bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel amoxicillin nanoparticles formulated as sustained release delivery system for poultry use
Authors: Güncüm E. , Bakırel T. , Anlaş C. , Ekici H. , Işıklan N.
Published: March 2018

Amoxicillin is used in the treatment and prevention of a wide range of diseases in poultry breeding. However, its short half‐life and low bioavailability restrict its clinical application in these species. Entrapment of drugs into polymeric nanoparticles (nps) presents a means to improve gastrointestinal absorption and oral bioavailability of drugs. This study was aimed to overcome limitation of amoxicillin use in poultry breeding. Amoxicillin was loaded into sodium alginate‐polyvinyl alcohol (NaAlg‐PVA) blend nps, and characterization of the prepared nps was performed. For pharmacokinetic study, commercial male broilers were used and comparative pharmacokinetics of free and nanoparticle form of amoxicillin were investigated. Twenty‐one broilers were divided into three groups. All groups received 10 mg/kg drug. Blood samples were collected, and drug plasma concentrations were determined by HPLC. The results demonstrated that the particle size, zeta potential, encapsulation efficiency, and loading capacity of the nps were 513.96 ± 19.46 nm, −45.36 ± 1.35 mV, 43.66 ± 3.30, and 12.06 ± 0.83%, respectively. In vitro drug release exhibited a biphasic pattern with an initial burst release of 18% within 2 hr followed by a sustained release over 22 hr. The pharmacokinetic results showed that amoxicillin nps have higher bioavailability and longer plasma half‐life (p < .01) than free amoxicillin. These results indicate that amoxicillin nano formulation is suitable for oral administration in broilers.
One shape fits all, but only in the aggregate: Diversity in sub‐stand scale diameter distributions
Authors: Zenner Eric K. , Peck JeriLynn E. , Sagheb‐Talebi Khosro
Published: March 2018

Questions

To what extent are the sub‐stand size class distributions at the neighbourhood patch scale masked at the stand level via spatial smoothing? What are the implications for naturalness assessment of obscuring, at the stand level, structures that arise from endogenous processes at the neighbourhood scale?

Location

Elborz Mountains, south of the Caspian Sea, Iran.

Methods

Natural uneven‐aged old‐growth Oriental beech (Fagus orientalis) forest subject to fine‐scale disturbances was stem‐mapped in a 1.2‐ha plot of live trees >7.5 cm DBH; neighbourhoods were delineated across multiple scales using the tree‐centred floating neighbourhood approach of spatial tessellation to connect trees to their natural neighbours. Cluster analysis was used to identify an optimal number of recurring diameter distribution types (DDT) based on the proportion of trees in each of the five size classes. The richness of DDTs was assessed and the extent of DDTs was modelled as a function of tree size.

Results

The number of member trees and spatial extent increased with neighbourhood scale. While the stand‐level tree size class distribution exhibited a rotated sigmoid shape, the nine most distinct DDTs were characterized by four different distribution shapes (negative exponential, increasing‐q, rotated sigmoid and unimodal) and varied considerably in the abundance of trees in different size classes. Each individual tree contributed to at least three of the nine DDTs, which were nonetheless spatially distinct and varied in extent with size class composition. As expected, all metrics exhibited spatial smoothing (i.e., increasing homogeneity with increasing scale) as small, heterogeneous tree neighbourhoods were expanded into larger neighbourhoods with more similar average composition, which converged on a rotated sigmoid shape at the broadest scale.

Conclusions

The stand‐level rotated sigmoid distribution reflected spatial smoothing across more heterogeneous fine‐scale tree neighbourhood patches. Further studies are needed to assess if a better measure of natural forest structure may be the diversity of sub‐stand structures and the contribution of individual trees to that diversity, rather than an aggregated metric that averages across the hallmark heterogeneity of neighbourhood dynamics.
Grasslands maintained with frequent fire promote cold‐tolerant species
Authors: Ladwig Laura M. , Damschen Ellen I. , Martin‐Blangy Soline , Alstad Amy O.
Published: March 2018

Question

In temperate grasslands and savannas that were historically maintained by frequent, low‐intensity fires, disturbance by fire may promote community resistance to winter climate change by favouring slow‐growing, resource‐conservative species that may also be more cold‐tolerant. The lack of functional trait data for measuring cold tolerance, however, has prevented testing this idea. We ask, are slower growing, resource‐conservative species more cold‐tolerant than fast‐growing species, and are plant responses to fire frequency and cold tolerance related?

