bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological facilitation of the giant tree fern Angiopteris evecta in the germination of the invasive velvet tree Miconia calvescens
Authors: Lee Jaemin
Published: January 2018

Background. Biological facilitation is a type of relationship between two taxa that benefits at least one of the participants and harms neither. Although invasive species are widely known to compete with native taxa, recent studies suggest that invasive and native species can have positive relationships. This study aims to examine the biological facilitation of the germination of invasive Miconia calvescens by giant tree fern Angiopteris evecta, native to French Polynesia.

Methods. Field surveys were conducted to measure A. evecta and M. calvescens by applying the 10×10 m2 quadrat survey method. The density of seedlings, saplings, and matures of M. calvescens growing on the rhizomes of A. evecta and on bare soil was compared, and the correlation between the size of the rhizomes and the number of M. calvescens growing on them was verified. Two separate sets of nutrient measurements of substrates were performed to compare the nutrient of A. evecta rhizome and other environments (abiotic and potential biotic environments). Leaf decomposition rate of five dominant tree species was compared to verify whether A. evecta has quickly decomposing leaves, and therefore induce the germination of M. calvescens indirectly.

Results. Field surveys show that there is a greater number of seedlings and saplings of M. calvescens growing on the rhizomes of A. evecta as compared to bare soil. Furthermore, there is a positive correlation between the size of rhizomes and the number of M. calvescens growing on them. Substrates of A. evecta had higher phosphorus and potassium contents compared to other soils and substrates, but did not differ from bark of other tree species that could potentially offer favorable microenvironments. A. evecta has quickly decomposing leaves.

Discussion. A. evecta facilitates the germination of M. calvescens, supported by the much higher number of seedlings and saplings growing on the rhizomes and the positive correlation between the size of the rhizome and the number of M. calvescens growing on it. Microslopes on the rhizomes of A. evecta prevent leaf litter from accumulating on the rhizomes, and enable more sunlight to reach and facilitate the germination of M. calvescens seeds. Also, quickly decomposing leaves of A. evecta prevent the accumulation of leaf litter on the ground and enable more light to reach seed bank. Although the chemical components is not different from other tree species, physical structure of the rhizome and consequent higher light availability, and higher amount of potassium than bare soil would be the possible reason for the facilitation. Biological facilitation of the germination of invasive M. calvescens by native A. evecta can give better understanding on the invasion success and the relationship between the native and invasive species. Invasion of A. evecta can induce and promote further invasion of M. calvescens. Therefore, thorough management of ongoing invasion of A. evecta is particularly required.
Models for exploring genome-fitness mapping in an introductory course
Authors: Thompson David
Published: January 2018

Evolutionary theory presents a number of conceptual hurdles for the undergraduate student. In addition, the extended timespan over which many evolutionary processes occur, coupled with the time constraints of the typical undergraduate laboratory, restricts the range of relevant laboratory exercises available to augment instruction in an undergraduate course. Computer-based simulations have the potential to overcome this barrier as they allow interaction with models of natural processes which occur on long timescales. Such simulations allow the student to pursue what would be impossible at the bench: to investigate multiple scenarios and to collect, visualize, and analyze large amounts of data. Here, we describe a set of agent-based models, developed using the NetLogo platform, designed to facilitate developing a better understanding of the interplay between random processes, organismal fitness, encoding, and genomic sequence space.
How do waterbirds respond to climate change? A study at a key wintering site in Europe
Authors: Marchowski Dominik , Jankowiak Łukasz , Wysocki Dariusz , Ławicki Łukasz , Girjatowicz Józef
Published: January 2018

Many species of birds react to climate change, for example, by wintering in areas closer to their breeding areas. We investigated the responses of two different functional groups of waterbirds to factors associated with climate change. The Odra River Estuary (SW Baltic Sea) is of key importance to wintering waterfowl. The most numerous birds here belong to two ecological groups: benthic feeders and fish feeders. We showed that numbers of all benthivorous waterbirds were negatively correlated with the presence of ice, but failed to find such a relationship for piscivores. We anticipated that, with ongoing global warming, the significance of this area would increase for benthic feeders but decrease for fish feeders: our results bore this out. The maximum range of ice cover in the Baltic Sea has a weak and negative effect on both groups of birds. Five of the seven target species are benthivores (Greater Scaup Aythya marila, Tufted Duck A. fuligula, Common Pochard A. ferina, Common Goldeneye Bucephala clangula and Eurasian Coot Fulica atra), while the other two are piscivores (Smew Mergellus albellus and Goosander Mergus merganser). Local changes at the level of particular species vary for different reasons. The local decline of Common Pochard may be a reflection of the species’ global decline. Climate change may be responsible for some of the local changes in the study area, namely, the significance of the area has increased for Greater Scaup and Tufted Duck but declined for Smew.
­Vulnerability of parrotfish functional diversity and coral reef health in transitioning island socio-ecosystems
Authors: Rice Katherine R
Published: January 2018

