterial growth was expressed by Flare (1.693cm) at all concentrations followed by Plant Protector (1.473 cm), Mancozeb (1.290 cm), Agrimycine (1.150 cm) and copper oxy-chloride (0.953) cm respectively while in case of plant extracts maximum inhibition was expressed by N. tabacum (0.650 cm) followed by A. indica (0.486), M. oleifera (0.350), D. alba (0.256 cm) and C. longa (0.168 cm). Green house experiment revealed that the best result was produced by the combination of Flare and N. tabacum by indicating lowest disease incidence (32.27%) at all the tested concentration. Same results were obtained in field experiment, where the lowest disease incidence (40.41%) was recorded when the ,Flare and N. tabacum were applied in combination although it was higher then green house. This study concludes that N. tabacum and Flare are better option against bacterial disease development and even their combination is more significant lowering the bacterial blight disease incidence on cotton. Selection of suitable formulation and method of application could be the future aspects of plant product especially N. tabacum related research.
Occurrence and characteristics of microplastics on insular beaches in the Western Tropical Atlantic Ocean
Authors: Ivar do Sul Juliana Assunção , Costa Monica , Fillmann Gilberto
Published: January 2018

Microplastics are widespread throughout oceans and seas and beaches are no exceptions. On beach sediments, microplastics (<5mm) are commonly prevalent over macroplastics (>5mm), where fragments of larger items are sampled in greater amounts. The occurrence and characteristics of microplastics were investigated on beaches of Fernando de Noronha, Abrolhos and Trindade islands located in the western tropical Atlantic Ocean. Despite no microplastic was identified in Abrolhos at this time, small spatial variations were detected in Fernando de Noronha and Trindade islands, highlighting the importance of oceanographic variables on plastics distribution and accumulation over time.
A comparison of planned radiotherapy dose distributions calculated by Monte Carlo with variation of technique, statistical uncertainty and voxel size on resulting gamma pass rates
Authors: Van Delinder Kurt W
Published: January 2018

Background: The gamma analysis index (γ) is the most commonly used method to compare a calculated and measured dose distribution. A caveat to the clinical use of γ is that the formalism does have a sensitivity to noise present in either distribution. Monte Carlo (MC) based dose calculation methods are widely accepted as the most accurate method to calculate a resulting patient dose distribution from a radiation therapy treatment plan [6]. However, noise is inherently present as random errors or statistical uncertainty within all MC based dose calculation methods and is inversely proportional to the dose calculation time [7]. A research experiment performed by Van Delinder et al. investigated the effect of decreasing voxel size and increasing statistical uncertainty for a Monte Carlo based dose calculation method using 10 clinical head and neck (H&N) IMRT treatment plans. The experimental result was a definitive increase in γ passing rates with combined decrease in voxel size [10]. In order to further clinical information regarding this phenomenon, a large comprehensive study is required using multiple treatment techniques, a different treatment site, and using a different type of radiation measurement device.

Methods/Design: A study consisting of (ntotal = 30) thirty total prostate cancer radiation therapy plans comprised of (n1 = 10) ten VMAT plans, (n2 = 10) ten IMRT plans and (n3 = 10) ten 3DCRT plans. All treatment plans consisting of three different treatment techniques are to be delivered with a total dose of 79.2 Gy prescribed to the PTV at a rate of 1.8 Gy in 44 fractions. 3DCRT will be delivered using 6 fields, IMRT delivered as 7 fields and VMAT consists of 2 arcs (CCW from 1o to 359o with a collimator angle of 170o and CW from 359o to 1o with a collimator angle of 190o). All three treatment techniques will be calculated using 6 and 10 MV energy to allow an intra-study comparison between energies. All QA plans will then be calculated with varied statistical uncertainty from 0.5%, 1%, 2%, 3%, 4% and 5%. The voxel sizes will also be varied from 3mm, 2mm and 1mm for each of the statistical uncertainty percentages. All treatment plans will be measured using ArcCHECK radiation dose measurement device and the γ will be applied within SNC Machine. Both 3%/3mm and 2%/2mm will be implemented for γ criteria for all of the treatment plans.

Discussion: The necessity for a comprehensive research experiment investigating the effects of statistical uncertainty and voxel size amongst multiple treatment techniques with additional variations is required to guarantee safe quality assurance with routine use of Monte Carlo dose calculation methods. This experimental design acts as a contrasting research experiment when combined with prior literature allowing the clinician the ability to use the direct results and develop clinical recommendations for IMRT QA involving the use of Monte Carlo based dose calculations.
Bacteria from hypersaline environments: a bioactivity reservoir of anti-methicillin resistant Staphylococcus aureus
Authors: Gad Ahmed H.
Published: January 2018