Location

Prairies and savannas of south‐central Wisconsin, USA.

Methods

We measured leaf cold tolerance for 120 plant species from prairies and savannas and compared cold tolerance to fire affinity as well as other functional traits describing plant strategies.

Results

As predicted, resource‐conservative species are more cold‐tolerant than fast‐growing species in temperate grasslands and savannas. Cold tolerance is also associated with disturbance regime such that species found in frequently burned sites are more cold‐tolerant.

Conclusions

The ability to predict the degree of susceptibility of species and communities to winter climate change and extreme climate events, such as freezing, will provide insight into the conservation and management practices to promote species persistence into the future. Under climate change, communities composed of more stress‐tolerant species may be more likely to persist. Our results demonstrate that cold‐tolerant species are more common in temperate grasslands and savannas managed with frequent, low‐intensity fire that simulate historic disturbance regimes. Identifying and maintaining ecosystems composed of stress‐tolerant species may play a key role in preserving natural communities under environmental uncertainty.
Impact of climate change environmental conditions on the resilience of different formulations of the biocontrol agent Candida sake CPA-1 on grapes
Authors: Carbó A. , Torres R. , Teixidó N. , Usall J. , Medina A. , Magan N.
Published: March 2018

Biocontrol agents have become components of integrated crop protection systems for controlling economically important fungal pathogens. Candida sake CPA-1 is a biocontrol agent of fungal pathogens of fruits, both pre- and post-harvest. While the efficacy of different formulations have been examined previously, few studies have considered the resilience of different formulations under changing climatic conditions of elevated temperature, drought stress and increased atmospheric CO2. This study examined the effect of (a) temperature × RH × elevated CO2 (400 vs 1000 ppm) on the temporal establishment and viability of two dry and one liquid C. sake CPA-1 formulations on grape berry surfaces; (b) temperature stress (25 vs 35°C); and (c) elevated CO2 levels. Results indicated that temperature, RH and CO2 concentration influenced the establishment and viability of the formulations but there was no significant difference between formulations. For the combined three-component factors, increased temperature (35°C) and lower RH (40%) reduced the viable populations on grapes. The interaction with elevated CO2 improved the establishment of viable populations of the formulations tested. Viable populations greater than Log 4 CFUs per g were recovered from the grape surfaces suggesting that these had conserved resilience for control of Botrytis rot in grapes.

Significance and Impact of the Study

The interaction between environmental factors that are expected to occur in response to climate change (CC) will have a significant impact on food security and availability. Little information exists on how elevated temperature, drought stress and increased CO2 will have on the efficacy of biocontrol agents. The impact of these factors on the viability of different formulations of the biocontrol yeast Candida sake on the surface of grapes berries was evaluated for the first time. Such knowledge is critical for projecting the efficacy of biocontrol under climate change conditions and to identify formulations that have the necessary resilience to perform under CC conditions.
Hepatotoxicity of immune checkpoint inhibitors: An evolving picture of risk associated with a vital class of immunotherapy agents
Authors: Suzman Daniel L. , Pelosof Lorraine , Rosenberg Amy , Avigan Mark I.
Published: March 2018