Mo’orea’s reefs have rebounded from environmental disturbance throughout the years largely due to herbivorous fish that deter damaging algal blooms. This resilience suggests herbivorous fishes act as a keystone species in the coral reef ecosystem, and the greater island community of Mo’orea. Parrotfish support reef health and stability, and reefs support the development of the local economy by way of tourism and access to medicine, nourishment, and protection. Because island communities rely heavily on coral reef ecosystems, identifying the impact of fishing on the morphology and ecosystem function of parrotfish in a time of marine management and demographic transition can increase our knowledge of the vulnerability and resilience of these complex socio-ecosystems. The 2016 study reported here seeks to understand to what extent changes in fisheries management and off-take rates have affected the historically sustainable relationship between Mo’orea’s fishing population, the lagoon’s supply of larger-sized parrotfish, and the ecological stability of the greater coral reef ecosystem. Specifically, this study measured average parrotfish size at various fishing zones and paired Marine Protected Areas (MPAs) around the island, and then used participatory surveys to quantify fishermen observation of changes in parrotfish size since they started fishing. Both field data and participatory survey data show a decrease in parrotfish size since the establishment of MPAs. Island-wide, parrotfish also appear to be smaller in fished sites than in MPAs. Results suggest that the joint effect of zoning, catch-size enforcements and increased fishing pressure have caused a size-selection of parrotfish in the fishing zones of studied lagoons. These findings highlight the vulnerability of Mo’orea’s coral reef ecosystem to transitions in marine management strategy and size-selective fishing.
Conus bonus! Facilitation of Conus gastropods by invasive mangroves in Mo'orea, French Polynesia
Authors: Witte Eric C
Published: January 2018

Background. Ecosystem engineers are organisms that modify habitats and in many cases community assemblages. Mangroves (Rhizophora stylosa) on Mo’orea displace native marsh grass habitats and affect the distribution of native and non-native gastropod species. This study aimed to determine the effect of mangrove facilitation on the expansion of geographic distribution of certain cone snail species (Conus eburneus,C. frigidus C. leopardus, C. miliaris, and C. pulicaris).

Methods. Comparisons of temperature as well as cone snail abundance and diversity were conducted between marsh grasses, mangroves and sand flat habitats. The effects of short-term exposure to high temperatures on oxygen consumption were compared based on habitat parameters.

Results. While cone snails were absent from salt marshes, cone snails varied in abundance and diversity in mangrove and sand flat habitats. Cone snails were slightly more abundant in mangroves than paired sand flat habitats. Conus species assemblages were comparable in paired mangrove and sand flat habitats. One effect of mangrove ecosystem engineering is reduced thermal maxima and variance, which did not have a clear effect on oxygen consumption.

Discussion. Cone snails are excluded from salt marshes dominated by Paspalum vaginatum, however they are present in mangrove salt marshes. Habitat usage by cone snails is comparable between adjacent sites, suggesting that sand-specialized cone snails may receive the greatest benefit from mangrove facilitation due to proximity between possible habitats. Despite well documented effects of temperature variance on intertidal gastropods, this study did not find a direct effect of temperature variance on cone snails. This study contributes to efforts to understand effects of invasive ecosystem engineers on native community assemblages. Redistribution of species on a global scale has varied and complex implications; understanding these effects is crucial to predicting effects on biodiversity.
Out of place: a study of the mangrove crab Cardisoma carnifex on Mo’orea, French Polynesia
Authors: Johnson Isabel L S
Published: January 2018

Background. Invasive plant species pose a significant threat to island biodiversity and ecosystems. Invasive mangrove trees in particular have been shown to be devastating to the shorelines of islands across the Pacific. Previous studies have assumed that the mangrove crab, Cardisoma carnifex, plays a significant role in controlling Rhizophora stylosa mangrove populations on Mo’orea, French Polynesia. Found across East Africa, Indonesia, and the Pacific, C. carnifex’s behavior can change drastically depending on the environment it’s found in.

Methods. From October-November 2016, a field study was conducted on Mo’orea to assess C. carnifex habitat and food preferences. A series of 30 meter transects were done to determine the population density of crabs in mangrove and non-mangrove sites. In addition, a set of food preference experiments were run to determine if C. carnifex preferred to eat R. stylosa leaves, propagules, Hibiscus tiliaceus leaves, flowers, and Paspalum vaginatum marsh grass.

