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opencc-zeroOct 2020View details →

Large mammalian herbivores contribute to conspecific negative density dependence in a temperate forest

1. The Janzen-Connell Hypothesis (JCH) predicts that density-responsive and host-specific natural enemies limit the population sizes of abundant species. Importantly, these interactions help to maintain local community diversity through time. While ample evidence exists for the demographic predictions of the JCH, it remains unclear which natural enemies drive these dynamics across different plant communities. 2. While large mammalian herbivores are often assumed to lack the specialized diet needed to drive Janzen-Connell effects, they do show a degree of host-preference that could drive density-dependent plant demography. However, the potential role of large mammalian herbivores in Janzen-Connell interactions has only rarely been investigated. 3. Using 204 seedling transects (1 x 10 m) at 51 sites across a 900-hectare forested reserve in southwestern Pennsylvania (USA), we examined the role that large mammals play in driving conspecific negative density dependence (CNDD) in temperate tree seedlings. Individual fences were erected around half of the transects (N=102) to exclude large mammals, and were paired with adjacent unfenced transects. Within transects, a total of ~15,000 individual seedlings were monitored over three growing seasons. 4. Demographic neighborhood models were constructed to examine the influence of neighborhood composition and density on seedling survival and growth. An interaction term between conspecific neighbor density and fencing treatment was included to test the hypothesis that large herbivores cause CNDD. 5. We found that seedling survival was influenced by both conspecific neighbor density and fencing. CNDD was strongest when large mammals were allowed access to seedlings, and these results were driven by two abundant taxa (Prunus serotina and Fraxinus spp). Despite evidence that large mammals mediate CNDD, we found no effect of fencing on rarified species richness or evenness in seedling transects during the study. 6. Synthesis: Debate regarding the role of large herbivores in fostering the diversity and stability of forest communities continues. Our results indicate that large mammalian herbivores can cause CNDD in some temperate tree species, but whether they help to promote community diversity over time remains unclear. Further research is needed to assess the role of large mammalian herbivores in driving conspecific negative density dependence in plant communities.

opencc-zeroOct 2020View details →

Scale-dependent drivers of the phylogenetic structure and similarity of tree communities in northwestern Amazonia

1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. 2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic relatedness and low phylogenetic turnover. ii) Geographical barriers triggered dispersal limitation, causing high local and subregional phylogenetic clustering and high regional phylogenetic turnover. iii) Edaphic properties and flooding were negatively associated to stem size and determined the tree phylogenetic structure and turnover at local and regional scales in Amazon forests. 3. We found that the extent to which environmental or evolutionary features shaped the phylogenetic structure and phylogenetic similarity of tree communities in NW Amazonia was scale dependent. Specifically, we show that the relative importance of environmental factors increases as spatial scale and species pool decreases. Further, we find that these results are generally robust for both adult and juvenile trees. Synthesis: Our analysis at the regional (NW Amazon) scale lends support to the idea of Amazonian forests as a large metacommunity primarily structured by historical dispersal at large spatial scales with an increasing importance of environmental factors at finer spatial scales. The convergence of ancestral lineages across habitat types may have been due to the relatively recent formation of geographical barriers that promoted local isolation and allopatric speciation.

Ecosystem recovery from disturbance depends on nutrient supply rate

Human disturbances alter the functioning and biodiversity of many ecosystems. These ecosystems may return to their pre-disturbance state after disturbance ceases, however humans have altered the environment in ways that may change the rate or direction of this recovery. For example, human activities have increased supplies of biologically-limiting nutrients, such as nitrogen (N) and phosphorus (P), which can reduce grassland diversity and increase productivity. We tracked the recovery of a grassland for two decades following an intensive agricultural disturbance under ambient and elevated nutrient conditions. Productivity returned to predisturbance levels quickly under ambient nutrient conditions, but nutrient addition slowed this recovery. In contrast, the effects of disturbance on diversity remained hidden for 15 years, at which point diversity began to increase in unfertilized plots. This work demonstrates that enrichment of terrestrial ecosystems by humans may alter the recovery of ecosystems and that disturbance effects may remain hidden for many years.

