Water-Limiting Conditions Alter the Structure and Biofilm-Forming Ability of Bacterial Multispecies Communities in the Alfalfa Rhizosphere

Biofilms are microbial communities that adhere to biotic or abiotic surfaces and are enclosed in a protective matrix of extracellular compounds. An important advantage of the biofilm lifestyle for soil bacteria (rhizobacteria) is protection against water deprivation (desiccation or osmotic effect). The rhizosphere is a crucial microhabitat for ecological, interactive, and agricultural production processes. The composition and functions of bacterial biofilms in soil microniches are poorly understood. We studied multibacterial communities established as biofilm-like structures in the rhizosphere of Medicago sativa (alfalfa) exposed to 3 experimental conditions of water limitation. The whole biofilm-forming ability (WBFA) for rhizospheric communities exposed to desiccation was higher than that of communities exposed to saline or nonstressful conditions. A culture-dependent ribotyping analysis indicated that communities exposed to desiccation or saline conditions were more diverse than those under the nonstressful condition. 16S rRNA gene sequencing of selected strains showed that the rhizospheric communities consisted primarily of members of the Actinobacteria and α- and γ-Proteobacteria, regardless of the water-limiting condition. Our findings contribute to improved understanding of the effects of environmental stress factors on plant-bacteria interaction processes and have potential application to agricultural management practices.     

Patterns and Ecological Correlates of Pollination Modes Among Bromeliad Communities of Andean Forests in Bolivia

Abstract: We studied the distribution of five pollination modes (ornithophily, chiropterophily, entomophily, mixed/unspecific, autogamy) among the bromeliad communities of 74 forest sites in the Bolivian Andes and adjacent lowlands. We recorded a total of 188 bromeliad species belonging to 16 genera, including 115 (61 %) ornithophilous, 14 (7 %) chiropterophilous, 45 (24 %) entomophilous, 8 (4 %) autogamous, and 6 (3 %) species with mixed pollination mode. Ornithophily was the dominant pollination mode at high elevations and in wet regions, while entomophily dominated in arid regions. Chiropterophily was most common in wet lowland regions, autogamy in arid sites, and mixed pollination in the lowlands. Pollination modes were rather evenly distributed among life-forms and ecophysiological types, with a few exceptions: terrestrial forest bromeliads, mostly belonging to unarmed, soft-leaved taxa, had a prevalence of entomophily and few ornithophilous species; large, spiny terrestrial bromeliads of Puya and Bromelioideae showed a prevalence of ornithophily; and autogamy was restricted to the neotenous subgenus Diaphoranthema of Tillandsia. The restriction of unspecific pollination modes to the lowlands is hypothesized to be related to the abundance of pollinators, eliminating the need for specialized co-evolution, or to the overall rarity of bromeliads in this environment, precluding the development of specialized relationships. The low representation of entomophilous species in small dry forest regions compared to extensive areas is assumed to be due to the seasonal influx of hummingbirds and/or bats. Overall, the frequency of individual pollination modes was related to the availability of pollinators as determined by temperatures and humidity.     

The Stability of Invertebrate Communities in Bromeliad Phytotelmata in a Rain Forest Subject to Hurricanes

Communities of invertebrate animals in lower canopy and saxicolous tank bromeliads, originally studied in 1993–1997, were resampled along an elevational gradient in tabonuco, palo colorado, and dwarf or cloud forest in Puerto Rico in 2010. These Puerto Rican montane rain forests were impacted strongly by hurricanes in 1989 and 1998, so the surveys in the 1990s represented 4–8 yr of post‐hurricane recovery, whereas our recent survey represents 12 yr of post‐hurricane recovery. At most elevations, species diversity, both within individual bromeliads and at the forest scale, declined between the 1990s and 2010. This decline in diversity between decades is associated with reductions in bromeliad density as the canopy progressively closed during recovery from hurricane damage. The observed decline in alpha and gamma diversity appears to have involved the loss of rarer species, as might be expected from standard metapopulation theory. By contrast, the most common species were remarkably stable in abundance, composition, and frequency of occurrence over the two decades. In the lowermost tabonuco forest, two endemic bromeliad specialists, restricted to bromeliads for their entire life cycle, were not found on resampling. This study also demonstrates that, at least in Puerto Rico, sets of ten plants from each forest were sufficient to monitor bromeliad invertebrate populations and their diversity over time.     

