bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of viral vectors to the study of neural connectivities and neural circuits in the marmoset brain
Authors: Watakabe Akiya , Sadakane Osamu , Hata Katsusuke , Ohtsuka Masanari , Takaji Masafumi , Yamamori Tetsuo 
Published: October 2016

ABSTRACTIt is important to study the neural connectivities and functions in primates. For this purpose, it is critical to be able to transfer genes to certain neurons in the primate brain so that we can image the neuronal signals and analyze the function of the transferred gene. Toward this end, our team has been developing gene transfer systems using viral vectors. In this review, we summarize our current achievements as follows. 1) We compared the features of gene transfer using five different AAV serotypes in combination with three different promoters, namely, CMV, mouse CaMKII (CaMKII), and human synapsin 1 (hSyn1), in the marmoset cortex with those in the mouse and macaque cortices. 2) We used target‐specific double‐infection techniques in combination with TET‐ON and TET‐OFF using lentiviral retrograde vectors for enhanced visualization of neural connections. 3) We used an AAV‐mediated gene transfer method to study the transcriptional control for amplifying fluorescent signals using the TET/TRE system in the primate neocortex. We also established systems for shRNA mediated gene targeting in a neocortical region where a gene is significantly expressed and for expressing the gene using the CMV promoter for an unexpressed neocortical area in the primate cortex using AAV vectors to understand the regulation of downstream genes. Our findings have demonstrated the feasibility of using viral vector mediated gene transfer systems for the study of primate cortical circuits using the marmoset as an animal model. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 354–372, 2017
Species distribution models may misdirect assisted migration: insights from the introduction of Douglas‐fir to Europe
Authors: Boiffin Juliette , Badeau Vincent , Bréda Nathalie 
Published: October 2016

AbstractSpecies distribution models (SDMs), which statistically relate species occurrence to climatic variables, are widely used to identify areas suitable for species growth under future climates and to plan for assisted migration. When SDMs are projected across times or spaces, it is assumed that species climatic requirements remain constant. However, empirical evidence supporting this assumption is rare, and SDM predictions could be biased. Historical human‐aided movements of tree species can shed light on the reliability of SDM predictions in planning for assisted migration. We used Douglas‐fir (Pseudotsuga menziesii(Mirb.) Franco), a North American conifer introduced into Europe during the mid‐19th century, as a case‐study to test niche conservatism. We combined transcontinental data sets of Douglas‐fir occurrence and climatic predictors to compare the realized niches between native and introduced ranges. We calibrated a SDM in the native range and compared areas predicted to be climatically suitable with observed presences. The realized niches in the native and introduced ranges showed very limited overlap. The SDM calibrated in North America had very high predictive power in the native range, but failed to predict climatic suitability in Europe where Douglas‐fir grows in climates that have no analogue in the native range. We review the ecological mechanisms and silvicultural practices that can trigger such shifts in realized niches. Retrospective analysis of tree species introduction revealed that the assumption of niche conservatism is erroneous. As a result, distributions predicted by SDM are importantly biased. There is a high risk that assisted migration programs may be misdirected and target inadequate species or introduction zones.
Detecting state changes for ecosystem conservation with long‐term monitoring of species composition
Authors: Mason T. J. , Keith D. A. , Letten A. D. 
Published: October 2016