Results. Cardisoma carnifex was found to be more prevalent in mangrove sites although the results were not statistically significant. There were no food preferences found regardless of habitat and the flow of food through both habitats was the same.

Discussion. Results do not give a clear indication of C. carnifex’s ability to impact R. stylosa populations. However, results do demonstrate C. carnifex’s opportunistic nature, suggesting that they are extremely adaptable and do not rely on one habitat or food source for survival. Cardisoma carnifex’s role in its habitat is still poorly understood and needs to be studied in more detail in the future.
The burrow morphology of mole crickets (Orthoptera: Gryllotalpidae): terminology and comparisons
Authors: Baker Edward
Published: January 2018

Since the publication of Baker (2016) three additional burrow casts, unknown to the author, were located in the Natural History Museum, London (NHM) collection by George Beccaloni. These casts were provisionally identified as Gryllotalpa vineae. In order to establish whether this identification was correct a literature survey of the casts of mole crickets (Orthoptera: Gryllotalpidae) was conducted. Through this process a standardised terminology for mole cricket burrows has been established.

The application of eccentricity measurements to burrow structures has identified measurements that can potentially be used to discriminate those species for which suitably detailed burrow descriptions have been made available. It is demonstrated that the eccentricity of the restrictions on either side of the bulb, as well as the eccentricity of the horn opening, are useful diagnostic characters.
The influence of predator type on ‘whirling’ defensive behavior of Pholcus ancoralis (Araneae, Pholcidae), a tropical web-building spider
Authors: Striegel Theodore
Published: January 2018

Background. The ‘whirling’ defensive behavior of Pholcus ancoralis (L. Koch, 1865) was studied in a forest and laboratory in Mo’orea, French Polynesia. This behavior involves fast web-borne gyration to dissuade predators and is widespread in the Pholcidae family.

Methods. Different local predators (Anterhyncium rufipes, Lipinia noctua, and Thorelliola ensifera) were placed in two-chambered systems with P. ancoralis individuals and qualitative data on whirling frequency and duration were obtained.

Results. Potter wasps (Anterhyncium rufipes) triggered whirling in 50% of trials and moth skinks (Lipinia noctua) triggered whirling in 20% of trials. The average durations of the behavior triggered by each were 853 and 455 seconds, respectively. Pacific horned jumping spiders (Thorelliola ensifera) triggered whirling in 10% of trials with an average duration of only 20 seconds.

Discussion. Wasps triggered whirling the most frequently and of a long average duration. This has not been seen in other studied pholcids. This difference in predator specificity of whirling may be due to differences in habitat between pholcid species.
The Neotropical land snails (Mollusca, Gastropoda) collected by the ‘Comisión Científica del Pacífico’
Authors: Breure Abraham SH , Araujo Rafael
Published: January 2018

The land snails collected by the ‘Comisión Científica del Pacifíco’ (CCP), a Spanish expedition to South and Central America from 1862–1866, are restudied and revised. The historical context of the expedition and the study of its collected material are described. Biographical data is given for the main persons involved. The land snails were previously studied by Joaquin Hidalgo between 1867 and 1893. A total of 3470 specimens belonging to 211 species are treated in this paper. Of 34 species mentioned by Hidalgo is his catalogue, the corresponding material could not be located. A lectotype is now designated for Drymaeus (Drymaeus) chanchamayensis (Hidalgo, 1870); Bulimus visendus Hidalgo, 1869 is now placed in the genus Synapterpes Pilsbry, 1896, a new combination.
A standard field protocol for testing relative disease resistance in Acropora palmata and Acropora cervicornis
Authors: Miller Margaret W , Williams Dana E
Published: January 2018

Coral disease has been identified as an ongoing threat to the recovery of sustainable coral populations. This document provides a standard field protocol for screening disease resistance traits in the imperiled coral species, Acropora palmata and Acropora cervicornis, particularly genotypes under nursery culture for population enhancement. It is intended to be implemented by practitioners and researchers in coral restoration and provide standardized information on disease resistance that can aid in the design and success of population enhancement efforts.
Ten simple rules for considering preprints
Authors: Bourne Philip E , Polka Jessica K , Vale Ron D , Kiley Robert
Published: January 2018

So why make your work available as preprints? There are perceived positives and negatives to disclosing scientific work in the form of a preprint, explored here in the form of 10 Simple Rules. These rules, if they pass review, will appear as part of the PLOS Computational Biology Ten Simple Rules Collection. The rules cover such issues as reward, incentives, speed of dissemination, quality, scooping, and record of priority. You cannot have an article describing preprints, without itself being a preprint!!
A comparison of least squares regression and geographically weighted regression modeling of West Nile virus risk based on environmental parameters
Authors: Kala Abhishek K , Tiwari Chetan , Mikler Armin R , Atkinson Samuel F
Published: January 2018