Transpinal and Transcortical Stimulation Alter Corticospinal Excitability and Increase Spinal Output

The objective of this study was to assess changes in corticospinal excitability and spinal output following noninvasive transpinal and transcortical stimulation in humans. The size of the motor evoked potentials (MEPs), induced by transcranial magnetic stimulation (TMS) and recorded from the right plantar flexor and extensor muscles, was assessed following transcutaneous electric stimulation of the spine (tsESS) over the thoracolumbar region at conditioning-test (C-T) intervals that ranged from negative 50 to positive 50 ms. The size of the transpinal evoked potentials (TEPs), induced by tsESS and recorded from the right and left plantar flexor and extensor muscles, was assessed following TMS over the left primary motor cortex at 0.7 and at 1.1× MEP resting threshold at C-T intervals that ranged from negative 50 to positive 50 ms. The recruitment curves of MEPs and TEPs had a similar shape, and statistically significant differences between the sigmoid function parameters of MEPs and TEPs were not found. Anodal tsESS resulted in early MEP depression followed by long-latency MEP facilitation of both ankle plantar flexors and extensors. TEPs of ankle plantar flexors and extensors were increased regardless TMS intensity level. Subthreshold and suprathreshold TMS induced short-latency TEP facilitation that was larger in the TEPs ipsilateral to TMS. Noninvasive transpinal stimulation affected ipsilateral and contralateral actions of corticospinal neurons, while corticocortical and corticospinal descending volleys increased TEPs in both limbs. Transpinal and transcortical stimulation is a noninvasive neuromodulation method that alters corticospinal excitability and increases motor output of multiple spinal segments in humans.     

F-Actin Binding Regions on the Androgen Receptor and Huntingtin Increase Aggregation and Alter Aggregate Characteristics

Protein aggregation is associated with neurodegeneration. Polyglutamine expansion diseases such as spinobulbar muscular atrophy and Huntington disease feature proteins that are destabilized by an expanded polyglutamine tract in their N-termini. It has previously been reported that intracellular aggregation of these target proteins, the androgen receptor (AR) and huntingtin (Htt), is modulated by actin-regulatory pathways. Sequences that flank the polyglutamine tract of AR and Htt might influence protein aggregation and toxicity through protein-protein interactions, but this has not been studied in detail. Here we have evaluated an N-terminal 127 amino acid fragment of AR and Htt exon 1. The first 50 amino acids of ARN127 and the first 14 amino acids of Htt exon 1 mediate binding to filamentous actin in vitro. Deletion of these actin-binding regions renders the polyglutamine-expanded forms of ARN127 and Htt exon 1 less aggregation-prone, and increases the SDS-solubility of aggregates that do form. These regions thus appear to alter the aggregation frequency and type of polyglutamine-induced aggregation. These findings highlight the importance of flanking sequences in determining the propensity of unstable proteins to misfold.     

Stochasticity and bistability in insect outbreak dynamics

Theoretical Ecology - There is a long history in ecology of using mathematical models to identify deterministic processes that may lead to dramatic population dynamic patterns like boom-and-bust...     

Structure Versus Stochasticity—The Role of Molecular Crowding and Intrinsic Disorder in Membrane Fission