AbstractEffective conservation requires an understanding not only of contemporary vegetation distributions in the landscape, but also cognizance of vegetation transitions over time with the goal of maintaining persistence of all states within the landscape. Using a state and transition model framework, we investigated temporal transitions over 31 years in species composition among five upland swamp vegetation communities in southeastern Australia. We applied fuzzy clustering to document transitions across communities; evaluated the resilience and resistance of communities to change; and explored the relationship between ecosystem states and major environmental factors posited to structure the system. We also evaluated the predictive ability of an established vegetation dynamics model. We found that community composition remained stable or underwent reversible or directional transitions depending on the vegetation type. Wetter communities (Ti‐tree thicket and Cyperoid heath) were more stable (i.e., resistant) while drier communities showed a greater propensity to transition (i.e., had lower resistance) under the observed disturbance regime (low variance fire intervals). The resilience of drier communities differed under this regime, with Banksia thicket showing reversible compositional change, while Restioid heath and Sedgeland showed directional change. In accord with an established conceptual model, we found that communities were distributed along a hydrological gradient. In addition, vegetation structure, along with light penetration to ground level, differentiated communities. However, internal dynamics of drier communities were complex: differences in fire regime (penultimate fire interval in 2014 and number of fires since 1965) were unable to predict differences in community membership among sites. Aspects of the fire regime are expected to be more important predictors if fire intervals vary more strongly among sites in the future. Fuzzy clustering of compositional data allows managers to track community transitions over time and facilitates planned interventions for conservation purposes.
Predicting North American Scolytinae invasions in the Southern Hemisphere
Authors: Lantschner Maria Victoria , Atkinson Thomas H. , Corley Juan C. , Liebhold Andrew M. 
Published: October 2016

AbstractScolytinae species are recognized as one of the most important tree mortality agents in coniferous forests worldwide, and many are known invaders because they are easily transported in wood products. Nonnative trees planted in novel habitats often exhibit exceptional growth, in part because they escape herbivore (such as Scolytinae) pressure from their native range. Increasing accidental introductions of forest pest species as a consequence of international trade, however, is expected to diminish enemy release of nonnative forest trees. In this context, there is need to characterize patterns of forest herbivore species invasion risks at global scales. In this study, we analyze the establishment potential of 64 North American Scolytinae species in the Southern Hemisphere. We use climate‐based ecological niche models (MaxEnt) to spatially define the potential distribution of these Scolytinae species in regions of the Southern Hemisphere were pines are planted. Our model predicts that all of the pine‐growing regions of the Southern Hemisphere are capable of supporting some species of North American Scolytinae, but there are certain “hotspot” regions, southeastern Argentina, Bolivia, Chile, Peru and southwestern Australia, that appear to be suitable for a particularly large number of species. The species with the highest predicted risk of establishment were Dendroctonus valens, Xyleborus intrusus, Hylastes tenuis, Ips grandicollis, Gnathotrichus sulcatus, and Ips calligraphus. Given that global commerce is anticipated to continue to increase, we can expect that more Scolytinae species will continue to establish outside their range. Our results provide information useful for identifying a global list of potential invasive species in pine plantations, and may assist in the design of comprehensive strategies aimed at reducing pest establishment in Southern Hemisphere forest plantations.
Effects of sulfate and sulfide on the life cycle ofZizania palustrisin hydroponic and mesocosm experiments
Authors: Pastor John , Dewey Brad , Johnson Nathan W. , Swain Edward B. , Monson Philip , Peters Emily B. , Myrbo Amy 
Published: October 2016

AbstractUnder oxygenated conditions, sulfate is relatively non‐toxic to aquatic plants. However, in water‐saturated soils, which are usually anoxic, sulfate can be reduced to toxic sulfide. Although the direct effects of sulfate and sulfide on the physiology of a few plant species have been studied in some detail, their cumulative effects on a plant's life cycle through inhibition of seed germination, seedling survival, growth, and seed production have been less well studied. We investigated the effect of sulfate and sulfide on the life cycle of wild rice (Zizania palustrisL.) in hydroponic solutions and in outdoor mesocosms with sediment from a wild rice lake. In hydroponic solutions, sulfate had no effect on seed germination or juvenile seedling growth and development, but sulfide greatly reduced juvenile seedling growth and development at concentrations greater than 320 μg/L. In outdoor mesocosms, sulfate additions to overlying water increased sulfide production in sediments. Wild rice seedling emergence, seedling survival, biomass growth, viable seed production, and seed mass all declined with sulfate additions and hence sulfide concentrations in sediment. These declines grew steeper during the course of the 5 yr of the mesocosm experiment and wild rice populations became extinct in most tanks with concentrations of 250 mg SO4/L or greater in the overlying water. Iron sulfide precipitated on the roots of wild rice plants, especially at high sulfate application rates. These precipitates, or the encroachment of reducing conditions that they indicate, may impede nutrient uptake and be partly responsible for the reduced seed production and viability.
Testing the reproductive and somatic trade‐off in female Columbian ground squirrels
Authors: Rubach Kristin , Wu Mingyan , Abebe Asheber , Dobson F. Stephen , Murie Jan O. , Viblanc Vincent A. 
Published: October 2016