The U-shaped pattern of size-dependent mortality and its driving factors in a subtropical monsoon evergreen forest

1. Tree mortality is an important ecological process influencing multiple functions of forest ecosystems. Previous studies have shown two basic size-mortality patterns, including a competition-driven declining and a disturbance-driven increasing mortality rate with tree size. Subtropical forests, which have a high species diversity and subject to frequent monsoon disturbances, are widely distributed in eastern Asia. However, the tree size-mortality pattern in the mature subtropical forests remains unclear. 2. Here we analyzed patterns of size-dependent mortality from tree species to forest community using a 5-year inventory data from 117 species and 163,612 individuals in a 20-ha forest dynamic plot in a mature subtropical monsoon evergreen forest in eastern China. To explain the spatial variability in mortality patterns, two major biotic drivers (competition and tree size) and multiple local-scale environmental factors were further analyzed. 3. Our results showed that tree size was the best predictor of tree mortality at the scales of both species and community. A species-level analysis identified four size-mortality patterns that are shaped by species-specific attributes such as maximum size and life form. For 27 out of 92 species that comprised 59% of tree individuals, the relationship between size and mortality exhibited a U-shaped pattern of a first decline followed by an increase. An overall community-scale size-dependent mortality also showed a U-shaped pattern. 4. Tree mortality was also influenced by the competition and environmental conditions, but the relative importance varied widely across tree sizes and species. The competition showed significant correlations with the mortality of small trees, while the effect of environmental conditions on mortality was strongest for large trees. A principal component analysis showed that a combination of biotic and abiotic factors explained 42.3% of the spatial variation in mortality at large sizes. Synthesis. Our results reveal four identifiable size-dependent mortality patterns that differ across diverse species, jointly leading to a U-shaped mortality size pattern at the community level. This finding calls for the need to establish the details of every potential size-mortality pattern with consideration of the different effects of biotic and abiotic factors on tree mortality of specific size.

Context-dependent variability in the population prevalence and individual fitness effects of plant-fungal symbiosis

1. Heritable symbionts, found within a diverse array of flora and fauna, are often observed at intermediate prevalence within host populations, despite expectations that positive fitness feedbacks should drive beneficial symbionts to fixation. Intermediate prevalence may reflect neutral dynamics of symbionts with weak fitness effects, transient dynamics of symbionts trending toward fixation (or elimination), or a stable intermediate outcome determined by the balance of fitness effects and failed symbiont transmission. Theory suggests these outcomes should depend on symbiont-conferred effects and vertical transmission efficiency, which may both depend on environmental context. 2. We tested these alternatives by tracking temporal change in population-level symbiont prevalence in a three-year field experiment with grasses and vertically transmitted fungal endophytes under the context of manipulated precipitation. Precipitation can mediate endophyte effects on host grasses, and is a relevant context, as global climate models predict changes in precipitation amount and seasonal distribution. 3. We found evidence for each of the three proposed mechanisms for intermediate symbiont prevalence, but the outcome differed qualitatively across years and precipitation treatments. Specifically, within the first study year, all populations under ambient precipitation trended toward symbiont fixation, whereas elevated precipitation literally neutralized the interaction resulting in no long-run equilibrium. The second study year yielded a different result with long-run equilibria at an intermediate prevalence for both ambient and elevated precipitation treatments. We linked these population-level outcomes with individual-level symbiont effects on grasses and showed that the benefits of symbiosis were concentrated at the seedling stage, especially under drought stress during the time period coinciding with recruitment. The drought stress evident during the first year of the study was not present in the second year due to greater ambient precipitation during this time period. Together, these findings provide the first experimental evidence that population-level outcomes of host-symbiont interactions, which arise from the composite outcome of demographic vital rates and transmission, can be dynamically stable and can fluctuate in response to shifts in spatio-temporal context. 4. Synthesis: Overall, these results indicate that intermediate prevalence of heritable microbial symbionts likely reflects a combination of neutral, transient, and stable mechanisms, and context-dependent fluctuations among them.

opencc-by-4.0May 2020View details →

the supplemental data of 'The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes'

This data set is the supplemental data of the manuscript ‘The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes’. Due to the size limitation of online storage, this data set contains partial data collected in this work, which consists of one experiment per condition. The full data that support the findings of this study are available from the corresponding author upon reasonable request.