Cellular membranes must undergo remodeling to facilitate critical functions including membrane trafficking, organelle biogenesis, and cell division. An essential step in membrane remodeling is membrane fission, in which an initially continuous membrane surface is divided into multiple, separate compartments. The established view has been that membrane fission requires proteins with conserved structural features such as helical scaffolds, hydrophobic insertions, and polymerized assemblies. In this review, we discuss these structure-based fission mechanisms and highlight recent findings from several groups that support an alternative, structure-independent mechanism of membrane fission. This mechanism relies on lateral collisions among crowded, membrane-bound proteins to generate sufficient steric pressure to drive membrane vesiculation. As a stochastic process, this mechanism contrasts with the paradigm that deterministic protein structures are required to drive fission, raising the prospect that many more proteins may participate in fission than previously thought. Paradoxically, our recent work suggests that intrinsically disordered domains may be among the most potent drivers of membrane fission, owing to their large hydrodynamic radii and substantial chain entropy. This stochastic view of fission also suggests new roles for the structure-based fission proteins. Specifically, we hypothesize that in addition to driving fission directly, the canonical fission machines may facilitate the enrichment and organization of bulky disordered protein domains in order to promote membrane fission by locally amplifying protein crowding.     

Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground‐rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of epiphytes is scanty in the literature. We evaluated the genetic variation and spatial genetic structure of the epiphytic bromeliad Guzmania monostachia (Bromeliaceae, Tillandsioideae) in montane secondary forest patches in Costa Rica. The sampling design included plants on the same trees (i.e., populations), populations within forest patches and patches within secondary forest at two different successional stages (early vs. mid‐succession). Six microsatellites revealed low levels of population genetic variation (A = 2.06, A_E = 1.61, H_E = 0.348), a marked deficiency of heterozygotes (H_O = 0.031) and high inbreeding (f = 0.908). Genetic differentiation was negligible among populations within the same forest patch, but moderate (G_ST = 0.123 ± 0.043) among forest patches. Genetic relatedness between individuals was significantly higher for plants located within the same forest patch and separated by <60 m and decreased as distance between plants increased, becoming significantly negative at distances >400 m. An analysis of molecular variance (AMOVA) showed significant genetic variation between forest patches, but non‐significant variation between successional stages. The selfing breeding system and limited seed dispersal capabilities in G. monostachia could explain the observed levels and partitioning of genetic diversity at this geographic scale. However, these results also suggest that forest fragmentation is likely to influence the degree of local genetic structuring of epiphytic plants by limiting gene flow.     

Hippocampal Extracellular Matrix Levels and Stochasticity in Synaptic Protein Expression Increase with Age and Are Associated with Age-dependent Cognitive Decline

Age-related cognitive decline is a serious health concern in our aging society. Decreased cognitive function observed during healthy brain aging is most likely caused by changes in brain connectivity and synaptic dysfunction in particular brain regions. Here we show that aged C57BL/6J wild-type mice have hippocampus-dependent spatial memory impairments. To identify the molecular mechanisms that are relevant to these memory deficits, we investigated the temporal profile of mouse hippocampal synaptic proteome changes at 20, 40, 50, 60, 70, 80, 90, and 100 weeks of age. Extracellular matrix proteins were the only group of proteins that showed robust and progressive up-regulation over time. This was confirmed by immunoblotting and histochemical analysis, which indicated that the increased levels of hippocampal extracellular matrix might limit synaptic plasticity as a potential cause of age-related cognitive decline. In addition, we observed that stochasticity in synaptic protein expression increased with age, in particular for proteins that were previously linked with various neurodegenerative diseases, whereas low variance in expression was observed for proteins that play a basal role in neuronal function and synaptic neurotransmission. Together, our findings show that both specific changes and increased variance in synaptic protein expression are associated with aging and may underlie reduced synaptic plasticity and impaired cognitive performance in old age.As the proportion of aged individuals in our population continues to grow, we are faced with an increase in age-related health problems. Brain aging invariably leads to functional decline and impairments in cognitive function and motor skills, which can seriously affect quality of life. A better understanding of the neurobiological mechanisms underlying age-related cognitive decline is crucial to facilitate maintenance of cognitive health in the elderly and to reveal potential causes of highly prevalent age-related forms of dementia, in particular Alzheimer disease, in which cognitive decline is severely impaired by yet unknown mechanisms.Several studies showed that normal brain aging is associated with subtle morphological and functional alterations in specific neuronal circuits (1, 2) and that reduced cognitive function with increasing age is likely due to synaptic dysfunction (3). Increasing evidence supports the idea that alterations in hippocampal activity are correlated with deficits in learning and memory in healthy aging humans (4, 5). In addition, rodent models of healthy aging demonstrate strong correlations between impaired performance in learning and memory tests and disturbed hippocampal network activity (6, 7). Electrophysiological studies provide additional evidence that age-related disturbances in the hippocampus involve changes in the principal cellular features of learning and memory, synaptic long-term potentiation and long-term depression (8, 9). Together, these observations suggest that a decline in hippocampal synaptic efficacy and plasticity plays a critical role in age-dependent cognitive impairment.Aging is also the primary risk factor for Alzheimer disease, which clinically manifests as severe and accelerated age-dependent cognitive decline (10). Genetic causes of familial early-onset Alzheimer disease all point to a key role in disease etiology for increased brain levels of the protein amyloid-β (11). Familial Alzheimer disease, however, is rare, and it is likely that increased amyloid-β levels in sporadic Alzheimer disease result from age-dependent and/or genetically determined alterations in the expression of other genes or proteins (12, 13). Thus, the identification of molecular mechanisms of normal brain aging might also contribute to our understanding of cognitive decline under pathological conditions, in particular in Alzheimer disease.Although the exact mechanisms underlying brain aging remain to be fully determined, they likely include changes at the molecular, cellular, and neuronal-network levels. In particular, characterization of alterations in the molecular composition and dynamics of hippocampal synapses could potentially reveal important aspects of the underlying mechanisms of brain aging. Age-related changes in global hippocampal gene and protein expression have been investigated previously (14, 15), but these studies were not geared to identify the specific synaptic molecular substrates of brain aging. Here, we made use of iTRAQ¹ technology and high-coverage mass spectrometry to study the effects of aging on the proteomic composition of mouse hippocampal synaptosomes. We investigated the synaptic proteomes of individual mice at 20, 40, 50, 60, 70, 80, 90, and 100 weeks of age. Our findings show that both specific changes and increased variance in synaptic protein expression are associated with age-related cognitive decline.     