AbstractEnergetic trade‐offs in resource allocation form the basis of life‐history theory, which predicts that reproductive allocation in a given season should negatively affect future reproduction or individual survival. We examined how allocation of resources differed between successful and unsuccessful breeding female Columbian ground squirrels to discern any effects of resource allocation on reproductive and somatic efforts. We compared the survival rates, subsequent reprodction, and mass gain of successful breeders (females that successfully weaned young) and unsuccessful breeders (females that failed to give birth or wean young) and investigated “carryover” effects to the next year. Starting capital was an important factor influencing whether successful reproduction was initiated or not, as females with the lowest spring emergence masses did not give birth to a litter in that year. Females that were successful and unsuccessful at breeding in one year, however, were equally likely to be successful breeders in the next year and at very similar litter sizes. Although successful and unsuccessful breeding females showed no difference in over winter survival, females that failed to wean a litter gained additional mass during the season when they failed. The next year, those females had increased energy “capital” in the spring, leading to larger litter sizes. Columbian ground squirrels appear to act as income breeders that also rely on stored capital to increase their propensity for future reproduction. Failed breeders in one year “prepare” for future reproduction by accumulating additional mass, which is “carried over” to the subsequent reproductive season.
The interplay between soil structure, roots, and microbiota as a determinant of plant–soil feedback
Authors: Bergmann Joana , Verbruggen Erik , Heinze Johannes , Xiang Dan , Chen Baodong , Joshi Jasmin , Rillig Matthias C. 
Published: October 2016

AbstractPlant–soil feedback (PSF) can influence plant community structure via changes in the soil microbiome. However, how these feedbacks depend on the soil environment remains poorly understood. We hypothesized that disintegrating a naturally aggregated soil may influence the outcome of PSF by affecting microbial communities. Furthermore, we expected plants to differentially interact with soil structure and the microbial communities due to varying root morphology. We carried out a feedback experiment with nine plant species (five forbs and four grasses) where the “training phase” consisted of aggregated versus disintegrated soil. In the feedback phase, a uniform soil was inoculated in a fully factorial design with soil washings from conspecific‐ versus heterospecific‐trained soil that had been either disintegrated or aggregated. This way, the effects of prior soil structure on plant performance in terms of biomass production and allocation were examined. In the training phase, soil structure did not affect plant biomass. But on disintegrated soil, plants with lower specific root length (SRL) allocated more biomass aboveground. PSF in the feedback phase was negative overall. With training on disintegrated soil, conspecific feedback was positively correlated with SRL and significantly differed between grasses and forbs. Plants with higher SRL were likely able to easily explore the disintegrated soil with smaller pores, while plants with lower SRL invested in belowground biomass for soil exploration and seemed to be more susceptible to fungal pathogens. This suggests that plants with low SRL could be more limited by PSF on disintegrated soils of early successional stages. This study is the first to examine the influence of soil structure on PSF. Our results suggest that soil structure determines the outcome of PSF mediated by SRL. We recommend to further explore the effects of soil structure and propose to include root performance when working with PSF.
Do foraging methods in winter affect morphology during growth in juvenile snow geese?
Authors: Jónsson Jón Einar , Afton Alan D. 
Published: October 2016