Immune checkpoint inhibitors (ICIs) block CTLA‐4, PD‐1 and PD‐L1, or other molecules that control antitumour activities of lymphocytes. These products are associated with a broad array of immune‐related toxicities affecting a variety of organs, including the liver. ICI‐associated immune‐mediated hepatitis (IMH) ranges in severity between mild and life‐threatening and is marked by findings that bear both similarities as well as differences with idiopathic autoimmune hepatitis. Hepatotoxic events are often detected in clinical trials of ICIs that are powered for efficacy. Risk levels for ICI‐induced liver injury may be impacted by the specific checkpoint molecule targeted for treatment, the ICI dose levels, and the presence of a pre‐existing autoimmune diathesis, chronic infection or tumour cells which infiltrate the liver parenchyma. When patients develop liver injury during ICI treatment, a prompt assessment of the cause of injury, in conjunction with the application of measures to optimally manage the adverse event, should be made. Strategies to manage the risk of IMH include the performance of pretreatment liver tests with regular monitoring during and after ICI treatment and patient education. Using Common Terminology Criteria for Adverse Events developed at the National Cancer Institute to measure the severity level of liver injury, recommended actions may include continued ICI treatment with close patient monitoring, ICI treatment suspension or discontinuation and/or administration of corticosteroids or, when necessary, a non‐steroidal immunosuppressive agent. The elucidation of reliable predictors of tumour‐specific ICI treatment responses, as well as an increased susceptibility for clinically serious immune‐related adverse events, would help optimize treatment decisions for individual patients.
Development of spatial similarity‐based modelling to improve integrated lake water quality management in Malaysia
Authors: Fazli Bashirah , Shafie Aziz , Mohamed Azuhan , Mohamad Mohd F. , Yahaya Nasehir K. E. M. , Noordin Normaliza
Published: March 2018

This study describes similarity‐based modelling techniques used to develop a spatially based water quality prediction model to facilitate sustainable lake water quality management. The lentic nature of lakes allows them to slowly absorb pollutants over a long period of time with readily noticeable signs, causing symptoms to appear only when the water quality has significantly degraded, meaning the risk of improper water quality management can be very high. Thus, failure to establish sustainable planning at the watershed scale was found to be a major threat of water quality degradation, from extemporary approaches often practised in lake management. Accordingly, the developed model is tailored for lakes facing moderate to serious water quality data limitation. The geodatabase integrates the identified driving factors of physical, social and water quality with significant influences on the status of lake water quality. A 1 km buffer radius with percentages of built‐up area, population, lake surface area and rainfall is measured. Calculation of a water quality index was then quantified on the basis of a similarity‐modelling technique. Lake Putrajaya was chosen as a control point for developing the indicator index. A total of 93 recreational lakes within Selangor and Kuala Lumpur were selected as modelling points. The results of this study indicated the similarity technique of spatial modelling is sufficiently reliable to be applied as an early assessment indicator. From the 93 lakes in this study, none feel in the category of either “bad” or “excellent,” with the majority being in class 3 (medium water quality status) and only four considered as having a good water quality condition. The balance of 35 lakes was considered to exhibit poor water quality. The model output is an indicator index, providing classification guidelines for the water quality status of the assessed lake as an early assessment tools.
An experimental study on impact‐induced alterations of planetary organic simulants
Authors: Sekine Yasuhito , Kodama Kenya , Kobayashi Takamichi , Obata Seiji , Chang Yu , Ogawa Nanako O. , Takano Yoshinori , Ohkouchi Naohiko , Saiki Koichiro , Sekine Toshimori
Published: March 2018

The present study systematically investigates shock‐induced alteration of organic simulants of planetary bodies (OSPBs) as a function of peak shock pressure and temperature by impact experiments. Our results show that the composition and structure of OSPBs are unchanged upon impacts at peak pressures ≤~5 GPa and temperatures ≤~350 °C. On the other hand, these are dramatically changed upon impacts at >7–8 GPa and > ~400 °C, through loss of hydrogen‐related bonds and concurrent carbonization, regardless of the initial compositions of OSPBs. Compared with previous results on static heating of organic matter, we suggest that shock‐induced alteration cannot be distinguished from static heating only by Raman and infrared spectroscopy. Our experimental results would provide a proxy indicator for assessing degree of shock‐induced alteration of organic matter contained in carbonaceous chondrites. We suggest that a remote‐sensing signature of the 3.3–3.6 μm absorption due to hydrogen‐related bonds on the surface of small bodies would be a promising indicator for the presence of less‐thermally‐altered (i.e., <350 °C) organic matter there, which will be a target for landing to collect primordial samples in sample‐return spacecraft missions, such as Hayabusa2 and OSIRIS‐REx.
Model‐based detection and analysis of introgressed Neanderthal ancestry in modern humans
Authors: Steinrücken Matthias , Spence Jeffrey P. , Kamm John A. , Wieczorek Emilia , Song Yun S.
Published: March 2018