Background. The primary aim of the study reported here was to determine the effectiveness of utilizing local spatial variations in environmental data to uncover the statistical relationships between West Nile Virus (WNV) risk and environmental factors. Because least squares regression methods do not account for spatial autocorrelation and non-stationarity of the type of spatial data analyzed for studies that explore the relationship between WNV and environmental determinants, we hypothesized that a geographically weighted regression model would help us better understand how environmental factors are related to WNV risk patterns without the confounding effects of spatial non-stationarity.

Methods. We examined commonly mapped environmental factors using both ordinary least squares regression (LSR) and geographically weighted regression (GWR). Both types of models were applied to examine the relationship between WNV-infected dead bird counts and various environmental factors for those locations. The goal was to determine which approach yielded a better predictive model.

Results. LSR efforts lead to identifying three environmental variables that were statistically significantly related to WNV infected dead birds (adjusted R2=0.61): stream density, road density, and land surface temperature. GWR efforts increased the explanatory value of these three environmental variables with better spatial precision (adjusted R2 = 0.71).

Conclusions. The spatial granularity resulting from the geographically weighted approach provides a better understanding of how environmental spatial heterogeneity is related to WNV risk as implied by WNV infected dead birds, which should allow improved planning of public health management strategies.
The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation
Authors: Bialevich Vitali , Sinha Dhiraj , Shamayeva Katsiaryna , Guzanova Alena , Řeha David , Csefalvay Eva , Carey Jannette , Weiserova Marie , Ettrich Rüdiger H
Published: January 2018

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types, HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.
Do you speak open science? Resources and tips to learn the language
Authors: Masuzzo Paola , Martens Lennart
Published: January 2018

The internet era, large-scale computing and storage resources, mobile devices, social media, and their high uptake among different groups of people, have all deeply changed the way knowledge is created, communicated, and further deployed. These advances have enabled a radical transformation of the practice of science, which is now more open, more global and collaborative, and closer to society than ever. Open science has therefore become an increasingly important topic. Moreover, as open science is actively pursued by several high-profile funders and institutions, it has fast become a crucial matter to all researchers. However, because this widespread interest in open science has emerged relatively recently, its definition and implementation are constantly shifting and evolving, sometimes leaving researchers in doubt about how to adopt open science, and which are the best practices to follow.

This article therefore aims to be a field guide for scientists who want to perform science in the open, offering resources and tips to make open science happen in the four key areas of data, code, publications and peer-review.
Expression and properties of lysyl oxidase from archeal halophile Haloterrigena turkmenica
Authors: Pestov Nikolay B , Kalinovsky Daniel V , Larionova Tatyana D , Zakirova Alia Z , Modyanov Nikolai N , Okkelman Irina A , Korneenko Tatyana V
Published: January 2018

Background: Lysyl oxidases (LOX) were studied mostly in mammals, whereas properties of recently found homologs in prokaryotic genomes remain enigmatic. Methods: LOX gene from Haloterrigena turkmenica has been cloned by PCR in a E. coli expression vector. Protein purification has been done using metal affinity chromatography under denaturing conditions followed by refolding. Catalytic activity has been fluorometrically a release of hydrogen peroxide coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results: H. turkmenica LOX (HTU-LOX) may be successfully expressed in E. coli with a high yield. However, full-length protein gives no catalytic activity. On the other hand, a deletion of putative signal peptide allows the protein to be refolded into an active enzyme. Further deletion until the boundary of the catalytic C-terminal domain greatly increases the activity. Refolding is optimal at pH around 6.0, with addition of Cu2+, and surprisingly does not respond to changing concentration s of NaCl. The active HTU-LOX is sensitive to the lysyl oxidase inhibitor β-aminopropionitrile. HTU-LOX is active towards usual substrates of mammalian LOX such as lysine-containing basic peptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed specificity of the former. HTU-LOX readily oxidizes various amines including such compounds as taurine and glycine. Moreover, it is active also towards aminoglycoside antibiotics. Benzyl amine is a poor substrate for HTU-LOX. H. turkmenica cells or culture medium do not contain any detectable amine oxidase activity. Polyclonal antibodies against HTU-LOX detect a band among H. turkmenica proteins with the molecular weight corresponding to the unprocessed enzyme. Conclusion: H. turkmenica contains a lysyl oxidase gene that may give active recombinant enzyme with important biochemical features conserved, for example, sensitivity to β-aminopropionitrile. However, its function in the host may be cryptic. Significance: This is the first report on some properties of lysyl oxidase that originated from a horizontal transfer event into Archea.
System-on-chip sensor fusion front-end self-healing design for network-on-chip digital communications
Authors: Seaman Emmanuel , Du Jason
Published: January 2018

