bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research note: the effect of strain amplitude produced by ultrasonic waves on its velocity
Authors: Nourifard Nazanin , Lebedev Maxim 
Published: July 2018

ABSTRACTThe effect of the amplitude of ultrasonic waves propagating through a sample is not often taken into account in laboratory experiments. However, ultrasonic waves can produce relatively large strain inside the sample, and thus change the properties of the sample. To investigate the effect of strain amplitude on the P‐wave velocity, a series of ultrasonic wave propagation experiments were carried out on three different media. All measurements were performed at 1 MHz central frequency and at the strain levels inside propagating waves of ∼3.0 × 10−6 to 6.0 × 10−5 without applying confining pressure to the sample. Strains in the waves were measured by a laser Doppler interferometer upon wave arrival on a free surface of the sample. The ultrasonic velocities were measured by a pair of P‐wave transducers located at the same measuring point as the laser beam of the LDI. The effect of strain on P‐wave velocity varied for different material. The P‐wave velocity was calculated using both a first arrival and a first maximum peak at different applied voltage. The P‐wave velocity remained unchanged for a pure elastic medium (aluminium); however, the velocity increased continuously with the increasing of the strain for polymethylmethacrylate and Gosford sandstone. For Gosford sandstone, velocity increases up to 0.8% with strain increase from 7.0 × 10−6 to 2.0 × 10−5. This effect of velocity increase with the strain induced by an ultrasonic wave can be explained by the in‐elasticity of both the polymethylmethacrylate and Gosford sandstone samples.
A novel approach to determining dynamic nitrogen thresholds for seagrass conservation
Authors: Fernandes Milena B. , van Gils Jos , Erftemeijer Paul L. A. , Daly Rob , Gonzalez Dennis , Rouse Karen 
Published: July 2018

Abstract

Seagrass decline is often related to eutrophication, with sudden and drastic losses attributed to tipping points in nutrient loads. The identification of these threshold loads is an important step in the sustainable management of nutrient discharges.

In this study, a novel methodological approach is presented to simulate the spatial and temporal dynamics of coastal nitrogen loads and its relationship with seagrass loss. The analysis allows the identification of nitrogen thresholds associated with the loss of Posidonia and Amphibolis spp. in Adelaide, South Australia.

The identified thresholds varied between 0.8 and 1.1 t N km−2 over 6 months and explained up to 95% of all seagrass losses in the region.

Posidonia spp. was predominantly lost nearshore, indicating a threshold for this species in the higher end of the values reported here. In contrast, Amphibolis spp. were selectively lost further offshore, suggesting a lower threshold for the onset of fragmentation and decline.

Nitrogen pressure was concentrated over the wetter months of the year between late autumn and early spring. Pulsed pressure peaking in August likely affected thresholds by reducing resilience in the system.

Synthesis and applications. This study derives, for the first time, nitrogen load thresholds for the loss of the seagrasses Posidonia and Amphibolis spp., highlighting the low tolerance of these keystone temperate species to nitrogen pressure. The methodology developed as part of the work provides a tool to inform planning and improved management of nutrient discharges from land to facilitate seagrass conservation.
Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability
Authors: Wang Mengmeng , Ding Junjun , Sun Bo , Zhang Junyu , Wyckoff Kristen N. , Yue Haowei , Zhao Mengxin , Liang Yuting , Wang Xiaoyue , Wen Chongqing , Zhou Jizhong , Yang Yunfeng 
Published: July 2018

SummaryEutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%–12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon‐degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4‐17 folds and recalcitrant carbon‐degrading genes by 23%–40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.
Spatial scaling of forest soil microbial communities across a temperature gradient
Authors: Deng Ye , Ning Daliang , Qin Yujia , Xue Kai , Wu Liyou , He Zhili , Yin Huaqun , Liang Yuting , Buzzard Vanessa , Michaletz Sean T. , Zhou Jizhong 
Published: July 2018

SummaryTemperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa‐area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental‐scale description of temperature‐dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama. Our results revealed that spatial scaling rates (z‐values) of microbial communities varied with both taxonomic resolutions and phylogenetic groups. Additionally, microbial TAR z‐values increased with temperature (r = 0.739, P < 0.05), but were not correlated with other environmental variables tested (P > 0.05), indicating that microbial spatial scaling rate is temperature‐dependent. Understanding how temperature affects the spatial scaling of microbial biodiversity is of fundamental importance for preservation of soil biodiversity and management of ecosystems.
Structure and function of high Arctic pelagic, particle‐associated and benthic bacterial communities
Authors: Balmonte John Paul , Teske Andreas , Arnosti Carol 
Published: July 2018