Genetic evidence has revealed that the ancestors of modern human populations outside Africa and their hominin sister groups, notably Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence tracts along modern‐day human genomes provides insight into the selective forces acting on them and the role of introgression in the evolutionary history of hominins. Studying introgression patterns on the X‐chromosome is of particular interest, as sex chromosomes are thought to play a special role in speciation. Recent studies have developed methods to localize introgressed ancestries, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair‐ and skin‐related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model‐based introgression detection method called dical‐admix. We demonstrate its efficiency and accuracy through extensive simulations and apply it to detect tracts of Neanderthal introgression in modern human individuals from the 1000 Genomes Project. Our findings are largely concordant with previous studies, consistent with weak selection against Neanderthal ancestry. We find evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals resulting from small effective population size, rather than widespread Dobzhansky–Müller incompatibilities (DMIs) that could contribute to reproductive isolation. Moreover, we confirm the previously reported low level of introgression on the X‐chromosome, but find little evidence that DMIs contributed to this pattern.
Genetic costructure in a meta‐community under threat of habitat fragmentation
Authors: De Kort Hanne , Baguette Michel , Prunier Jérôme G. , Tessier Marc , Monsimet Jérémy , Turlure Camille , Stevens Virginie
Published: March 2018

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the eco‐evolutionary processes underlying fragmentation‐compromised communities in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community module experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community module comprises a parasitic butterfly of conservation concern and its two obligatory host species, a plant and an ant. We show that both historical dispersal and ongoing habitat fragmentation shape population genetic diversity of the butterfly Phengaris alcon and its most limited host species (the plant Gentiana pneumonanthe). Genetic structure of each species was strongly driven by geographical structure, altitude and landscape connectivity. Strikingly, however, was the strong degree of genetic costructure among the three species that could not be explained by the spatial variables under study. This finding suggests that factors other than spatial configuration, including co‐evolutionary dynamics and shared dispersal pathways, cause parallel genetic structure among interacting species. While the exact contribution of co‐evolution and shared dispersal routes on the genetic variation within and among communities deserves further attention, our findings demonstrate a considerable degree of genetic parallelism in natural meta‐communities. The significant effect of landscape connectivity on the genetic diversity and structure of the butterfly also suggests that habitat fragmentation may threaten the functioning of the community module on the long run.
A high‐quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal
Authors: Wells David A. , Cant Michael A. , Nichols Hazel J. , Hoffman Joseph I.
Published: March 2018

Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life‐history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg) whereas in theory with enough molecular markers realized IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life‐history traits in a wild population of banded mongooses using pedigree‐based inbreeding coefficients (fped) and standardized multilocus heterozygosity (sMLH) measured at 35–43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped. We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality‐related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait‐specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBDg above and beyond the pedigree expectation.
Selection outweighs drift at a fine scale: Lack of MHC differentiation within a family living lizard across geographically close but disconnected rocky outcrops
Authors: Pearson Sarah K. , Bull C. Michael , Gardner Michael G.
Published: March 2018