With the ultra-scaling of CMOS technology, high-speed and low-power millimeter-wave communication systems for network-on-chip have been attracting more and more attentions due to the wider bandwidth and higher data rate that can meet the ever-increasing needs for multimedia, massive external data storage, or even biomedical applications. However, from manufacturing’s perspective, the circuits implementations are increasingly susceptible to fabrication process variations with the scaling of CMOS technology, which results in loss of yield rate. To solve this issue, a sensor-fusion solution is proposed in this paper by adding multiple on-chip sensors, including power detectors, temperature sensors, information envelope detectors and related filters, instrumentation amplifiers using a standard CMOS process. These sensors and detectors aim to collect critical system performance and environmental parameters, which will be utilized by a self-healing and optimization algorithm to adjust the state of system components by digitized control knobs.
System-on-chip sensor fusion front-end self-healing design for network-on-chip digital communications
Authors: Seaman Emmanuel , Du Jason Yuan
Published: January 2018

With the ultra-scaling of CMOS technology, high-speed and low-power millimeter-wave communication systems for network-on-chip have been attracting more and more attentions due to the wider bandwidth and higher data rate that can meet the ever-increasing needs for multimedia, massive external data storage, or even biomedical applications. However, from manufacturing’s perspective, the circuits implementations are increasingly susceptible to fabrication process variations with the scaling of CMOS technology, which results in loss of yield rate. To solve this issue, a sensor-fusion solution is proposed in this paper by adding multiple on-chip sensors, including power detectors, temperature sensors, information envelope detectors and related filters, instrumentation amplifiers using a standard CMOS process. These sensors and detectors aim to collect critical system performance and environmental parameters, which will be utilized by a self-healing and optimization algorithm to adjust the state of system components by digitized control knobs.
Imagining the ‘open’ university: Sharing scholarship to improve research and education
Authors: McKiernan Erin C
Published: January 2018

Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education, as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship, and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship, and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding, but rather a redistribution of existing funds and a rewriting of internal policies to better align with university missions of knowledge dissemination and societal impact.
Abundance of microorganisms and enzyme activity in the rapids-pool-benchland systems in natural Douliu River of China
Authors: Wang Zhen Hong , Wang Zhenhong , Chen Chen , Wu Qing
Published: January 2018

River structures and their ecosystem funtciotns have been greatly destructed due to the human disturbance during the last decades. It is a pressing task to understand the complete structures and ecosystem functions of a natural river to restore the impired river ecosystems. We found a basic structure of a natural river, i.e., the rapid-pool-benchland system, in the previous studies, so we selected the rapid-pool-benchland systems in the upper, middle and lower reaches of Duliu River, a natural river in China and tested the abundance of microorganisms and the enzyme activity in the sediments in these systems. Results indicated that the number of bacteria was far more than ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments of all river reaches. In the upper reach, the microbial abundance in the sediments was more than the middle and lower reaches. In each of the rapid-pool-benchland system, the microbial abundance in the sediemnets of the pool was always highest, and that of the rapid was lowest. The catalase activity in the sediments of the benchland was higher than the rapid and pool but the phosphatase activity in the pool was higher than the rapid and benchland. The phosphatas and urease activities were significantly correlated to the abundance of the bacteria, ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments. The rapid-pool-benchland system in a river obviously regulates the microbial abundance and the catalase and phosphatase activities in the sediments. However, the abuncance of microorganisms only indicated a 0.434-0.836 level of significant correlatioships with the activity of four enzymes, and further influences biochemical functions.
Abundance of microorganisms and enzyme activity in the rapid-pool-benchland systems in natural Douliu River of China
Authors: Wang Zhen Hong , Wang Zhenhong , Chen Chen , Wu Qing
Published: January 2018