Oxygen and the Spatial Structure of Microbial Communities

Oxygen has two faces. On one side it is the terminal electron acceptor of aerobic respiration – the most efficient engine of energy metabolism. On the other hand, oxygen is toxic because the reduction of molecular O₂ creates reactive oxygen species such as the superoxide anion, peroxide, and the hydroxyl radical. Probably most prokaryotes, and virtually all eukaryotes, depend on oxygen respiration, and we show that the ambiguous relation to oxygen is both an evolutionary force and a dominating factor driving functional interactions and the spatial structure of microbial communities.We focus on microbial communities that are specialised for life in concentration gradients of oxygen, where they acquire the full panoply of specific requirements from limited ranges of PO₂ , which also support the spatial organisation of microbial communities. Marine and lake sediments provide examples of steep O₂ gradients, which arise because consumption or production of oxygen exceeds transport rates of molecular diffusion. Deep lakes undergo thermal stratification in warm waters, resulting in seasonal anaerobiosis below the thermocline, and lakes with a permanent pycnocline often have permanent anoxic deep water. The oxycline is here biologically similar to sediments, and it harbours similar microbial biota, the main difference being the spatial scale. In sediments, transport is dominated by molecular diffusion, and in the water column, turbulent mixing dominates vertical transport.Cell size determines the minimum requirement of aerobic organisms. For bacteria (and mitochondria), the half‐saturation constant for oxygen uptake ranges within 0.05 – 0.1% atmospheric saturation; for the amoeba Acanthamoeba castellanii it is 0.2%, and for two ciliate species measuring around 150 μm, it is 1‐2 % atmospheric saturation. Protection against O₂ toxicity has an energetic cost that increases with increasing ambient O₂ tension. Oxygen sensing seems universal in aquatic organisms. Many aspects of oxygen sensing are incompletely understood, but the mechanisms seem to be evolutionarily conserved. A simple method of studying oxygen preference in microbes is to identify the preferred oxygen tension accumulating in O₂ gradients. Microorganisms cannot sense the direction of a chemical gradient directly, so they use other devices to orient themselves. Different mechanisms in different prokaryotic and eukaryotic microbes are described. In O₂ gradients, many bacteria and protozoa are vertically distributed according to oxygen tension and they show a very limited range of preferred PO₂. In some pigmented protists the required PO₂ is contingent on light due to photochemically generated reactive oxygen species. In protists that harbour endosymbiotic phototrophs, orientation towards light is mediated through the oxygen production of their photosynthetic symbionts. Oxygen plays a similar role for the distribution of small metazoans (meiofauna) in sediments, but there is little experimental evidence for this. Thus the oxygenated sediments surrounding ventilated animal burrows provide a special habitat for metazoan meiofauna as well as unicellular organisms.     