SummaryArctic marine microbes are affected by environmental changes that may ultimately influence their functions in carbon cycling. Here, we investigated in concert the structure and enzymatic activities of pelagic, particle‐associated and benthic bacterial communities in the central Arctic Ocean, and used these data to evaluate microbial structure–function relationships. Our findings showed influences of hydrographic conditions and particle association on community composition, and sharp pelagic‐benthic contrasts. In addition to community compositional differences, regional and depth‐related patterns in enzymatic activities were observed. Peptide hydrolysis rates were highest in surface waters, especially at ice‐free and first year ice‐covered regions, and decreased with depth. While the range of hydrolysed polysaccharides showed varying geographic patterns, particles often showed a wider spectrum of polysaccharide hydrolase activities. Summed benthic peptidase rates differed across stations but showed similar proportions of individual enzyme activities. Analysing for potential linkages between structure and function after subtracting the effect of environmental conditions revealed no direct link, indicating functional redundancy to carry out peptide hydrolysis among pelagic microbes. Thus, while community composition and activities are influenced by environmental conditions, bacterial functional redundancy suggests that compositional shifts – in response to the changing Arctic – may have complex and less predictable functional consequences than previously anticipated. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd
Exploring plant‐microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR‐Cas9 system
Authors: Yi Yanglei , Li Zhibo , Song Chunxu , Kuipers Oscar P. 
Published: July 2018

Summary
Bacillus subtilis HS3 and Bacillus mycoides EC18 are two rhizosphere‐associated bacteria with plant growth‐promoting activity. The CRISPR‐Cas9 system was implemented to study various aspects of plant‐microbe interaction mechanisms of these two environmental isolates. The results show that fengycin and surfactin are involved in the antifungal activity of B. subtilis HS3. Moreover, this strain emits several other volatile organic compounds than 2,3‐butanediol, contributing to plant growth promotion. Confocal laser scanning microscopy observations of the GFP‐labelled strain showed that HS3 selectively colonizes root hairs of grass (Lolium perenne) in a hydroponic system. For B. mycoides EC18, we found that the wild‐type EC18 strain and a ΔasbA (petropectin‐deficient) mutant, but not the ΔdhbB (bacillibactin‐deficient) and ADKO (asbA and dhbB double knockout) mutants, can increase the plant biomass and total chlorophyll. All the mutant strains have a reduced colonization capability on Chinese cabbage (Brassica rapa) roots, at the root tip and root hair region compared with the wild‐type strain. These results indicate that the siderophore, bacillibactin, is involved in the plant growth promoting activity and could affect the root colonization of B. mycoides. Collectively, the CRISPR‐Cas9 system we developed for environmental isolates is broadly applicable and will facilitate deciphering the mechanisms of Bacillus‐plant interactions. © 2018 The Authors.
Evidence of differential adaptation to decreased temperature by anammox bacteria
Authors: Lin Ximao , Wang Yayi , Ma Xiao , Yan Yuan , Wu Min , Bond Philip L. , Guo Jianhua 
Published: July 2018

SummaryLow temperature is recognized as one of the major barriers for the application of the anaerobic ammonium oxidation (anammox) process to treat mainstream wastewater. Studies are yet to reveal the underlying biological limitations and molecular mechanisms associated with the inhibition of low temperature on the anammox process. In this study, metaproteomics was used to examine proteome modulation patterns of the anammox community occurring at different temperatures. The anammox community remarkably altered their proteomes when the temperature decreased from 35 °C to 20 °C. This was especially for proteins involved in energy conversion, transcription and translation and inorganic ion transport. However, at 15 °C the anammox activities became distinctly inhibited, and there was evidence of energy limitations and severe stress in Candidatus Kuenenia and to a lesser degree in Candidatus Brocadia. Candidatus Jettenia exhibited more changes in its proteome at 15 °C. From the proteomes, at the lower temperatures there was evidence of stress caused by toxic nitrogen compounds or reactive oxygen species in the anammox bacteria. Hydroxylamine oxidoreductase (HAO)‐like proteins and an oxidative stress response protein (a catalase) were in high abundance to potentially ameliorate these inhibitory effects. This study offers metaproteomic insight into the anammox community‐based physiological response to decreasing temperatures.
Community dynamics and functional characteristics of naphthalene‐degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater
Authors: Wilhelm Roland C. , Hanson Buck T. , Chandra Subhash , Madsen Eugene 
Published: July 2018