AbstractPhysical exertion during growth can affect ultimate size and density of skeletal structures. Such changes from different exercise regimes may explain morphological differences between groups, such as those exhibited by lesser snow geese (Chen caerulescens caerulescens; hereafter snow geese) foraging in southwest Louisiana. In rice‐prairie habitats (hereafter rice‐prairies), snow geese bite off or graze aboveground vegetation, whereas they dig or grub for subterranean plant parts in adjacent coastal marshes. Grubbing involves considerably more muscular exertion than does grazing. Thus, we hypothesized that rates of bone formation and growth would be lower for juveniles wintering in rice‐prairies than those in coastal marshes, resulting in smaller bill and skull features at adulthood. First, we tested this exertion hypothesis by measuring bills, skulls, and associated musculature from arrival to departure (November–February) in both habitats in southwest Louisiana, using both banded birds and collected specimens. Second, we used the morphological data to test an alternative hypothesis, which states that smaller bill dimensions in rice‐prairies evolved because of hybridization with Ross's geese (C. rossii). Under the exertion hypothesis, we predicted that bill and skull bones of juveniles would grow at different rates between habitats. However, we found that bill and skull bones of juveniles grew similarly between habitats, thus failing to support the exertion hypothesis. Morphometrics were more likely to differ by sex or change with sampling date than to differ by habitat. We predicted that significant, consistent skewness toward smaller birds could indicate hybridization with Ross's geese, but no skewness was observed in our morphological data, which fails to support the hybridization hypothesis. Further research is needed to clarify whether snow geese wintering in Louisiana represent a single polymorphic population that segregates into individually preferred habitats, which we believe at present to be more likely as an explanation than two ecologically and spatially distinct morphotypes.
Higher efficiency of ISSR markers over plastid psbA‐trnH region in resolving taxonomical status of genus Ocimum L.
Authors: Kumar Amit , Mishra Priyanka , Baskaran Kuppusamy , Shukla Ashutosh K. , Shasany Ajit K. , Sundaresan Velusamy 
Published: October 2016

AbstractHigh level of morphological as well as chemical variability exists within the genus Ocimum, and its taxonomy and phylogenetic relationships are still doubtful. For evaluating interspecific genetic relationships among the Ocimum species, genotyping with intersimple sequence repeat (ISSR) markers and sequence analyses of noncoding psbA‐trnH intergenic region belonging to chloroplast DNA were carried out. Although ISSR markers are highly efficient and reproducible, they have not been used extensively in phylogenetic studies. The use of the plastidial barcode candidate was expected to provide more variable and informative insight into evolutionary rates, and was thus employed as a phylogenetic marker to assess interspecific relationships. This study revealed that the ISSR markers were more efficient than psbA‐trnH sequences in resolving the current status of Ocimum L. genus. Distance‐ and character‐based methodological approaches applied on the molecular data with biparental and maternal inheritance were used for deducing the phylogenetic relationships among Ocimum species. Average polymorphic information content (0.344) and resolving power (6.285) depicted through ISSR markers proved to be efficient in discriminating the studied species of Ocimum. The primers used in this study revealed 99.585% polymorphism across the species demonstrating the polymorphic nature of ISSR markers.
Citations increase with manuscript length, author number, and references cited in ecology journals
Authors: Fox Charles W. , Paine C. E. Timothy , Sauterey Boris 
Published: October 2016