How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from complex environments with many obstacles.     

HPV Clearance and the Neglected Role of Stochasticity

Clearance of anogenital and oropharyngeal HPV infections is attributed primarily to a successful adaptive immune response. To date, little attention has been paid to the potential role of stochastic cell dynamics in the time it takes to clear an HPV infection. In this study, we combine mechanistic mathematical models at the cellular level with epidemiological data at the population level to disentangle the respective roles of immune capacity and cell dynamics in the clearing mechanism. Our results suggest that chance—in form of the stochastic dynamics of basal stem cells—plays a critical role in the elimination of HPV-infected cell clones. In particular, we find that in immunocompetent adolescents with cervical HPV infections, the immune response may contribute less than 20% to virus clearance—the rest is taken care of by the stochastic proliferation dynamics in the basal layer. In HIV-negative individuals, the contribution of the immune response may be negligible.     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

Origins of Stochasticity and Burstiness in High-Dimensional Biochemical Networks

Two major approaches are known in the field of stochastic dynamics of intracellular biochemical networks. The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluctuations. The second approach treats the regulatory process as essentially continuous. Complex pseudostochastic behavior in such processes may occur due to multistability and oscillatory motions within limit cycles. In this paper we outline the third scenario of stochasticity in the regulatory process. This scenario is only conceivable in high-dimensional highly nonlinear systems. In particular, we show that burstiness, a well-known phenomenon in the biology of gene expression, is a natural consequence of high dimensionality coupled with high nonlinearity. In mathematical terms, burstiness is associated with heavy-tailed probability distributions of stochastic processes describing the dynamics of the system. We demonstrate how the "shot" noise originates from purely deterministic behavior of the underlying dynamical system. We conclude that the limiting stochastic process may be accurately approximated by the "heavy-tailed" generalized Pareto process which is a direct mathematical expression of burstiness.     

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes

Insulin-dependent or type 1 diabetes is a prototypic autoimmune disease whose incidence steadily increased over the past decades in industrialized countries. Recent evidence suggests the importance of the gut microbiota to explain this trend. Here, non-obese diabetic (NOD) mice that spontaneously develop autoimmune type 1 diabetes were treated with different antibiotics to explore the influence of a targeted intestinal dysbiosis in the progression of the disease. A mixture of wide spectrum antibiotics (i.e. streptomycin, colistin and ampicillin) or vancomycin alone were administered orally from the moment of conception, treating breeding pairs, and during the postnatal and adult life until the end of follow-up at 40 weeks. Diabetes incidence significantly and similarly increased in male mice following treatment with these two antibiotic regimens. In NOD females a slight yet not significant trend towards an increase in disease incidence was observed. Changes in gut microbiota composition were assessed by sequencing the V3 region of bacterial 16S rRNA genes. Administration of the antibiotic mixture resulted in near complete ablation of the gut microbiota. Vancomycin treatment led to increased Escherichia, Lactobacillus and Sutterella genera and decreased members of the Clostridiales order and Lachnospiraceae, Prevotellaceae and Rikenellaceae families, as compared to control mice. Massive elimination of IL-17-producing cells, both CD4+TCRαβ+ and TCRγδ+ T cells was observed in the lamina propria of the ileum and the colon of vancomycin-treated mice. These results show that a directed even partial ablation of the gut microbiota, as induced by vancomycin, significantly increases type 1 diabetes incidence in male NOD mice thus prompting for caution in the use of antibiotics in pregnant women and newborns.