SummaryEarlier research on the biogeochemical factors affecting natural attenuation in coal‐tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field‐based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single‐cell imaging and shotgun metagenomics now provide cultivation‐independent tools for their study. We tracked carbon from 13C‐labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant‐based trophic web. Contaminant‐exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome‐assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
Metagenome analysis of Russian and Georgian Pyophage cocktails and a placebo‐controlled safety trial of single phage versus phage cocktail in healthy Staphylococcus aureus carriers
Authors: McCallin Shawna , Sarker Shafiqul A. , Sultana Shamima , Oechslin Frank , Brüssow Harald 
Published: July 2018

SummaryBacteriophage therapy is a commonly used treatment for Staphylococcus aureus infections in countries of the former Soviet Union, using both single phages and phage cocktails. The scarce data available on Eastern phage cocktails prompted an investigation into commercially‐available Pyophage cocktails from two different manufacturers used to treat skin and wound infections. Comparison of the metagenomic composition of two Pyophage products from Georgia and Russia revealed substantial differences in phage‐types targeting Escherichia, Enterococcus, Salmonella, Pseudomonas aeruginosa and Proteus, therefore indicating multiple strategies for composing phage cocktails against these bacterial pathogens. Closely‐related Kayvirus‐like Myoviruses were, however, a shared component against S. aureus within all products, except for the inclusion of a secondary S. aureus Podovirus in one Microgen cocktail. Metagenomic analysis also revealed the presence of several probable prophage sequences but detected no genetic safety risks in terms of virulence factors or antibiotic resistance genes. The safety of broad‐spectrum cocktails was tested by comparing the effects of nasal and oral exposure to Eliava Pyophage, a monospecies counterpart and placebo in healthy human carriers of S. aureus. The lack of adverse effects in any treatment groups supports the clinical safety of S. aureus phages administered as a single phage or as phage cocktail.
Temporal and spatial dynamics in microbial community composition within a temperate stream network
Authors: Hassell Norman , Tinker Kara A. , Moore Thomas , Ottesen Elizabeth A. 
Published: July 2018

SummaryThe water column of streams hosts a unique microbial community that is distinct from the microbial communities of the stream benthos and surrounding soil. This community is shaped by complex interacting forces, including microbial dispersal from surrounding environments and in‐stream selection. However, how the processes structuring stream communities change over space and time remains poorly understood. In this study, we characterize spatial and temporal trends in microbial community composition throughout a stream network spanning first through fifth order streams. We found that the microbial communities of headwater streams are compositionally diverse, with low representation of freshwater microbial taxa and high representation of soil and sediment‐associated taxa. In three out of five seasonal samplings, a successional pattern was identified in which phylotype richness and compositional heterogeneity decreased while the proportion of known freshwater taxa increased with increasing cumulative upstream dendritic distance. However, in two samplings, streams instead exhibited uniformly high microbial diversity across the watershed, and the fraction of freshwater taxa showed no relationship with dendritic distance. Overall, our data suggest that the successional processes that drive microbial diversity in streams are highly dynamic and can be disrupted at landscape scales, potentially in response to variation in temperature and precipitation.
The Inhibition of Advanced Glycation End Products by Carnosine and Other Natural Dipeptides to Reduce Diabetic and Age‐Related Complications
Authors: Freund Michael A. , Chen Bingcan , Decker Eric A. 
Published: July 2018

AbstractAs people age they are at a greater risk for many disorders including cardiovascular, renal, and neurodegenerative diseases, and these conditions are exacerbated by diabetes. An important cause of the maladies associated with both age and diabetes is the formation of advanced glycation end products (AGEs). AGE formation is initiated by glycation reactions between reducing sugars and free amine groups. A cascade of other reactions follows, leading to alterations in membrane function and damage to the proteome, such as protein crosslinking. Compounds that prevent these reactions are currently being researched, but peptides hold great potential as they tend to lack toxicity, are absorbed intact, are easily produced, and are cheaper than other options. Of the peptides researched, carnosine is the most promising. Research suggests that carnosine is absorbed into the plasma unaltered and intact. Carnosine has been shown to prevent AGE formations through reduction of blood glucose, prevention of early glycation, and even reversing previously formed AGEs. Other promising peptides and amino acids include β‐alanine, L‐histidine, homocarnosine, anserine, and glutathione. If bioactive peptides and amino acids can minimize the formation of AGEs, foods containing these peptides could be used to improve health.
Increased transport of acetyl‐CoA into the endoplasmic reticulum causes a progeria‐like phenotype
Authors: Peng Yajing , Shapiro Samantha L. , Banduseela Varuna C. , Dieterich Inca A. , Hewitt Kyle J. , Bresnick Emery H. , Kong Guangyao , Zhang Jing , Schueler Kathryn L. , Keller Mark P. , Attie Alan D. , Hacker Timothy A. , Sullivan Ruth , Kielar‐Grevstad Elle , Arriola Apelo Sebastian I. , Lamming Dudley W. , Anderson Rozalyn M. , Puglielli Luigi 
Published: July 2018