The highly polymorphic genes of the major histocompatibility complex (MHC) are involved in disease resistance, mate choice and kin recognition. Therefore, they are widely used markers for investigating adaptive variation. Although selection is the key driver, gene flow and genetic drift also influence adaptive genetic variation, sometimes in opposing ways and with consequences for adaptive potential. To further understand the processes that generate MHC variation, it is helpful to compare variation at the MHC with that at neutral genetic loci. Differences in MHC and neutral genetic variation are useful for inferring the relative influence of selection, gene flow and drift on MHC variation. To date, such investigations have usually been undertaken at a broad spatial scale. Yet, evolutionary and ecological processes can occur at a fine spatial scale, particularly in small or fragmented populations. We investigated spatial patterns of MHC variation among three geographically close, naturally discrete, sampling sites of Egernia stokesii, an Australian lizard. The MHC of E. stokesii has recently been characterized, and there is evidence for historical selection on the MHC. We found E. stokesii MHC weakly differentiated among sites compared to microsatellites, suggesting selection, acting similarly at each site, has outweighed any effects of low gene flow or of genetic drift on E. stokesii MHC variation. Our findings demonstrate the strength of selection in shaping patterns of MHC variation or consistency at a fine spatial scale.
Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards
Authors: Akashi Hiroshi D. , Saito Shigeru , Cádiz Díaz Antonio , Makino Takashi , Tominaga Makoto , Kawata Masakado
Published: March 2018

Thermal tolerances of organisms play a role in defining geographic ranges and occurrence of species. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, Anolis homolechis and Anolis sagrei) inhabit different thermal microhabitats. A previous study found that these species showed distinct gene expression patterns in response to temperature stimuli, suggesting the genetically distinct thermal physiology among species. To investigate whether the Anolis species inhabiting locally distinct thermal habitats diverge their thermal tolerances, we first conducted behavioural experiments to analyse the temperatures at which the three Anolis species escape from heat source. Then, for each of the three species, we isolated cDNA encoding a putative molecular heat sensor, transient receptor potential ion channel ankyrin 1 (TRPA1), which has been suggested to play a role on eliciting behavioural responses to heat stimuli. We performed electrophysiological analysis to quantify activation temperature of Anolis TRPA1 to see whether the pattern of divergence in TRPA1 responses is congruent with that of divergence in behavioural responses. We found that temperatures triggering behavioural and TRPA1 responses were significantly lower for shade‐dwelling species (A. allogus) than for sun‐dwelling species (A. homolechis and A. sagrei). The ambient temperature of shade habitats where A. allogus occurs stays relatively cool compared to that of open habitats where A. homolechis and A. sagrei occur and bask. The high temperature thresholds of A. homolechis and A. sagrei may reflect their heat tolerances that would benefit these species to inhabit the open habitats.
Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia
Authors: Reyes‐Velasco Jacobo , Manthey Joseph D. , Freilich Xenia , Boissinot Stéphane
Published: March 2018

The frog genus Leptopelis is composed of ~50 species that occur across sub‐Saharan Africa. The majority of these frogs are typically arboreal; however, a few species have evolved a fossorial lifestyle. Most species inhabit lowland forests, but a few species have adapted to high elevations. Five species of Leptopelis occupy the Ethiopian highlands and provide a good opportunity to study the evolutionary transition from an arboreal to a fossorial lifestyle, as well as the diversification in this biodiversity hot spot. We sequenced 14 nuclear and three mitochondrial genes, and generated thousands of SNPs from ddRAD sequencing to study the evolutionary relationships of Ethiopian Leptopelis. The five species of highland Leptopelis form a monophyletic group, which diversified during the late Miocene and Pliocene. We found strong population structure in the fossorial species L. gramineus, with levels of genetic differentiation between populations similar to those found between arboreal species. This could indicate that L. gramineus is a complex of cryptic species. We propose that after the original colonization of the Ethiopian highlands by the ancestor of the L. gramineus group, episodes of vicariance fragmented the ancestral populations of this group. We also report the re‐evolution of arboreality in L. susanae, which evolved from a fossorial ancestor, a rare ecological switch in frogs that had previously been reported only once.
Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing
Authors: Gauthier Jérémy , Gayral Philippe , Le Ru Bruno Pierre , Jancek Séverine , Dupas Stéphane , Kaiser Laure , Gyapay Gabor , Herniou Elisabeth A.
Published: March 2018