Ecosystem functions of rivers have been greatly impaired due to the negative effects of human actions on river structures in different regions of the Earth during the last decades. It is an urgent task to understand the complete structures and ecosystem functions of a natural rive for restoration of the impaired river ecosystems. A natural river is composed of the repeatedly occurring rapid-pool-benchland system, i.e., a basic structural unit. We respectively selected three of the rapid-pool-benchland systems in the upper, middle and lower reaches of the Duliu River, a natural river in China as materials and tested the abundance of microorganisms in the sediments of these systems with plate counting method and a MPN (most-probable-number) method and the activity of enzymes with titration or colorimetric methods. Results indicated that the number of bacteria was far more than ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments of all these rapid-pool-benchland systems. In each of the rapid-pool-benchland systems, all the microbial abundance in the sediments of the pools was always highest, and that of the rapids was lowest. In the upper reach, the microbial abundance was more than the middle and lower reaches. Catalase activity in the sediments of the benchlands was higher than the rapids and pools but phosphatase activity in the pools was higher than the rapids and benchlands. Phosphatas and urease activities were significantly correlated to the abundance of the bacteria, ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments. The rapid-pool-benchland systems in a river obviously affect the microbial abundance and catalase and phosphatase activities related to biochemical functions in the sediments. However, the microbial abundance only indicated a middle-level correlations (r ranges from 0.434 to 0.836, p<0.05) with the activity of four extracellular enzymes. The study clarifies if the repeatedly occurring rapid-pool-benchland systems, a kind of habitat heterogeneity in a river have an effect on the microbial abundance and enzyme activity in the sediments, and further the relationships between the microbial abundance and enzyme activity.
The use of computational modeling to link sensory processing with behavior in Drosophila
Authors: Clemens Jan , Murthy Mala
Published: January 2018

A major goal of systems neuroscience is to understand how the brain represents information, and how those representations are used to drive behavior. Even though genetic model organisms like Drosophila grant unprecedented experimental access to the nervous system for manipulating and recording neural activity, the complexity of natural stimuli and natural behaviors still poses a challenge for solving the connections between neural activity and behavior. Here, we advocate for the use of computational modeling to complement (and enhance) the Drosophila toolkit. We first lay out a modelling framework for making sense of the relation between natural sensory stimuli, neuronal responses, and natural behavior. We then highlight how this framework can be used to reveal how neural circuits drive behavior, using selected case studies.
Long-term resource addition to a detrital food web yields a pattern of responses more complex than pervasive bottom-up control
Authors: Lawrence Kendra L. , Wise David H
Published: January 2018

Background. Theory predicts strong bottom-up control in detritus-based food webs, yet field experiments with detritus-based terrestrial systems have uncovered contradictory evidence regarding the strength and pervasiveness of bottom-up control processes. Two factors likely leading to contradictory results are experiment duration, which influences exposure to temporal variation in abiotic factors such as rainfall and affects the likelihood of detecting approach to a new equilibrium; and openness of the experimental units to immigration and migration. To investigate the contribution of these two factors, we conducted a long-term experiment with open and fenced plots in the forest that was the site of an earlier, short-term experiment (3.5 months) with open plots (Chen & Wise 1999) that produced evidence of strong bottom-up control for 14 taxonomic groupings of primary consumers of litter and fungi (microbi-detritivores) and their predators. Methods. We added artificial high-quality detritus to ten 2 x 2-m forest-floor plots at bi-weekly intervals from April through September in three consecutive years (Supplemented treatment). Ten comparable Ambient plots were controls. Half of the Supplemented and Ambient plots were enclosed by metal fencing. Results. Arthropod community structure (based upon 18 response variables) diverged over time between Supplemented and Ambient treatments, with no effect of Fencing on the multivariate response pattern. Fencing possibly influenced only ca. 20% of the subsequent univariate analyses. Multi- and univariate analyses revealed bottom-up control by fall of Year 1 of some, but not all, microbi-detritivores and predators. During the following two years the pattern of responses became more complex than that observed by Chen & Wise (1999). Some taxa showed consistent bottom-up control whereas many did not. Variation across years could not be explained completely by differences in rainfall because some taxa exhibited negative, not positive, responses to detrital supplementation. Discussion. Our 3-yr experiment did not confirm the conclusion of strong, pervasive bottom-up control of microbi-detritivores and predators reported by Chen and Wise (1999). Our longer-term experiment revealed a more complex pattern of responses, a pattern much closer to the range of outcomes reported in the literature for many short-term experiments. Much of the variation in responses across studies likely reflects variation in factors such as rainfall and the quality of added detritus. Nevertheless, it is also possible that long-term resource enhancement can drive a community towards a new equilibrium state that differs from what would have been predicted from the initial short-term responses exhibited by primary and secondary consumers.
Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time
Authors: van Dijk Aalt D.J. , Molenaar Jaap
Published: January 2018

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.
Influence of season and feeding intensity on the fatty acid composition of wild cobia (Rachycentron canadum, Linnaeus, 1766) in the Dungun coast, Malaysia
Authors: Babatunde Taofik Ademola , Amin S. M. Nurul , Yusoff Fatimah Md , Arshad Aziz , Esa Yuzine B , Ebrahimi Mahdi M
Published: January 2018