Tree mycorrhizal type mediates the strength of negative density dependence in temperate forests

1. Recent plant-soil feedback experiments suggest that arbuscular mycorrhizal (AM) tree species experience stronger conspecific negative density dependence (CNDD) than ectomycorrhizal (EM) tree species. Yet how these findings inform our understanding of natural systems is limited because the roles of local soil conditions, light environments and tree species abundances in influencing CNDD for AM and EM species are not clear. 2. Here we examined seedling and sapling survival in two temperate old-growth forests (broadleaved pine and spruce-fir forests) in Northeast China, to evaluate the effects of both conspecific and heterospecific neighbour density, as well as the soil and light environments, on the survival of AM and EM-dependent trees at early life stages. 3. While light availability increased the survival of EM seedlings, soil organic resources increased EM sapling survival in the spruce-fir plot. AM seedlings suffered stronger CNDD than did EM seedlings in both plots. In the spruce-fir plot, soil factors and light availability mediated species CNDD but their effects differed for AM and EM species, and also between seedlings and saplings. For seedlings in both plots, we found that AM species exhibited a positive relationship between species abundance and CNDD strength, whereas this relationship was negative for EM species. 4. Synthesis. Our results provide one of the few tests of how fungal symbioses determine species responses to intra- and interspecific interactions and the direct effects of local environmental conditions on seedling and sapling survival. We show that mycorrhizal type mediates the strength of CNDD and its relationship with species abundance. These results suggest that tree mycorrhizal association can determine the strength of CNDD effects on both rare and common species, and these CNDD differences are likely to influence the community composition of temperate forests.

opencc-by-4.0Nov 2020View details →

The Age-dependent Changes of the Human Adrenal Cortical Zones Are Not Congruent SUPPLEMENTAL DATA

Supplemental tables 1 and 2.

opencc-by-4.0Nov 2020View details →

Data and Scripts for "Real-Time Time-Dependent Density Functional Theory Implementation of Electronic Circular Dichroism Applied to Nanoscale Metal-Organic Clusters"

The xyz files were used for the ECD calculation in the paper :https://arxiv.org/abs/2007.08560 gsrun.py: ground-state calculation td_calc.py: time -propagation for ECD cdspecX.py: get rotatory strength for plotting

opencc-by-4.0Dec 2020View details →

Identification of distinct pH-and zeaxanthin-dependent quenching in LHCSR3 from C. reinhardtii - single-molecule photon stream

Photon stream used in the article "Identification of distinct pH-and zeaxanthin-dependent quenching in LHCSR3 from Chlamydomonas reinhardtii" to analyze single-molecule fluorescence emission. Detected emission of WT LHCSR3 and stop-LHCSR3 at pH 7.5 and pH 5 along with associated instrument response function (IRF) and measurements of background fluorescence (BG). Each detected photon is described by its time within the collected photon stream and its time relative to the excitation laser.

The sodium/proton exchanger NHA2 regulates blood pressure through a WNK4-NCC dependent pathway in the kidney

NHA2 is sodium/hydrogen exchanger that was associated with arterial hypertension in humans, but the role of NHA2 in kidney function and blood pressure homeostasis is currently unknown. Here we show that NHA2 localizes almost exclusively to distal convoluted tubules in the kidney. NHA2 knock-out mice displayed reduced blood pressure, normocalcemic hypocalciuria and an attenuated response to the thiazide diuretic hydrochlorothiazide. Phosphorylation of the thiazide-sensitive sodium/chloride cotransporter NCC and its upstream activating kinase Ste20/SPS1-related proline/alaninerich kinase (SPAK), as well as the abundance of with no lysine [K] kinase 4 (WNK4), were significantly reduced in kidneys of NHA2 knock-out mice. In vitro experiments recapitulated these findings and revealed increased WNK4 ubiquitylation and enhanced proteasomal WNK4 degradation upon loss of NHA2. The effect of NHA2 on WNK4 stability was Kelch-like 3 (KLHL3)-dependent. More specifically, loss of NHA2 selectively attenuated KLHL3 phosphorylation and the physiologically important PKAand PKC-mediated decrease of WNK4 degradation was blunted upon loss of NHA2. Phenotype analysis of NHA2/NCC double knock-out mice supported the notion that NHA2 affects blood pressure homeostasis by an intrarenal and NCC-dependent mechanism. In summary, our data reveal NHA2 as a critical component of the WNK4-NCC pathway and hence as a novel regulator of blood pressure homeostasis in the kidney.

Datasets used for the publication: State-dependence explains individual variation in nest defence behaviour in a long-lived bird

The uploaded datasets were used to test if variation in states predicts nest defence behaviour (a 'risky' behaviour) in a long-lived species, the barnacle goose (Branta leucopsis). Repeated measures of nest defence towards a human intruder (flight initiation distance or FID) of females of known age were collected during 15 breeding seasons. Increasing values of FID represent increasing shyness. Adaptive models have predicted that an individual's residual reproductive value or 'asset' is an important state variable underlying variation in such risk-taking behaviour. Hence, we used this data to investigate how nest defence varies as a function of time of the season and individual age, two state variables that can vary between and within individuals and determine asset.