The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of Cotesia typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples, allowing the study of genetic variation between wasp populations and species. By combining population genetic estimations, such as nucleotide diversity (π), relative differentiation (FST) and absolute divergence (dxy), with branch‐site dN/dS measures, we identified six of 98 bracovirus genes showing significant divergence and evidence of positive selection. These genes, belonging to different gene families, are potentially involved in host adaptation and in the specialization process. Fine‐scale analyses of genetic variation also revealed mutations and large deletions in certain genes inducing pseudogenization and loss of function. The image emerging from these results is that adaptation mediated by bracovirus genes happens through selection of particularly adaptive alleles and loss of nonadaptive genes. These results highlight the central role of the bracovirus in the molecular interactions between the wasps and their hosts and in the evolutionary processes of specialization.
Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
Authors: Erlandson Sonya , Wei Xiaojing , Savage Jessica , Cavender‐Bares Jeannine , Peay Kabir
Published: March 2018

Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity and their interactions in shaping soil microbial communities. Using a multifactor, split‐plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity—habitat specialization, phylogenetic distance and species identity—influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi and archaea, while Salicaceae identity influenced <1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments—showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
Co‐evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella
Authors: Brandis Gerrit , Cao Sha , Hughes Diarmaid
Published: March 2018

Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF‐Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. We measured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but for insertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.
Regulons and protein–protein interactions of PRD‐containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions
Authors: Raynor Malik J. , Roh Jung‐Hyeob , Widen Stephen G. , Wood Thomas G. , Koehler Theresa M.
Published: March 2018

Bacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed ‘PCVRs’ (Phosphoenolpyruvate‐dependent phosphotransferase regulation Domain‐Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. AcpA and AcpB independently positively control transcription of the capsule biosynthetic operon capBCADE, and culture conditions that enhance AtxA level or activity result in capBCADE transcription in strains lacking acpA and acpB. We used RNA‐Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels. Plasmid and chromosome‐borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ≥ 4‐fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. We determined that AcpA and AcpB form homomultimers, as shown previously for AtxA, and we detected AtxA‐AcpA heteromultimers. In co‐expression experiments, AcpA activity was reduced by increased levels of AtxA. Our data show that the PCVRs have specific and overlapping activity and that PCVR stoichiometry and potential heteromultimerization can influence target gene expression.
Distribution and abundance of beaked whales (Family Ziphiidae) Off Cape Hatteras, North Carolina, U.S.A.
Authors: McLellan William A. , McAlarney Ryan J. , Cummings Erin W. , Read Andrew J. , Paxton Charles G. M. , Bell Joel T. , Pabst D. Ann
Published: March 2018

Beaked whales are vulnerable to the impacts of disturbance from several sources of anthropogenic sound. Here we report the distribution and abundance of beaked whales off Cape Hatteras, North Carolina, U.S.A., an area utilized by the U.S. Navy for training exercises, and of particular interest for seismic geophysical surveys. From May 2011 through November 2015, monthly aerial surveys were conducted at the site. Beaked whales were encountered 74 times (n = 205 individuals) during these surveys.Ziphius cavirostris, the most commonly encountered species, was observed in every month of the year.Mesoplodonspp. were encountered in ten months of the year. Photographs of adult males with erupted teeth permitted six sightings to be identified conclusively asM. europaeus;M. miruswas also photographed just outside the study area. Beaked whale surface densities stratified by depth (0.005–0.007/km2) were among the highest reported in the world for small ziphiids. A quantitative comparison of sightings and stranding records suggests that strandings do not accurately reflect the relative abundance of beaked whale species in this area. We conclude that Cape Hatteras, at the convergence of the Labrador Current and Gulf Stream, is a particularly important year‐round habitat for several species of beaked whales.
The status of Demodex cornei: description of the species and developmental stages, and data on demodecid mites in the domestic dog Canis lupus familiaris
Authors: Izdebska J. N. , Rolbiecki L.
Published: March 2018