Cobia, Rachycentron canadum, is an important recreational marine fish of growing popularity in the aquaculture industry. Knowledge of the impact of environment on their fatty acids (FAs) utilization may contribute to the understanding their feeding in culture condition especially as cobia is been considered for low salinity culture. This study investigates the variations in the fatty acid contents of cobia from Dungun coast, Malaysia with respect to the changes in seasons and feeding intensity. Saturated fatty acids (FAs) comprised the majority of FAs in muscle, followed by monoenes, total poly-unsaturated fatty acids (PUFAs) (n-3) and then total PUFAs (n-6) with no seasonal variation in the quantity. A similar trend was observed in liver but total saturated FAs was significantly higher during the inter-monsoon while total monoenes significantly accumulate during monsoon. During low feeding intensity, there was a significant accumulation of PUFAs (n-6) in the muscle tissue (P < 0.05). Gut content analyses showed that cobia significantly increased the consumption of mollusks during the inter-monsoon (P < 0.05), although bony fishes dominated their diet throughout the year with no significant seasonal differences (P > 0.05). Our results suggest that cobia lipids are composed of a significant quantity of omega-3 and omega-6 FAs, which are considered to have important health benefits. While the environmental variability especially salinity fluctuations and prey abundance that accompany seasonal changes have a significant impact on the nutritional composition of cobia in Malaysian waters, their nutritional quality is maintained.
A residence-time framework for biodiversity
Authors: Locey Kenneth J , Lennon Jay T
Published: January 2018

Much of Earth’s biodiversity is at the mercy of currents and physical turnover. Residence time (τ) is the average time that particles spend in a system and is estimated from the ratio of volume to flow rate. Here, we present a framework for how τ influences biodiversity by coupling dispersal and resource supply. We test a suite of predictions with >20,000 individual-based models that impose ecological selection and energetic costs. Altogether, 24 patterns of growth, productivity, abundance, diversity, turnover, commonness and rarity, and trait syndromes simultaneously emerged across six orders of magnitude in τ. Abundance, productivity, and species richness were greatest when dilution rate, i.e., 1/τ, approximated basal metabolic rate. The emergence of τ-based relationships alongside realistic patterns of biodiversity and metabolic scaling suggest that manifold influences of τ, from the individual to ecosystem-levels, are powerful and congruous with ecological paradigms.
Development rate rather than social environment influences cognitive performance in Australian black field crickets, Teleogryllus commodus
Authors: Anderson Caitlin , Kasumovic Michael M
Published: January 2018

Cognitive functioning is vital for enabling animals of all taxa to optimise their chances of survival and reproductive success. Learning and memory in particular are drivers of many evolutionary processes. The field of cognitive ecology explores how the environment can affect investment into cognitive capacity and learning ability. In this study, we examine how developmental plasticity can affect cognitive ability by exploring the role of early social environment on influencing problem solving ability and learning of female black field crickets, Teleogryllus commodus. We used two learning paradigms, an analog of the Morris water maze and a novel linear maze, to examine cognitive differences between individuals reared in two acoustic treatments: silence or calling. Although there was no evidence of learning or memory, individuals that took longer to mature solved the Morris water maze more quickly. This suggests that increased investment into cognitive development is likely associated with increased development time during immature stages. Inconsistent individual performance and motivation during the novel linear maze task highlights the difficulties of designing ecologically relevant learning tasks within a lab setting. The role of experimental design in understanding cognitive ability and learning in more natural circumstances is discussed.
Pollen extracts increase growth of a trypanosome parasite of bumble bees
Authors: Palmer-Young Evan C
Published: January 2018

Phytochemicals produced by plants, including at flowers, function in protection against plant diseases, and have a long history of use against trypanosome infection. Floral nectar and pollen, the sole food sources for many species of insect pollinators, contain phytochemicals that have been shown to reduce trypanosome infection in bumble and honey bees when fed as isolated compounds. Nectar and pollen, however, consist of phytochemical mixtures, which can have greater antimicrobial activity than do single compounds. This study tested the hypothesis that pollen extracts would inhibit parasite growth.Extracts of six different pollens were tested for direct inhibitory activity against cell cultures of the bumble bee trypanosome gut parasite Crithidia bombi.