AbstractMost top impact factor ecology journals indicate a preference or requirement for short manuscripts; some state clearly defined word limits, whereas others indicate a preference for more concise papers. Yet evidence from a variety of academic fields indicates that within journals longer papers are both more positively reviewed by referees and more highly cited. We examine the relationship between citations received and manuscript length, number of authors, and number of references cited for papers published in 32 ecology journals between 2009 and 2012. We find that longer papers, those with more authors, and those that cite more references are cited more. Although paper length, author count, and references cited all positively covary, an increase in each independently predicts an increase in citations received, with estimated relationships positive for all the journals we examined. That all three variables covary positively with citations suggests that papers presenting more and a greater diversity of data and ideas are more impactful. We suggest that the imposition of arbitrary manuscript length limits discourages the publication of more impactful studies. We propose that journals abolish arbitrary word or page limits, avoid declining papers (or requiring shortening) on the basis of length alone (irrespective of content), and adopt the philosophy that papers should be as long as they need to be.
Using hydrogen isotopes of freshwater fish tissue as a tracer of provenance
Authors: Soto David X. , Hobson Keith A. , Wassenaar Leonard I. 
Published: October 2016

AbstractHydrogen isotope (δ2H) measurements of consumer tissues in aquatic food webs are useful tracers of diet and provenance and may be combined with δ13C and δ15N analyses to evaluate complex trophic relationships in aquatic systems. However, δ2H measurements of organic tissues are complicated by analytical issues (e.g., H exchangeability, lack of matrix‐equivalent calibration standards, and lipid effects) and physiological mechanisms, such as H isotopic exchange with ambient water during protein synthesis and the influence of metabolic water. In this study, δ2H (and δ15N) values were obtained from fish muscle samples from Lake Winnipeg, Canada, 2007–2010, and were assessed for the effects of species, feeding habits, and ambient water δ2H values. After lipid removal, we used comparative equilibration to calibrate muscle δ2H values to nonexchangeable δ2H equivalents and controlled for H isotopic exchange between sample and laboratory ambient water vapor. We then examined the data for evidence of trophic δ2H enrichment by comparing δ2H values with δ15N values. Our results showed a significant logarithmic correlation between fork length and δ2H values, and no strong relationships between δ15N and δ2H. This suggests the so‐called apparent trophic compounding effect and the influence of metabolic water into tissue H were the potential mechanisms for δ2H enrichment. We evaluated the importance of water in controlling δ2H values of fish tissues and, consequently, the potential of H isotopes as a tracer of provenance by taking account of confounding variables such as body size and trophic effects. The δ2H values of fish appear to be a good tracer for tracking provenance, and we present a protocol for the use of H isotopes in aquatic ecosystems, which should be applicable to a broad range of marine and freshwater fish species. We advise assessing size effects or working with fish of relatively similar mass when inferring fish movements using δ2H measurements.
Responses of riparian plants to habitat changes following restoration of channelized streams
Authors: Kuglerová Lenka , Botková Kamila , Jansson Roland 
Published: October 2016

AbstractThe ecological effects of stream restoration were evaluated by comparing riparian vegetation, flooding, and habitat properties between channelized and two types of restored streams in northern Sweden. Channelized streams were straightened and cleared of in‐stream boulders and wood >50 years ago to facilitate timber floating. Basic restoration (performed 8–10 years ago) returned cleared material back to the channels, and enhanced restoration (3 years ago) added large structural elements (boulders and downed trees) to previously basic‐restored streams. Riparian inundation duration increased only after enhanced restoration. Similarly, enhanced‐restored reaches had the highest amount of substrate available for plant establishment compared to channelized and basic‐restored streams. In contrast, soil biochemical properties (pH and C:N ratio) did not improve following either restoration effort. Riparian plant cover was higher at both restored types than channelized reaches. Plant species richness was higher at plot‐scale level (0.25 m2) at both restored types in the most species‐rich elevation levels compared to channelized reaches, whereas at the reach‐scale (>700 m2 of riparian area), species richness did not differ among stream types. Similarly, species composition segregated between channelized and restored reaches only at the plot scale. We found no significant differences in riparian vegetation between the two restored types. The lack of positive responses of vegetation to enhanced restoration and to variables that changed immediately after restoration (inundation, habitat area) implies that responses were either slower than expected or the changes in hydrology and substrate availability were not as important for riparian flora as believed.