Demodecosis canina is one of the most important dog parasitoses, but its aetiology is still not well known. There are currently two known species of demodecid mite specific to the domestic dog Canis lupus familiaris Linnaeus, 1758 (Carnivora: Canidae). These are Demodex canis Leydig, 1859 (Acariformes: Demodecidae) and Demodex injai Desch & Hillier, 2003. There have also been many reports of the so‐called ‘short form’, considered to be a separate species functioning under the name Demodex cornei nomen nudum, for which, however, no formal valid description has been documented. Taxonomic analysis of short forms of dog demodecid mites, associated with the stratum corneum, was performed, in line with the taxonomic criteria of Demodecidae systematics. This form was found to be a distinct species with features that differ from those of the other known species of this family. The species, including the adult and immature stages, is described. It is likely that different Demodex species parasitizing the domestic dog may be responsible for differentiated symptoms and different courses of demodecosis. However, the basis for clarifying this issue should be the correct, unambiguous identification of the species causing parasitosis.
On God in Lacan: A Response to Tina Beattie
Authors: Dalzell Thomas
Published: March 2018

Tina Beattie has re-read Aquinas in the light of Lacanian theory and found the later Lacan's transition to what he calls the register of “the Real” to be significant for a revitalised theology beyond traditional intellectual categories. She argues for a maternal Trinity which she believes to lie hidden in Thomas and, in support of this, she contends that Lacan left behind Freud's paternal preoccupations in favour of maternity. This response to Beattie will re-examine Lacan's trajectory from “the Symbolic” register to “the Real” through the lens of what he said in his year-long seminars about Moses, whom he regarded as a representative of “the Symbolic”, and it will demonstrate that paternity remained a constant in Lacan, who even came to see “the Real” itself as a name of the father.
Francisco Suárez and His Sources on the Gift of Tongues
Authors: Salas Victor
Published: March 2018

This paper considers the grace of the gift of tongues both as it is currently practiced among many members of the Catholic Charismatic Renewal (CCR) and how it has traditionally been understood in medieval and post-medieval theology. The paper especially considers the perspective of Francisco Suárez on the subject insofar as he, as in most matters, is able to frame the status quaestionis of the topic and presents a uniform view of the Catholic theological tradition's understanding of the gift. Ultimately, I point out that there are significant points of divergence between the nature of this gift as the CCR understands and practices it and as it has traditionally been understood historically.
GLT‐1 mediates exercise‐induced fatigue through modulation of glutamate and lactate in rats
Authors: Wang Dongmei , Wang Xingtong
Published: March 2018

Glutamate has been implicated in exercise‐induced fatigue, but the underlying mechanism is unknown. This study aimed to determine whether glutamate transporter‐1 (GLT‐1) has a key role in the regulation of exercise‐induced fatigue. The expressions of GLT‐1 and glial fibrillary acidic protein (GFAP) in the supplementary motor area of rats exposed to exhaustion were analyzed by immunohistochemistry. The expression of GLT‐1 was further confirmed by Western blotting. The effects of GLT‐1 on extracellular levels of glutamate and lactate and on exercise endurance were studied by microdialysis. GLT‐1 expression was decreased in rats subjected to exercise‐induced fatigue. Functional inhibition of GLT‐1 using dihydrokainate and transcriptional inhibition of GLT‐1 using antisense oligodeoxynucleotides led to a decrease in exercise endurance with a subsequent increase in extracellular glutamate concentration and decrease in extracellular lactate concentration. The expression of GLT‐1 in the supplementary motor area is reduced after strenuous exercise, resulting in an increased extracellular glutamate concentration and decreased extracellular lactate level that may be responsible for the development of fatigue. GLT‐1‐mediated uptake of glutamate ameliorates exercise‐induced fatigue in rat models.
Change in ecological stoichiometry of Carex brevicuspis in response to seasonal dynamics and elevation in Dongting Lake, China
Authors: Fu Xiaohua , Li Feng , Zhu Lianlian , Xie Yonghong , Hu Cong , Chen Xinsheng , Deng Zhengmiao
Published: March 2018