In the past decades, novel pharmaceutical compounds have been produced by a wide diverse groups of marine bacteria. These marine bacteria are potential reservoirs for antimicrobial products. In this study, we investigated 40 soil samples collected from the Great Salt Plain of Oklahoma GSP for anti-methicillin resistant Staphylococcus aureus bioactivities. A total number of 499 heterotrophic bacterial isolates (202 mesophilic halotolerant isolates, 125 thermophilic isolates, 84 halophilic isolates and 88 thermophile-halophile isolates) were recovered by culture dependent isolation and subjected to high-throughput screening to investigate their bioactivities against two strains of methicillin resistant Staphylococcus aureus MRSA. A total of 101 isolates (20.2%) out of 499 isolates possessed bioactivities against MRSA strains. They included; eighty (40%) isolates out of the 202 mesophilic halotolerant isolates showed anti-MRSA bioactivity. Twenty one bioactive (7%) isolates out of the 297 enrichment isolates showed anti-MRSA bioactivity. They involved; eleven bioactive (11%) isolates out of 125 of the thermophilic group and ten bioactive isolates (10%) out of 84 halophilic group isolates. No anti-MRSA bioactivity was revealed by the 88 isolates of the thermophile-halophile group. These 101 bioactive isolates (80 mesophilic halotolerant, 11 thermophilic and 10 halophilic) exhibited bioactivities against at least one Staphylococcus aureus MRSA using well diffusion technique. In regard to biogeographical distribution, a total of 29 (29%) and 72 (71%) bioactive isolates were isolated from vegetation and salt flat areas respectively. Thirty four (34%) isolates showed bioactivity against both methicillin resistant Staphylococcus aureus strains and fourteen (14%) isolates showed antimicrobial bioactivity against Staphylococcus aureus B-8-41-D-4, whereas fifty two (52%) isolates revealed antagonism against Staphylococcus aureus 4656. Furthermore, 16S rRNA-based study exposed that, Firmicutes harbored the highest number of bioactive isolates 77 (77%) including Bacillus (n=45 isolates), Halobacillus (n=13 isolates), Virgibacillus (n=7 isolates), Brevibacillus (n=7 isolates), Paenibacillus (n=1 isolates), Sediminibacillus (n=2 isolates), Oceanobacillus (n=1 isolates) and Staphylococcus (n=1 isolate). Proteobacteria- Gammaproteobacteria contained seven bioactive isolates (7%), including Halomonas (n=5 isolates), Marinobacter (n=1 isolate) and Pseudomonas (n=1 isolate). Actinobacteria were the third group and contained two bioactive isolates (2%), including, Cellulomonas (n=1 isolate) and Micrococcus (n=1 isolates). To our knowledge, this is the first study to explore the anti- methicillin resistant Staphylococcus aureus bioactivities of bacteria isolated from GSP. We consider our findings promising for further research to develop novel antimicrobial antibiotics.
Using metagenomic methods to detect organismal contaminants in microbial materials
Authors: Olson Nathan D , Zook Justin M , Morrow Jayne B , Lin Nancy J
Published: January 2018

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Therefore, high sensitivity methods not requiring a priori assumptions about the contaminant are needed. We demonstrate the use of whole genome sequencing (WGS) and a metagenomic taxonomic classification algorithm for assessing the organismal purity of a microbial material. Using this proposed method we characterized the types of false positive contaminants reported and the dependence of detectable contaminant concentration on material and contaminant genome using simulated WGS data. Using the proposed method to characterize microbial material purity will help to ensure that the materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods are free of contaminants adversely impacting measurement results.
Early warning indicators of grassland degradation in inner Mongolia
Authors: Qin Jie , Han Guodong , Wang Zhongwu , Hu Linxi , Zhang Jun
Published: January 2018

Backgroung: With the implementation of the Household Production Responsibility System in China almost 30 years ago, obvious spatial heterogeneity has developed over rangeland.

Methods: We examined lifeform functional groups over 5 years on household ranches in different grazing utilization rate (30%-95%) ecosystems in Inner Mongolia to identify the early warning indicators of grassland degradation.

Results: The results showed that a similar grassland utilization threshold occurred in different types of steppe, with 78-89% utilization for meadow steppe, 81-89% for typical steppe and 70-85% for desert steppe. The vegetation composition above these utilization thresholds did not show obvious signs of degradation; therefore, the risk of degradation was difficult to determine. The spatial threshold (WD: L) had a value of 31.40:100 for meadow steppe, 8.53:100 for typical steppe and 42.21:100 for desert steppe.

Conclusion: Land managers cannot easily determine the risk of degeneration according to the vegetation composition or function group. So the spatial threshold is important for implemented strategies to prevent degradation, and our study provides new insights to improve the management and restoration of degraded grassland in Inner Mongolia.
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Authors: Gerritsen Jacoline , Hornung Bastian , Renckens Bernadette , van Hijum Sacha A.F.T. , Martins dos Santos Vitor A.P. , Rijkers Ger T. , Schaap Peter J. , de Vos Willem M. , Smidt Hauke
Published: January 2018

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.

Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC.

Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.

Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.