AbstractThe membrane transporter AT‐1/SLC33A1 translocates cytosolic acetyl‐CoA into the lumen of the endoplasmic reticulum (ER), participating in quality control mechanisms within the secretory pathway. Mutations and duplication events in AT‐1/SLC33A1 are highly pleiotropic and have been linked to diseases such as spastic paraplegia, developmental delay, autism spectrum disorder, intellectual disability, propensity to seizures, and dysmorphism. Despite these known associations, the biology of this key transporter is only beginning to be uncovered. Here, we show that systemic overexpression of AT‐1 in the mouse leads to a segmental form of progeria with dysmorphism and metabolic alterations. The phenotype includes delayed growth, short lifespan, alopecia, skin lesions, rectal prolapse, osteoporosis, cardiomegaly, muscle atrophy, reduced fertility, and anemia. In terms of homeostasis, the AT‐1 overexpressing mouse displays hypocholesterolemia, altered glycemia, and increased indices of systemic inflammation. Mechanistically, the phenotype is caused by a block in Atg9a‐Fam134b‐LC3β and Atg9a‐Sec62‐LC3β interactions, and defective reticulophagy, the autophagic recycling of the ER. Inhibition of ATase1/ATase2 acetyltransferase enzymes downstream of AT‐1 restores reticulophagy and rescues the phenotype of the animals. These data suggest that inappropriately elevated acetyl‐CoA flux into the ER directly induces defects in autophagy and recycling of subcellular structures and that this diversion of acetyl‐CoA from cytosol to ER is causal in the progeria phenotype. Collectively, these data establish the cytosol‐to‐ER flux of acetyl‐CoA as a novel event that dictates the pace of aging phenotypes and identify intracellular acetyl‐CoA‐dependent homeostatic mechanisms linked to metabolism and inflammation.
Leukocyte telomere length in the Thoroughbred racehorse
Authors: Denham J. , Denham M. M. 
Published: July 2018

SummaryThoroughbred racehorses possess superior cardiorespiratory fitness levels and are at the pinnacle of athletic performance compared to other breeds of horses. Although equine athletes have undergone years of artificial selection for racing performance, musculoskeletal injuries and illnesses are common and concerns relating to animal welfare have been proposed. Leukocyte telomere length is indicative of biological age, and accelerated telomere shortening occurs with excess physical and psychological stress. This study was designed to explore the association between leukocyte telomere length, biological factors (age, sex and coat colour), training status, winnings and race history parameters. Blood was collected from 146 Thoroughbred racehorses from around Geelong, Victoria, Australia. DNA was extracted from leukocytes; telomere length was measured using qPCR and analysed in context with traits obtained from the Racing Australia website. Age was inversely correlated with telomere length (r = −0.194, P = 0.019). The oldest horses (≥11 years) in the highest age quartile possessed shorter telomeres compared to younger horses in the first, second and third quartiles (≤2, 3–5 and 6–10 years respectively; P < 0.05). No statistically significant associations were observed between telomere length and biological factors, training status, winnings or race history parameters in age‐adjusted analyses. The study findings suggest that Thoroughbred horses may undergo age‐related telomere shortening similar to other mixed breeds and humans. Despite concerns from some quarters regarding the welfare of racehorses, there was a lack of accelerated biological ageing observed in the present study, as indicated by leukocyte telomere length.
Seroprevalence of antibodies to Pestivirus infections in South Australian sheep flocks
Authors: Evans CA , Lanyon SR , O’Handley RM , Reichel MP , Cockcroft PD 
Published: July 2018

ObjectiveBovine viral diarrhoea virus (BVDV) and border disease virus (BDV) are of the genus Pestivirus. They are known to cause significant reproductive and production losses, with BVDV acknowledged as a major source of economic loss to the Australian cattle industry. Very little is currently known about the prevalence and effect of pestiviruses in the Australian sheep industry. The present study aimed to examine the seroprevalence and effect of both BVDV and BDV in South Australian sheep flocks.MethodsIn total, 875 breeding ewes on 29 properties were serologically tested by ELISA, AGID and VNT assays for the presence of Pestivirus‐specific antibodies.ResultsThree (0.34%) individual animals returned serological results suggestive of previous BDV infection. All three positive animals were collected from one property, giving a property level seroprevalence of 3.45% and a within‐flock seroprevalence of 10%.ConclusionThe results suggested that BDV infection is present, albeit at a very low incidence, in the South Australian sheep flock and BVDV infection appears to be absent. Consequently, pestiviruses are unlikely to impair production in South Australian sheep populations.