Plant nutrient stoichiometry is affected by both environmental factors and plant physiological processes. However, we know little about how small elevation gradients (influencing e.g. flooding regimes) and seasonality combine with soil physicochemical properties to influence nutrient stoichiometry in wetland plants. In this study, we examined these factors in Carex brevicuspis at Dongting Lake, China, during the non‐flooding periods in March, May and December of 2015 and February of 2016. We found that total foliar C concentration increased as elevation increased, especially during December 2015 and February 2016. At the low‐elevation site, total foliar C concentration decreased over the season, whereas it first increased and then decreased over time at higher elevations. Foliar total N and P concentrations decreased from March to May and subsequently increased throughout the season, and these concentrations were always much higher at the low‐elevation site. The C:N and C:P ratios first increased and then decreased over the season, while increasing with rising elevation. The N:P ratio was lower at the low‐elevation site, especially during May 2015 and February 2016; its variation over time differed across the elevations. A canonical correspondence analysis revealed that soil organic C, total N and soil nitrate N are important for determining C. brevicuspis stoichiometry. Our results suggest that both elevation and plant life stage have a significant influence on plant stoichiometry. This study improves our understanding of the seasonal dynamics of plant nutrients under different geographical conditions.
Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
Authors: Morales‐Briones Diego F. , Liston Aaron , Tank David C.
Published: March 2018

Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence.

We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches.

All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera.

Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
Rare genotype advantage promotes survival and genetic diversity of a tropical palm
Authors: Browne Luke , Karubian Jordan
Published: March 2018

Negative density dependence, where survival decreases as density increases, is a well‐established driver of species diversity at the community level, but the degree to which a similar process might act on the density or frequency of genotypes within a single plant species to maintain genetic diversity has not been well studied in natural systems.

In this study, we determined the maternal genotype of naturally dispersed seeds of the palm Oenocarpus bataua within a tropical forest in northwest Ecuador, tracked the recruitment of each seed, and assessed the role of individual‐level genotypic rarity on survival.

We demonstrate that negative frequency‐dependent selection within this species conferred a survival advantage to rare maternal genotypes and promoted population‐level genetic diversity. The strength of the observed rare genotype survival advantage was comparable to the effect of conspecific density regardless of genotype.

These findings corroborate an earlier, experimental study and implicate negative frequency‐dependent selection of genotypes as an important, but currently underappreciated, determinant of plant recruitment and within‐species genetic diversity. Incorporating intraspecific genetic variation into studies and theory of forest dynamics may improve our ability to understand and manage forests, and the processes that maintain their diversity.
Steal the light: shade vs fire adapted vegetation in forest–savanna mosaics
Authors: Charles‐Dominique Tristan , Midgley Guy F. , Tomlinson Kyle W. , Bond William J.
Published: March 2018

Shade cast by trees, which suppresses grass growth, and fire fuelled by grass biomass, which prevents tree sapling establishment, are mutually exclusive and self‐reinforcing drivers of biome distribution in savanna–forest mosaics.

We investigated how shade depth, represented by canopy leaf area index (LAI), is generated by adult trees across savanna–forest boundaries and how a shade gradient filters tree functioning, and grass composition and biomass.

Forest trees exerted greater shading through increased stem density and greater light interception per unit biomass. A critical transition at LAI c. 1.5 was linked to tree shifts from savanna to forest species, functional shifts from fire‐tolerant to light‐competitive species, and grass composition shifts from C4 to C3 pathways. A second transition to grass fuel loads too low to support fires, occurred at a lower canopy density (LAI > 0.5), accompanied by shifts in C4 subtype dominance.

This pattern suggests that shade suppression of grass biomass is an essential first step for the maintenance of alternative stable states.
Biodiversity of arbuscular mycorrhizal fungi and ecosystem function
Authors: Powell Jeff R. , Rillig Matthias C.
Published: March 2018

Contents

Summary
1059

I.
Introduction: pathways of influence and pervasiveness of effects
1060

II.
AM fungal richness effects on ecosystem functions
1062

III.
Other dimensions of biodiversity
1062

IV.
Back to basics – primary axes of niche differentiation by AM fungi
1066

V.
Functional diversity of AM fungi – a role for biological stoichiometry?
1067

VI.
Past, novel and future ecosystems
1068

VII.
Opportunities and the way forward
1071

Acknowledgements
1072

References
1072

Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal‐centric view of AM fungal biodiversity–ecosystem function relationships that focuses on the direct and specific links between AM fungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research.