Data from: Abiotic and biotic context dependency of perennial crop yield

Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass—Thinopyrum intermedium-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (Silphium intregrifolium), and alfalfa (Medicago sativa). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both Silphium and alfalfa strongly benefit from AM fungi. The presence of native prairie AM fungi had a greater benefit to Silphium in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of Silphium and alfalfa. This study identifies importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.

opencc-zeroDec 2019View details →

Plant community assembly in suburban vacant lots depends on earthmoving legacy, habitat connectivity, and current mowing frequency

In suburban regions, vacant lots potentially offer significant opportunities for biodiversity conservation. Recently, in Japan, due to an economic recession, some previously developed lands have become vacant. Little is known, however, about the legacy of earlier earthmoving, which involves topsoil removal and ground levelling before residential construction, on plant community composition in such vacant lots. To understand (dis)assembly processes in vacant lots, we studied 24 grasslands in a suburban region in Japan: 12 grasslands that had experienced earthmoving and 12 that had not. We surveyed plant community composition and species richness, and clarified compositional turnover (replacement of species) and nestedness (non-random species loss) by distance-based β-diversities, which were summarized by PCoA analysis. We used piecewise structural equation modeling to examine the effects of soil properties, mowing frequency, past and present habitat connectivities on compositional changes. As a result, past earthmoving, mowing frequency, soil properties, and past habitat connectivity were found to be the drivers of compositional turnover. In particular, we found legacy effects of earthmoving: earthmoving promoted turnover from native grassland species to weeds in arable lands or roadside by altering soil properties. Mowing frequency also promoted the same turnover, implying that extensive rather than intensive mowing can modify the negative legacy effects and maintain grassland species. Decrease in present habitat connectivity marginally enhanced non-random loss of native grassland species (nestedness). Present habitat connectivity had a positive effect on species richness, highlighting the important roles of contemporary dispersal. Our study demonstrates that community assembly is a result of multiple processes differing in spatial and temporal scales. We suggest that extensive mowing at local scale, as well as giving a high conservation priority to grasslands with high habitat connectivity at regional scale, are the promising actions to maintain endangered native grassland species in suburban landscapes with negative legacy effects of earthmoving.

Data from: Functional diversity of phyllostomid bats in an urban-rural landscape: a scale-dependent analysis

Urbanization is one of the most pervasive landscape transformational processes responsible for novel selection agents promoting functional community homogenization. Bats may persist in those human environments, but the mechanisms responsible for their adaptability and the spatial scales in which landscape imposes environmental filtering remain poorly studied in the Neotropics. We tested the hypothesis that landscape composition interacts with the spatial scale to affect the functional diversity of phyllostomids in an urban-rural gradient. Based on functional traits, we calculated indices of functional richness, divergence, evenness, community-weighted means of morphological traits, and classified species into functional groups. We evaluated the changes of those variables in response to forest, grassland, and urbanized areas at 0.5, 1.25 and, 2 km scales. The number of functional groups, functional richness, and functional evenness tended to be higher in areas far from cities and with higher forest cover, whereas functional divergence increased in more urbanized areas. Our results show that the mean value of wing loading in the assemblage was negatively associated to landscape transformation at several spatial scales. However, environmental filtering driven by grass cover was particularly robust at the 500 m scale, affecting big-sized species with long pointed wings. Retaining natural forest in cattle ranging systems at ~12 km2 appears to favor bat abundance evenness among functional types in the urban-rural landscape. Recognizing the scale of the effect on phyllostomid functional responses appears to be a fundamental issue for elucidating the spatial extent to which phyllostomid conservation planning in urban-rural landscapes should be addressed.

opencc-zeroDec 2019View details →

Fungal root-endophytes influence plants in a species-specific manner that depends on plant's growth stage