Surprisingly, pollen extracts increased parasite growth rather than inhibiting it. Experimental manipulations of growth media showed that supplemental monosaccharides (glucose and fructose) were sufficient to promote growth, while a common floral phytochemical (caffeic acid) with inhibitory activity against other trypanosomes had only weak inhibitory effects on Crithidia bombi. These results indicate that, although pollen is essential for bees and other pollinators, pollen may promote growth of intestinal parasites that are uninhibited by pollen phytochemicals and, as a result, can benefit from the nutrients that pollen provides.
Differential drivers of chemical defenses in three widespread pine species along a 1500-m elevational gradient: a test of the elevational gradient in plant defense hypothesis
Authors: Ferrenberg Scott , Langenhan Joseph M , Loskot Steven A , Rozal Leonardo M , Mitton Jeffry B
Published: January 2018

1. The elevational gradient in plant defense (EGPD) hypothesis posits that natural enemy pressures increase positively alongside temperature across elevational climatic gradients, thereby selecting for enhanced defenses at lower elevations while leaving plants less defended at higher elevations. Phylogenetically constrained tests of this hypothesis in tree populations are exceedingly rare. Nevertheless, the presumed presence of poorly-defended trees has been invoked as an important driver of recent pest outbreaks at higher elevations than historically common.

2. Tree age, growth rate, and size have all been correlated with levels of tree defenses. Thus, we sought to disentangle the interacting influences of these properties from possible elevational climatic effects on monoterpene composition, concentrations, and diversity of constitutive resin within three widespread pines (Pinus contorta, Pinus ponderosa, and Pinus flexilis) across a 1532 m elevational transect in the Rocky Mountains, Colorado, USA.

3. Collectively, elevation and tree properties were relatively weak predictors of defenses in P. ponderosa and P. flexilis, but explained ~ 75% of variation in monoterpene concentration and ~ 50% of diversity in P. contorta.

4. Increasing tree age had the greatest positive influence on monoterpene concentration and diversity in P. contorta, while increasing tree size had a negative influence suggesting a potential lifelong tradeoff between tree growth and defense. Elevation had a significant, negative influence on monoterpene concentration but little to no effect on monoterpene diversity in P. contorta.

5. Overall, we found some support for the EGPD hypothesis within P. contorta, but no support within P. ponderosa or P. flexilis. Our results suggest the presence of divergent conifer defense allocation strategies and drivers even among congeners growing in shared environments. An improved understanding of the controls on tree defenses, particularly possible influences of climate-based drivers, is necessary for predicting forest pest dynamics under global change scenarios.
Testing the hypothesis that routine sea ice coverage of 3-5 mkm2 results in a greater than 30% decline in population size of polar bears (Ursus maritimus)
Authors: Crockford Susan J
Published: January 2018

The polar bear (Ursus maritimus) was the first species to be classified as threatened with extinction based on predictions of future conditions rather than current status. These predictions were made using expert-opinion forecasts of population declines linked to modeled habitat loss – first by the International Union for the Conservation of Nature (IUCN)’s Red List in 2006, and then by the United States Fish and Wildlife Service (USFWS) in 2008 under the Endangered Species Act (ESA), based on data collected to 2005 and 2006, respectively. Both assessments predicted significant population declines of polar bears would result by mid-century as a consequence of summer sea ice extent reaching 3-5 mkm2 on a regular basis: the IUCN predicted a >30% decline in total population, while the USFWS predicted the global population would decline by 67% (including total extirpation of ten subpopulations within two vulnerable ecoregions). Biologists involved in these conservation assessments had to make several critical assumptions about how polar bears might be affected by future habitat loss, since sea ice conditions predicted to occur by 2050 had not occurred prior to 2006. However, summer sea ice declines have been much faster than expected: low ice levels not expected until mid-century (about 3-5 mkm2) have occurred regularly since 2007. Realization of predicted sea ice levels allows the ‘sea ice decline = population decline’ assumption for polar bears to be treated as a testable hypothesis. Data collected between 2007 and 2015 reveal that polar bear numbers have not declined as predicted and no subpopulation has been extirpated. Several subpopulations expected to be at high risk of decline have remained stable and at least one showed a marked increase in population size over the entire period. Another at-risk subpopulation was not counted but showed marked improvement in reproductive parameters and body condition with less summer ice. As a consequence, the hypothesis that repeated summer sea ice levels of below 5 mkm2 will cause significant population declines in polar bears is rejected. This result indicates that the ESA and IUCN judgments to list polar bears as threatened based on future risks of habitat loss were hasty generalizations that were scientifically unfounded, which suggests that similar predictions for Arctic seals and walrus may be likewise flawed, while the lack of a demonstrable ‘sea ice decline = population decline’ relationship for polar bears invalidates updated survival model outputs that predict catastrophic population declines should the Arctic become ice-free in summer.