The mycobiome (fungal microbiome) influences plants— from seed germination to full maturation. While many studies on fungal-plant interaction studies have focused on known mutualistic and pathogenic fungi, the functional role of ubiquitous endophytic fungi remains little explored. We examined how root-inhabiting fungi (endophytes) influence range expanding plant species. We isolated endophytes from three European intra-continental range-expanders and three congenerics that are native both in the range-expander's original (southern Europe) and new (northern Europe) range. To standardize our collection, endophytes were obtained from all six plant species growing under controlled conditions in northern (new range of the range-expander) and southern (native range of the range-expander) soils. We cultivated, molecularly identified and tested the effects of all isolates on seed germination, and growth of seedlings and older plants. Most of the 34 isolates could not be functionally characterized based on their taxonomic identity and literature information on functions. Endophytes affected plant growth in a plant species-endophyte specific manner, but overall differed between range-expanders and natives. While endophytes reduced germination and growth of range-expanders compared to natives, they reduced seedling growth of natives more than of range-expanders. Synthesis: We conclude that endophytic fungi have a direct effect on plant growth in a plant growth stage-dependent manner. While these effects differed between range expanders and natives, the effect strength and significance varied among the plant genera included in the present study. Nevertheless, endophytes likely influence establishment of newly arriving plants and influence vegetation dynamics

Ligand-dependent effects of methionine-8 oxidation in parathyroid hormone peptide analogs

LA-PTH is a long-acting parathyroid hormone (PTH) peptide analog in pre-clinical development for hypoparathyroidism (HP). Like native PTH, LA-PTH contains a methionine at position 8 that is predicted to be critical for function. We assessed the impact of methionine oxidation on the functional properties of LA-PTH and control PTH ligands. Oxidation of PTH(1-34) resulted in marked (~20-fold) reductions in binding affinity on the PTH receptor-1 (PTHR1) in cell membranes, similarly diminished potency for cAMP signaling in osteoblastic cell lines (SaOS-2 and UMR106), and impaired efficacy for raising blood calcium in mice. Surprisingly, oxidation of LA-PTH resulted in little or no change in these functional responses. The signaling potency of oxidized-LA-PTH was, however, reduced ~40-fold compared to LA-PTH in cells expressing a PTHR1 construct that lacks the N-terminal extracellular domain (ECD). Molecular modeling revealed that while Met8 of both LA-PTH and PTH(1-34) is situated within the orthosteric ligand-binding pocket of the receptor's transmembrane domain bundle (TMD), the Met8 sidechain position is shifted for the two ligands such that upon Met8 oxidation of PTH(1-34) steric clashes occur that are not seen with oxidized LA-PTH. The findings suggest that LA-PTH and PTH(1-34) engage the receptor differently in the Met8-interaction environment of the TMD bundle, and that this interaction environment can be allosterically influenced by the ECD component of the ligand-receptor complex. The findings should be useful for the future development of novel PTH-based peptide therapeutics for diseases of bone and mineral ion metabolism.

opencc-by-4.0Jan 2021View details →

An Extended Viscoacoustic Wave Equation for Frequency-dependent Wavefields Modeling in Viscoacoustic Media

An excel file containing the velocity of three viscoacoustic media (velocity.xlsx); A mat file containing the wavefields of viscoacoustic media (model_viscoacoustic.mat); A mat file containing the wavefields of acoustic media (model_acoustic.mat); A mat file containing the wavefields of viscoacoustic media with changed dispersion parameters  (model_diffusion.mat); A mat file containing the wavefields of viscoacoustic media with changed viscous parameters  (model_viscous.mat);

opencc-zeroJan 2021View details →

Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure

Physiological states can determine the ability of organisms to handle stress. Does this mean that the same selection pressure will lead to different evolutionary outcomes, depending on the organisms' physiological state? If yes, what will be the genomic signatures of such adaptation(s)? We used experimental evolution in Escherichia coli followed by whole-genome whole-population sequencing to investigate these questions. The sensitivity of Escherichia coli to ultraviolet (UV) radiation depends on the growth phase during which it experiences the radiation. We evolved replicate E. coli populations under two different conditions of UV exposures, namely exposure during the lag and the exponential growth phases. Initially, the UV sensitivity of the ancestor was greater during the exponential phase than the lag phase. However, at the end of 100 cycles of exposure, UV resistance evolved to similar extents in both treatments. Genome analysis showed that mutations in genes involved in DNA repair, cell membrane structure and RNA polymerase were common in both treatments. However, different functional groups were found mutated in populations experiencing lag and exponential UV treatment. In the former, genes involved in transcriptional and translational regulations and cellular transport were mutated, whereas the latter treatment showed mutations in genes involved in signal transduction and cell adhesion. Interestingly, the treatments showed no phenotypic differences in a number of novel environments. Taken together, these results suggest that selection pressures at different physiological stages can lead to differences in the genomic signatures of adaptation, which need not necessarily translate into observable phenotypic differences.